From waveflux at gmail.com  Thu Jan  9 16:52:01 2020
From: waveflux at gmail.com (Tom Beaudry)
Date: Thu, 9 Jan 2020 16:52:01 -0500
Subject: [Loris-dev] upgrading centos dev server to v21
Message-ID: <CALzz+FPNwVkHmTgmMn1DEXRB12qeNmGi8_w8NXzYZTGsjs9big@mail.gmail.com>

Hi Guys,

I'm trying to upgrade a dev server to v21 that runs on centos from the
official release.  I followed the instruction on the release page, and I'm
running PHP 7.1.33.

After the upgrade, when i try and access the login page, i get:

This page isn?t workinglorisdev.concordia.ca is currently unable to handle
this request.
HTTP ERROR 500

and my apache logs says:

PHP Parse error:  syntax error, unexpected '?', expecting variable
(T_VARIABLE) in /var/www/loris/php/libraries/NDB_Client.class.inc on line 49

Any help would be greatly appreciated,

Thanks,
Tom
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From lingyun.ma at mcin.ca  Thu Jan  9 17:35:44 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Thu, 9 Jan 2020 17:35:44 -0500
Subject: [Loris-dev] upgrading centos dev server to v21
In-Reply-To: <CALzz+FPNwVkHmTgmMn1DEXRB12qeNmGi8_w8NXzYZTGsjs9big@mail.gmail.com>
References: <CALzz+FPNwVkHmTgmMn1DEXRB12qeNmGi8_w8NXzYZTGsjs9big@mail.gmail.com>
Message-ID: <CAMpvQ9j7CLa21Xm5ouMxL_CBgZpMKDJc2HVEoZh5-Q8v7KRVUg@mail.gmail.com>

Hi Tom,

It looks most likely that even your PHP shows 7.1.33, your web server is
somehow still running with PHP7.0, PHP 5.6 or even more ancient versions.

Please verify.


Best regards,
Ling Ma
Development Consultant

On Thu, Jan 9, 2020 at 4:52 PM Tom Beaudry <waveflux at gmail.com> wrote:

> Hi Guys,
>
> I'm trying to upgrade a dev server to v21 that runs on centos from the
> official release.  I followed the instruction on the release page, and I'm
> running PHP 7.1.33.
>
> After the upgrade, when i try and access the login page, i get:
>
> This page isn?t workinglorisdev.concordia.ca is currently unable to
> handle this request.
> HTTP ERROR 500
>
> and my apache logs says:
>
> PHP Parse error:  syntax error, unexpected '?', expecting variable
> (T_VARIABLE) in /var/www/loris/php/libraries/NDB_Client.class.inc on line 49
>
> Any help would be greatly appreciated,
>
> Thanks,
> Tom
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
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From dave.macfarlane at mcin.ca  Fri Jan 10 09:27:18 2020
From: dave.macfarlane at mcin.ca (Dave MacFarlane)
Date: Fri, 10 Jan 2020 09:27:18 -0500
Subject: [Loris-dev] upgrading centos dev server to v21
In-Reply-To: <CALzz+FPNwVkHmTgmMn1DEXRB12qeNmGi8_w8NXzYZTGsjs9big@mail.gmail.com>
References: <CALzz+FPNwVkHmTgmMn1DEXRB12qeNmGi8_w8NXzYZTGsjs9big@mail.gmail.com>
Message-ID: <CAN9cDwFqf_P-UMi6PibNF3KwL3Dv8QGXONjrJndAjZo5KbgYOg@mail.gmail.com>

"?" to mean nullable in type hinting was added in PHP 7.1, so that suggests
that Ling Ma is right and your web server might
be running a different version of PHP than your command line.

You can verify by making a simple php page that calls phpinfo() and seeing
what it says when you visit page in your browser.


On Thu, Jan 9, 2020 at 4:52 PM Tom Beaudry <waveflux at gmail.com> wrote:

> Hi Guys,
>
> I'm trying to upgrade a dev server to v21 that runs on centos from the
> official release.  I followed the instruction on the release page, and I'm
> running PHP 7.1.33.
>
> After the upgrade, when i try and access the login page, i get:
>
> This page isn?t workinglorisdev.concordia.ca is currently unable to
> handle this request.
> HTTP ERROR 500
>
> and my apache logs says:
>
> PHP Parse error:  syntax error, unexpected '?', expecting variable
> (T_VARIABLE) in /var/www/loris/php/libraries/NDB_Client.class.inc on line 49
>
> Any help would be greatly appreciated,
>
> Thanks,
> Tom
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
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From waveflux at gmail.com  Fri Jan 10 12:53:46 2020
From: waveflux at gmail.com (Tom Beaudry)
Date: Fri, 10 Jan 2020 12:53:46 -0500
Subject: [Loris-dev] upgrading centos dev server to v21
In-Reply-To: <CAN9cDwFqf_P-UMi6PibNF3KwL3Dv8QGXONjrJndAjZo5KbgYOg@mail.gmail.com>
References: <CALzz+FPNwVkHmTgmMn1DEXRB12qeNmGi8_w8NXzYZTGsjs9big@mail.gmail.com>
 <CAN9cDwFqf_P-UMi6PibNF3KwL3Dv8QGXONjrJndAjZo5KbgYOg@mail.gmail.com>
Message-ID: <CALzz+FNRwb7L=gsgYpcf3R9mO8=2Zn9Ye9QOQpzAd7jqyNTqTQ@mail.gmail.com>

Hey guys,

Problem solved, apache needed a restart after upgrading to php 7.1.

Take care,
Tom

On Fri, Jan 10, 2020 at 9:27 AM Dave MacFarlane <dave.macfarlane at mcin.ca>
wrote:

> "?" to mean nullable in type hinting was added in PHP 7.1, so that
> suggests that Ling Ma is right and your web server might
> be running a different version of PHP than your command line.
>
> You can verify by making a simple php page that calls phpinfo() and seeing
> what it says when you visit page in your browser.
>
>
> On Thu, Jan 9, 2020 at 4:52 PM Tom Beaudry <waveflux at gmail.com> wrote:
>
>> Hi Guys,
>>
>> I'm trying to upgrade a dev server to v21 that runs on centos from the
>> official release.  I followed the instruction on the release page, and I'm
>> running PHP 7.1.33.
>>
>> After the upgrade, when i try and access the login page, i get:
>>
>> This page isn?t workinglorisdev.concordia.ca is currently unable to
>> handle this request.
>> HTTP ERROR 500
>>
>> and my apache logs says:
>>
>> PHP Parse error:  syntax error, unexpected '?', expecting variable
>> (T_VARIABLE) in /var/www/loris/php/libraries/NDB_Client.class.inc on line 49
>>
>> Any help would be greatly appreciated,
>>
>> Thanks,
>> Tom
>> _______________________________________________
>> Loris-dev mailing list
>> Loris-dev at bic.mni.mcgill.ca
>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>
>
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From rolando.acosta at cnbp.ca  Thu Jan 16 10:55:27 2020
From: rolando.acosta at cnbp.ca (Rolando Acosta)
Date: Thu, 16 Jan 2020 10:55:27 -0500
Subject: [Loris-dev] Issue when trying to use "pselectOne" and "pselect"
 functions with an " IN " sql statement
Message-ID: <CACYwi7aXe_ezx2BGdG3JZpPAyx4BaLY+LsgCA7ryM0ApTYTXqw@mail.gmail.com>

Hi LORIS team,

A while ago I faced the following issue in one of the PRs I was working on:

/////////////////////////////////////////

The structure:

$recruitmentStartDate = $DB->pselectOne(
    "SELECT MIN(Date_registered)
     FROM candidate

* WHERE RegistrationCenterID IN (:Sites)",    array('Sites' => implode(",",
array_keys($list_of_sites)))*
);

Doesn't seem to be working for me. Only the first element of the array
$list_of_sites is been passed to the IN SQL clause. Not sure if I'm using
correctly this way. For the moment I write it as:

$recruitmentStartDate = $DB->pselectOne(
    "SELECT MIN(Date_registered)
     FROM candidate

*WHERE RegistrationCenterID IN (" . $sitesString . ")",    array()*
);

//////////////////////////////////////////////////


I'm having the same behavior with the function *pselect(string $query,
array $params): array*
from the *class Database*.

I'm wondering if you could take a look and see if there is a way to pass an
array as one of the elements in the *$params* array? The issue rises when
need to do an IN statement as part of the query.

Cheers,
Rolando Acosta (CHU Sainte-Justine)
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From melanie.legault2 at mcgill.ca  Thu Jan 16 11:15:23 2020
From: melanie.legault2 at mcgill.ca (Melanie Legault, Mrs)
Date: Thu, 16 Jan 2020 16:15:23 +0000
Subject: [Loris-dev] Issue when trying to use "pselectOne" and "pselect"
 functions with an " IN " sql statement
In-Reply-To: <CACYwi7aXe_ezx2BGdG3JZpPAyx4BaLY+LsgCA7ryM0ApTYTXqw@mail.gmail.com>
References: <CACYwi7aXe_ezx2BGdG3JZpPAyx4BaLY+LsgCA7ryM0ApTYTXqw@mail.gmail.com>
Message-ID: <YTOPR0101MB161167E7DD043366193C0A4BCF360@YTOPR0101MB1611.CANPRD01.PROD.OUTLOOK.COM>

Hello Rolando,

Sorry if I misled you on the wrong track. You can't use `in` using pselect() or pselectOne().
In order to use `in` you have to use run().


M?lanie


________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Rolando Acosta <rolando.acosta at cnbp.ca>
Sent: January 16, 2020 10:55
To: loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
Subject: [Loris-dev] Issue when trying to use "pselectOne" and "pselect" functions with an " IN " sql statement

Hi LORIS team,

A while ago I faced the following issue in one of the PRs I was working on:

/////////////////////////////////////////

The structure:

$recruitmentStartDate = $DB->pselectOne(
    "SELECT MIN(Date_registered)
     FROM candidate
     WHERE RegistrationCenterID IN (:Sites)",
    array('Sites' => implode(",", array_keys($list_of_sites)))
);

Doesn't seem to be working for me. Only the first element of the array $list_of_sites is been passed to the IN SQL clause. Not sure if I'm using correctly this way. For the moment I write it as:

$recruitmentStartDate = $DB->pselectOne(
    "SELECT MIN(Date_registered)
     FROM candidate
     WHERE RegistrationCenterID IN (" . $sitesString . ")",
    array()
);

//////////////////////////////////////////////////


I'm having the same behavior with the function pselect(string $query, array $params): array
from the class Database.

I'm wondering if you could take a look and see if there is a way to pass an array as one of the elements in the $params array? The issue rises when need to do an IN statement as part of the query.

Cheers,
Rolando Acosta (CHU Sainte-Justine)
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From lingyun.ma at mcin.ca  Thu Jan 16 11:26:11 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Thu, 16 Jan 2020 11:26:11 -0500
Subject: [Loris-dev] Issue when trying to use "pselectOne" and "pselect"
 functions with an " IN " sql statement
In-Reply-To: <YTOPR0101MB161167E7DD043366193C0A4BCF360@YTOPR0101MB1611.CANPRD01.PROD.OUTLOOK.COM>
References: <CACYwi7aXe_ezx2BGdG3JZpPAyx4BaLY+LsgCA7ryM0ApTYTXqw@mail.gmail.com>
 <YTOPR0101MB161167E7DD043366193C0A4BCF360@YTOPR0101MB1611.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <CAMpvQ9hSo=_YB0YZ2QNSCsscTx7KOmwUV-UQBPtk5px+XShKqw@mail.gmail.com>

Hi Melanie and Rolando,

In fact, you can use pselect in this case. If you use pselect, you have to
pass each "in" clause item as a parameter, not as a whole. For example, the
following code could solve your problem.

$params = array();
$values = array();
foreach ($list as $key => $id) {
    $params[]         = ":id$key";
    $values["id$key"] = $id;
}
$results = $DB->pselect(
    "SELECT * FROM x WHERE ID in (" .
    implode(', ', $params) . ")",
    $values
)

Best regards,

Ling Ma
Development consultant

On Thu, Jan 16, 2020 at 11:15 AM Melanie Legault, Mrs <
melanie.legault2 at mcgill.ca> wrote:

> Hello Rolando,
>
> Sorry if I misled you on the wrong track. You can't use `in` using
> pselect() or pselectOne().
> In order to use `in` you have to use run().
>
> M?lanie
>
> ------------------------------
> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Rolando Acosta <
> rolando.acosta at cnbp.ca>
> *Sent:* January 16, 2020 10:55
> *To:* loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
> *Subject:* [Loris-dev] Issue when trying to use "pselectOne" and
> "pselect" functions with an " IN " sql statement
>
> Hi LORIS team,
>
> A while ago I faced the following issue in one of the PRs I was working on:
>
> /////////////////////////////////////////
>
> The structure:
>
> $recruitmentStartDate = $DB->pselectOne(
>     "SELECT MIN(Date_registered)
>      FROM candidate
>
> * WHERE RegistrationCenterID IN (:Sites)",     array('Sites' =>
> implode(",", array_keys($list_of_sites)))*
> );
>
> Doesn't seem to be working for me. Only the first element of the array
> $list_of_sites is been passed to the IN SQL clause. Not sure if I'm using
> correctly this way. For the moment I write it as:
>
> $recruitmentStartDate = $DB->pselectOne(
>     "SELECT MIN(Date_registered)
>      FROM candidate
>
> *WHERE RegistrationCenterID IN (" . $sitesString . ")",     array()*
> );
>
> //////////////////////////////////////////////////
>
>
> I'm having the same behavior with the function *pselect(string $query,
> array $params): array*
> from the *class Database*.
>
> I'm wondering if you could take a look and see if there is a way to pass
> an array as one of the elements in the *$params* array? The issue rises
> when need to do an IN statement as part of the query.
>
> Cheers,
> Rolando Acosta (CHU Sainte-Justine)
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
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From rolando.acosta at cnbp.ca  Fri Jan 17 14:24:28 2020
From: rolando.acosta at cnbp.ca (Rolando Acosta)
Date: Fri, 17 Jan 2020 14:24:28 -0500
Subject: [Loris-dev] Issue when trying to use "pselectOne" and "pselect"
 functions with an " IN " sql statement
In-Reply-To: <CAMpvQ9hSo=_YB0YZ2QNSCsscTx7KOmwUV-UQBPtk5px+XShKqw@mail.gmail.com>
References: <CACYwi7aXe_ezx2BGdG3JZpPAyx4BaLY+LsgCA7ryM0ApTYTXqw@mail.gmail.com>
 <YTOPR0101MB161167E7DD043366193C0A4BCF360@YTOPR0101MB1611.CANPRD01.PROD.OUTLOOK.COM>
 <CAMpvQ9hSo=_YB0YZ2QNSCsscTx7KOmwUV-UQBPtk5px+XShKqw@mail.gmail.com>
Message-ID: <CACYwi7YSY+uQ7pjK4dd_DgAqAkwDLby-M3LJPTOT1QiwXvafqg@mail.gmail.com>

Hi Melanie and Ling,

Thank you very much for helping me with this. It seems that both approaches
do work.

Nice one @Ling!

Best,
Rolando Acosta (CHU Sainte-Justine)

On Thu, Jan 16, 2020 at 11:26 AM Ling Ma <lingyun.ma at mcin.ca> wrote:

> Hi Melanie and Rolando,
>
> In fact, you can use pselect in this case. If you use pselect, you have to
> pass each "in" clause item as a parameter, not as a whole. For example, the
> following code could solve your problem.
>
> $params = array();
> $values = array();
> foreach ($list as $key => $id) {
>     $params[]         = ":id$key";
>     $values["id$key"] = $id;
> }
> $results = $DB->pselect(
>     "SELECT * FROM x WHERE ID in (" .
>     implode(', ', $params) . ")",
>     $values
> )
>
> Best regards,
>
> Ling Ma
> Development consultant
>
> On Thu, Jan 16, 2020 at 11:15 AM Melanie Legault, Mrs <
> melanie.legault2 at mcgill.ca> wrote:
>
>> Hello Rolando,
>>
>> Sorry if I misled you on the wrong track. You can't use `in` using
>> pselect() or pselectOne().
>> In order to use `in` you have to use run().
>>
>> M?lanie
>>
>> ------------------------------
>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Rolando Acosta <
>> rolando.acosta at cnbp.ca>
>> *Sent:* January 16, 2020 10:55
>> *To:* loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
>> *Subject:* [Loris-dev] Issue when trying to use "pselectOne" and
>> "pselect" functions with an " IN " sql statement
>>
>> Hi LORIS team,
>>
>> A while ago I faced the following issue in one of the PRs I was working
>> on:
>>
>> /////////////////////////////////////////
>>
>> The structure:
>>
>> $recruitmentStartDate = $DB->pselectOne(
>>     "SELECT MIN(Date_registered)
>>      FROM candidate
>>
>> * WHERE RegistrationCenterID IN (:Sites)",     array('Sites' =>
>> implode(",", array_keys($list_of_sites)))*
>> );
>>
>> Doesn't seem to be working for me. Only the first element of the array
>> $list_of_sites is been passed to the IN SQL clause. Not sure if I'm using
>> correctly this way. For the moment I write it as:
>>
>> $recruitmentStartDate = $DB->pselectOne(
>>     "SELECT MIN(Date_registered)
>>      FROM candidate
>>
>> *WHERE RegistrationCenterID IN (" . $sitesString . ")",     array()*
>> );
>>
>> //////////////////////////////////////////////////
>>
>>
>> I'm having the same behavior with the function *pselect(string $query,
>> array $params): array*
>> from the *class Database*.
>>
>> I'm wondering if you could take a look and see if there is a way to pass
>> an array as one of the elements in the *$params* array? The issue rises
>> when need to do an IN statement as part of the query.
>>
>> Cheers,
>> Rolando Acosta (CHU Sainte-Justine)
>> _______________________________________________
>> Loris-dev mailing list
>> Loris-dev at bic.mni.mcgill.ca
>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>
>
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From sotirisnik at gmail.com  Wed Jan 29 10:35:06 2020
From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos)
Date: Wed, 29 Jan 2020 17:35:06 +0200
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAKHj7uSEegvE1apPBGVyHmjyVzF+YxJjDMg0b+hDE4_-ON+dYw@mail.gmail.com>
References: <mailman.1851.1573565332.16403.loris-dev@bic.mni.mcgill.ca>
 <CAEfMBom1HCWLo4NWgt5XG4625tCBfRT_Z_HepvtT_Er2LKbJoA@mail.gmail.com>
 <CAKHj7uS1AdMDjnacouTvxZgziYVgp5NNUeOuMkpDyrTskGTh-Q@mail.gmail.com>
 <CALbt7NDej8FGUUS6_oKbK5Fp-FnwsVz9AgZ6ZcJEZhmoKZmv8w@mail.gmail.com>
 <CAKHj7uSx-qqcXHZsWsZmSJ7sC1DgF+XapT5Y1+QdoVic37_DDg@mail.gmail.com>
 <CAMkiY3fQBGDGeNO8EHxwYAgbhTggNSQ+AVuCfdraDXwULMjjUg@mail.gmail.com>
 <CAKHj7uT5xXi=pOPdH=W9BroSphMHdTszdgW+GxuES=8wZox9eQ@mail.gmail.com>
 <CAMkiY3eUouxaRVdC4wH+vdjeQ=q_Nx8bcDNzcWgD_OgN77m3mw@mail.gmail.com>
 <CAKHj7uSxu4+tm+=x4+qJ1sAbrjmxG2H7LovDb7-2KMnyYQhrgg@mail.gmail.com>
 <CAMkiY3fdPZec2jx-cc2Zq37j3ekmTu_o819yBUv-bC7M98bkVw@mail.gmail.com>
 <CAKHj7uSZHozpuQ_YwGmy6wQ4tm43vJa556V0o2+JGDVsYaqN4g@mail.gmail.com>
 <CAMkiY3dge=x93bQDv0fHGMcrX0PA8Z_imLb_zSTh=nTrx5weFg@mail.gmail.com>
 <CAKHj7uR81gCkjvccMxwMA08dGSEgyTLJBJ+pZPkoUQDtGP_hFA@mail.gmail.com>
 <CAMkiY3fGhvExZ-JOvxeHe7dJQPvtPAHx3oJuiMVX7f1JgF1GAg@mail.gmail.com>
 <CAKHj7uRExO98Yyn9_07aw44wbh0bCL9_C1VFTAURKsxQLUuAeQ@mail.gmail.com>
 <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>
 <CAKHj7uRueb5fgh4VVCAyaq8tC9WM4gJ7k6Q=dxsqWzFgDqPfVQ@mail.gmail.com>
 <CAMkiY3d-Vt=3gQqwJ+GSRSacbLp2QxrB0g-_C7ONd8j_g1ipoQ@mail.gmail.com>
 <CAKHj7uQt9=nokz5g1zBuBx1-rJ8q7qKOuNVkQugC9wfvNFcjVA@mail.gmail.com>
 <CAMkiY3cAuQfT_5iMzYoF2BXVceu_vgz4eCq2sAtoyse+zUYeSg@mail.gmail.com>
 <CAMkiY3dq1O3V8+r4tTAWQ8N=rVFg=DNY-UPeMqbec+MSayj=Cg@mail.gmail.com>
 <CAKHj7uSEegvE1apPBGVyHmjyVzF+YxJjDMg0b+hDE4_-ON+dYw@mail.gmail.com>
Message-ID: <CAKHj7uRx1NT7CycFq65uFpgPiOVwvT-jtK1NJX6_3rrLNFwdbA@mail.gmail.com>

Hello,

We are making a dockerized version of Loris 21 and when we execute the
batch_uploads_imageuploader.pl we get an error about xargs. What could be
the casue?

Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/
batch_uploads_imageuploader.pl line 144.
Running now the following command: /data/loris/data//uploadNeuroDB/
imaging_upload_file.pl -profile prod -upload_id 13
/data/incoming/DCC0007_854380_V1.tar.gz -verbose

 find -path \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml -name '__MACOSX'
-delete
xargs: file: No such file or directory

dicomTar.pl \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml
\/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
 Source: /data/tmp/ImagingUpload-15-31-U_O5ml
Target: /data/loris/data/tarchive

Thanks

???? ???, 10 ??? 2019 ???? 7:21 ?.?., ?/? Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> ??????:

> Hi,
>
> i opened an issue and looked up for the values of Volume they suggested
> https://github.com/BIC-MNI/minc-toolkit-v2/issues/95. The only attributes
> associated with it i saw are [0x00089206] and [0x00089207]
>
> [image: image.png]
>
> I looked up for the file that was being viewed fine in the BrainBrowser
> and saw that it had that attribute empty so i used this command because i
> couldn't find a way to modify the attribute via pydicom
>
> dcmodify -ma "(0008,9206)=" *.dcm
>
> and that command reported the warning about the Endian Syntax. I also used
> the corresponding command for 9207 and got the message "Tag not found'
>
> Lastly I tried to upload some dicoms and now i am getting the SNR and i
> can view them fine. I believe now that all of them will pass successfully,
> i will report back later.
>
> Thanks,
>
> Sotirios
>
> ???? ???, 9 ??? 2019 ???? 8:10 ?.?., ?/? Cecile Madjar <
> cecile.madjar at mcin.ca> ??????:
>
>> Hi Sotirios,
>>
>> The issue you are having is a indeed a dcm2mnc issue. The converter does
>> not seem to work on your dataset for some reason. Unfortunately, there is
>> not much we can do on our front to fix this...
>>
>> I would recommend creating an issue on the MINC tools repository
>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> so they can fix your
>> problem.
>>
>> Very sorry that you are having that problem.
>>
>> Best,
>>
>> C?cile
>>
>> On Wed, Dec 4, 2019 at 8:59 AM Cecile Madjar <cecile.madjar at mcin.ca>
>> wrote:
>>
>>> Hi Sotirios,
>>>
>>> Could you please share a dataset with us that produces the error you get
>>> and the weird display in BrainBrowser? You could use the same SFTP
>>> credential that Nicolas gave you.
>>>
>>> The message errors you got from imaging_install.sh are probably due to
>>> the fact that you reran the install script and it tried to reinstall
>>> something that was already there. I would not worry about it. FYI, the only
>>> thing you needed to do was to update the MINC tools path in the environment
>>> file as you did after re-running imaging_install.sh and source the
>>> environment file.
>>>
>>> Best,
>>>
>>> C?cile
>>>
>>> On Wed, Dec 4, 2019 at 8:03 AM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>>>  Hi Cecile,
>>>>
>>>> We used minctool 1.9.7 and we still get this error
>>>>
>>>> <<Restructuring...
>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>> Default GSL error handler invoked.
>>>> noise_estimate --snr /data/loris/data>>
>>>>
>>>
>>>> One dicom folder hadn't that error and is being viewed fine in the
>>>> BrainBrowser of Loris.
>>>>
>>>
>>>> When i used dpkg to the 1.9.17 the installation reported fine
>>>> <<Unpacking minc-toolkit-v2 (1.9.17) over (1.9.16) ...>>
>>>>
>>>> and then i used source /opt/minc/1.9.17/minc-toolkit-config.sh
>>>>
>>>> and aftewards runned bash ./imaging_install.sh just to be sure.
>>>>
>>>> We also had to modify /data/loris/bin/mri/environment because it still
>>>> pointed to the old version.
>>>>
>>>> What i found strange is this during the run of imaging_install.sh
>>>>
>>>> <<already using interpreter
>>>> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/bin/python3
>>>> Please use the *system* python to run this script
>>>> Traceback (most recent call last):
>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>>> 2632, in <module>
>>>>     main()
>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>>> 870, in main
>>>>     symlink=options.symlink,
>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>>> 1156, in create_environment
>>>>     install_python(home_dir, lib_dir, inc_dir, bin_dir,
>>>> site_packages=site_packages, clear=clear, symlink=symlink)
>>>>   File
>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>> line 357, in abspath
>>>>     if not isabs(path):
>>>>   File
>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>> line 64, in isabs
>>>>     return s.startswith(sep)
>>>> AttributeError: 'NoneType' object has no attribute 'startswith'
>>>> Installing the Python libraries into the loris-mri virtualenv...
>>>> Requirement already satisfied: mysqlclient in
>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (1.4.4)
>>>> Requirement already satisfied: mysql-connector in
>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (2.2.9)
>>>> Requirement already satisfied: pybids in
>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (0.9.4)
>>>> Requirement already satisfied: nibabel>=2.1 in ./python_virtua>>
>>>>
>>>> So should i open an issue for that error? or is there something else to
>>>> try?
>>>>
>>>> Thanks
>>>>
>>>> Sotirios
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ???? ???, 3 ??? 2019 ???? 10:39 ?.?., ?/? Cecile Madjar <
>>>> cecile.madjar at mcin.ca> ??????:
>>>>
>>>>> Hi Sotirios,
>>>>>
>>>>> Does the pic screenshot in the imaging browser module also shows 1
>>>>> slice? If so, that would mean there was an issue with the dcm2mnc
>>>>> conversion. Once again, installing the latest version of the MINC tools
>>>>> should help but if this issue persists I would recommend creating an issue
>>>>> for that too on their repository
>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> (if not already
>>>>> reported there, there are a few known issue reported).
>>>>>
>>>>> Other viewer for MINCs are register and Display (both part of the MINC
>>>>> tools). For NIfTI, you have FSLeye, MRICron and probably many other viewers
>>>>> that exists.
>>>>>
>>>>> Hope this helps,
>>>>>
>>>>> C?cile
>>>>>
>>>>> On Tue, Dec 3, 2019 at 3:26 PM Sotirios Nikoloutsopoulos <
>>>>> sotirisnik at gmail.com> wrote:
>>>>>
>>>>>> Hi Cecile,
>>>>>>
>>>>>> Yes, Nifti files are mandatory for our work. From what we saw at a
>>>>>> 3rd vm we setted up, the nifti files are being created ( i haven't verified
>>>>>> if that is the case at the 2nd vm ). I will install the latest version and
>>>>>> will report back, but do you know any nifti/minc viewer? because the
>>>>>> Brainbrowser of Loris does not output them well, it's like it is loading
>>>>>> only 1 slice and we would like to verify it with another tool too. We
>>>>>> verified that the dcmconv command didn't affect the quality of the
>>>>>> .dcm files.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Sotirios
>>>>>>
>>>>>> ???? ???, 2 ??? 2019 ???? 6:59 ?.?., ?/? Cecile Madjar <
>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>
>>>>>>> Hi Sotirios,
>>>>>>>
>>>>>>> It looks like for some reason your binary mnc2nii is not working and
>>>>>>> reports that error. Do you want to create NIfTI files or are you happy with
>>>>>>> just the MINC files?
>>>>>>>
>>>>>>> If you don't need the NIfTI files, then maybe you can set the Config
>>>>>>> setting "NIfTI file creation" to No instead of Yes and this error
>>>>>>> will not appear anymore.
>>>>>>>
>>>>>>> If you need the NIfTI files to be created, then I would
>>>>>>> recommend installing the latest version of the MINC tools (1.9.17). They
>>>>>>> can be found there:
>>>>>>>
>>>>>>>    - pre-built packages:
>>>>>>>    https://packages.bic.mni.mcgill.ca/minc-toolkit/
>>>>>>>    - from the source code with installation instructions in the
>>>>>>>    README: https://github.com/BIC-MNI/minc-toolkit-v2
>>>>>>>
>>>>>>> If the problem persists by using the latest release of MINC tools,
>>>>>>> then create an issue on Github for the MINC developers here
>>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues>.
>>>>>>>
>>>>>>> Hope this helps,
>>>>>>>
>>>>>>> C?cile
>>>>>>>
>>>>>>> On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi Cecile,
>>>>>>>>
>>>>>>>> Thanks to Nicholas i was able to create all the mincs images. The
>>>>>>>> problem was that the files were in Little-Endian-Implicit transfer syntax
>>>>>>>> and i had to convert them Little-Endian-Explicit transfer syntax with this
>>>>>>>> command
>>>>>>>>
>>>>>>>> find <root_of_my_DICOM_files_directory> -type f | xargs -i
>>>>>>>> dcmconv --write-xfer-little {} {}
>>>>>>>>
>>>>>>>>
>>>>>>>> Looking back at our mails i saw that Little-Endian error had
>>>>>>>> occurred when i used dcmodify, but i switcthed to using pydicom instead.
>>>>>>>>
>>>>>>>>
>>>>>>>> [image: image.png]
>>>>>>>>
>>>>>>>>
>>>>>>>> In the output i see an error sometimes about "gsl: bessel_I0.c:216:
>>>>>>>> ERROR: overflow". Is this okay?
>>>>>>>>
>>>>>>>> Restructuring...
>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>> Default GSL error handler invoked.
>>>>>>>> noise_estimate --snr
>>>>>>>> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
>>>>>>>> SNR is:
>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>> Default GSL error handler invoked.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Sotirios
>>>>>>>>
>>>>>>>>
>>>>>>>> ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar <
>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>
>>>>>>>>> Hi Sotirios,
>>>>>>>>>
>>>>>>>>> Thank you for the details!
>>>>>>>>>
>>>>>>>>> A few things to try:
>>>>>>>>>
>>>>>>>>>    - modify the TMPDIR to be on your /data directory where there
>>>>>>>>>    might be more space to do processing (could create a /data/tmp where the
>>>>>>>>>    temporary files would be created)
>>>>>>>>>    - how many files are there for that upload in tarchive_files?
>>>>>>>>>    Are they different from the ones showing the warning message?
>>>>>>>>>       - FYI: query to get that: SELECT tf.* FROM tarchive_files
>>>>>>>>>       tf JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your uploadID> (the
>>>>>>>>>       output of that query would be very useful if you can provide it)
>>>>>>>>>       - how many series are there for that upload in
>>>>>>>>>    tarchive_series?
>>>>>>>>>    - FYI: query to get that: SELECT ts.* FROM tarchive_series ts
>>>>>>>>>       JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your uploadID> (the
>>>>>>>>>       output of that query would be very useful if you can provide it)
>>>>>>>>>    - things are failing when the scripts try running the
>>>>>>>>>    following command: find
>>>>>>>>>    /tmp/TarLoad-23-43-ccugaa/ImagingUpload-23-43-6JCOTO -type f  |
>>>>>>>>>    /data/loris/bin/mri/dicom-archive/get_dicom_info.pl -studyuid
>>>>>>>>>    -series -echo -image -file  -attvalue 0018 0024 -series_descr -stdin | sort
>>>>>>>>>    -n -k1 -k2 -k7 -k3 -k6 -k4  | cut -f 5 | dcm2mnc -dname '' -stdin -clobber
>>>>>>>>>    -usecoordinates /tmp/TarLoad-23-43-ccugaa
>>>>>>>>>       - clearly the problems come from get_dicom_info.pl but I
>>>>>>>>>       cannot pinpoint the error yet. I will ask around and get back to you
>>>>>>>>>
>>>>>>>>> If I cannot figure it out remotely, is there a way to have a call
>>>>>>>>> using zoom? This way you could share your screen with me and run the
>>>>>>>>> debugger on that script and hopefully we can figure out what is going on
>>>>>>>>> with those datasets?
>>>>>>>>>
>>>>>>>>> Thanks!
>>>>>>>>>
>>>>>>>>> C?cile
>>>>>>>>>
>>>>>>>>> On Tue, Nov 26, 2019 at 5:17 PM Sotirios Nikoloutsopoulos <
>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Cecile,
>>>>>>>>>>
>>>>>>>>>> In both my virtual machines
>>>>>>>>>> export TMPDIR=/tmp
>>>>>>>>>>
>>>>>>>>>> In both vm also with dcm2mnc i get this output. Just to verify
>>>>>>>>>> that this passed in my 1st vm and produced mincs.
>>>>>>>>>>
>>>>>>>>>> I attached the spool as a csv.
>>>>>>>>>>
>>>>>>>>>> [image: image.png]
>>>>>>>>>>
>>>>>>>>>> And also one difference i found was this in the Loris-mri code (
>>>>>>>>>> left 1st workable vm, right 2nd vm that has to be fixed, although i changed
>>>>>>>>>> it seems to be independent of the uninitialized value $_ )
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> [image: image.png]
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> Sotirios
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar <
>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> that is puzzling... A few additional questions:
>>>>>>>>>>>
>>>>>>>>>>>    - what is the bash variable TMPDIR set to on the environment
>>>>>>>>>>>    file?
>>>>>>>>>>>    - could you try running separately dcm2mnc on the DICOM
>>>>>>>>>>>    folder to see if that works?
>>>>>>>>>>>    - could you send us the detailed log from the notification
>>>>>>>>>>>    spool table (SELECT * FROM notification_spool WHERE UploadID=<your
>>>>>>>>>>>    uploadID>) and send it back to us? Maybe there are some additional clues
>>>>>>>>>>>    that could help figuring out what is going on.
>>>>>>>>>>>
>>>>>>>>>>> Thank you!
>>>>>>>>>>>
>>>>>>>>>>> C?cile
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Nov 26, 2019 at 10:12 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>
>>>>>>>>>>>> I checked for the StudyInstacueUID at the files with "The
>>>>>>>>>>>> target directory does not contain a single DICOM file"" and their attribute
>>>>>>>>>>>> has a value.
>>>>>>>>>>>>
>>>>>>>>>>>> Regarding the scouter and localizer, i modified the settings in
>>>>>>>>>>>> the imaging pipeline and now i don't get that error message, but still it
>>>>>>>>>>>> doesn't create the mnics.
>>>>>>>>>>>>
>>>>>>>>>>>> The errors i am getting are ( uninitialized value $_ is not
>>>>>>>>>>>> important? because i haven't got comments about that )
>>>>>>>>>>>>
>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>> Running now the following command:
>>>>>>>>>>>> /data/loris/data//uploadNeuroDB/imaging_upload_file.pl
>>>>>>>>>>>> -profile prod -upload_id 134 /data/incoming/DCC0025_118008_V1.tar.gz
>>>>>>>>>>>> -verbose
>>>>>>>>>>>>
>>>>>>>>>>>> and
>>>>>>>>>>>>
>>>>>>>>>>>> Number of MINC files that will be considered for inserting into
>>>>>>>>>>>> the database: 0
>>>>>>>>>>>>
>>>>>>>>>>>> No data could be converted into valid MINC files.
>>>>>>>>>>>>
>>>>>>>>>>>> The tarchiveLoader.pl insertion script has failed.
>>>>>>>>>>>> Use of uninitialized value $mail_user in concatenation (.) or
>>>>>>>>>>>> string at /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>> line 249.
>>>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>>>>>>>> batch_uploads_imageuploader.pl line 250.
>>>>>>>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>>>>>>>> batch_uploads_imageuploader.pl line 251.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks
>>>>>>>>>>>>
>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>
>>>>>>>>>>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>
>>>>>>>>>>>>> OK. So the issue I mentioned should not be a problem for you.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Is the StudyInstanceUID DICOM header set in your images? If it
>>>>>>>>>>>>> is not set, then you would end up with the error message "The target
>>>>>>>>>>>>> directory does not contain a single DICOM file". So maybe this is the issue
>>>>>>>>>>>>> you are having with those datasets?
>>>>>>>>>>>>>
>>>>>>>>>>>>> Regarding not excluding series descriptions, you can configure
>>>>>>>>>>>>> that in the Config module under the Imaging Pipeline section. Simply remove
>>>>>>>>>>>>> all entries for the "Series description to exclude from imaging insertion"
>>>>>>>>>>>>> setting.
>>>>>>>>>>>>>
>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Mon, Nov 25, 2019 at 9:58 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> We are using this version
>>>>>>>>>>>>>> https://github.com/aces/Loris/archive/v21.0.0.zip. Is it
>>>>>>>>>>>>>> possible to insert low resolution now?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, <
>>>>>>>>>>>>>> cecile.madjar at mcin.ca> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Which version of LORIS-MRI are you using?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> There was a bug that got resolved in 20.2 in
>>>>>>>>>>>>>>> get_dicom_info.pl. Basically, if a DICOM did not have the
>>>>>>>>>>>>>>> (0020,0032) header, get_dicom_info.pl considered that the
>>>>>>>>>>>>>>> file was not a DICOM, which was a mistake. This got fixed in version 20.2
>>>>>>>>>>>>>>> of LORIS-MRI. Hopefully this is the issue you are encountering.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> About scout and localizer, they are a type of short and low
>>>>>>>>>>>>>>> resolution sequence that is used by the tech but is of no interest
>>>>>>>>>>>>>>> scientifically, which is why we tend to no insert them.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> i executed the find command and the output i got per folder
>>>>>>>>>>>>>>>> was "DICOM medical imaging data. Maybe there is something wrong with the
>>>>>>>>>>>>>>>> find command in the warning that it is unable to check if the file is a
>>>>>>>>>>>>>>>> dicom file? Also when i use get_dicom_info.pl i don't get
>>>>>>>>>>>>>>>> any output data. Finally i don't understand what scout or localizer is (
>>>>>>>>>>>>>>>> something like if and only if a file fails then the whole session is
>>>>>>>>>>>>>>>> invalid? ).
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I took a closer look to the
>>>>>>>>>>>>>>>>> batch_uploader_multiple_output.txt file you sent. It looks like there are
>>>>>>>>>>>>>>>>> different reasons for failure depending on the DICOM folder uploaded.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>    - For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908
>>>>>>>>>>>>>>>>>    DCC0007 V1: it looks like there is no file of type DICOM in the folder.
>>>>>>>>>>>>>>>>>    Have you checked to see if that is indeed the case? Maybe you can try
>>>>>>>>>>>>>>>>>    running the following command on that folder to see what are the types of
>>>>>>>>>>>>>>>>>    the files? If it does not return at least one DICOM medical imaging data
>>>>>>>>>>>>>>>>>    file, then that is why you get the error message from the pipeline:
>>>>>>>>>>>>>>>>>       -
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>       find <my_dicom_archive_root_folder> -type f | xargs -i file {}|cut -d: -f2|sort|uniq
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>       - For 864173 DCC0001 V1: it looks like there are
>>>>>>>>>>>>>>>>>    two different DICOM studies within the same folder. You will need to split
>>>>>>>>>>>>>>>>>    that study in two based on the StudyUID field as the insertion pipeline
>>>>>>>>>>>>>>>>>    does not allow for more than one StudyUID per upload.
>>>>>>>>>>>>>>>>>    - For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975
>>>>>>>>>>>>>>>>>    DCC0006 V1: it looks like the dcm2mnc command did not produce any MINC
>>>>>>>>>>>>>>>>>    files. Can you check in the DICOM archive what are the series present in
>>>>>>>>>>>>>>>>>    the tarchive for that visit? Maybe only a scout or localizer was acquired
>>>>>>>>>>>>>>>>>    for that session, hence the no valid MINC files (scout and localizer being
>>>>>>>>>>>>>>>>>    skipped for the conversion)
>>>>>>>>>>>>>>>>>    - For 397410 DCC0003 V1: it looks like everything went
>>>>>>>>>>>>>>>>>    well for this one.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> One script that is called by our pipeline is called
>>>>>>>>>>>>>>>>> get_dicom_info.pl and this does all kind of checks on the
>>>>>>>>>>>>>>>>> DICOM files (it is being called when running the dcm2mnc conversion). You
>>>>>>>>>>>>>>>>> could run it independently on your folder if needed.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Since one of the study got in, it does not look like you
>>>>>>>>>>>>>>>>> are having a problem with the setup. It seems more likely to be a problem
>>>>>>>>>>>>>>>>> with the data themselves.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hope this helps.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> In my first vm i am able to create the minc files and
>>>>>>>>>>>>>>>>>> view them at the mri browser (except of candidate 102761034 ), meanwhile
>>>>>>>>>>>>>>>>>> the same files gives warnings at the 2nd vm. The output  of the batch
>>>>>>>>>>>>>>>>>> upload can be seen in the file attached.
>>>>>>>>>>>>>>>>>> Also a colleague of us has built a pre-validation tool
>>>>>>>>>>>>>>>>>> for dicom
>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/
>>>>>>>>>>>>>>>>>> which had found all the files that Loris gave as warning . Basically I
>>>>>>>>>>>>>>>>>> confirmed that the total amount of files per dicom was the same amount as
>>>>>>>>>>>>>>>>>> stated in Loris and checked some filenames given from warning to confirm
>>>>>>>>>>>>>>>>>> that they match with our tool. But that was months ago and my colleague had
>>>>>>>>>>>>>>>>>> changed some parameters for MIP and now our tool doesn't find all the
>>>>>>>>>>>>>>>>>> invalid files, that's why i asked for the dicom header specification of
>>>>>>>>>>>>>>>>>> Loris. In a discussion we had he mentioned that he doesn't check for some
>>>>>>>>>>>>>>>>>> tags e.x. orientation. Lastly to mention that in my first vm i didn't use
>>>>>>>>>>>>>>>>>> our tool to remove invalid dcm files.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>> Can you provide us with some fresh particulars of the
>>>>>>>>>>>>>>>>>>> current issue and we'll take it from there?
>>>>>>>>>>>>>>>>>>> Yang's team has built these scripts which can definitely
>>>>>>>>>>>>>>>>>>> serve as a model for your pre-validation of your DICOM collections.
>>>>>>>>>>>>>>>>>>> cheers,
>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios
>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> HI Yang,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> We make use of pydicom library too. Now about the
>>>>>>>>>>>>>>>>>>>> validate.py i see that you check if some attributes are missing such as
>>>>>>>>>>>>>>>>>>>> PatientID, PatientName which all of our files contains that info. Maybe i
>>>>>>>>>>>>>>>>>>>> have missed something on the setup of my other virtual machine ( although
>>>>>>>>>>>>>>>>>>>> one dicom passed on the new vm successfully, the others that were inserted
>>>>>>>>>>>>>>>>>>>> correctly on my old vm fails on the new one ), i think that i had asked
>>>>>>>>>>>>>>>>>>>> about this error "Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>> line 144." but i don't remember the solution.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding <
>>>>>>>>>>>>>>>>>>>> it at cnbp.ca> ??????:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Hey, Sotirios,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Christine from the LORIS team mentioned you had some
>>>>>>>>>>>>>>>>>>>>> issue with DICOM.  I am a fellow developer for an external project using
>>>>>>>>>>>>>>>>>>>>> LORIS, kind of just like you. We had to implement DICOM upload as well but
>>>>>>>>>>>>>>>>>>>>> more as a fully automated pipeline actually.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> While we were building CNBP, we had coded up some
>>>>>>>>>>>>>>>>>>>>> minor Python functions to check DICOM integrity (and simple validations)
>>>>>>>>>>>>>>>>>>>>> and you might be able to gain some inspiration from it and help you with
>>>>>>>>>>>>>>>>>>>>> your cause. For more comprehensive solution, PyDICOM (
>>>>>>>>>>>>>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#)  seems
>>>>>>>>>>>>>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks
>>>>>>>>>>>>>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can
>>>>>>>>>>>>>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty
>>>>>>>>>>>>>>>>>>>>> rough around the edges but hopefully point you in the right direcitons
>>>>>>>>>>>>>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Yang Ding, PhD.
>>>>>>>>>>>>>>>>>>>>> Canadian Neonatal Brain Platform Architect
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM <
>>>>>>>>>>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Send Loris-dev mailing list submissions to
>>>>>>>>>>>>>>>>>>>>>>         loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> To subscribe or unsubscribe via the World Wide Web,
>>>>>>>>>>>>>>>>>>>>>> visit
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>> or, via email, send a message with subject or body
>>>>>>>>>>>>>>>>>>>>>> 'help' to
>>>>>>>>>>>>>>>>>>>>>>         loris-dev-request at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> You can reach the person managing the list at
>>>>>>>>>>>>>>>>>>>>>>         loris-dev-owner at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> When replying, please edit your Subject line so it is
>>>>>>>>>>>>>>>>>>>>>> more specific
>>>>>>>>>>>>>>>>>>>>>> than "Re: Contents of Loris-dev digest..."
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Today's Topics:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>    1. Re: Import mri - scripts (Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos)
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Message: 1
>>>>>>>>>>>>>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200
>>>>>>>>>>>>>>>>>>>>>> From: Sotirios Nikoloutsopoulos <sotirisnik at gmail.com
>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>> To: Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>> Message-ID:
>>>>>>>>>>>>>>>>>>>>>>         <CAKHj7uST=
>>>>>>>>>>>>>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com
>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Could we send you a link with 10 anonymized dicom
>>>>>>>>>>>>>>>>>>>>>> files to diagnose the
>>>>>>>>>>>>>>>>>>>>>> warnings we get?
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> > Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>> > We were wondering whether Loris has a tool to check
>>>>>>>>>>>>>>>>>>>>>> if there are problems
>>>>>>>>>>>>>>>>>>>>>> > with the dcm files, before trying to upload them.
>>>>>>>>>>>>>>>>>>>>>> Something that could
>>>>>>>>>>>>>>>>>>>>>> > provide the same results provided in the
>>>>>>>>>>>>>>>>>>>>>> warning_output, this is the
>>>>>>>>>>>>>>>>>>>>>> > summary from the mri_upload at the front-page. Also
>>>>>>>>>>>>>>>>>>>>>> which attributes of the
>>>>>>>>>>>>>>>>>>>>>> > dcm header would trigger a warning? is there a dcm
>>>>>>>>>>>>>>>>>>>>>> file header
>>>>>>>>>>>>>>>>>>>>>> > specification for Loris?
>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>> > Thanks
>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>> > Sotirios
>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> > sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp function
>>>>>>>>>>>>>>>>>>>>>> it worked,but i
>>>>>>>>>>>>>>>>>>>>>> >> thought that something else was causing the 2nd
>>>>>>>>>>>>>>>>>>>>>> issue.
>>>>>>>>>>>>>>>>>>>>>> >> Thanks
>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher,
>>>>>>>>>>>>>>>>>>>>>> Mr, <
>>>>>>>>>>>>>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> The first error occurs because the
>>>>>>>>>>>>>>>>>>>>>> QCFirstChangeTime and columns are of
>>>>>>>>>>>>>>>>>>>>>> >>> type `unsigned integer` and not `datatime`. You
>>>>>>>>>>>>>>>>>>>>>> should be using
>>>>>>>>>>>>>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW().
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> The second error occurs because the trigger
>>>>>>>>>>>>>>>>>>>>>> triggers a rollback of the
>>>>>>>>>>>>>>>>>>>>>> >>> insert statement in the files table.
>>>>>>>>>>>>>>>>>>>>>> >>> See mysql documentation for trigger error
>>>>>>>>>>>>>>>>>>>>>> handling.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> An error during either a BEFORE or AFTER trigger
>>>>>>>>>>>>>>>>>>>>>> results in failure of
>>>>>>>>>>>>>>>>>>>>>> >>> the entire statement that caused trigger
>>>>>>>>>>>>>>>>>>>>>> invocation.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thank you for sharing that. I hope it helps.
>>>>>>>>>>>>>>>>>>>>>> >>> -- Xavier
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf
>>>>>>>>>>>>>>>>>>>>>> of Sotirios
>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM
>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>> >>> Christine Rogers, Ms. <christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> When mincs are inserted their corresponding rows
>>>>>>>>>>>>>>>>>>>>>> at the file table are
>>>>>>>>>>>>>>>>>>>>>> >>> inserted too
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> i would like to insert their rows at
>>>>>>>>>>>>>>>>>>>>>> file_qcstatus as well, because i
>>>>>>>>>>>>>>>>>>>>>> >>> don't want manually to label them as passed
>>>>>>>>>>>>>>>>>>>>>> throught the interface
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> That is the trigger i wrote
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER
>>>>>>>>>>>>>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER
>>>>>>>>>>>>>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW
>>>>>>>>>>>>>>>>>>>>>> >>> BEGIN
>>>>>>>>>>>>>>>>>>>>>> >>> INSERT INTO files_qcstatus
>>>>>>>>>>>>>>>>>>>>>> >>> SET FileID = NEW.FileID,
>>>>>>>>>>>>>>>>>>>>>> >>>      SeriesUID = NEW.SeriesUID,
>>>>>>>>>>>>>>>>>>>>>> >>>      EchoTime = NEW.EchoTime,
>>>>>>>>>>>>>>>>>>>>>> >>>      QCStatus = "Pass",
>>>>>>>>>>>>>>>>>>>>>> >>>      QCFirstChangeTime = NOW(),
>>>>>>>>>>>>>>>>>>>>>> >>>      QCLastChangeTime = NOW();
>>>>>>>>>>>>>>>>>>>>>> >>> END
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> although it contains some errors
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range value for
>>>>>>>>>>>>>>>>>>>>>> column
>>>>>>>>>>>>>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at
>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm
>>>>>>>>>>>>>>>>>>>>>> line 823.
>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a
>>>>>>>>>>>>>>>>>>>>>> child row: a foreign
>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`parameter_file`,
>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT
>>>>>>>>>>>>>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`)
>>>>>>>>>>>>>>>>>>>>>> REFERENCES `files` (`FileID`))
>>>>>>>>>>>>>>>>>>>>>> >>> at
>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>>>>>> Madjar <
>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> In the mri_upload table, there is a TarchiveID
>>>>>>>>>>>>>>>>>>>>>> column associated with
>>>>>>>>>>>>>>>>>>>>>> >>> the MRI upload you inserted. When this value is
>>>>>>>>>>>>>>>>>>>>>> NULL, it means no DICOMs
>>>>>>>>>>>>>>>>>>>>>> >>> were inserted into the tarchive tables. At the
>>>>>>>>>>>>>>>>>>>>>> end of the insertion of the
>>>>>>>>>>>>>>>>>>>>>> >>> DICOMs in the tarchive tables, this value is
>>>>>>>>>>>>>>>>>>>>>> updated with the correct
>>>>>>>>>>>>>>>>>>>>>> >>> TarchiveID associated with the upload.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Could this correspond to what you want to do?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Regarding the files_qcstatus, this table is only
>>>>>>>>>>>>>>>>>>>>>> linked to the files
>>>>>>>>>>>>>>>>>>>>>> >>> table (hence, the MINC files). You could always
>>>>>>>>>>>>>>>>>>>>>> create a new table for
>>>>>>>>>>>>>>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive table?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> i would like whenever a dicom is imported to mark
>>>>>>>>>>>>>>>>>>>>>> all their
>>>>>>>>>>>>>>>>>>>>>> >>> coressponding qc_status to "pass". I was thinking
>>>>>>>>>>>>>>>>>>>>>> of creating a trigger for
>>>>>>>>>>>>>>>>>>>>>> >>> that, but which tables do i need to add entries
>>>>>>>>>>>>>>>>>>>>>> to? So far from what i see
>>>>>>>>>>>>>>>>>>>>>> >>> i need to add entres at  the table "files"
>>>>>>>>>>>>>>>>>>>>>> whenever an insertion happens to
>>>>>>>>>>>>>>>>>>>>>> >>> files_qcstatus.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Oh, sorry i should have asked for StudyID, at the
>>>>>>>>>>>>>>>>>>>>>> beginning of my email
>>>>>>>>>>>>>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID).
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> that's the Study Instance UID, not the StudyID.
>>>>>>>>>>>>>>>>>>>>>> So the StudyID i am
>>>>>>>>>>>>>>>>>>>>>> >>> looking for is not stored in the database?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thanks.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>>>>>> Madjar <
>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> The StudyUID is stored in the DicomArchiveID
>>>>>>>>>>>>>>>>>>>>>> field of the
>>>>>>>>>>>>>>>>>>>>>> >>> tarchive table. It can also be found in the
>>>>>>>>>>>>>>>>>>>>>> metadata field but it is mixed
>>>>>>>>>>>>>>>>>>>>>> >>> with many other information.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Is StudyUID stored somewhere at the tables? At
>>>>>>>>>>>>>>>>>>>>>> the tarchive table,
>>>>>>>>>>>>>>>>>>>>>> >>> specifically at the AcquisitonMetadata column i
>>>>>>>>>>>>>>>>>>>>>> found something called
>>>>>>>>>>>>>>>>>>>>>> >>> 'Unique Study ID" in its context, but that must
>>>>>>>>>>>>>>>>>>>>>> be the Study Instance UID.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>>>>>> Madjar <
>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Your observation is correct. A little explanation
>>>>>>>>>>>>>>>>>>>>>> below.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> MINC files get inserted into the MRI violation
>>>>>>>>>>>>>>>>>>>>>> tables if:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>    - the scan type could not be identified (not
>>>>>>>>>>>>>>>>>>>>>> matching an entry in
>>>>>>>>>>>>>>>>>>>>>> >>>    the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>> >>>    - one parameter of the scan type is out of the
>>>>>>>>>>>>>>>>>>>>>> expected range
>>>>>>>>>>>>>>>>>>>>>> >>>    present in the mri_protocol_checks (extra
>>>>>>>>>>>>>>>>>>>>>> filtering in case you need to be
>>>>>>>>>>>>>>>>>>>>>> >>>    stricker on some parameters not present in the
>>>>>>>>>>>>>>>>>>>>>> mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>> >>>    - if the CandID and PSCID do not match
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> The following cases do not get in the MRI
>>>>>>>>>>>>>>>>>>>>>> violation tables as it happens
>>>>>>>>>>>>>>>>>>>>>> >>> before the conversion of the DICOM to MINC files
>>>>>>>>>>>>>>>>>>>>>> and only MINC files
>>>>>>>>>>>>>>>>>>>>>> >>> violations are logged there:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>    - "No single DICOM" (since no valid DICOM
>>>>>>>>>>>>>>>>>>>>>> could be found to convert
>>>>>>>>>>>>>>>>>>>>>> >>>    to MINC)
>>>>>>>>>>>>>>>>>>>>>> >>>    - "Study already inserted" (duplicate
>>>>>>>>>>>>>>>>>>>>>> StudyUID) since this error
>>>>>>>>>>>>>>>>>>>>>> >>>    happens at the dicomTar.pl level (way before
>>>>>>>>>>>>>>>>>>>>>> conversion into MINC files)
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Glad everything is working out!!
>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> the mri passed, for some reason it consumed
>>>>>>>>>>>>>>>>>>>>>> 5.12GB of ram. Now about the
>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations, dicoms are triggered to be
>>>>>>>>>>>>>>>>>>>>>> inserted there only if there is
>>>>>>>>>>>>>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general for
>>>>>>>>>>>>>>>>>>>>>> its header parameter?
>>>>>>>>>>>>>>>>>>>>>> >>> Because i don't see the cases of 'No single
>>>>>>>>>>>>>>>>>>>>>> dicom" or with the 2 studyiuid
>>>>>>>>>>>>>>>>>>>>>> >>> to be there.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>>>>>> Madjar <
>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Sorry to hear you are having issues with the
>>>>>>>>>>>>>>>>>>>>>> memory. I think most of our
>>>>>>>>>>>>>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you
>>>>>>>>>>>>>>>>>>>>>> should be fine.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> about that dicom that had that insertion error
>>>>>>>>>>>>>>>>>>>>>> it's about 30mb and when
>>>>>>>>>>>>>>>>>>>>>> >>> it is being processed the ram is being
>>>>>>>>>>>>>>>>>>>>>> drastically increased from 2gb to
>>>>>>>>>>>>>>>>>>>>>> >>> 3.28 and then the whole virtual machine is
>>>>>>>>>>>>>>>>>>>>>> frozen. What is the recommended
>>>>>>>>>>>>>>>>>>>>>> >>> size of ram for using Loris?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>>>>>> Madjar <
>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Glad to see that the StudyUID problem was fixed!
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> For the delete script issue, if you are
>>>>>>>>>>>>>>>>>>>>>> absolutely certain that no
>>>>>>>>>>>>>>>>>>>>>> >>> processes are run for that uploadID, you can
>>>>>>>>>>>>>>>>>>>>>> update the mri_upload table
>>>>>>>>>>>>>>>>>>>>>> >>> and set the column Inserting to 0 instead of 1
>>>>>>>>>>>>>>>>>>>>>> for that uploadID. It
>>>>>>>>>>>>>>>>>>>>>> >>> looks like for some reason the scripts did not
>>>>>>>>>>>>>>>>>>>>>> update this field when it
>>>>>>>>>>>>>>>>>>>>>> >>> stopped the insertion. Not sure why that would be
>>>>>>>>>>>>>>>>>>>>>> the case though.
>>>>>>>>>>>>>>>>>>>>>> >>> Note: only do that update if you are certain that
>>>>>>>>>>>>>>>>>>>>>> there is no processing
>>>>>>>>>>>>>>>>>>>>>> >>> happening.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> about the Dicoms i reported that didn't have a
>>>>>>>>>>>>>>>>>>>>>> StudyID they actually do
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> I thought that this might be a permission because
>>>>>>>>>>>>>>>>>>>>>> "w" was missing at the
>>>>>>>>>>>>>>>>>>>>>> >>> group. After using chmod -R 775 only 102809579
>>>>>>>>>>>>>>>>>>>>>> passed, but with no mnic
>>>>>>>>>>>>>>>>>>>>>> >>> files. Also now i have this error
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox
>>>>>>>>>>>>>>>>>>>>>> :/data/loris/bin/mri/tools$
>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore
>>>>>>>>>>>>>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is
>>>>>>>>>>>>>>>>>>>>>> currently processing it.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> How can solve this?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Here is our auto dicom uploading python script:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> To give you a brief idea:
>>>>>>>>>>>>>>>>>>>>>> >>> Per folder it will:
>>>>>>>>>>>>>>>>>>>>>> >>> 1) Delete all the .bak files
>>>>>>>>>>>>>>>>>>>>>> >>> 2) Locate .dcm files and update the Patient header
>>>>>>>>>>>>>>>>>>>>>> >>> 3) Furthermore we are interesting in finding
>>>>>>>>>>>>>>>>>>>>>> TR_min, TR_max, TE_min,
>>>>>>>>>>>>>>>>>>>>>> >>> TE_max parameters of T1 protocol and do an update
>>>>>>>>>>>>>>>>>>>>>> at the mri_protocol table
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205
>>>>>>>>>>>>>>>>>>>>>> >>> For some reason some files are missing
>>>>>>>>>>>>>>>>>>>>>> SeriesDescription/ProtocolName
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> In total i have 7 folders
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> 3/7 passed
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Also about the first patient with DC0000 had a
>>>>>>>>>>>>>>>>>>>>>> violation "T1 AXIAL SE
>>>>>>>>>>>>>>>>>>>>>> >>> GADO", but my script didn't output a TE of 17
>>>>>>>>>>>>>>>>>>>>>> nowhere and i find that weird
>>>>>>>>>>>>>>>>>>>>>> >>> since Loris detects the SeriesDescription.
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Now about the 4/7 that didn't passed
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> 102327840 and 102809579 outputs "The target
>>>>>>>>>>>>>>>>>>>>>> directory does not contain a
>>>>>>>>>>>>>>>>>>>>>> >>> single DICOM file.", therefore they are missing
>>>>>>>>>>>>>>>>>>>>>> their StudyUID
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it with
>>>>>>>>>>>>>>>>>>>>>> data from multiple
>>>>>>>>>>>>>>>>>>>>>> >>> studies."
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> and 102761034 "No data could be converted into
>>>>>>>>>>>>>>>>>>>>>> valid MINC files.
>>>>>>>>>>>>>>>>>>>>>> >>> localizer, scout will not be considered!" What is
>>>>>>>>>>>>>>>>>>>>>> this?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> If i wanted to force the insertion of 102327840,
>>>>>>>>>>>>>>>>>>>>>> 102809579 and 102506134
>>>>>>>>>>>>>>>>>>>>>> >>> can i just pass a flag parameter to
>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl? or
>>>>>>>>>>>>>>>>>>>>>> >>> modify imaging_upload_file.pl?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thank you,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Sotirios
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> PS
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> To diagnose a folder search the name of the
>>>>>>>>>>>>>>>>>>>>>> folder at dicom_output.txt.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear about your progress.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Yes, the script you used to delete imaging data
>>>>>>>>>>>>>>>>>>>>>> is fully documented here
>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>> >>> -- let us know if you didn't find the answers you
>>>>>>>>>>>>>>>>>>>>>> were looking for there.
>>>>>>>>>>>>>>>>>>>>>> >>> (Is it possible the null row in *mri_scanner*
>>>>>>>>>>>>>>>>>>>>>> seen in your database
>>>>>>>>>>>>>>>>>>>>>> >>> management software is a visual placeholder for
>>>>>>>>>>>>>>>>>>>>>> you as the user?  I'm not
>>>>>>>>>>>>>>>>>>>>>> >>> sure why a scanner would ever be registered with
>>>>>>>>>>>>>>>>>>>>>> ID='0' as your screenshot
>>>>>>>>>>>>>>>>>>>>>> >>> showed.)
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> I fixed it with this
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> I tried to create a new candidate using the API,
>>>>>>>>>>>>>>>>>>>>>> is there something
>>>>>>>>>>>>>>>>>>>>>> >>> wrong with the structure? why did i receive a 500
>>>>>>>>>>>>>>>>>>>>>> internal error? In the
>>>>>>>>>>>>>>>>>>>>>> >>> loris-error log it state that there is something
>>>>>>>>>>>>>>>>>>>>>> wrong with token, but i
>>>>>>>>>>>>>>>>>>>>>> >>> verfied that the type of the token is a string.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error]
>>>>>>>>>>>>>>>>>>>>>> [pid 4535] [client
>>>>>>>>>>>>>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error:  Uncaught
>>>>>>>>>>>>>>>>>>>>>> TypeError: Argument 1
>>>>>>>>>>>>>>>>>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate()
>>>>>>>>>>>>>>>>>>>>>> must be of the type string,
>>>>>>>>>>>>>>>>>>>>>> >>> null given, called in
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and
>>>>>>>>>>>>>>>>>>>>>> >>> defined in
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
>>>>>>>>>>>>>>>>>>>>>> >>> trace:\n#0
>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):
>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2
>>>>>>>>>>>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
>>>>>>>>>>>>>>>>>>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
>>>>>>>>>>>>>>>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
>>>>>>>>>>>>>>>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST',
>>>>>>>>>>>>>>>>>>>>>> Array)\n#5 {main}\n  thrown in
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Is there a way also to delete candidates? Just to
>>>>>>>>>>>>>>>>>>>>>> let you know what i
>>>>>>>>>>>>>>>>>>>>>> >>> did to clear candidates, because maybe i may have
>>>>>>>>>>>>>>>>>>>>>> missed dependencies.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> First i deleted all their uploads
>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is
>>>>>>>>>>>>>>>>>>>>>> there a way to omit
>>>>>>>>>>>>>>>>>>>>>> >>> the backup file ? )
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Afterwards i had some scanner candidates, so i
>>>>>>>>>>>>>>>>>>>>>> deleted all the entries
>>>>>>>>>>>>>>>>>>>>>> >>> from mri_scanner except that i couldn't delete
>>>>>>>>>>>>>>>>>>>>>> this entry with the 0 ID.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Lastly i deleted the session and then the
>>>>>>>>>>>>>>>>>>>>>> candidate table.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> We recommend that you use our existing tools for
>>>>>>>>>>>>>>>>>>>>>> creating new candidates
>>>>>>>>>>>>>>>>>>>>>> >>> - either the LORIS API or if you are using a PHP
>>>>>>>>>>>>>>>>>>>>>> script, by calling the Candidate
>>>>>>>>>>>>>>>>>>>>>> >>> class's createNew()
>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200
>>>>>>>>>>>>>>>>>>>>>> >function.
>>>>>>>>>>>>>>>>>>>>>> >>> These will create the necessary records for you.
>>>>>>>>>>>>>>>>>>>>>> (It's not recommended to
>>>>>>>>>>>>>>>>>>>>>> >>> make direct modifications to mysql database
>>>>>>>>>>>>>>>>>>>>>> tables in your script, if I
>>>>>>>>>>>>>>>>>>>>>> >>> understand you.)
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> The CandID should be a randomized 6 digit
>>>>>>>>>>>>>>>>>>>>>> randomized ID, and there are
>>>>>>>>>>>>>>>>>>>>>> >>> multiple reasons for this.
>>>>>>>>>>>>>>>>>>>>>> >>> You can use the PSCID for project-specific IDs
>>>>>>>>>>>>>>>>>>>>>> and the External ID field
>>>>>>>>>>>>>>>>>>>>>> >>> in the candidate table can also be used for any
>>>>>>>>>>>>>>>>>>>>>> values you like.
>>>>>>>>>>>>>>>>>>>>>> >>> Additionally, any number of custom IDs can be
>>>>>>>>>>>>>>>>>>>>>> added in parallel - these
>>>>>>>>>>>>>>>>>>>>>> >>> are entered/visible in the Candidate Information
>>>>>>>>>>>>>>>>>>>>>> module and added in the
>>>>>>>>>>>>>>>>>>>>>> >>> back-end as candidate parameters.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> We are building a script that will auto insert
>>>>>>>>>>>>>>>>>>>>>> the candidates based on
>>>>>>>>>>>>>>>>>>>>>> >>> their ExternalID. We would like to know whethere
>>>>>>>>>>>>>>>>>>>>>> when we are creating a new
>>>>>>>>>>>>>>>>>>>>>> >>> profile in the candidate table, if we also have
>>>>>>>>>>>>>>>>>>>>>> to insert a new record at
>>>>>>>>>>>>>>>>>>>>>> >>> another table? Furthermore is there a problem
>>>>>>>>>>>>>>>>>>>>>> that in our case CandID won't
>>>>>>>>>>>>>>>>>>>>>> >>> be a 6digit? ( should we start it from 100000?)
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie
>>>>>>>>>>>>>>>>>>>>>> Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> That would normally be the case but the numeric
>>>>>>>>>>>>>>>>>>>>>> part of the PSCID get
>>>>>>>>>>>>>>>>>>>>>> >>> paded with 0 on the left.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Ex. for sequential ID made of center ID of `ABC`
>>>>>>>>>>>>>>>>>>>>>> plus 4 numerical char
>>>>>>>>>>>>>>>>>>>>>> >>> with a min value of 1, the sequence would be:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ABC0001
>>>>>>>>>>>>>>>>>>>>>> >>> ABC0002
>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>> >>> ABC0010
>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> thus sorting them ascending will always get the
>>>>>>>>>>>>>>>>>>>>>> latest value generated
>>>>>>>>>>>>>>>>>>>>>> >>> as the max value.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15
>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>> melanie.legault2 at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> I see, although the PSCID value is varchar(255),
>>>>>>>>>>>>>>>>>>>>>> it must be stored
>>>>>>>>>>>>>>>>>>>>>> >>> within a specific length of characters. Otherwise
>>>>>>>>>>>>>>>>>>>>>> if we were to sort
>>>>>>>>>>>>>>>>>>>>>> >>> strings with different lengths the result would
>>>>>>>>>>>>>>>>>>>>>> not be sorted correctly (
>>>>>>>>>>>>>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10,
>>>>>>>>>>>>>>>>>>>>>> 11, 2 ).
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie
>>>>>>>>>>>>>>>>>>>>>> Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hello Sotirios,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> There is no `last value` stored anywhere.
>>>>>>>>>>>>>>>>>>>>>> >>> The code simply look for the PSCID with the max
>>>>>>>>>>>>>>>>>>>>>> value and increase that
>>>>>>>>>>>>>>>>>>>>>> >>> value by 1 in order to generate the next PSCID.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hope this info help.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie Legault | Software developer | Faculty of
>>>>>>>>>>>>>>>>>>>>>> Medicine | McGill
>>>>>>>>>>>>>>>>>>>>>> >>> University
>>>>>>>>>>>>>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf
>>>>>>>>>>>>>>>>>>>>>> of Sotirios
>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43
>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> how does Loris determine the next available PSCID
>>>>>>>>>>>>>>>>>>>>>> value for a new
>>>>>>>>>>>>>>>>>>>>>> >>> candidate?
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization
>>>>>>>>>>>>>>>>>>>>>> >>> e.x in the default case the PSCID is sequential,
>>>>>>>>>>>>>>>>>>>>>> but where do we store the
>>>>>>>>>>>>>>>>>>>>>> >>> last value for the sequential sequence?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> the parameters in the mri_protocol you have
>>>>>>>>>>>>>>>>>>>>>> assigned are global
>>>>>>>>>>>>>>>>>>>>>> >>> standard? or were assigned after trial and error?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Given you have done the initial setup of your
>>>>>>>>>>>>>>>>>>>>>> tables to match your
>>>>>>>>>>>>>>>>>>>>>> >>> intended protocol/parameters according to
>>>>>>>>>>>>>>>>>>>>>> instructions --
>>>>>>>>>>>>>>>>>>>>>> >>> the Troubleshooting guide documentation recommends
>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes
>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>> >>> re-running the pipeline (and first deleting prior
>>>>>>>>>>>>>>>>>>>>>> uploads).
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> *if i were to change their status to resolve what
>>>>>>>>>>>>>>>>>>>>>> would happen?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> I noticed that i can view the mnics at the
>>>>>>>>>>>>>>>>>>>>>> brainbrowser from the
>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations page ( those mnics are stored at
>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/trashbin/
>>>>>>>>>>>>>>>>>>>>>> >>> if i were to click their issue to resolve what
>>>>>>>>>>>>>>>>>>>>>> would happend? would they
>>>>>>>>>>>>>>>>>>>>>> >>> appear in the dicom_archive view too? ).
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> The defaut values of the schema exists in my
>>>>>>>>>>>>>>>>>>>>>> local database. If i adjust
>>>>>>>>>>>>>>>>>>>>>> >>> the default values of TR_min and TE_min the mincs
>>>>>>>>>>>>>>>>>>>>>> will be uploaded?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Is it possible that you haven't set up your
>>>>>>>>>>>>>>>>>>>>>> mri_protocol table ?   (and
>>>>>>>>>>>>>>>>>>>>>> >>> mri_scan_type table too, for additional types of
>>>>>>>>>>>>>>>>>>>>>> scans)
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Like the psc table, this is a pre-requisite for
>>>>>>>>>>>>>>>>>>>>>> the Imaging insertion
>>>>>>>>>>>>>>>>>>>>>> >>> setup : See the install/setup documentation :
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> To add new rows, just use MySQL insert
>>>>>>>>>>>>>>>>>>>>>> statements.  You can adapt the
>>>>>>>>>>>>>>>>>>>>>> >>> insert statements which load the default table
>>>>>>>>>>>>>>>>>>>>>> values --> e.g. Here on
>>>>>>>>>>>>>>>>>>>>>> >>> GitHub :
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>>>>>>>>>>>>>>>>>>>>> >>> (see also the mri_scan_type table)
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> I see that i can edit the values but not how to
>>>>>>>>>>>>>>>>>>>>>> insert new rows.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> If i choose Inserted with flag then will the minc
>>>>>>>>>>>>>>>>>>>>>> be inserted?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear that *dcmodify* worked correctly.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> For the MRI Violations module, the screenshot is
>>>>>>>>>>>>>>>>>>>>>> enough.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> It says "could not identify scan type", which we
>>>>>>>>>>>>>>>>>>>>>> knew already.  Did you
>>>>>>>>>>>>>>>>>>>>>> >>> click on the link on those words?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> It will take you to the next page of the module,
>>>>>>>>>>>>>>>>>>>>>> showing for each scan
>>>>>>>>>>>>>>>>>>>>>> >>> what the scan parameters were, and will also show
>>>>>>>>>>>>>>>>>>>>>> for comparison what's
>>>>>>>>>>>>>>>>>>>>>> >>> stored in your *mri_protocol* table.
>>>>>>>>>>>>>>>>>>>>>> >>> Compare these values to find which parameter was
>>>>>>>>>>>>>>>>>>>>>> not correct according
>>>>>>>>>>>>>>>>>>>>>> >>> to your *mri_protocol* table scan type
>>>>>>>>>>>>>>>>>>>>>> definitions.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> You may end up broadening your mri_protocol value
>>>>>>>>>>>>>>>>>>>>>> ranges (e.g. TR, TE)
>>>>>>>>>>>>>>>>>>>>>> >>> for scans.
>>>>>>>>>>>>>>>>>>>>>> >>> This can be done in the front-end, by editing the
>>>>>>>>>>>>>>>>>>>>>> database table
>>>>>>>>>>>>>>>>>>>>>> >>> directly in the same subpage of the MRI
>>>>>>>>>>>>>>>>>>>>>> Violations module.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> The MRI Violations module features are explained
>>>>>>>>>>>>>>>>>>>>>> in more detail in the
>>>>>>>>>>>>>>>>>>>>>> >>> Help text for this module inside LORIS (click
>>>>>>>>>>>>>>>>>>>>>> the  ["?"] icon in the menu
>>>>>>>>>>>>>>>>>>>>>> >>> bar.)
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide
>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>> >>> :  no MINCs inserted- violated scans
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> looks like my previous email's attachment wasn't
>>>>>>>>>>>>>>>>>>>>>> delivered due to
>>>>>>>>>>>>>>>>>>>>>> >>> security reasons, i uploaded my file at google
>>>>>>>>>>>>>>>>>>>>>> drive
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> From Dicat's view seems that dcmodify worked in
>>>>>>>>>>>>>>>>>>>>>> both cases
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> For the mri_violations i attached the .html
>>>>>>>>>>>>>>>>>>>>>> output from webbrowser, so
>>>>>>>>>>>>>>>>>>>>>> >>> that you can check the filelds easier.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios --
>>>>>>>>>>>>>>>>>>>>>> >>> Great, sounds like more progress.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> About the dcmodify command -- I'm not sure why
>>>>>>>>>>>>>>>>>>>>>> you're getting an Endian
>>>>>>>>>>>>>>>>>>>>>> >>> warning.  (it's a warning not an error, correct?)
>>>>>>>>>>>>>>>>>>>>>> >>> To clarify -- Were the DICOM headers
>>>>>>>>>>>>>>>>>>>>>> (PatientName) all successfully
>>>>>>>>>>>>>>>>>>>>>> >>> relabelled, after the command ran?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> You can use also our DICAT tool (
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/DICAT) to
>>>>>>>>>>>>>>>>>>>>>> >>> verify and/or update local DICOM headers --
>>>>>>>>>>>>>>>>>>>>>> though your dcmodify command is
>>>>>>>>>>>>>>>>>>>>>> >>> a great and fast solution for bulk header updates.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> If you're concerned about fields being changed
>>>>>>>>>>>>>>>>>>>>>> (e.g. "(2001,105f)" from
>>>>>>>>>>>>>>>>>>>>>> >>> the warning message)  - you can also dcmdump a
>>>>>>>>>>>>>>>>>>>>>> DICOM slice before and look
>>>>>>>>>>>>>>>>>>>>>> >>> at these fields specifically.
>>>>>>>>>>>>>>>>>>>>>> >>> It's also not a bad "sanity check" to backup your
>>>>>>>>>>>>>>>>>>>>>> DICOMS before/after
>>>>>>>>>>>>>>>>>>>>>> >>> running dcmodify, and use dcmdump on each version
>>>>>>>>>>>>>>>>>>>>>> to diff the outputs --
>>>>>>>>>>>>>>>>>>>>>> >>> this will pinpoint what changed.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Re the protocol violation -- AcquisitionProtocol
>>>>>>>>>>>>>>>>>>>>>> not recognized or
>>>>>>>>>>>>>>>>>>>>>> >>> unknown :   this means your scans did not match
>>>>>>>>>>>>>>>>>>>>>> what is stored in your
>>>>>>>>>>>>>>>>>>>>>> >>> mri_protocol table.
>>>>>>>>>>>>>>>>>>>>>> >>> Check the MRI Violations front-end module -- can
>>>>>>>>>>>>>>>>>>>>>> you see why they didn't
>>>>>>>>>>>>>>>>>>>>>> >>> match?
>>>>>>>>>>>>>>>>>>>>>> >>> Send us an example, in addition to the contents
>>>>>>>>>>>>>>>>>>>>>> of the mri_protocol
>>>>>>>>>>>>>>>>>>>>>> >>> table, if you can't find the source of the
>>>>>>>>>>>>>>>>>>>>>> mismatch.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>  Here is the psc table
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> I created 2 candidates profiles through the
>>>>>>>>>>>>>>>>>>>>>> interface
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> then runned dcmodify command to a dicom file
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1"
>>>>>>>>>>>>>>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> and got those warning: is this okay?
>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and
>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN and
>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and
>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify at another Dicom didn't show warnings.
>>>>>>>>>>>>>>>>>>>>>> Below you can see the
>>>>>>>>>>>>>>>>>>>>>> >>> execution for the second dicom. Mnics could not
>>>>>>>>>>>>>>>>>>>>>> be inserted due to
>>>>>>>>>>>>>>>>>>>>>> >>> AcquisitionProtocol being unknown.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Running now the following command:
>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>> >>> imaging_upload_file.pl -profile prod -upload_id
>>>>>>>>>>>>>>>>>>>>>> 12
>>>>>>>>>>>>>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>  find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX'
>>>>>>>>>>>>>>>>>>>>>> >>> -delete
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>>>>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database
>>>>>>>>>>>>>>>>>>>>>> -profile prod -verbose
>>>>>>>>>>>>>>>>>>>>>> >>>  Source: /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>> >>> Target: /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Testing for database connectivity.
>>>>>>>>>>>>>>>>>>>>>> >>> Database is available.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> You will archive the dir :
>>>>>>>>>>>>>>>>>>>>>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> You are creating a tar with the following command:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> tar -cf
>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> getting md5sums and gzipping!!
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :    127.0.1.1
>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :    Linux
>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :    lorisadmin
>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>> 2019-09-06 18:36:50
>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814
>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f
>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar.gz
>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e
>>>>>>>>>>>>>>>>>>>>>> >>>  DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Adding archive info into database
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Removing temporary files from target location
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Done adding archive info into database
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation
>>>>>>>>>>>>>>>>>>>>>> >>> -profile prod
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>>>>>>>>>>>>>>>>>>>>> >>> -uploadID 12 -verbose
>>>>>>>>>>>>>>>>>>>>>> >>>  md5sum
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>> >>> Set centerID = 1
>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Number of MINC files that will be considered for
>>>>>>>>>>>>>>>>>>>>>> inserting into the
>>>>>>>>>>>>>>>>>>>>>> >>> database: 2
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is
>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is
>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>> cat
>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Acquisition protocol is unknown
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>   --> The minc file cannot be registered since
>>>>>>>>>>>>>>>>>>>>>> the AcquisitionProtocol
>>>>>>>>>>>>>>>>>>>>>> >>> is unknown
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Sure -- you can delete imaging datasets with the
>>>>>>>>>>>>>>>>>>>>>> *delete_imaging_upload*
>>>>>>>>>>>>>>>>>>>>>> >>> script --
>>>>>>>>>>>>>>>>>>>>>> >>> details here:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> What's in your *psc* table?  (Is it properly
>>>>>>>>>>>>>>>>>>>>>> populated? This is a
>>>>>>>>>>>>>>>>>>>>>> >>> pre-requisite to loading imaging data.
>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database
>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>> >>> The foreign key constraint error on the candidate
>>>>>>>>>>>>>>>>>>>>>> record is curious.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> There are also a few options for creating
>>>>>>>>>>>>>>>>>>>>>> candidates when inserting
>>>>>>>>>>>>>>>>>>>>>> >>> imaging data:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then DICOM
>>>>>>>>>>>>>>>>>>>>>> insertion pipeline
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> a. via the LORIS API -- Create the candidates
>>>>>>>>>>>>>>>>>>>>>> (and visits, optionally I
>>>>>>>>>>>>>>>>>>>>>> >>> think)
>>>>>>>>>>>>>>>>>>>>>> >>> How to:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>>>>>>>>>>>>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by LORIS.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Then as a second step:
>>>>>>>>>>>>>>>>>>>>>> >>> b. Use the imaging insertion pipeline
>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets
>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>> >>> to load your DICOMs.
>>>>>>>>>>>>>>>>>>>>>> >>> You will want to first ensure that the
>>>>>>>>>>>>>>>>>>>>>> PatientName header in the DICOMs
>>>>>>>>>>>>>>>>>>>>>> >>> as well as tar package are correctly labelled
>>>>>>>>>>>>>>>>>>>>>> with PSCID_DCCID_VisitLabel
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets:
>>>>>>>>>>>>>>>>>>>>>> >>> How to :
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options when
>>>>>>>>>>>>>>>>>>>>>> running the bids_import script,
>>>>>>>>>>>>>>>>>>>>>> >>> to automatically create your candidates and
>>>>>>>>>>>>>>>>>>>>>> sessions.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> How do i delete a Study? And everytime do i have
>>>>>>>>>>>>>>>>>>>>>> to create a new
>>>>>>>>>>>>>>>>>>>>>> >>> candidate to get DCCID and a PSCID?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> *First execution:*
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod <
>>>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match
>>>>>>>>>>>>>>>>>>>>>> (m//) at ./
>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a
>>>>>>>>>>>>>>>>>>>>>> child row: a foreign
>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`,
>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_candidate_1`
>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES
>>>>>>>>>>>>>>>>>>>>>> `psc` (`CenterID`)) at
>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm
>>>>>>>>>>>>>>>>>>>>>> line 1060.
>>>>>>>>>>>>>>>>>>>>>> >>> ERROR: Failed to insert record in table
>>>>>>>>>>>>>>>>>>>>>> mri_scanner:
>>>>>>>>>>>>>>>>>>>>>> >>> The following database commands failed:
>>>>>>>>>>>>>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';
>>>>>>>>>>>>>>>>>>>>>> >>> SET
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
>>>>>>>>>>>>>>>>>>>>>> >>> Medical Systems';
>>>>>>>>>>>>>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>>>>>>>>>>>>>>>>>>>>> >>> Error obtained:Cannot add or update a child row:
>>>>>>>>>>>>>>>>>>>>>> a foreign key
>>>>>>>>>>>>>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`,
>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_mri_scanner_1`
>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate`
>>>>>>>>>>>>>>>>>>>>>> (`CandID`)) (error code 1452)
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>  ERROR: The validation has failed. Either re-run
>>>>>>>>>>>>>>>>>>>>>> the validation again
>>>>>>>>>>>>>>>>>>>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl
>>>>>>>>>>>>>>>>>>>>>> using -force to force the
>>>>>>>>>>>>>>>>>>>>>> >>> execution.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> The tarchiveLoader.pl insertion script has failed.
>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./
>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> *And second execution: *
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod <
>>>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match
>>>>>>>>>>>>>>>>>>>>>> (m//) at ./
>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> PROBLEM:
>>>>>>>>>>>>>>>>>>>>>> >>> The user 'lorisadmin' has already inserted this
>>>>>>>>>>>>>>>>>>>>>> study.
>>>>>>>>>>>>>>>>>>>>>> >>> The unique study ID is
>>>>>>>>>>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
>>>>>>>>>>>>>>>>>>>>>> >>> This is the information retained from the first
>>>>>>>>>>>>>>>>>>>>>> time the study was
>>>>>>>>>>>>>>>>>>>>>> >>> inserted:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy
>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :    127.0.1.1
>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :    Linux
>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :    lorisadmin
>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>> 2019-09-04 18:33:05
>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d
>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec
>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar.gz
>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053
>>>>>>>>>>>>>>>>>>>>>> >>>  DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Last update of record:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> The dicomTar.pl execution has failed.
>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./
>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Ok, this sounds like good progress.  Let us know
>>>>>>>>>>>>>>>>>>>>>> when you next encounter
>>>>>>>>>>>>>>>>>>>>>> >>> issues as you progress through the Imaging
>>>>>>>>>>>>>>>>>>>>>> Install/Setup docs
>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>> >.
>>>>>>>>>>>>>>>>>>>>>> >>> I'll look into how we can better handle the
>>>>>>>>>>>>>>>>>>>>>> incoming/ directory next
>>>>>>>>>>>>>>>>>>>>>> >>> time.
>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is
>>>>>>>>>>>>>>>>>>>>>> >>> populated correctly except its port is  'port'
>>>>>>>>>>>>>>>>>>>>>> : ''. Also i have tested
>>>>>>>>>>>>>>>>>>>>>> >>> that i can connect to MySQL with lorisuser.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> I executed the script again, because the only
>>>>>>>>>>>>>>>>>>>>>> error i had previously was
>>>>>>>>>>>>>>>>>>>>>> >>> that the /data/incoming folder didn't exist and
>>>>>>>>>>>>>>>>>>>>>> there are no errors
>>>>>>>>>>>>>>>>>>>>>> >>> reported back except of warnings <<mysql:
>>>>>>>>>>>>>>>>>>>>>> [Warning] Using a password on the
>>>>>>>>>>>>>>>>>>>>>> >>> command line interface can be insecure>>.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> It's possible -- if the script was unable to
>>>>>>>>>>>>>>>>>>>>>> connect to the database
>>>>>>>>>>>>>>>>>>>>>> >>> during its execution (e.g. typo in the password),
>>>>>>>>>>>>>>>>>>>>>> that would explain the
>>>>>>>>>>>>>>>>>>>>>> >>> underpopulated Image path and Loris-MRI code path
>>>>>>>>>>>>>>>>>>>>>> you saw in the Config
>>>>>>>>>>>>>>>>>>>>>> >>> module.
>>>>>>>>>>>>>>>>>>>>>> >>> It's hard to tell without seeing the output from
>>>>>>>>>>>>>>>>>>>>>> your script run -- Did
>>>>>>>>>>>>>>>>>>>>>> >>> you see a sign of any such error?
>>>>>>>>>>>>>>>>>>>>>> >>> The Config fields are populated by the
>>>>>>>>>>>>>>>>>>>>>> imaging_install.sh script (starting
>>>>>>>>>>>>>>>>>>>>>> >>> at line 222
>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222
>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> For example, check if the database connection
>>>>>>>>>>>>>>>>>>>>>> information was populated
>>>>>>>>>>>>>>>>>>>>>> >>> accurately in
>>>>>>>>>>>>>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> If you are referring to the imaging_install.sh
>>>>>>>>>>>>>>>>>>>>>> here is an image with the
>>>>>>>>>>>>>>>>>>>>>> >>> configurations i typed. Maybe the problem is
>>>>>>>>>>>>>>>>>>>>>> somewhere at the last part
>>>>>>>>>>>>>>>>>>>>>> >>> which asks to configure as much as possible
>>>>>>>>>>>>>>>>>>>>>> automatically?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear your LORIS core install is up and
>>>>>>>>>>>>>>>>>>>>>> working and all the
>>>>>>>>>>>>>>>>>>>>>> >>> front-end pages are loading.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$
>>>>>>>>>>>>>>>>>>>>>> chmod 775 project
>>>>>>>>>>>>>>>>>>>>>> >>> > and the web interface worked.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Yes, it's important that project/ have 775
>>>>>>>>>>>>>>>>>>>>>> permissions and that
>>>>>>>>>>>>>>>>>>>>>> >>> lorisadmin be part of the sudoers group, per step
>>>>>>>>>>>>>>>>>>>>>> 1 in the install
>>>>>>>>>>>>>>>>>>>>>> >>> Readme <
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris#install-steps>.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image
>>>>>>>>>>>>>>>>>>>>>> should change LORIS to
>>>>>>>>>>>>>>>>>>>>>> >>> loris, right?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> These imaging paths will be updated during your
>>>>>>>>>>>>>>>>>>>>>> imaging installation
>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup> by an
>>>>>>>>>>>>>>>>>>>>>> automated script --
>>>>>>>>>>>>>>>>>>>>>> >>> you do not need to set them manually via the
>>>>>>>>>>>>>>>>>>>>>> Config module.
>>>>>>>>>>>>>>>>>>>>>> >>> Please continue to follow the Setup Guide
>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup> for
>>>>>>>>>>>>>>>>>>>>>> detailed steps to follow.
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image should
>>>>>>>>>>>>>>>>>>>>>> change LORIS to loris,
>>>>>>>>>>>>>>>>>>>>>> >>> right?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> i used
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x |
>>>>>>>>>>>>>>>>>>>>>> sudo -E bash -
>>>>>>>>>>>>>>>>>>>>>> >>> sudo apt-get install -y nodejs
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> you had suggested in the past, make worked and
>>>>>>>>>>>>>>>>>>>>>> now i can see all the
>>>>>>>>>>>>>>>>>>>>>> >>> contents in the web-interface, but i don't need
>>>>>>>>>>>>>>>>>>>>>> make install?
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>> -------------- next part --------------
>>>>>>>>>>>>>>>>>>>>>> An HTML attachment was scrubbed...
>>>>>>>>>>>>>>>>>>>>>> URL: <
>>>>>>>>>>>>>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html
>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16
>>>>>>>>>>>>>>>>>>>>>> *****************************************
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
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From cecile.madjar at mcin.ca  Wed Jan 29 12:59:21 2020
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Wed, 29 Jan 2020 12:59:21 -0500
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAKHj7uRx1NT7CycFq65uFpgPiOVwvT-jtK1NJX6_3rrLNFwdbA@mail.gmail.com>
References: <mailman.1851.1573565332.16403.loris-dev@bic.mni.mcgill.ca>
 <CAEfMBom1HCWLo4NWgt5XG4625tCBfRT_Z_HepvtT_Er2LKbJoA@mail.gmail.com>
 <CAKHj7uS1AdMDjnacouTvxZgziYVgp5NNUeOuMkpDyrTskGTh-Q@mail.gmail.com>
 <CALbt7NDej8FGUUS6_oKbK5Fp-FnwsVz9AgZ6ZcJEZhmoKZmv8w@mail.gmail.com>
 <CAKHj7uSx-qqcXHZsWsZmSJ7sC1DgF+XapT5Y1+QdoVic37_DDg@mail.gmail.com>
 <CAMkiY3fQBGDGeNO8EHxwYAgbhTggNSQ+AVuCfdraDXwULMjjUg@mail.gmail.com>
 <CAKHj7uT5xXi=pOPdH=W9BroSphMHdTszdgW+GxuES=8wZox9eQ@mail.gmail.com>
 <CAMkiY3eUouxaRVdC4wH+vdjeQ=q_Nx8bcDNzcWgD_OgN77m3mw@mail.gmail.com>
 <CAKHj7uSxu4+tm+=x4+qJ1sAbrjmxG2H7LovDb7-2KMnyYQhrgg@mail.gmail.com>
 <CAMkiY3fdPZec2jx-cc2Zq37j3ekmTu_o819yBUv-bC7M98bkVw@mail.gmail.com>
 <CAKHj7uSZHozpuQ_YwGmy6wQ4tm43vJa556V0o2+JGDVsYaqN4g@mail.gmail.com>
 <CAMkiY3dge=x93bQDv0fHGMcrX0PA8Z_imLb_zSTh=nTrx5weFg@mail.gmail.com>
 <CAKHj7uR81gCkjvccMxwMA08dGSEgyTLJBJ+pZPkoUQDtGP_hFA@mail.gmail.com>
 <CAMkiY3fGhvExZ-JOvxeHe7dJQPvtPAHx3oJuiMVX7f1JgF1GAg@mail.gmail.com>
 <CAKHj7uRExO98Yyn9_07aw44wbh0bCL9_C1VFTAURKsxQLUuAeQ@mail.gmail.com>
 <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>
 <CAKHj7uRueb5fgh4VVCAyaq8tC9WM4gJ7k6Q=dxsqWzFgDqPfVQ@mail.gmail.com>
 <CAMkiY3d-Vt=3gQqwJ+GSRSacbLp2QxrB0g-_C7ONd8j_g1ipoQ@mail.gmail.com>
 <CAKHj7uQt9=nokz5g1zBuBx1-rJ8q7qKOuNVkQugC9wfvNFcjVA@mail.gmail.com>
 <CAMkiY3cAuQfT_5iMzYoF2BXVceu_vgz4eCq2sAtoyse+zUYeSg@mail.gmail.com>
 <CAMkiY3dq1O3V8+r4tTAWQ8N=rVFg=DNY-UPeMqbec+MSayj=Cg@mail.gmail.com>
 <CAKHj7uSEegvE1apPBGVyHmjyVzF+YxJjDMg0b+hDE4_-ON+dYw@mail.gmail.com>
 <CAKHj7uRx1NT7CycFq65uFpgPiOVwvT-jtK1NJX6_3rrLNFwdbA@mail.gmail.com>
Message-ID: <CAMkiY3dAnkLdc4N=REmeCpX2qBfsQf=wRb=YtHtt20f8adXFyw@mail.gmail.com>

Hi Sotirios,

It looks like xargs is not installed in your docker environment.

This is being used by the following command in dicomTar.pl (and a few other
places but that is the one causing the error at the moment):

$cmd = "cd " . $dcm_source . "; find -type f -name '.*' | *xargs* rm -f";

So you need to install xargs in your docker for the command to run.

Hope this helps,

C?cile
On Wed, Jan 29, 2020 at 10:35 AM Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:

> Hello,
>
> We are making a dockerized version of Loris 21 and when we execute the
> batch_uploads_imageuploader.pl we get an error about xargs. What could be
> the casue?
>
> Use of uninitialized value $_ in pattern match (m//) at
> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
> Running now the following command: /data/loris/data//uploadNeuroDB/
> imaging_upload_file.pl -profile prod -upload_id 13
> /data/incoming/DCC0007_854380_V1.tar.gz -verbose
>
>  find -path \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml -name '__MACOSX'
> -delete
> xargs: file: No such file or directory
>
> dicomTar.pl \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml
> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>  Source: /data/tmp/ImagingUpload-15-31-U_O5ml
> Target: /data/loris/data/tarchive
>
> Thanks
>
> ???? ???, 10 ??? 2019 ???? 7:21 ?.?., ?/? Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> ??????:
>
>> Hi,
>>
>> i opened an issue and looked up for the values of Volume they suggested
>> https://github.com/BIC-MNI/minc-toolkit-v2/issues/95. The only
>> attributes associated with it i saw are [0x00089206] and [0x00089207]
>>
>> [image: image.png]
>>
>> I looked up for the file that was being viewed fine in the BrainBrowser
>> and saw that it had that attribute empty so i used this command because i
>> couldn't find a way to modify the attribute via pydicom
>>
>> dcmodify -ma "(0008,9206)=" *.dcm
>>
>> and that command reported the warning about the Endian Syntax. I also
>> used the corresponding command for 9207 and got the message "Tag not found'
>>
>> Lastly I tried to upload some dicoms and now i am getting the SNR and i
>> can view them fine. I believe now that all of them will pass successfully,
>> i will report back later.
>>
>> Thanks,
>>
>> Sotirios
>>
>> ???? ???, 9 ??? 2019 ???? 8:10 ?.?., ?/? Cecile Madjar <
>> cecile.madjar at mcin.ca> ??????:
>>
>>> Hi Sotirios,
>>>
>>> The issue you are having is a indeed a dcm2mnc issue. The converter does
>>> not seem to work on your dataset for some reason. Unfortunately, there is
>>> not much we can do on our front to fix this...
>>>
>>> I would recommend creating an issue on the MINC tools repository
>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> so they can fix
>>> your problem.
>>>
>>> Very sorry that you are having that problem.
>>>
>>> Best,
>>>
>>> C?cile
>>>
>>> On Wed, Dec 4, 2019 at 8:59 AM Cecile Madjar <cecile.madjar at mcin.ca>
>>> wrote:
>>>
>>>> Hi Sotirios,
>>>>
>>>> Could you please share a dataset with us that produces the error you
>>>> get and the weird display in BrainBrowser? You could use the same SFTP
>>>> credential that Nicolas gave you.
>>>>
>>>> The message errors you got from imaging_install.sh are probably due to
>>>> the fact that you reran the install script and it tried to reinstall
>>>> something that was already there. I would not worry about it. FYI, the only
>>>> thing you needed to do was to update the MINC tools path in the environment
>>>> file as you did after re-running imaging_install.sh and source the
>>>> environment file.
>>>>
>>>> Best,
>>>>
>>>> C?cile
>>>>
>>>> On Wed, Dec 4, 2019 at 8:03 AM Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> wrote:
>>>>
>>>>>  Hi Cecile,
>>>>>
>>>>> We used minctool 1.9.7 and we still get this error
>>>>>
>>>>> <<Restructuring...
>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>> Default GSL error handler invoked.
>>>>> noise_estimate --snr /data/loris/data>>
>>>>>
>>>>
>>>>> One dicom folder hadn't that error and is being viewed fine in the
>>>>> BrainBrowser of Loris.
>>>>>
>>>>
>>>>> When i used dpkg to the 1.9.17 the installation reported fine
>>>>> <<Unpacking minc-toolkit-v2 (1.9.17) over (1.9.16) ...>>
>>>>>
>>>>> and then i used source /opt/minc/1.9.17/minc-toolkit-config.sh
>>>>>
>>>>> and aftewards runned bash ./imaging_install.sh just to be sure.
>>>>>
>>>>> We also had to modify /data/loris/bin/mri/environment because it still
>>>>> pointed to the old version.
>>>>>
>>>>> What i found strange is this during the run of imaging_install.sh
>>>>>
>>>>> <<already using interpreter
>>>>> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/bin/python3
>>>>> Please use the *system* python to run this script
>>>>> Traceback (most recent call last):
>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>>>> 2632, in <module>
>>>>>     main()
>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>>>> 870, in main
>>>>>     symlink=options.symlink,
>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>>>> 1156, in create_environment
>>>>>     install_python(home_dir, lib_dir, inc_dir, bin_dir,
>>>>> site_packages=site_packages, clear=clear, symlink=symlink)
>>>>>   File
>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>> line 357, in abspath
>>>>>     if not isabs(path):
>>>>>   File
>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>> line 64, in isabs
>>>>>     return s.startswith(sep)
>>>>> AttributeError: 'NoneType' object has no attribute 'startswith'
>>>>> Installing the Python libraries into the loris-mri virtualenv...
>>>>> Requirement already satisfied: mysqlclient in
>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (1.4.4)
>>>>> Requirement already satisfied: mysql-connector in
>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (2.2.9)
>>>>> Requirement already satisfied: pybids in
>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (0.9.4)
>>>>> Requirement already satisfied: nibabel>=2.1 in ./python_virtua>>
>>>>>
>>>>> So should i open an issue for that error? or is there something else
>>>>> to try?
>>>>>
>>>>> Thanks
>>>>>
>>>>> Sotirios
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ???? ???, 3 ??? 2019 ???? 10:39 ?.?., ?/? Cecile Madjar <
>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>
>>>>>> Hi Sotirios,
>>>>>>
>>>>>> Does the pic screenshot in the imaging browser module also shows 1
>>>>>> slice? If so, that would mean there was an issue with the dcm2mnc
>>>>>> conversion. Once again, installing the latest version of the MINC tools
>>>>>> should help but if this issue persists I would recommend creating an issue
>>>>>> for that too on their repository
>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> (if not already
>>>>>> reported there, there are a few known issue reported).
>>>>>>
>>>>>> Other viewer for MINCs are register and Display (both part of the
>>>>>> MINC tools). For NIfTI, you have FSLeye, MRICron and probably many other
>>>>>> viewers that exists.
>>>>>>
>>>>>> Hope this helps,
>>>>>>
>>>>>> C?cile
>>>>>>
>>>>>> On Tue, Dec 3, 2019 at 3:26 PM Sotirios Nikoloutsopoulos <
>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>
>>>>>>> Hi Cecile,
>>>>>>>
>>>>>>> Yes, Nifti files are mandatory for our work. From what we saw at a
>>>>>>> 3rd vm we setted up, the nifti files are being created ( i haven't verified
>>>>>>> if that is the case at the 2nd vm ). I will install the latest version and
>>>>>>> will report back, but do you know any nifti/minc viewer? because the
>>>>>>> Brainbrowser of Loris does not output them well, it's like it is loading
>>>>>>> only 1 slice and we would like to verify it with another tool too. We
>>>>>>> verified that the dcmconv command didn't affect the quality of the
>>>>>>> .dcm files.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Sotirios
>>>>>>>
>>>>>>> ???? ???, 2 ??? 2019 ???? 6:59 ?.?., ?/? Cecile Madjar <
>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>
>>>>>>>> Hi Sotirios,
>>>>>>>>
>>>>>>>> It looks like for some reason your binary mnc2nii is not working
>>>>>>>> and reports that error. Do you want to create NIfTI files or are you happy
>>>>>>>> with just the MINC files?
>>>>>>>>
>>>>>>>> If you don't need the NIfTI files, then maybe you can set the
>>>>>>>> Config setting "NIfTI file creation" to No instead of Yes and this
>>>>>>>> error will not appear anymore.
>>>>>>>>
>>>>>>>> If you need the NIfTI files to be created, then I would
>>>>>>>> recommend installing the latest version of the MINC tools (1.9.17). They
>>>>>>>> can be found there:
>>>>>>>>
>>>>>>>>    - pre-built packages:
>>>>>>>>    https://packages.bic.mni.mcgill.ca/minc-toolkit/
>>>>>>>>    - from the source code with installation instructions in the
>>>>>>>>    README: https://github.com/BIC-MNI/minc-toolkit-v2
>>>>>>>>
>>>>>>>> If the problem persists by using the latest release of MINC tools,
>>>>>>>> then create an issue on Github for the MINC developers here
>>>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues>.
>>>>>>>>
>>>>>>>> Hope this helps,
>>>>>>>>
>>>>>>>> C?cile
>>>>>>>>
>>>>>>>> On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi Cecile,
>>>>>>>>>
>>>>>>>>> Thanks to Nicholas i was able to create all the mincs images. The
>>>>>>>>> problem was that the files were in Little-Endian-Implicit transfer syntax
>>>>>>>>> and i had to convert them Little-Endian-Explicit transfer syntax with this
>>>>>>>>> command
>>>>>>>>>
>>>>>>>>> find <root_of_my_DICOM_files_directory> -type f | xargs -i
>>>>>>>>> dcmconv --write-xfer-little {} {}
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Looking back at our mails i saw that Little-Endian error had
>>>>>>>>> occurred when i used dcmodify, but i switcthed to using pydicom instead.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> [image: image.png]
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> In the output i see an error sometimes about "gsl:
>>>>>>>>> bessel_I0.c:216: ERROR: overflow". Is this okay?
>>>>>>>>>
>>>>>>>>> Restructuring...
>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>> noise_estimate --snr
>>>>>>>>> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
>>>>>>>>> SNR is:
>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> Sotirios
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar <
>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>
>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>
>>>>>>>>>> Thank you for the details!
>>>>>>>>>>
>>>>>>>>>> A few things to try:
>>>>>>>>>>
>>>>>>>>>>    - modify the TMPDIR to be on your /data directory where there
>>>>>>>>>>    might be more space to do processing (could create a /data/tmp where the
>>>>>>>>>>    temporary files would be created)
>>>>>>>>>>    - how many files are there for that upload in tarchive_files?
>>>>>>>>>>    Are they different from the ones showing the warning message?
>>>>>>>>>>       - FYI: query to get that: SELECT tf.* FROM tarchive_files
>>>>>>>>>>       tf JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your uploadID> (the
>>>>>>>>>>       output of that query would be very useful if you can provide it)
>>>>>>>>>>       - how many series are there for that upload in
>>>>>>>>>>    tarchive_series?
>>>>>>>>>>    - FYI: query to get that: SELECT ts.* FROM tarchive_series ts
>>>>>>>>>>       JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your uploadID> (the
>>>>>>>>>>       output of that query would be very useful if you can provide it)
>>>>>>>>>>    - things are failing when the scripts try running the
>>>>>>>>>>    following command: find
>>>>>>>>>>    /tmp/TarLoad-23-43-ccugaa/ImagingUpload-23-43-6JCOTO -type f  |
>>>>>>>>>>    /data/loris/bin/mri/dicom-archive/get_dicom_info.pl -studyuid
>>>>>>>>>>    -series -echo -image -file  -attvalue 0018 0024 -series_descr -stdin | sort
>>>>>>>>>>    -n -k1 -k2 -k7 -k3 -k6 -k4  | cut -f 5 | dcm2mnc -dname '' -stdin -clobber
>>>>>>>>>>    -usecoordinates /tmp/TarLoad-23-43-ccugaa
>>>>>>>>>>       - clearly the problems come from get_dicom_info.pl but I
>>>>>>>>>>       cannot pinpoint the error yet. I will ask around and get back to you
>>>>>>>>>>
>>>>>>>>>> If I cannot figure it out remotely, is there a way to have a call
>>>>>>>>>> using zoom? This way you could share your screen with me and run the
>>>>>>>>>> debugger on that script and hopefully we can figure out what is going on
>>>>>>>>>> with those datasets?
>>>>>>>>>>
>>>>>>>>>> Thanks!
>>>>>>>>>>
>>>>>>>>>> C?cile
>>>>>>>>>>
>>>>>>>>>> On Tue, Nov 26, 2019 at 5:17 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>
>>>>>>>>>>> In both my virtual machines
>>>>>>>>>>> export TMPDIR=/tmp
>>>>>>>>>>>
>>>>>>>>>>> In both vm also with dcm2mnc i get this output. Just to verify
>>>>>>>>>>> that this passed in my 1st vm and produced mincs.
>>>>>>>>>>>
>>>>>>>>>>> I attached the spool as a csv.
>>>>>>>>>>>
>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>
>>>>>>>>>>> And also one difference i found was this in the Loris-mri code (
>>>>>>>>>>> left 1st workable vm, right 2nd vm that has to be fixed, although i changed
>>>>>>>>>>> it seems to be independent of the uninitialized value $_ )
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>>
>>>>>>>>>>> Sotirios
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>
>>>>>>>>>>>> that is puzzling... A few additional questions:
>>>>>>>>>>>>
>>>>>>>>>>>>    - what is the bash variable TMPDIR set to on the
>>>>>>>>>>>>    environment file?
>>>>>>>>>>>>    - could you try running separately dcm2mnc on the DICOM
>>>>>>>>>>>>    folder to see if that works?
>>>>>>>>>>>>    - could you send us the detailed log from the notification
>>>>>>>>>>>>    spool table (SELECT * FROM notification_spool WHERE UploadID=<your
>>>>>>>>>>>>    uploadID>) and send it back to us? Maybe there are some additional clues
>>>>>>>>>>>>    that could help figuring out what is going on.
>>>>>>>>>>>>
>>>>>>>>>>>> Thank you!
>>>>>>>>>>>>
>>>>>>>>>>>> C?cile
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Nov 26, 2019 at 10:12 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>
>>>>>>>>>>>>> I checked for the StudyInstacueUID at the files with "The
>>>>>>>>>>>>> target directory does not contain a single DICOM file"" and their attribute
>>>>>>>>>>>>> has a value.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Regarding the scouter and localizer, i modified the settings
>>>>>>>>>>>>> in the imaging pipeline and now i don't get that error message, but still
>>>>>>>>>>>>> it doesn't create the mnics.
>>>>>>>>>>>>>
>>>>>>>>>>>>> The errors i am getting are ( uninitialized value $_ is not
>>>>>>>>>>>>> important? because i haven't got comments about that )
>>>>>>>>>>>>>
>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>> Running now the following command:
>>>>>>>>>>>>> /data/loris/data//uploadNeuroDB/imaging_upload_file.pl
>>>>>>>>>>>>> -profile prod -upload_id 134 /data/incoming/DCC0025_118008_V1.tar.gz
>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>
>>>>>>>>>>>>> and
>>>>>>>>>>>>>
>>>>>>>>>>>>> Number of MINC files that will be considered for inserting
>>>>>>>>>>>>> into the database: 0
>>>>>>>>>>>>>
>>>>>>>>>>>>> No data could be converted into valid MINC files.
>>>>>>>>>>>>>
>>>>>>>>>>>>> The tarchiveLoader.pl insertion script has failed.
>>>>>>>>>>>>> Use of uninitialized value $mail_user in concatenation (.) or
>>>>>>>>>>>>> string at /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>>> line 249.
>>>>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 250.
>>>>>>>>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 251.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>
>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>
>>>>>>>>>>>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> OK. So the issue I mentioned should not be a problem for you.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Is the StudyInstanceUID DICOM header set in your images? If
>>>>>>>>>>>>>> it is not set, then you would end up with the error message "The target
>>>>>>>>>>>>>> directory does not contain a single DICOM file". So maybe this is the issue
>>>>>>>>>>>>>> you are having with those datasets?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Regarding not excluding series descriptions, you can
>>>>>>>>>>>>>> configure that in the Config module under the Imaging Pipeline section.
>>>>>>>>>>>>>> Simply remove all entries for the "Series description to exclude from
>>>>>>>>>>>>>> imaging insertion" setting.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Mon, Nov 25, 2019 at 9:58 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> We are using this version
>>>>>>>>>>>>>>> https://github.com/aces/Loris/archive/v21.0.0.zip. Is it
>>>>>>>>>>>>>>> possible to insert low resolution now?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, <
>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Which version of LORIS-MRI are you using?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> There was a bug that got resolved in 20.2 in
>>>>>>>>>>>>>>>> get_dicom_info.pl. Basically, if a DICOM did not have the
>>>>>>>>>>>>>>>> (0020,0032) header, get_dicom_info.pl considered that the
>>>>>>>>>>>>>>>> file was not a DICOM, which was a mistake. This got fixed in version 20.2
>>>>>>>>>>>>>>>> of LORIS-MRI. Hopefully this is the issue you are encountering.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> About scout and localizer, they are a type of short and low
>>>>>>>>>>>>>>>> resolution sequence that is used by the tech but is of no interest
>>>>>>>>>>>>>>>> scientifically, which is why we tend to no insert them.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> i executed the find command and the output i got per
>>>>>>>>>>>>>>>>> folder was "DICOM medical imaging data. Maybe there is something wrong with
>>>>>>>>>>>>>>>>> the find command in the warning that it is unable to check if the file is a
>>>>>>>>>>>>>>>>> dicom file? Also when i use get_dicom_info.pl i don't get
>>>>>>>>>>>>>>>>> any output data. Finally i don't understand what scout or localizer is (
>>>>>>>>>>>>>>>>> something like if and only if a file fails then the whole session is
>>>>>>>>>>>>>>>>> invalid? ).
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> I took a closer look to the
>>>>>>>>>>>>>>>>>> batch_uploader_multiple_output.txt file you sent. It looks like there are
>>>>>>>>>>>>>>>>>> different reasons for failure depending on the DICOM folder uploaded.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>    - For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908
>>>>>>>>>>>>>>>>>>    DCC0007 V1: it looks like there is no file of type DICOM in the folder.
>>>>>>>>>>>>>>>>>>    Have you checked to see if that is indeed the case? Maybe you can try
>>>>>>>>>>>>>>>>>>    running the following command on that folder to see what are the types of
>>>>>>>>>>>>>>>>>>    the files? If it does not return at least one DICOM medical imaging data
>>>>>>>>>>>>>>>>>>    file, then that is why you get the error message from the pipeline:
>>>>>>>>>>>>>>>>>>       -
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>       find <my_dicom_archive_root_folder> -type f | xargs -i file {}|cut -d: -f2|sort|uniq
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>       - For 864173 DCC0001 V1: it looks like there are
>>>>>>>>>>>>>>>>>>    two different DICOM studies within the same folder. You will need to split
>>>>>>>>>>>>>>>>>>    that study in two based on the StudyUID field as the insertion pipeline
>>>>>>>>>>>>>>>>>>    does not allow for more than one StudyUID per upload.
>>>>>>>>>>>>>>>>>>    - For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975
>>>>>>>>>>>>>>>>>>    DCC0006 V1: it looks like the dcm2mnc command did not produce any MINC
>>>>>>>>>>>>>>>>>>    files. Can you check in the DICOM archive what are the series present in
>>>>>>>>>>>>>>>>>>    the tarchive for that visit? Maybe only a scout or localizer was acquired
>>>>>>>>>>>>>>>>>>    for that session, hence the no valid MINC files (scout and localizer being
>>>>>>>>>>>>>>>>>>    skipped for the conversion)
>>>>>>>>>>>>>>>>>>    - For 397410 DCC0003 V1: it looks like everything
>>>>>>>>>>>>>>>>>>    went well for this one.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> One script that is called by our pipeline is called
>>>>>>>>>>>>>>>>>> get_dicom_info.pl and this does all kind of checks on
>>>>>>>>>>>>>>>>>> the DICOM files (it is being called when running the dcm2mnc conversion).
>>>>>>>>>>>>>>>>>> You could run it independently on your folder if needed.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Since one of the study got in, it does not look like you
>>>>>>>>>>>>>>>>>> are having a problem with the setup. It seems more likely to be a problem
>>>>>>>>>>>>>>>>>> with the data themselves.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hope this helps.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos
>>>>>>>>>>>>>>>>>> <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> In my first vm i am able to create the minc files and
>>>>>>>>>>>>>>>>>>> view them at the mri browser (except of candidate 102761034 ), meanwhile
>>>>>>>>>>>>>>>>>>> the same files gives warnings at the 2nd vm. The output  of the batch
>>>>>>>>>>>>>>>>>>> upload can be seen in the file attached.
>>>>>>>>>>>>>>>>>>> Also a colleague of us has built a pre-validation tool
>>>>>>>>>>>>>>>>>>> for dicom
>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/
>>>>>>>>>>>>>>>>>>> which had found all the files that Loris gave as warning . Basically I
>>>>>>>>>>>>>>>>>>> confirmed that the total amount of files per dicom was the same amount as
>>>>>>>>>>>>>>>>>>> stated in Loris and checked some filenames given from warning to confirm
>>>>>>>>>>>>>>>>>>> that they match with our tool. But that was months ago and my colleague had
>>>>>>>>>>>>>>>>>>> changed some parameters for MIP and now our tool doesn't find all the
>>>>>>>>>>>>>>>>>>> invalid files, that's why i asked for the dicom header specification of
>>>>>>>>>>>>>>>>>>> Loris. In a discussion we had he mentioned that he doesn't check for some
>>>>>>>>>>>>>>>>>>> tags e.x. orientation. Lastly to mention that in my first vm i didn't use
>>>>>>>>>>>>>>>>>>> our tool to remove invalid dcm files.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>> Can you provide us with some fresh particulars of the
>>>>>>>>>>>>>>>>>>>> current issue and we'll take it from there?
>>>>>>>>>>>>>>>>>>>> Yang's team has built these scripts which can
>>>>>>>>>>>>>>>>>>>> definitely serve as a model for your pre-validation of your DICOM
>>>>>>>>>>>>>>>>>>>> collections.
>>>>>>>>>>>>>>>>>>>> cheers,
>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> HI Yang,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> We make use of pydicom library too. Now about the
>>>>>>>>>>>>>>>>>>>>> validate.py i see that you check if some attributes are missing such as
>>>>>>>>>>>>>>>>>>>>> PatientID, PatientName which all of our files contains that info. Maybe i
>>>>>>>>>>>>>>>>>>>>> have missed something on the setup of my other virtual machine ( although
>>>>>>>>>>>>>>>>>>>>> one dicom passed on the new vm successfully, the others that were inserted
>>>>>>>>>>>>>>>>>>>>> correctly on my old vm fails on the new one ), i think that i had asked
>>>>>>>>>>>>>>>>>>>>> about this error "Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>> line 144." but i don't remember the solution.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding <
>>>>>>>>>>>>>>>>>>>>> it at cnbp.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hey, Sotirios,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Christine from the LORIS team mentioned you had some
>>>>>>>>>>>>>>>>>>>>>> issue with DICOM.  I am a fellow developer for an external project using
>>>>>>>>>>>>>>>>>>>>>> LORIS, kind of just like you. We had to implement DICOM upload as well but
>>>>>>>>>>>>>>>>>>>>>> more as a fully automated pipeline actually.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> While we were building CNBP, we had coded up some
>>>>>>>>>>>>>>>>>>>>>> minor Python functions to check DICOM integrity (and simple validations)
>>>>>>>>>>>>>>>>>>>>>> and you might be able to gain some inspiration from it and help you with
>>>>>>>>>>>>>>>>>>>>>> your cause. For more comprehensive solution, PyDICOM (
>>>>>>>>>>>>>>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#)  seems
>>>>>>>>>>>>>>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks
>>>>>>>>>>>>>>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can
>>>>>>>>>>>>>>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty
>>>>>>>>>>>>>>>>>>>>>> rough around the edges but hopefully point you in the right direcitons
>>>>>>>>>>>>>>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Yang Ding, PhD.
>>>>>>>>>>>>>>>>>>>>>> Canadian Neonatal Brain Platform Architect
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM <
>>>>>>>>>>>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Send Loris-dev mailing list submissions to
>>>>>>>>>>>>>>>>>>>>>>>         loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> To subscribe or unsubscribe via the World Wide Web,
>>>>>>>>>>>>>>>>>>>>>>> visit
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>> or, via email, send a message with subject or body
>>>>>>>>>>>>>>>>>>>>>>> 'help' to
>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-request at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> You can reach the person managing the list at
>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-owner at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> When replying, please edit your Subject line so it
>>>>>>>>>>>>>>>>>>>>>>> is more specific
>>>>>>>>>>>>>>>>>>>>>>> than "Re: Contents of Loris-dev digest..."
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Today's Topics:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>    1. Re: Import mri - scripts (Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos)
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Message: 1
>>>>>>>>>>>>>>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200
>>>>>>>>>>>>>>>>>>>>>>> From: Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>> To: Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>> Message-ID:
>>>>>>>>>>>>>>>>>>>>>>>         <CAKHj7uST=
>>>>>>>>>>>>>>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com
>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Could we send you a link with 10 anonymized dicom
>>>>>>>>>>>>>>>>>>>>>>> files to diagnose the
>>>>>>>>>>>>>>>>>>>>>>> warnings we get?
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> > Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>> > We were wondering whether Loris has a tool to
>>>>>>>>>>>>>>>>>>>>>>> check if there are problems
>>>>>>>>>>>>>>>>>>>>>>> > with the dcm files, before trying to upload them.
>>>>>>>>>>>>>>>>>>>>>>> Something that could
>>>>>>>>>>>>>>>>>>>>>>> > provide the same results provided in the
>>>>>>>>>>>>>>>>>>>>>>> warning_output, this is the
>>>>>>>>>>>>>>>>>>>>>>> > summary from the mri_upload at the front-page.
>>>>>>>>>>>>>>>>>>>>>>> Also which attributes of the
>>>>>>>>>>>>>>>>>>>>>>> > dcm header would trigger a warning? is there a dcm
>>>>>>>>>>>>>>>>>>>>>>> file header
>>>>>>>>>>>>>>>>>>>>>>> > specification for Loris?
>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>> > Thanks
>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>> > Sotirios
>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> > sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp
>>>>>>>>>>>>>>>>>>>>>>> function it worked,but i
>>>>>>>>>>>>>>>>>>>>>>> >> thought that something else was causing the 2nd
>>>>>>>>>>>>>>>>>>>>>>> issue.
>>>>>>>>>>>>>>>>>>>>>>> >> Thanks
>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher,
>>>>>>>>>>>>>>>>>>>>>>> Mr, <
>>>>>>>>>>>>>>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> The first error occurs because the
>>>>>>>>>>>>>>>>>>>>>>> QCFirstChangeTime and columns are of
>>>>>>>>>>>>>>>>>>>>>>> >>> type `unsigned integer` and not `datatime`. You
>>>>>>>>>>>>>>>>>>>>>>> should be using
>>>>>>>>>>>>>>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW().
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> The second error occurs because the trigger
>>>>>>>>>>>>>>>>>>>>>>> triggers a rollback of the
>>>>>>>>>>>>>>>>>>>>>>> >>> insert statement in the files table.
>>>>>>>>>>>>>>>>>>>>>>> >>> See mysql documentation for trigger error
>>>>>>>>>>>>>>>>>>>>>>> handling.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> An error during either a BEFORE or AFTER trigger
>>>>>>>>>>>>>>>>>>>>>>> results in failure of
>>>>>>>>>>>>>>>>>>>>>>> >>> the entire statement that caused trigger
>>>>>>>>>>>>>>>>>>>>>>> invocation.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you for sharing that. I hope it helps.
>>>>>>>>>>>>>>>>>>>>>>> >>> -- Xavier
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf
>>>>>>>>>>>>>>>>>>>>>>> of Sotirios
>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM
>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>> >>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> When mincs are inserted their corresponding rows
>>>>>>>>>>>>>>>>>>>>>>> at the file table are
>>>>>>>>>>>>>>>>>>>>>>> >>> inserted too
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> i would like to insert their rows at
>>>>>>>>>>>>>>>>>>>>>>> file_qcstatus as well, because i
>>>>>>>>>>>>>>>>>>>>>>> >>> don't want manually to label them as passed
>>>>>>>>>>>>>>>>>>>>>>> throught the interface
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> That is the trigger i wrote
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER
>>>>>>>>>>>>>>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER
>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW
>>>>>>>>>>>>>>>>>>>>>>> >>> BEGIN
>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT INTO files_qcstatus
>>>>>>>>>>>>>>>>>>>>>>> >>> SET FileID = NEW.FileID,
>>>>>>>>>>>>>>>>>>>>>>> >>>      SeriesUID = NEW.SeriesUID,
>>>>>>>>>>>>>>>>>>>>>>> >>>      EchoTime = NEW.EchoTime,
>>>>>>>>>>>>>>>>>>>>>>> >>>      QCStatus = "Pass",
>>>>>>>>>>>>>>>>>>>>>>> >>>      QCFirstChangeTime = NOW(),
>>>>>>>>>>>>>>>>>>>>>>> >>>      QCLastChangeTime = NOW();
>>>>>>>>>>>>>>>>>>>>>>> >>> END
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> although it contains some errors
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range value for
>>>>>>>>>>>>>>>>>>>>>>> column
>>>>>>>>>>>>>>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at
>>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm
>>>>>>>>>>>>>>>>>>>>>>> line 823.
>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a
>>>>>>>>>>>>>>>>>>>>>>> child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`parameter_file`,
>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT
>>>>>>>>>>>>>>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`)
>>>>>>>>>>>>>>>>>>>>>>> REFERENCES `files` (`FileID`))
>>>>>>>>>>>>>>>>>>>>>>> >>> at
>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>>>>>>> Madjar <
>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> In the mri_upload table, there is a TarchiveID
>>>>>>>>>>>>>>>>>>>>>>> column associated with
>>>>>>>>>>>>>>>>>>>>>>> >>> the MRI upload you inserted. When this value is
>>>>>>>>>>>>>>>>>>>>>>> NULL, it means no DICOMs
>>>>>>>>>>>>>>>>>>>>>>> >>> were inserted into the tarchive tables. At the
>>>>>>>>>>>>>>>>>>>>>>> end of the insertion of the
>>>>>>>>>>>>>>>>>>>>>>> >>> DICOMs in the tarchive tables, this value is
>>>>>>>>>>>>>>>>>>>>>>> updated with the correct
>>>>>>>>>>>>>>>>>>>>>>> >>> TarchiveID associated with the upload.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Could this correspond to what you want to do?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Regarding the files_qcstatus, this table is only
>>>>>>>>>>>>>>>>>>>>>>> linked to the files
>>>>>>>>>>>>>>>>>>>>>>> >>> table (hence, the MINC files). You could always
>>>>>>>>>>>>>>>>>>>>>>> create a new table for
>>>>>>>>>>>>>>>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive table?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> i would like whenever a dicom is imported to
>>>>>>>>>>>>>>>>>>>>>>> mark all their
>>>>>>>>>>>>>>>>>>>>>>> >>> coressponding qc_status to "pass". I was
>>>>>>>>>>>>>>>>>>>>>>> thinking of creating a trigger for
>>>>>>>>>>>>>>>>>>>>>>> >>> that, but which tables do i need to add entries
>>>>>>>>>>>>>>>>>>>>>>> to? So far from what i see
>>>>>>>>>>>>>>>>>>>>>>> >>> i need to add entres at  the table "files"
>>>>>>>>>>>>>>>>>>>>>>> whenever an insertion happens to
>>>>>>>>>>>>>>>>>>>>>>> >>> files_qcstatus.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Oh, sorry i should have asked for StudyID, at
>>>>>>>>>>>>>>>>>>>>>>> the beginning of my email
>>>>>>>>>>>>>>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID).
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> that's the Study Instance UID, not the StudyID.
>>>>>>>>>>>>>>>>>>>>>>> So the StudyID i am
>>>>>>>>>>>>>>>>>>>>>>> >>> looking for is not stored in the database?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>>>>>>> Madjar <
>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> The StudyUID is stored in the DicomArchiveID
>>>>>>>>>>>>>>>>>>>>>>> field of the
>>>>>>>>>>>>>>>>>>>>>>> >>> tarchive table. It can also be found in the
>>>>>>>>>>>>>>>>>>>>>>> metadata field but it is mixed
>>>>>>>>>>>>>>>>>>>>>>> >>> with many other information.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Is StudyUID stored somewhere at the tables? At
>>>>>>>>>>>>>>>>>>>>>>> the tarchive table,
>>>>>>>>>>>>>>>>>>>>>>> >>> specifically at the AcquisitonMetadata column i
>>>>>>>>>>>>>>>>>>>>>>> found something called
>>>>>>>>>>>>>>>>>>>>>>> >>> 'Unique Study ID" in its context, but that must
>>>>>>>>>>>>>>>>>>>>>>> be the Study Instance UID.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>>>>>>> Madjar <
>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Your observation is correct. A little
>>>>>>>>>>>>>>>>>>>>>>> explanation below.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> MINC files get inserted into the MRI violation
>>>>>>>>>>>>>>>>>>>>>>> tables if:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>    - the scan type could not be identified (not
>>>>>>>>>>>>>>>>>>>>>>> matching an entry in
>>>>>>>>>>>>>>>>>>>>>>> >>>    the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>> >>>    - one parameter of the scan type is out of
>>>>>>>>>>>>>>>>>>>>>>> the expected range
>>>>>>>>>>>>>>>>>>>>>>> >>>    present in the mri_protocol_checks (extra
>>>>>>>>>>>>>>>>>>>>>>> filtering in case you need to be
>>>>>>>>>>>>>>>>>>>>>>> >>>    stricker on some parameters not present in
>>>>>>>>>>>>>>>>>>>>>>> the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>> >>>    - if the CandID and PSCID do not match
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> The following cases do not get in the MRI
>>>>>>>>>>>>>>>>>>>>>>> violation tables as it happens
>>>>>>>>>>>>>>>>>>>>>>> >>> before the conversion of the DICOM to MINC files
>>>>>>>>>>>>>>>>>>>>>>> and only MINC files
>>>>>>>>>>>>>>>>>>>>>>> >>> violations are logged there:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>    - "No single DICOM" (since no valid DICOM
>>>>>>>>>>>>>>>>>>>>>>> could be found to convert
>>>>>>>>>>>>>>>>>>>>>>> >>>    to MINC)
>>>>>>>>>>>>>>>>>>>>>>> >>>    - "Study already inserted" (duplicate
>>>>>>>>>>>>>>>>>>>>>>> StudyUID) since this error
>>>>>>>>>>>>>>>>>>>>>>> >>>    happens at the dicomTar.pl level (way before
>>>>>>>>>>>>>>>>>>>>>>> conversion into MINC files)
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Glad everything is working out!!
>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> the mri passed, for some reason it consumed
>>>>>>>>>>>>>>>>>>>>>>> 5.12GB of ram. Now about the
>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations, dicoms are triggered to be
>>>>>>>>>>>>>>>>>>>>>>> inserted there only if there is
>>>>>>>>>>>>>>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general for
>>>>>>>>>>>>>>>>>>>>>>> its header parameter?
>>>>>>>>>>>>>>>>>>>>>>> >>> Because i don't see the cases of 'No single
>>>>>>>>>>>>>>>>>>>>>>> dicom" or with the 2 studyiuid
>>>>>>>>>>>>>>>>>>>>>>> >>> to be there.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>>>>>>> Madjar <
>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Sorry to hear you are having issues with the
>>>>>>>>>>>>>>>>>>>>>>> memory. I think most of our
>>>>>>>>>>>>>>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you
>>>>>>>>>>>>>>>>>>>>>>> should be fine.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> about that dicom that had that insertion error
>>>>>>>>>>>>>>>>>>>>>>> it's about 30mb and when
>>>>>>>>>>>>>>>>>>>>>>> >>> it is being processed the ram is being
>>>>>>>>>>>>>>>>>>>>>>> drastically increased from 2gb to
>>>>>>>>>>>>>>>>>>>>>>> >>> 3.28 and then the whole virtual machine is
>>>>>>>>>>>>>>>>>>>>>>> frozen. What is the recommended
>>>>>>>>>>>>>>>>>>>>>>> >>> size of ram for using Loris?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to see that the StudyUID problem was fixed!
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> For the delete script issue, if you are
>>>>>>>>>>>>>>>>>>>>>>> absolutely certain that no
>>>>>>>>>>>>>>>>>>>>>>> >>> processes are run for that uploadID, you can
>>>>>>>>>>>>>>>>>>>>>>> update the mri_upload table
>>>>>>>>>>>>>>>>>>>>>>> >>> and set the column Inserting to 0 instead of 1
>>>>>>>>>>>>>>>>>>>>>>> for that uploadID. It
>>>>>>>>>>>>>>>>>>>>>>> >>> looks like for some reason the scripts did not
>>>>>>>>>>>>>>>>>>>>>>> update this field when it
>>>>>>>>>>>>>>>>>>>>>>> >>> stopped the insertion. Not sure why that would
>>>>>>>>>>>>>>>>>>>>>>> be the case though.
>>>>>>>>>>>>>>>>>>>>>>> >>> Note: only do that update if you are certain
>>>>>>>>>>>>>>>>>>>>>>> that there is no processing
>>>>>>>>>>>>>>>>>>>>>>> >>> happening.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> about the Dicoms i reported that didn't have a
>>>>>>>>>>>>>>>>>>>>>>> StudyID they actually do
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> I thought that this might be a permission
>>>>>>>>>>>>>>>>>>>>>>> because "w" was missing at the
>>>>>>>>>>>>>>>>>>>>>>> >>> group. After using chmod -R 775 only 102809579
>>>>>>>>>>>>>>>>>>>>>>> passed, but with no mnic
>>>>>>>>>>>>>>>>>>>>>>> >>> files. Also now i have this error
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox
>>>>>>>>>>>>>>>>>>>>>>> :/data/loris/bin/mri/tools$
>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore
>>>>>>>>>>>>>>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is
>>>>>>>>>>>>>>>>>>>>>>> currently processing it.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> How can solve this?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Here is our auto dicom uploading python script:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> To give you a brief idea:
>>>>>>>>>>>>>>>>>>>>>>> >>> Per folder it will:
>>>>>>>>>>>>>>>>>>>>>>> >>> 1) Delete all the .bak files
>>>>>>>>>>>>>>>>>>>>>>> >>> 2) Locate .dcm files and update the Patient
>>>>>>>>>>>>>>>>>>>>>>> header
>>>>>>>>>>>>>>>>>>>>>>> >>> 3) Furthermore we are interesting in finding
>>>>>>>>>>>>>>>>>>>>>>> TR_min, TR_max, TE_min,
>>>>>>>>>>>>>>>>>>>>>>> >>> TE_max parameters of T1 protocol and do an
>>>>>>>>>>>>>>>>>>>>>>> update at the mri_protocol table
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205
>>>>>>>>>>>>>>>>>>>>>>> >>> For some reason some files are missing
>>>>>>>>>>>>>>>>>>>>>>> SeriesDescription/ProtocolName
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> In total i have 7 folders
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> 3/7 passed
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Also about the first patient with DC0000 had a
>>>>>>>>>>>>>>>>>>>>>>> violation "T1 AXIAL SE
>>>>>>>>>>>>>>>>>>>>>>> >>> GADO", but my script didn't output a TE of 17
>>>>>>>>>>>>>>>>>>>>>>> nowhere and i find that weird
>>>>>>>>>>>>>>>>>>>>>>> >>> since Loris detects the SeriesDescription.
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Now about the 4/7 that didn't passed
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> 102327840 and 102809579 outputs "The target
>>>>>>>>>>>>>>>>>>>>>>> directory does not contain a
>>>>>>>>>>>>>>>>>>>>>>> >>> single DICOM file.", therefore they are missing
>>>>>>>>>>>>>>>>>>>>>>> their StudyUID
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it with
>>>>>>>>>>>>>>>>>>>>>>> data from multiple
>>>>>>>>>>>>>>>>>>>>>>> >>> studies."
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> and 102761034 "No data could be converted into
>>>>>>>>>>>>>>>>>>>>>>> valid MINC files.
>>>>>>>>>>>>>>>>>>>>>>> >>> localizer, scout will not be considered!" What
>>>>>>>>>>>>>>>>>>>>>>> is this?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> If i wanted to force the insertion of 102327840,
>>>>>>>>>>>>>>>>>>>>>>> 102809579 and 102506134
>>>>>>>>>>>>>>>>>>>>>>> >>> can i just pass a flag parameter to
>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl? or
>>>>>>>>>>>>>>>>>>>>>>> >>> modify imaging_upload_file.pl?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> PS
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> To diagnose a folder search the name of the
>>>>>>>>>>>>>>>>>>>>>>> folder at dicom_output.txt.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear about your progress.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, the script you used to delete imaging data
>>>>>>>>>>>>>>>>>>>>>>> is fully documented here
>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>> >>> -- let us know if you didn't find the answers
>>>>>>>>>>>>>>>>>>>>>>> you were looking for there.
>>>>>>>>>>>>>>>>>>>>>>> >>> (Is it possible the null row in *mri_scanner*
>>>>>>>>>>>>>>>>>>>>>>> seen in your database
>>>>>>>>>>>>>>>>>>>>>>> >>> management software is a visual placeholder for
>>>>>>>>>>>>>>>>>>>>>>> you as the user?  I'm not
>>>>>>>>>>>>>>>>>>>>>>> >>> sure why a scanner would ever be registered with
>>>>>>>>>>>>>>>>>>>>>>> ID='0' as your screenshot
>>>>>>>>>>>>>>>>>>>>>>> >>> showed.)
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> I fixed it with this
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> I tried to create a new candidate using the API,
>>>>>>>>>>>>>>>>>>>>>>> is there something
>>>>>>>>>>>>>>>>>>>>>>> >>> wrong with the structure? why did i receive a
>>>>>>>>>>>>>>>>>>>>>>> 500 internal error? In the
>>>>>>>>>>>>>>>>>>>>>>> >>> loris-error log it state that there is something
>>>>>>>>>>>>>>>>>>>>>>> wrong with token, but i
>>>>>>>>>>>>>>>>>>>>>>> >>> verfied that the type of the token is a string.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error]
>>>>>>>>>>>>>>>>>>>>>>> [pid 4535] [client
>>>>>>>>>>>>>>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error:  Uncaught
>>>>>>>>>>>>>>>>>>>>>>> TypeError: Argument 1
>>>>>>>>>>>>>>>>>>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate()
>>>>>>>>>>>>>>>>>>>>>>> must be of the type string,
>>>>>>>>>>>>>>>>>>>>>>> >>> null given, called in
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and
>>>>>>>>>>>>>>>>>>>>>>> >>> defined in
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
>>>>>>>>>>>>>>>>>>>>>>> >>> trace:\n#0
>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
>>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):
>>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2
>>>>>>>>>>>>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
>>>>>>>>>>>>>>>>>>>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST',
>>>>>>>>>>>>>>>>>>>>>>> Array)\n#5 {main}\n  thrown in
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Is there a way also to delete candidates? Just
>>>>>>>>>>>>>>>>>>>>>>> to let you know what i
>>>>>>>>>>>>>>>>>>>>>>> >>> did to clear candidates, because maybe i may
>>>>>>>>>>>>>>>>>>>>>>> have missed dependencies.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> First i deleted all their uploads
>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc (
>>>>>>>>>>>>>>>>>>>>>>> is there a way to omit
>>>>>>>>>>>>>>>>>>>>>>> >>> the backup file ? )
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Afterwards i had some scanner candidates, so i
>>>>>>>>>>>>>>>>>>>>>>> deleted all the entries
>>>>>>>>>>>>>>>>>>>>>>> >>> from mri_scanner except that i couldn't delete
>>>>>>>>>>>>>>>>>>>>>>> this entry with the 0 ID.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Lastly i deleted the session and then the
>>>>>>>>>>>>>>>>>>>>>>> candidate table.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> We recommend that you use our existing tools for
>>>>>>>>>>>>>>>>>>>>>>> creating new candidates
>>>>>>>>>>>>>>>>>>>>>>> >>> - either the LORIS API or if you are using a PHP
>>>>>>>>>>>>>>>>>>>>>>> script, by calling the Candidate
>>>>>>>>>>>>>>>>>>>>>>> >>> class's createNew()
>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200
>>>>>>>>>>>>>>>>>>>>>>> >function.
>>>>>>>>>>>>>>>>>>>>>>> >>> These will create the necessary records for
>>>>>>>>>>>>>>>>>>>>>>> you.  (It's not recommended to
>>>>>>>>>>>>>>>>>>>>>>> >>> make direct modifications to mysql database
>>>>>>>>>>>>>>>>>>>>>>> tables in your script, if I
>>>>>>>>>>>>>>>>>>>>>>> >>> understand you.)
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> The CandID should be a randomized 6 digit
>>>>>>>>>>>>>>>>>>>>>>> randomized ID, and there are
>>>>>>>>>>>>>>>>>>>>>>> >>> multiple reasons for this.
>>>>>>>>>>>>>>>>>>>>>>> >>> You can use the PSCID for project-specific IDs
>>>>>>>>>>>>>>>>>>>>>>> and the External ID field
>>>>>>>>>>>>>>>>>>>>>>> >>> in the candidate table can also be used for any
>>>>>>>>>>>>>>>>>>>>>>> values you like.
>>>>>>>>>>>>>>>>>>>>>>> >>> Additionally, any number of custom IDs can be
>>>>>>>>>>>>>>>>>>>>>>> added in parallel - these
>>>>>>>>>>>>>>>>>>>>>>> >>> are entered/visible in the Candidate Information
>>>>>>>>>>>>>>>>>>>>>>> module and added in the
>>>>>>>>>>>>>>>>>>>>>>> >>> back-end as candidate parameters.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> We are building a script that will auto insert
>>>>>>>>>>>>>>>>>>>>>>> the candidates based on
>>>>>>>>>>>>>>>>>>>>>>> >>> their ExternalID. We would like to know whethere
>>>>>>>>>>>>>>>>>>>>>>> when we are creating a new
>>>>>>>>>>>>>>>>>>>>>>> >>> profile in the candidate table, if we also have
>>>>>>>>>>>>>>>>>>>>>>> to insert a new record at
>>>>>>>>>>>>>>>>>>>>>>> >>> another table? Furthermore is there a problem
>>>>>>>>>>>>>>>>>>>>>>> that in our case CandID won't
>>>>>>>>>>>>>>>>>>>>>>> >>> be a 6digit? ( should we start it from 100000?)
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> That would normally be the case but the numeric
>>>>>>>>>>>>>>>>>>>>>>> part of the PSCID get
>>>>>>>>>>>>>>>>>>>>>>> >>> paded with 0 on the left.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Ex. for sequential ID made of center ID of `ABC`
>>>>>>>>>>>>>>>>>>>>>>> plus 4 numerical char
>>>>>>>>>>>>>>>>>>>>>>> >>> with a min value of 1, the sequence would be:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0001
>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0002
>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0010
>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> thus sorting them ascending will always get the
>>>>>>>>>>>>>>>>>>>>>>> latest value generated
>>>>>>>>>>>>>>>>>>>>>>> >>> as the max value.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15
>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>> melanie.legault2 at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> I see, although the PSCID value is varchar(255),
>>>>>>>>>>>>>>>>>>>>>>> it must be stored
>>>>>>>>>>>>>>>>>>>>>>> >>> within a specific length of characters.
>>>>>>>>>>>>>>>>>>>>>>> Otherwise if we were to sort
>>>>>>>>>>>>>>>>>>>>>>> >>> strings with different lengths the result would
>>>>>>>>>>>>>>>>>>>>>>> not be sorted correctly (
>>>>>>>>>>>>>>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10,
>>>>>>>>>>>>>>>>>>>>>>> 11, 2 ).
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hello Sotirios,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> There is no `last value` stored anywhere.
>>>>>>>>>>>>>>>>>>>>>>> >>> The code simply look for the PSCID with the max
>>>>>>>>>>>>>>>>>>>>>>> value and increase that
>>>>>>>>>>>>>>>>>>>>>>> >>> value by 1 in order to generate the next PSCID.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this info help.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie Legault | Software developer | Faculty
>>>>>>>>>>>>>>>>>>>>>>> of Medicine | McGill
>>>>>>>>>>>>>>>>>>>>>>> >>> University
>>>>>>>>>>>>>>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf
>>>>>>>>>>>>>>>>>>>>>>> of Sotirios
>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43
>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> how does Loris determine the next available
>>>>>>>>>>>>>>>>>>>>>>> PSCID value for a new
>>>>>>>>>>>>>>>>>>>>>>> >>> candidate?
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization
>>>>>>>>>>>>>>>>>>>>>>> >>> e.x in the default case the PSCID is sequential,
>>>>>>>>>>>>>>>>>>>>>>> but where do we store the
>>>>>>>>>>>>>>>>>>>>>>> >>> last value for the sequential sequence?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> the parameters in the mri_protocol you have
>>>>>>>>>>>>>>>>>>>>>>> assigned are global
>>>>>>>>>>>>>>>>>>>>>>> >>> standard? or were assigned after trial and error?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Given you have done the initial setup of your
>>>>>>>>>>>>>>>>>>>>>>> tables to match your
>>>>>>>>>>>>>>>>>>>>>>> >>> intended protocol/parameters according to
>>>>>>>>>>>>>>>>>>>>>>> instructions --
>>>>>>>>>>>>>>>>>>>>>>> >>> the Troubleshooting guide documentation
>>>>>>>>>>>>>>>>>>>>>>> recommends
>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes
>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>> >>> re-running the pipeline (and first deleting
>>>>>>>>>>>>>>>>>>>>>>> prior uploads).
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> *if i were to change their status to resolve
>>>>>>>>>>>>>>>>>>>>>>> what would happen?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> I noticed that i can view the mnics at the
>>>>>>>>>>>>>>>>>>>>>>> brainbrowser from the
>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations page ( those mnics are stored at
>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/trashbin/
>>>>>>>>>>>>>>>>>>>>>>> >>> if i were to click their issue to resolve what
>>>>>>>>>>>>>>>>>>>>>>> would happend? would they
>>>>>>>>>>>>>>>>>>>>>>> >>> appear in the dicom_archive view too? ).
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> The defaut values of the schema exists in my
>>>>>>>>>>>>>>>>>>>>>>> local database. If i adjust
>>>>>>>>>>>>>>>>>>>>>>> >>> the default values of TR_min and TE_min the
>>>>>>>>>>>>>>>>>>>>>>> mincs will be uploaded?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Is it possible that you haven't set up your
>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table ?   (and
>>>>>>>>>>>>>>>>>>>>>>> >>> mri_scan_type table too, for additional types of
>>>>>>>>>>>>>>>>>>>>>>> scans)
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Like the psc table, this is a pre-requisite for
>>>>>>>>>>>>>>>>>>>>>>> the Imaging insertion
>>>>>>>>>>>>>>>>>>>>>>> >>> setup : See the install/setup documentation :
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> To add new rows, just use MySQL insert
>>>>>>>>>>>>>>>>>>>>>>> statements.  You can adapt the
>>>>>>>>>>>>>>>>>>>>>>> >>> insert statements which load the default table
>>>>>>>>>>>>>>>>>>>>>>> values --> e.g. Here on
>>>>>>>>>>>>>>>>>>>>>>> >>> GitHub :
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>>>>>>>>>>>>>>>>>>>>>> >>> (see also the mri_scan_type table)
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> I see that i can edit the values but not how to
>>>>>>>>>>>>>>>>>>>>>>> insert new rows.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> If i choose Inserted with flag then will the
>>>>>>>>>>>>>>>>>>>>>>> minc be inserted?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear that *dcmodify* worked correctly.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> For the MRI Violations module, the screenshot is
>>>>>>>>>>>>>>>>>>>>>>> enough.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> It says "could not identify scan type", which we
>>>>>>>>>>>>>>>>>>>>>>> knew already.  Did you
>>>>>>>>>>>>>>>>>>>>>>> >>> click on the link on those words?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> It will take you to the next page of the module,
>>>>>>>>>>>>>>>>>>>>>>> showing for each scan
>>>>>>>>>>>>>>>>>>>>>>> >>> what the scan parameters were, and will also
>>>>>>>>>>>>>>>>>>>>>>> show for comparison what's
>>>>>>>>>>>>>>>>>>>>>>> >>> stored in your *mri_protocol* table.
>>>>>>>>>>>>>>>>>>>>>>> >>> Compare these values to find which parameter was
>>>>>>>>>>>>>>>>>>>>>>> not correct according
>>>>>>>>>>>>>>>>>>>>>>> >>> to your *mri_protocol* table scan type
>>>>>>>>>>>>>>>>>>>>>>> definitions.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> You may end up broadening your mri_protocol
>>>>>>>>>>>>>>>>>>>>>>> value ranges (e.g. TR, TE)
>>>>>>>>>>>>>>>>>>>>>>> >>> for scans.
>>>>>>>>>>>>>>>>>>>>>>> >>> This can be done in the front-end, by editing
>>>>>>>>>>>>>>>>>>>>>>> the database table
>>>>>>>>>>>>>>>>>>>>>>> >>> directly in the same subpage of the MRI
>>>>>>>>>>>>>>>>>>>>>>> Violations module.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> The MRI Violations module features are explained
>>>>>>>>>>>>>>>>>>>>>>> in more detail in the
>>>>>>>>>>>>>>>>>>>>>>> >>> Help text for this module inside LORIS (click
>>>>>>>>>>>>>>>>>>>>>>> the  ["?"] icon in the menu
>>>>>>>>>>>>>>>>>>>>>>> >>> bar.)
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide
>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>> >>> :  no MINCs inserted- violated scans
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> looks like my previous email's attachment wasn't
>>>>>>>>>>>>>>>>>>>>>>> delivered due to
>>>>>>>>>>>>>>>>>>>>>>> >>> security reasons, i uploaded my file at google
>>>>>>>>>>>>>>>>>>>>>>> drive
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> From Dicat's view seems that dcmodify worked in
>>>>>>>>>>>>>>>>>>>>>>> both cases
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> For the mri_violations i attached the .html
>>>>>>>>>>>>>>>>>>>>>>> output from webbrowser, so
>>>>>>>>>>>>>>>>>>>>>>> >>> that you can check the filelds easier.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios --
>>>>>>>>>>>>>>>>>>>>>>> >>> Great, sounds like more progress.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> About the dcmodify command -- I'm not sure why
>>>>>>>>>>>>>>>>>>>>>>> you're getting an Endian
>>>>>>>>>>>>>>>>>>>>>>> >>> warning.  (it's a warning not an error, correct?)
>>>>>>>>>>>>>>>>>>>>>>> >>> To clarify -- Were the DICOM headers
>>>>>>>>>>>>>>>>>>>>>>> (PatientName) all successfully
>>>>>>>>>>>>>>>>>>>>>>> >>> relabelled, after the command ran?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> You can use also our DICAT tool (
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/DICAT) to
>>>>>>>>>>>>>>>>>>>>>>> >>> verify and/or update local DICOM headers --
>>>>>>>>>>>>>>>>>>>>>>> though your dcmodify command is
>>>>>>>>>>>>>>>>>>>>>>> >>> a great and fast solution for bulk header
>>>>>>>>>>>>>>>>>>>>>>> updates.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> If you're concerned about fields being changed
>>>>>>>>>>>>>>>>>>>>>>> (e.g. "(2001,105f)" from
>>>>>>>>>>>>>>>>>>>>>>> >>> the warning message)  - you can also dcmdump a
>>>>>>>>>>>>>>>>>>>>>>> DICOM slice before and look
>>>>>>>>>>>>>>>>>>>>>>> >>> at these fields specifically.
>>>>>>>>>>>>>>>>>>>>>>> >>> It's also not a bad "sanity check" to backup
>>>>>>>>>>>>>>>>>>>>>>> your DICOMS before/after
>>>>>>>>>>>>>>>>>>>>>>> >>> running dcmodify, and use dcmdump on each
>>>>>>>>>>>>>>>>>>>>>>> version to diff the outputs --
>>>>>>>>>>>>>>>>>>>>>>> >>> this will pinpoint what changed.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Re the protocol violation -- AcquisitionProtocol
>>>>>>>>>>>>>>>>>>>>>>> not recognized or
>>>>>>>>>>>>>>>>>>>>>>> >>> unknown :   this means your scans did not match
>>>>>>>>>>>>>>>>>>>>>>> what is stored in your
>>>>>>>>>>>>>>>>>>>>>>> >>> mri_protocol table.
>>>>>>>>>>>>>>>>>>>>>>> >>> Check the MRI Violations front-end module -- can
>>>>>>>>>>>>>>>>>>>>>>> you see why they didn't
>>>>>>>>>>>>>>>>>>>>>>> >>> match?
>>>>>>>>>>>>>>>>>>>>>>> >>> Send us an example, in addition to the contents
>>>>>>>>>>>>>>>>>>>>>>> of the mri_protocol
>>>>>>>>>>>>>>>>>>>>>>> >>> table, if you can't find the source of the
>>>>>>>>>>>>>>>>>>>>>>> mismatch.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>  Here is the psc table
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> I created 2 candidates profiles through the
>>>>>>>>>>>>>>>>>>>>>>> interface
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> then runned dcmodify command to a dicom file
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1"
>>>>>>>>>>>>>>>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> and got those warning: is this okay?
>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify at another Dicom didn't show warnings.
>>>>>>>>>>>>>>>>>>>>>>> Below you can see the
>>>>>>>>>>>>>>>>>>>>>>> >>> execution for the second dicom. Mnics could not
>>>>>>>>>>>>>>>>>>>>>>> be inserted due to
>>>>>>>>>>>>>>>>>>>>>>> >>> AcquisitionProtocol being unknown.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Running now the following command:
>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>> >>> imaging_upload_file.pl -profile prod -upload_id
>>>>>>>>>>>>>>>>>>>>>>> 12
>>>>>>>>>>>>>>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>  find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX'
>>>>>>>>>>>>>>>>>>>>>>> >>> -delete
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database
>>>>>>>>>>>>>>>>>>>>>>> -profile prod -verbose
>>>>>>>>>>>>>>>>>>>>>>> >>>  Source: /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>> >>> Target: /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Testing for database connectivity.
>>>>>>>>>>>>>>>>>>>>>>> >>> Database is available.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> You will archive the dir :
>>>>>>>>>>>>>>>>>>>>>>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> You are creating a tar with the following
>>>>>>>>>>>>>>>>>>>>>>> command:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> tar -cf
>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> getting md5sums and gzipping!!
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :    127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :    Linux
>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>> 2019-09-06 18:36:50
>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814
>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f
>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar.gz
>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e
>>>>>>>>>>>>>>>>>>>>>>> >>>  DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Removing temporary files from target location
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Done adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation
>>>>>>>>>>>>>>>>>>>>>>> >>> -profile prod
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>>>>>>>>>>>>>>>>>>>>>> >>> -uploadID 12 -verbose
>>>>>>>>>>>>>>>>>>>>>>> >>>  md5sum
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>> >>> Set centerID = 1
>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Number of MINC files that will be considered for
>>>>>>>>>>>>>>>>>>>>>>> inserting into the
>>>>>>>>>>>>>>>>>>>>>>> >>> database: 2
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is
>>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is
>>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>> cat
>>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Acquisition protocol is unknown
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>   --> The minc file cannot be registered since
>>>>>>>>>>>>>>>>>>>>>>> the AcquisitionProtocol
>>>>>>>>>>>>>>>>>>>>>>> >>> is unknown
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Sure -- you can delete imaging datasets with the
>>>>>>>>>>>>>>>>>>>>>>> *delete_imaging_upload*
>>>>>>>>>>>>>>>>>>>>>>> >>> script --
>>>>>>>>>>>>>>>>>>>>>>> >>> details here:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> What's in your *psc* table?  (Is it properly
>>>>>>>>>>>>>>>>>>>>>>> populated? This is a
>>>>>>>>>>>>>>>>>>>>>>> >>> pre-requisite to loading imaging data.
>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database
>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>> >>> The foreign key constraint error on the
>>>>>>>>>>>>>>>>>>>>>>> candidate record is curious.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> There are also a few options for creating
>>>>>>>>>>>>>>>>>>>>>>> candidates when inserting
>>>>>>>>>>>>>>>>>>>>>>> >>> imaging data:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then DICOM
>>>>>>>>>>>>>>>>>>>>>>> insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> a. via the LORIS API -- Create the candidates
>>>>>>>>>>>>>>>>>>>>>>> (and visits, optionally I
>>>>>>>>>>>>>>>>>>>>>>> >>> think)
>>>>>>>>>>>>>>>>>>>>>>> >>> How to:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>>>>>>>>>>>>>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by
>>>>>>>>>>>>>>>>>>>>>>> LORIS.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Then as a second step:
>>>>>>>>>>>>>>>>>>>>>>> >>> b. Use the imaging insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets
>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>> >>> to load your DICOMs.
>>>>>>>>>>>>>>>>>>>>>>> >>> You will want to first ensure that the
>>>>>>>>>>>>>>>>>>>>>>> PatientName header in the DICOMs
>>>>>>>>>>>>>>>>>>>>>>> >>> as well as tar package are correctly labelled
>>>>>>>>>>>>>>>>>>>>>>> with PSCID_DCCID_VisitLabel
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets:
>>>>>>>>>>>>>>>>>>>>>>> >>> How to :
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options when
>>>>>>>>>>>>>>>>>>>>>>> running the bids_import script,
>>>>>>>>>>>>>>>>>>>>>>> >>> to automatically create your candidates and
>>>>>>>>>>>>>>>>>>>>>>> sessions.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> How do i delete a Study? And everytime do i have
>>>>>>>>>>>>>>>>>>>>>>> to create a new
>>>>>>>>>>>>>>>>>>>>>>> >>> candidate to get DCCID and a PSCID?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> *First execution:*
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod <
>>>>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match
>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a
>>>>>>>>>>>>>>>>>>>>>>> child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`,
>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_candidate_1`
>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES
>>>>>>>>>>>>>>>>>>>>>>> `psc` (`CenterID`)) at
>>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm
>>>>>>>>>>>>>>>>>>>>>>> line 1060.
>>>>>>>>>>>>>>>>>>>>>>> >>> ERROR: Failed to insert record in table
>>>>>>>>>>>>>>>>>>>>>>> mri_scanner:
>>>>>>>>>>>>>>>>>>>>>>> >>> The following database commands failed:
>>>>>>>>>>>>>>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';
>>>>>>>>>>>>>>>>>>>>>>> >>> SET
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
>>>>>>>>>>>>>>>>>>>>>>> >>> Medical Systems';
>>>>>>>>>>>>>>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>>>>>>>>>>>>>>>>>>>>>> >>> Error obtained:Cannot add or update a child row:
>>>>>>>>>>>>>>>>>>>>>>> a foreign key
>>>>>>>>>>>>>>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`,
>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_mri_scanner_1`
>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate`
>>>>>>>>>>>>>>>>>>>>>>> (`CandID`)) (error code 1452)
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>  ERROR: The validation has failed. Either re-run
>>>>>>>>>>>>>>>>>>>>>>> the validation again
>>>>>>>>>>>>>>>>>>>>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl
>>>>>>>>>>>>>>>>>>>>>>> using -force to force the
>>>>>>>>>>>>>>>>>>>>>>> >>> execution.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> The tarchiveLoader.pl insertion script has
>>>>>>>>>>>>>>>>>>>>>>> failed.
>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> *And second execution: *
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod <
>>>>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match
>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> PROBLEM:
>>>>>>>>>>>>>>>>>>>>>>> >>> The user 'lorisadmin' has already inserted this
>>>>>>>>>>>>>>>>>>>>>>> study.
>>>>>>>>>>>>>>>>>>>>>>> >>> The unique study ID is
>>>>>>>>>>>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
>>>>>>>>>>>>>>>>>>>>>>> >>> This is the information retained from the first
>>>>>>>>>>>>>>>>>>>>>>> time the study was
>>>>>>>>>>>>>>>>>>>>>>> >>> inserted:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy
>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :    127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :    Linux
>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>> 2019-09-04 18:33:05
>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d
>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec
>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar.gz
>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053
>>>>>>>>>>>>>>>>>>>>>>> >>>  DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Last update of record:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> The dicomTar.pl execution has failed.
>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Ok, this sounds like good progress.  Let us know
>>>>>>>>>>>>>>>>>>>>>>> when you next encounter
>>>>>>>>>>>>>>>>>>>>>>> >>> issues as you progress through the Imaging
>>>>>>>>>>>>>>>>>>>>>>> Install/Setup docs
>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>> >.
>>>>>>>>>>>>>>>>>>>>>>> >>> I'll look into how we can better handle the
>>>>>>>>>>>>>>>>>>>>>>> incoming/ directory next
>>>>>>>>>>>>>>>>>>>>>>> >>> time.
>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is
>>>>>>>>>>>>>>>>>>>>>>> >>> populated correctly except its port is  'port'
>>>>>>>>>>>>>>>>>>>>>>>   : ''. Also i have tested
>>>>>>>>>>>>>>>>>>>>>>> >>> that i can connect to MySQL with lorisuser.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> I executed the script again, because the only
>>>>>>>>>>>>>>>>>>>>>>> error i had previously was
>>>>>>>>>>>>>>>>>>>>>>> >>> that the /data/incoming folder didn't exist and
>>>>>>>>>>>>>>>>>>>>>>> there are no errors
>>>>>>>>>>>>>>>>>>>>>>> >>> reported back except of warnings <<mysql:
>>>>>>>>>>>>>>>>>>>>>>> [Warning] Using a password on the
>>>>>>>>>>>>>>>>>>>>>>> >>> command line interface can be insecure>>.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> It's possible -- if the script was unable to
>>>>>>>>>>>>>>>>>>>>>>> connect to the database
>>>>>>>>>>>>>>>>>>>>>>> >>> during its execution (e.g. typo in the
>>>>>>>>>>>>>>>>>>>>>>> password), that would explain the
>>>>>>>>>>>>>>>>>>>>>>> >>> underpopulated Image path and Loris-MRI code
>>>>>>>>>>>>>>>>>>>>>>> path you saw in the Config
>>>>>>>>>>>>>>>>>>>>>>> >>> module.
>>>>>>>>>>>>>>>>>>>>>>> >>> It's hard to tell without seeing the output from
>>>>>>>>>>>>>>>>>>>>>>> your script run -- Did
>>>>>>>>>>>>>>>>>>>>>>> >>> you see a sign of any such error?
>>>>>>>>>>>>>>>>>>>>>>> >>> The Config fields are populated by the
>>>>>>>>>>>>>>>>>>>>>>> imaging_install.sh script (starting
>>>>>>>>>>>>>>>>>>>>>>> >>> at line 222
>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222
>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> For example, check if the database connection
>>>>>>>>>>>>>>>>>>>>>>> information was populated
>>>>>>>>>>>>>>>>>>>>>>> >>> accurately in
>>>>>>>>>>>>>>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> If you are referring to the imaging_install.sh
>>>>>>>>>>>>>>>>>>>>>>> here is an image with the
>>>>>>>>>>>>>>>>>>>>>>> >>> configurations i typed. Maybe the problem is
>>>>>>>>>>>>>>>>>>>>>>> somewhere at the last part
>>>>>>>>>>>>>>>>>>>>>>> >>> which asks to configure as much as possible
>>>>>>>>>>>>>>>>>>>>>>> automatically?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear your LORIS core install is up and
>>>>>>>>>>>>>>>>>>>>>>> working and all the
>>>>>>>>>>>>>>>>>>>>>>> >>> front-end pages are loading.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$
>>>>>>>>>>>>>>>>>>>>>>> chmod 775 project
>>>>>>>>>>>>>>>>>>>>>>> >>> > and the web interface worked.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, it's important that project/ have 775
>>>>>>>>>>>>>>>>>>>>>>> permissions and that
>>>>>>>>>>>>>>>>>>>>>>> >>> lorisadmin be part of the sudoers group, per
>>>>>>>>>>>>>>>>>>>>>>> step 1 in the install
>>>>>>>>>>>>>>>>>>>>>>> >>> Readme <
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris#install-steps>.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image
>>>>>>>>>>>>>>>>>>>>>>> should change LORIS to
>>>>>>>>>>>>>>>>>>>>>>> >>> loris, right?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> These imaging paths will be updated during your
>>>>>>>>>>>>>>>>>>>>>>> imaging installation
>>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup> by
>>>>>>>>>>>>>>>>>>>>>>> an automated script --
>>>>>>>>>>>>>>>>>>>>>>> >>> you do not need to set them manually via the
>>>>>>>>>>>>>>>>>>>>>>> Config module.
>>>>>>>>>>>>>>>>>>>>>>> >>> Please continue to follow the Setup Guide
>>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup> for
>>>>>>>>>>>>>>>>>>>>>>> detailed steps to follow.
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image
>>>>>>>>>>>>>>>>>>>>>>> should change LORIS to loris,
>>>>>>>>>>>>>>>>>>>>>>> >>> right?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> i used
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x |
>>>>>>>>>>>>>>>>>>>>>>> sudo -E bash -
>>>>>>>>>>>>>>>>>>>>>>> >>> sudo apt-get install -y nodejs
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> you had suggested in the past, make worked and
>>>>>>>>>>>>>>>>>>>>>>> now i can see all the
>>>>>>>>>>>>>>>>>>>>>>> >>> contents in the web-interface, but i don't need
>>>>>>>>>>>>>>>>>>>>>>> make install?
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>> -------------- next part --------------
>>>>>>>>>>>>>>>>>>>>>>> An HTML attachment was scrubbed...
>>>>>>>>>>>>>>>>>>>>>>> URL: <
>>>>>>>>>>>>>>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html
>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16
>>>>>>>>>>>>>>>>>>>>>>> *****************************************
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
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From sotirisnik at gmail.com  Wed Jan 29 18:57:02 2020
From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos)
Date: Thu, 30 Jan 2020 01:57:02 +0200
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAMkiY3dAnkLdc4N=REmeCpX2qBfsQf=wRb=YtHtt20f8adXFyw@mail.gmail.com>
References: <mailman.1851.1573565332.16403.loris-dev@bic.mni.mcgill.ca>
 <CAEfMBom1HCWLo4NWgt5XG4625tCBfRT_Z_HepvtT_Er2LKbJoA@mail.gmail.com>
 <CAKHj7uS1AdMDjnacouTvxZgziYVgp5NNUeOuMkpDyrTskGTh-Q@mail.gmail.com>
 <CALbt7NDej8FGUUS6_oKbK5Fp-FnwsVz9AgZ6ZcJEZhmoKZmv8w@mail.gmail.com>
 <CAKHj7uSx-qqcXHZsWsZmSJ7sC1DgF+XapT5Y1+QdoVic37_DDg@mail.gmail.com>
 <CAMkiY3fQBGDGeNO8EHxwYAgbhTggNSQ+AVuCfdraDXwULMjjUg@mail.gmail.com>
 <CAKHj7uT5xXi=pOPdH=W9BroSphMHdTszdgW+GxuES=8wZox9eQ@mail.gmail.com>
 <CAMkiY3eUouxaRVdC4wH+vdjeQ=q_Nx8bcDNzcWgD_OgN77m3mw@mail.gmail.com>
 <CAKHj7uSxu4+tm+=x4+qJ1sAbrjmxG2H7LovDb7-2KMnyYQhrgg@mail.gmail.com>
 <CAMkiY3fdPZec2jx-cc2Zq37j3ekmTu_o819yBUv-bC7M98bkVw@mail.gmail.com>
 <CAKHj7uSZHozpuQ_YwGmy6wQ4tm43vJa556V0o2+JGDVsYaqN4g@mail.gmail.com>
 <CAMkiY3dge=x93bQDv0fHGMcrX0PA8Z_imLb_zSTh=nTrx5weFg@mail.gmail.com>
 <CAKHj7uR81gCkjvccMxwMA08dGSEgyTLJBJ+pZPkoUQDtGP_hFA@mail.gmail.com>
 <CAMkiY3fGhvExZ-JOvxeHe7dJQPvtPAHx3oJuiMVX7f1JgF1GAg@mail.gmail.com>
 <CAKHj7uRExO98Yyn9_07aw44wbh0bCL9_C1VFTAURKsxQLUuAeQ@mail.gmail.com>
 <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>
 <CAKHj7uRueb5fgh4VVCAyaq8tC9WM4gJ7k6Q=dxsqWzFgDqPfVQ@mail.gmail.com>
 <CAMkiY3d-Vt=3gQqwJ+GSRSacbLp2QxrB0g-_C7ONd8j_g1ipoQ@mail.gmail.com>
 <CAKHj7uQt9=nokz5g1zBuBx1-rJ8q7qKOuNVkQugC9wfvNFcjVA@mail.gmail.com>
 <CAMkiY3cAuQfT_5iMzYoF2BXVceu_vgz4eCq2sAtoyse+zUYeSg@mail.gmail.com>
 <CAMkiY3dq1O3V8+r4tTAWQ8N=rVFg=DNY-UPeMqbec+MSayj=Cg@mail.gmail.com>
 <CAKHj7uSEegvE1apPBGVyHmjyVzF+YxJjDMg0b+hDE4_-ON+dYw@mail.gmail.com>
 <CAKHj7uRx1NT7CycFq65uFpgPiOVwvT-jtK1NJX6_3rrLNFwdbA@mail.gmail.com>
 <CAMkiY3dAnkLdc4N=REmeCpX2qBfsQf=wRb=YtHtt20f8adXFyw@mail.gmail.com>
Message-ID: <CAKHj7uRpA-8kzkoEnAk7JBNLP7v4cmK4zW-gMutHESiFGj7xjw@mail.gmail.com>

Hi Cecile,

it seems that xargs is already installed in our docker container.

[image: image.png]


???? ???, 29 ??? 2020 ???? 7:59 ?.?., ?/? Cecile Madjar <
cecile.madjar at mcin.ca> ??????:

> Hi Sotirios,
>
> It looks like xargs is not installed in your docker environment.
>
> This is being used by the following command in dicomTar.pl (and a few
> other places but that is the one causing the error at the moment):
>
> $cmd = "cd " . $dcm_source . "; find -type f -name '.*' | *xargs* rm -f";
>
> So you need to install xargs in your docker for the command to run.
>
> Hope this helps,
>
> C?cile
> On Wed, Jan 29, 2020 at 10:35 AM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> Hello,
>>
>> We are making a dockerized version of Loris 21 and when we execute the
>> batch_uploads_imageuploader.pl we get an error about xargs. What could
>> be the casue?
>>
>> Use of uninitialized value $_ in pattern match (m//) at
>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>> Running now the following command: /data/loris/data//uploadNeuroDB/
>> imaging_upload_file.pl -profile prod -upload_id 13
>> /data/incoming/DCC0007_854380_V1.tar.gz -verbose
>>
>>  find -path \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml -name '__MACOSX'
>> -delete
>> xargs: file: No such file or directory
>>
>> dicomTar.pl \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml
>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>>  Source: /data/tmp/ImagingUpload-15-31-U_O5ml
>> Target: /data/loris/data/tarchive
>>
>> Thanks
>>
>> ???? ???, 10 ??? 2019 ???? 7:21 ?.?., ?/? Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> ??????:
>>
>>> Hi,
>>>
>>> i opened an issue and looked up for the values of Volume they suggested
>>> https://github.com/BIC-MNI/minc-toolkit-v2/issues/95. The only
>>> attributes associated with it i saw are [0x00089206] and [0x00089207]
>>>
>>> [image: image.png]
>>>
>>> I looked up for the file that was being viewed fine in the BrainBrowser
>>> and saw that it had that attribute empty so i used this command because i
>>> couldn't find a way to modify the attribute via pydicom
>>>
>>> dcmodify -ma "(0008,9206)=" *.dcm
>>>
>>> and that command reported the warning about the Endian Syntax. I also
>>> used the corresponding command for 9207 and got the message "Tag not found'
>>>
>>> Lastly I tried to upload some dicoms and now i am getting the SNR and i
>>> can view them fine. I believe now that all of them will pass successfully,
>>> i will report back later.
>>>
>>> Thanks,
>>>
>>> Sotirios
>>>
>>> ???? ???, 9 ??? 2019 ???? 8:10 ?.?., ?/? Cecile Madjar <
>>> cecile.madjar at mcin.ca> ??????:
>>>
>>>> Hi Sotirios,
>>>>
>>>> The issue you are having is a indeed a dcm2mnc issue. The converter
>>>> does not seem to work on your dataset for some reason. Unfortunately, there
>>>> is not much we can do on our front to fix this...
>>>>
>>>> I would recommend creating an issue on the MINC tools repository
>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> so they can fix
>>>> your problem.
>>>>
>>>> Very sorry that you are having that problem.
>>>>
>>>> Best,
>>>>
>>>> C?cile
>>>>
>>>> On Wed, Dec 4, 2019 at 8:59 AM Cecile Madjar <cecile.madjar at mcin.ca>
>>>> wrote:
>>>>
>>>>> Hi Sotirios,
>>>>>
>>>>> Could you please share a dataset with us that produces the error you
>>>>> get and the weird display in BrainBrowser? You could use the same SFTP
>>>>> credential that Nicolas gave you.
>>>>>
>>>>> The message errors you got from imaging_install.sh are probably due to
>>>>> the fact that you reran the install script and it tried to reinstall
>>>>> something that was already there. I would not worry about it. FYI, the only
>>>>> thing you needed to do was to update the MINC tools path in the environment
>>>>> file as you did after re-running imaging_install.sh and source the
>>>>> environment file.
>>>>>
>>>>> Best,
>>>>>
>>>>> C?cile
>>>>>
>>>>> On Wed, Dec 4, 2019 at 8:03 AM Sotirios Nikoloutsopoulos <
>>>>> sotirisnik at gmail.com> wrote:
>>>>>
>>>>>>  Hi Cecile,
>>>>>>
>>>>>> We used minctool 1.9.7 and we still get this error
>>>>>>
>>>>>> <<Restructuring...
>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>> Default GSL error handler invoked.
>>>>>> noise_estimate --snr /data/loris/data>>
>>>>>>
>>>>>
>>>>>> One dicom folder hadn't that error and is being viewed fine in the
>>>>>> BrainBrowser of Loris.
>>>>>>
>>>>>
>>>>>> When i used dpkg to the 1.9.17 the installation reported fine
>>>>>> <<Unpacking minc-toolkit-v2 (1.9.17) over (1.9.16) ...>>
>>>>>>
>>>>>> and then i used source /opt/minc/1.9.17/minc-toolkit-config.sh
>>>>>>
>>>>>> and aftewards runned bash ./imaging_install.sh just to be sure.
>>>>>>
>>>>>> We also had to modify /data/loris/bin/mri/environment because it
>>>>>> still pointed to the old version.
>>>>>>
>>>>>> What i found strange is this during the run of imaging_install.sh
>>>>>>
>>>>>> <<already using interpreter
>>>>>> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/bin/python3
>>>>>> Please use the *system* python to run this script
>>>>>> Traceback (most recent call last):
>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>>>>> 2632, in <module>
>>>>>>     main()
>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>>>>> 870, in main
>>>>>>     symlink=options.symlink,
>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>>>>> 1156, in create_environment
>>>>>>     install_python(home_dir, lib_dir, inc_dir, bin_dir,
>>>>>> site_packages=site_packages, clear=clear, symlink=symlink)
>>>>>>   File
>>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>>> line 357, in abspath
>>>>>>     if not isabs(path):
>>>>>>   File
>>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>>> line 64, in isabs
>>>>>>     return s.startswith(sep)
>>>>>> AttributeError: 'NoneType' object has no attribute 'startswith'
>>>>>> Installing the Python libraries into the loris-mri virtualenv...
>>>>>> Requirement already satisfied: mysqlclient in
>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (1.4.4)
>>>>>> Requirement already satisfied: mysql-connector in
>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (2.2.9)
>>>>>> Requirement already satisfied: pybids in
>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (0.9.4)
>>>>>> Requirement already satisfied: nibabel>=2.1 in ./python_virtua>>
>>>>>>
>>>>>> So should i open an issue for that error? or is there something else
>>>>>> to try?
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Sotirios
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ???? ???, 3 ??? 2019 ???? 10:39 ?.?., ?/? Cecile Madjar <
>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>
>>>>>>> Hi Sotirios,
>>>>>>>
>>>>>>> Does the pic screenshot in the imaging browser module also shows 1
>>>>>>> slice? If so, that would mean there was an issue with the dcm2mnc
>>>>>>> conversion. Once again, installing the latest version of the MINC tools
>>>>>>> should help but if this issue persists I would recommend creating an issue
>>>>>>> for that too on their repository
>>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> (if not already
>>>>>>> reported there, there are a few known issue reported).
>>>>>>>
>>>>>>> Other viewer for MINCs are register and Display (both part of the
>>>>>>> MINC tools). For NIfTI, you have FSLeye, MRICron and probably many other
>>>>>>> viewers that exists.
>>>>>>>
>>>>>>> Hope this helps,
>>>>>>>
>>>>>>> C?cile
>>>>>>>
>>>>>>> On Tue, Dec 3, 2019 at 3:26 PM Sotirios Nikoloutsopoulos <
>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi Cecile,
>>>>>>>>
>>>>>>>> Yes, Nifti files are mandatory for our work. From what we saw at a
>>>>>>>> 3rd vm we setted up, the nifti files are being created ( i haven't verified
>>>>>>>> if that is the case at the 2nd vm ). I will install the latest version and
>>>>>>>> will report back, but do you know any nifti/minc viewer? because the
>>>>>>>> Brainbrowser of Loris does not output them well, it's like it is loading
>>>>>>>> only 1 slice and we would like to verify it with another tool too. We
>>>>>>>> verified that the dcmconv command didn't affect the quality of the
>>>>>>>> .dcm files.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Sotirios
>>>>>>>>
>>>>>>>> ???? ???, 2 ??? 2019 ???? 6:59 ?.?., ?/? Cecile Madjar <
>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>
>>>>>>>>> Hi Sotirios,
>>>>>>>>>
>>>>>>>>> It looks like for some reason your binary mnc2nii is not working
>>>>>>>>> and reports that error. Do you want to create NIfTI files or are you happy
>>>>>>>>> with just the MINC files?
>>>>>>>>>
>>>>>>>>> If you don't need the NIfTI files, then maybe you can set the
>>>>>>>>> Config setting "NIfTI file creation" to No instead of Yes and
>>>>>>>>> this error will not appear anymore.
>>>>>>>>>
>>>>>>>>> If you need the NIfTI files to be created, then I would
>>>>>>>>> recommend installing the latest version of the MINC tools (1.9.17). They
>>>>>>>>> can be found there:
>>>>>>>>>
>>>>>>>>>    - pre-built packages:
>>>>>>>>>    https://packages.bic.mni.mcgill.ca/minc-toolkit/
>>>>>>>>>    - from the source code with installation instructions in the
>>>>>>>>>    README: https://github.com/BIC-MNI/minc-toolkit-v2
>>>>>>>>>
>>>>>>>>> If the problem persists by using the latest release of MINC tools,
>>>>>>>>> then create an issue on Github for the MINC developers here
>>>>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues>.
>>>>>>>>>
>>>>>>>>> Hope this helps,
>>>>>>>>>
>>>>>>>>> C?cile
>>>>>>>>>
>>>>>>>>> On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Cecile,
>>>>>>>>>>
>>>>>>>>>> Thanks to Nicholas i was able to create all the mincs images. The
>>>>>>>>>> problem was that the files were in Little-Endian-Implicit transfer syntax
>>>>>>>>>> and i had to convert them Little-Endian-Explicit transfer syntax with this
>>>>>>>>>> command
>>>>>>>>>>
>>>>>>>>>> find <root_of_my_DICOM_files_directory> -type f | xargs -i
>>>>>>>>>> dcmconv --write-xfer-little {} {}
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Looking back at our mails i saw that Little-Endian error had
>>>>>>>>>> occurred when i used dcmodify, but i switcthed to using pydicom instead.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> [image: image.png]
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> In the output i see an error sometimes about "gsl:
>>>>>>>>>> bessel_I0.c:216: ERROR: overflow". Is this okay?
>>>>>>>>>>
>>>>>>>>>> Restructuring...
>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>> noise_estimate --snr
>>>>>>>>>> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
>>>>>>>>>> SNR is:
>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> Sotirios
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar <
>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> Thank you for the details!
>>>>>>>>>>>
>>>>>>>>>>> A few things to try:
>>>>>>>>>>>
>>>>>>>>>>>    - modify the TMPDIR to be on your /data directory where
>>>>>>>>>>>    there might be more space to do processing (could create a /data/tmp where
>>>>>>>>>>>    the temporary files would be created)
>>>>>>>>>>>    - how many files are there for that upload in
>>>>>>>>>>>    tarchive_files? Are they different from the ones showing the warning
>>>>>>>>>>>    message?
>>>>>>>>>>>       - FYI: query to get that: SELECT tf.* FROM tarchive_files
>>>>>>>>>>>       tf JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your uploadID> (the
>>>>>>>>>>>       output of that query would be very useful if you can provide it)
>>>>>>>>>>>       - how many series are there for that upload in
>>>>>>>>>>>    tarchive_series?
>>>>>>>>>>>    - FYI: query to get that: SELECT ts.* FROM tarchive_series
>>>>>>>>>>>       ts JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your uploadID> (the
>>>>>>>>>>>       output of that query would be very useful if you can provide it)
>>>>>>>>>>>    - things are failing when the scripts try running the
>>>>>>>>>>>    following command: find
>>>>>>>>>>>    /tmp/TarLoad-23-43-ccugaa/ImagingUpload-23-43-6JCOTO -type f  |
>>>>>>>>>>>    /data/loris/bin/mri/dicom-archive/get_dicom_info.pl
>>>>>>>>>>>    -studyuid -series -echo -image -file  -attvalue 0018 0024 -series_descr
>>>>>>>>>>>    -stdin | sort -n -k1 -k2 -k7 -k3 -k6 -k4  | cut -f 5 | dcm2mnc -dname ''
>>>>>>>>>>>    -stdin -clobber -usecoordinates /tmp/TarLoad-23-43-ccugaa
>>>>>>>>>>>       - clearly the problems come from get_dicom_info.pl but I
>>>>>>>>>>>       cannot pinpoint the error yet. I will ask around and get back to you
>>>>>>>>>>>
>>>>>>>>>>> If I cannot figure it out remotely, is there a way to have a
>>>>>>>>>>> call using zoom? This way you could share your screen with me and run the
>>>>>>>>>>> debugger on that script and hopefully we can figure out what is going on
>>>>>>>>>>> with those datasets?
>>>>>>>>>>>
>>>>>>>>>>> Thanks!
>>>>>>>>>>>
>>>>>>>>>>> C?cile
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Nov 26, 2019 at 5:17 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>
>>>>>>>>>>>> In both my virtual machines
>>>>>>>>>>>> export TMPDIR=/tmp
>>>>>>>>>>>>
>>>>>>>>>>>> In both vm also with dcm2mnc i get this output. Just to verify
>>>>>>>>>>>> that this passed in my 1st vm and produced mincs.
>>>>>>>>>>>>
>>>>>>>>>>>> I attached the spool as a csv.
>>>>>>>>>>>>
>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>
>>>>>>>>>>>> And also one difference i found was this in the Loris-mri code
>>>>>>>>>>>> ( left 1st workable vm, right 2nd vm that has to be fixed, although i
>>>>>>>>>>>> changed it seems to be independent of the uninitialized value $_ )
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>
>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>
>>>>>>>>>>>>> that is puzzling... A few additional questions:
>>>>>>>>>>>>>
>>>>>>>>>>>>>    - what is the bash variable TMPDIR set to on the
>>>>>>>>>>>>>    environment file?
>>>>>>>>>>>>>    - could you try running separately dcm2mnc on the DICOM
>>>>>>>>>>>>>    folder to see if that works?
>>>>>>>>>>>>>    - could you send us the detailed log from the notification
>>>>>>>>>>>>>    spool table (SELECT * FROM notification_spool WHERE UploadID=<your
>>>>>>>>>>>>>    uploadID>) and send it back to us? Maybe there are some additional clues
>>>>>>>>>>>>>    that could help figuring out what is going on.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you!
>>>>>>>>>>>>>
>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, Nov 26, 2019 at 10:12 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I checked for the StudyInstacueUID at the files with "The
>>>>>>>>>>>>>> target directory does not contain a single DICOM file"" and their attribute
>>>>>>>>>>>>>> has a value.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Regarding the scouter and localizer, i modified the settings
>>>>>>>>>>>>>> in the imaging pipeline and now i don't get that error message, but still
>>>>>>>>>>>>>> it doesn't create the mnics.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The errors i am getting are ( uninitialized value $_ is not
>>>>>>>>>>>>>> important? because i haven't got comments about that )
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>> Running now the following command:
>>>>>>>>>>>>>> /data/loris/data//uploadNeuroDB/imaging_upload_file.pl
>>>>>>>>>>>>>> -profile prod -upload_id 134 /data/incoming/DCC0025_118008_V1.tar.gz
>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> and
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Number of MINC files that will be considered for inserting
>>>>>>>>>>>>>> into the database: 0
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> No data could be converted into valid MINC files.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The tarchiveLoader.pl insertion script has failed.
>>>>>>>>>>>>>> Use of uninitialized value $mail_user in concatenation (.) or
>>>>>>>>>>>>>> string at /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>>>> line 249.
>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 250.
>>>>>>>>>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 251.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> OK. So the issue I mentioned should not be a problem for you.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Is the StudyInstanceUID DICOM header set in your images? If
>>>>>>>>>>>>>>> it is not set, then you would end up with the error message "The target
>>>>>>>>>>>>>>> directory does not contain a single DICOM file". So maybe this is the issue
>>>>>>>>>>>>>>> you are having with those datasets?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Regarding not excluding series descriptions, you can
>>>>>>>>>>>>>>> configure that in the Config module under the Imaging Pipeline section.
>>>>>>>>>>>>>>> Simply remove all entries for the "Series description to exclude from
>>>>>>>>>>>>>>> imaging insertion" setting.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Mon, Nov 25, 2019 at 9:58 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> We are using this version
>>>>>>>>>>>>>>>> https://github.com/aces/Loris/archive/v21.0.0.zip. Is it
>>>>>>>>>>>>>>>> possible to insert low resolution now?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, <
>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Which version of LORIS-MRI are you using?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> There was a bug that got resolved in 20.2 in
>>>>>>>>>>>>>>>>> get_dicom_info.pl. Basically, if a DICOM did not have the
>>>>>>>>>>>>>>>>> (0020,0032) header, get_dicom_info.pl considered that the
>>>>>>>>>>>>>>>>> file was not a DICOM, which was a mistake. This got fixed in version 20.2
>>>>>>>>>>>>>>>>> of LORIS-MRI. Hopefully this is the issue you are encountering.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> About scout and localizer, they are a type of short and
>>>>>>>>>>>>>>>>> low resolution sequence that is used by the tech but is of no interest
>>>>>>>>>>>>>>>>> scientifically, which is why we tend to no insert them.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> i executed the find command and the output i got per
>>>>>>>>>>>>>>>>>> folder was "DICOM medical imaging data. Maybe there is something wrong with
>>>>>>>>>>>>>>>>>> the find command in the warning that it is unable to check if the file is a
>>>>>>>>>>>>>>>>>> dicom file? Also when i use get_dicom_info.pl i don't
>>>>>>>>>>>>>>>>>> get any output data. Finally i don't understand what scout or localizer is
>>>>>>>>>>>>>>>>>> ( something like if and only if a file fails then the whole session is
>>>>>>>>>>>>>>>>>> invalid? ).
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> I took a closer look to the
>>>>>>>>>>>>>>>>>>> batch_uploader_multiple_output.txt file you sent. It looks like there are
>>>>>>>>>>>>>>>>>>> different reasons for failure depending on the DICOM folder uploaded.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>    - For 465466 DCC0000 V1; 727195 DCC0004 V1 and
>>>>>>>>>>>>>>>>>>>    684908 DCC0007 V1: it looks like there is no file of type DICOM in the
>>>>>>>>>>>>>>>>>>>    folder. Have you checked to see if that is indeed the case? Maybe you can
>>>>>>>>>>>>>>>>>>>    try running the following command on that folder to see what are the types
>>>>>>>>>>>>>>>>>>>    of the files? If it does not return at least one DICOM medical imaging data
>>>>>>>>>>>>>>>>>>>    file, then that is why you get the error message from the pipeline:
>>>>>>>>>>>>>>>>>>>       -
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>       find <my_dicom_archive_root_folder> -type f | xargs -i file {}|cut -d: -f2|sort|uniq
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>       - For 864173 DCC0001 V1: it looks like there are
>>>>>>>>>>>>>>>>>>>    two different DICOM studies within the same folder. You will need to split
>>>>>>>>>>>>>>>>>>>    that study in two based on the StudyUID field as the insertion pipeline
>>>>>>>>>>>>>>>>>>>    does not allow for more than one StudyUID per upload.
>>>>>>>>>>>>>>>>>>>    - For 890807 DCC0002 V1; 637025 DCC0005 V1 and
>>>>>>>>>>>>>>>>>>>    239975 DCC0006 V1: it looks like the dcm2mnc command did not produce any
>>>>>>>>>>>>>>>>>>>    MINC files. Can you check in the DICOM archive what are the series present
>>>>>>>>>>>>>>>>>>>    in the tarchive for that visit? Maybe only a scout or localizer was
>>>>>>>>>>>>>>>>>>>    acquired for that session, hence the no valid MINC files (scout and
>>>>>>>>>>>>>>>>>>>    localizer being skipped for the conversion)
>>>>>>>>>>>>>>>>>>>    - For 397410 DCC0003 V1: it looks like everything
>>>>>>>>>>>>>>>>>>>    went well for this one.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> One script that is called by our pipeline is called
>>>>>>>>>>>>>>>>>>> get_dicom_info.pl and this does all kind of checks on
>>>>>>>>>>>>>>>>>>> the DICOM files (it is being called when running the dcm2mnc conversion).
>>>>>>>>>>>>>>>>>>> You could run it independently on your folder if needed.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Since one of the study got in, it does not look like you
>>>>>>>>>>>>>>>>>>> are having a problem with the setup. It seems more likely to be a problem
>>>>>>>>>>>>>>>>>>> with the data themselves.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hope this helps.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios
>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> In my first vm i am able to create the minc files and
>>>>>>>>>>>>>>>>>>>> view them at the mri browser (except of candidate 102761034 ), meanwhile
>>>>>>>>>>>>>>>>>>>> the same files gives warnings at the 2nd vm. The output  of the batch
>>>>>>>>>>>>>>>>>>>> upload can be seen in the file attached.
>>>>>>>>>>>>>>>>>>>> Also a colleague of us has built a pre-validation tool
>>>>>>>>>>>>>>>>>>>> for dicom
>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/
>>>>>>>>>>>>>>>>>>>> which had found all the files that Loris gave as warning . Basically I
>>>>>>>>>>>>>>>>>>>> confirmed that the total amount of files per dicom was the same amount as
>>>>>>>>>>>>>>>>>>>> stated in Loris and checked some filenames given from warning to confirm
>>>>>>>>>>>>>>>>>>>> that they match with our tool. But that was months ago and my colleague had
>>>>>>>>>>>>>>>>>>>> changed some parameters for MIP and now our tool doesn't find all the
>>>>>>>>>>>>>>>>>>>> invalid files, that's why i asked for the dicom header specification of
>>>>>>>>>>>>>>>>>>>> Loris. In a discussion we had he mentioned that he doesn't check for some
>>>>>>>>>>>>>>>>>>>> tags e.x. orientation. Lastly to mention that in my first vm i didn't use
>>>>>>>>>>>>>>>>>>>> our tool to remove invalid dcm files.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>> Can you provide us with some fresh particulars of the
>>>>>>>>>>>>>>>>>>>>> current issue and we'll take it from there?
>>>>>>>>>>>>>>>>>>>>> Yang's team has built these scripts which can
>>>>>>>>>>>>>>>>>>>>> definitely serve as a model for your pre-validation of your DICOM
>>>>>>>>>>>>>>>>>>>>> collections.
>>>>>>>>>>>>>>>>>>>>> cheers,
>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios
>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> HI Yang,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> We make use of pydicom library too. Now about the
>>>>>>>>>>>>>>>>>>>>>> validate.py i see that you check if some attributes are missing such as
>>>>>>>>>>>>>>>>>>>>>> PatientID, PatientName which all of our files contains that info. Maybe i
>>>>>>>>>>>>>>>>>>>>>> have missed something on the setup of my other virtual machine ( although
>>>>>>>>>>>>>>>>>>>>>> one dicom passed on the new vm successfully, the others that were inserted
>>>>>>>>>>>>>>>>>>>>>> correctly on my old vm fails on the new one ), i think that i had asked
>>>>>>>>>>>>>>>>>>>>>> about this error "Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>> line 144." but i don't remember the solution.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding <
>>>>>>>>>>>>>>>>>>>>>> it at cnbp.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hey, Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Christine from the LORIS team mentioned you had some
>>>>>>>>>>>>>>>>>>>>>>> issue with DICOM.  I am a fellow developer for an external project using
>>>>>>>>>>>>>>>>>>>>>>> LORIS, kind of just like you. We had to implement DICOM upload as well but
>>>>>>>>>>>>>>>>>>>>>>> more as a fully automated pipeline actually.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> While we were building CNBP, we had coded up some
>>>>>>>>>>>>>>>>>>>>>>> minor Python functions to check DICOM integrity (and simple validations)
>>>>>>>>>>>>>>>>>>>>>>> and you might be able to gain some inspiration from it and help you with
>>>>>>>>>>>>>>>>>>>>>>> your cause. For more comprehensive solution, PyDICOM (
>>>>>>>>>>>>>>>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#)  seems
>>>>>>>>>>>>>>>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks
>>>>>>>>>>>>>>>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can
>>>>>>>>>>>>>>>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty
>>>>>>>>>>>>>>>>>>>>>>> rough around the edges but hopefully point you in the right direcitons
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Yang Ding, PhD.
>>>>>>>>>>>>>>>>>>>>>>> Canadian Neonatal Brain Platform Architect
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM <
>>>>>>>>>>>>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Send Loris-dev mailing list submissions to
>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> To subscribe or unsubscribe via the World Wide Web,
>>>>>>>>>>>>>>>>>>>>>>>> visit
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>> or, via email, send a message with subject or body
>>>>>>>>>>>>>>>>>>>>>>>> 'help' to
>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-request at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> You can reach the person managing the list at
>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-owner at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> When replying, please edit your Subject line so it
>>>>>>>>>>>>>>>>>>>>>>>> is more specific
>>>>>>>>>>>>>>>>>>>>>>>> than "Re: Contents of Loris-dev digest..."
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Today's Topics:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>    1. Re: Import mri - scripts (Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos)
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Message: 1
>>>>>>>>>>>>>>>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200
>>>>>>>>>>>>>>>>>>>>>>>> From: Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>> To: Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>>> Message-ID:
>>>>>>>>>>>>>>>>>>>>>>>>         <CAKHj7uST=
>>>>>>>>>>>>>>>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com
>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Could we send you a link with 10 anonymized dicom
>>>>>>>>>>>>>>>>>>>>>>>> files to diagnose the
>>>>>>>>>>>>>>>>>>>>>>>> warnings we get?
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> > Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>> > We were wondering whether Loris has a tool to
>>>>>>>>>>>>>>>>>>>>>>>> check if there are problems
>>>>>>>>>>>>>>>>>>>>>>>> > with the dcm files, before trying to upload them.
>>>>>>>>>>>>>>>>>>>>>>>> Something that could
>>>>>>>>>>>>>>>>>>>>>>>> > provide the same results provided in the
>>>>>>>>>>>>>>>>>>>>>>>> warning_output, this is the
>>>>>>>>>>>>>>>>>>>>>>>> > summary from the mri_upload at the front-page.
>>>>>>>>>>>>>>>>>>>>>>>> Also which attributes of the
>>>>>>>>>>>>>>>>>>>>>>>> > dcm header would trigger a warning? is there a
>>>>>>>>>>>>>>>>>>>>>>>> dcm file header
>>>>>>>>>>>>>>>>>>>>>>>> > specification for Loris?
>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>> > Thanks
>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>> > Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> > sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp
>>>>>>>>>>>>>>>>>>>>>>>> function it worked,but i
>>>>>>>>>>>>>>>>>>>>>>>> >> thought that something else was causing the 2nd
>>>>>>>>>>>>>>>>>>>>>>>> issue.
>>>>>>>>>>>>>>>>>>>>>>>> >> Thanks
>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours
>>>>>>>>>>>>>>>>>>>>>>>> Boucher, Mr, <
>>>>>>>>>>>>>>>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> The first error occurs because the
>>>>>>>>>>>>>>>>>>>>>>>> QCFirstChangeTime and columns are of
>>>>>>>>>>>>>>>>>>>>>>>> >>> type `unsigned integer` and not `datatime`. You
>>>>>>>>>>>>>>>>>>>>>>>> should be using
>>>>>>>>>>>>>>>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW().
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> The second error occurs because the trigger
>>>>>>>>>>>>>>>>>>>>>>>> triggers a rollback of the
>>>>>>>>>>>>>>>>>>>>>>>> >>> insert statement in the files table.
>>>>>>>>>>>>>>>>>>>>>>>> >>> See mysql documentation for trigger error
>>>>>>>>>>>>>>>>>>>>>>>> handling.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> An error during either a BEFORE or AFTER
>>>>>>>>>>>>>>>>>>>>>>>> trigger results in failure of
>>>>>>>>>>>>>>>>>>>>>>>> >>> the entire statement that caused trigger
>>>>>>>>>>>>>>>>>>>>>>>> invocation.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you for sharing that. I hope it helps.
>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Xavier
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf
>>>>>>>>>>>>>>>>>>>>>>>> of Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM
>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> When mincs are inserted their corresponding
>>>>>>>>>>>>>>>>>>>>>>>> rows at the file table are
>>>>>>>>>>>>>>>>>>>>>>>> >>> inserted too
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> i would like to insert their rows at
>>>>>>>>>>>>>>>>>>>>>>>> file_qcstatus as well, because i
>>>>>>>>>>>>>>>>>>>>>>>> >>> don't want manually to label them as passed
>>>>>>>>>>>>>>>>>>>>>>>> throught the interface
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> That is the trigger i wrote
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER
>>>>>>>>>>>>>>>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER
>>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW
>>>>>>>>>>>>>>>>>>>>>>>> >>> BEGIN
>>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT INTO files_qcstatus
>>>>>>>>>>>>>>>>>>>>>>>> >>> SET FileID = NEW.FileID,
>>>>>>>>>>>>>>>>>>>>>>>> >>>      SeriesUID = NEW.SeriesUID,
>>>>>>>>>>>>>>>>>>>>>>>> >>>      EchoTime = NEW.EchoTime,
>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCStatus = "Pass",
>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCFirstChangeTime = NOW(),
>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCLastChangeTime = NOW();
>>>>>>>>>>>>>>>>>>>>>>>> >>> END
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> although it contains some errors
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range value
>>>>>>>>>>>>>>>>>>>>>>>> for column
>>>>>>>>>>>>>>>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823.
>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update
>>>>>>>>>>>>>>>>>>>>>>>> a child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`parameter_file`,
>>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT
>>>>>>>>>>>>>>>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`)
>>>>>>>>>>>>>>>>>>>>>>>> REFERENCES `files` (`FileID`))
>>>>>>>>>>>>>>>>>>>>>>>> >>> at
>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>>>>>>>> Madjar <
>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> In the mri_upload table, there is a TarchiveID
>>>>>>>>>>>>>>>>>>>>>>>> column associated with
>>>>>>>>>>>>>>>>>>>>>>>> >>> the MRI upload you inserted. When this value is
>>>>>>>>>>>>>>>>>>>>>>>> NULL, it means no DICOMs
>>>>>>>>>>>>>>>>>>>>>>>> >>> were inserted into the tarchive tables. At the
>>>>>>>>>>>>>>>>>>>>>>>> end of the insertion of the
>>>>>>>>>>>>>>>>>>>>>>>> >>> DICOMs in the tarchive tables, this value is
>>>>>>>>>>>>>>>>>>>>>>>> updated with the correct
>>>>>>>>>>>>>>>>>>>>>>>> >>> TarchiveID associated with the upload.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Could this correspond to what you want to do?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Regarding the files_qcstatus, this table is
>>>>>>>>>>>>>>>>>>>>>>>> only linked to the files
>>>>>>>>>>>>>>>>>>>>>>>> >>> table (hence, the MINC files). You could always
>>>>>>>>>>>>>>>>>>>>>>>> create a new table for
>>>>>>>>>>>>>>>>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive
>>>>>>>>>>>>>>>>>>>>>>>> table?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> i would like whenever a dicom is imported to
>>>>>>>>>>>>>>>>>>>>>>>> mark all their
>>>>>>>>>>>>>>>>>>>>>>>> >>> coressponding qc_status to "pass". I was
>>>>>>>>>>>>>>>>>>>>>>>> thinking of creating a trigger for
>>>>>>>>>>>>>>>>>>>>>>>> >>> that, but which tables do i need to add entries
>>>>>>>>>>>>>>>>>>>>>>>> to? So far from what i see
>>>>>>>>>>>>>>>>>>>>>>>> >>> i need to add entres at  the table "files"
>>>>>>>>>>>>>>>>>>>>>>>> whenever an insertion happens to
>>>>>>>>>>>>>>>>>>>>>>>> >>> files_qcstatus.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Oh, sorry i should have asked for StudyID, at
>>>>>>>>>>>>>>>>>>>>>>>> the beginning of my email
>>>>>>>>>>>>>>>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID).
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> that's the Study Instance UID, not the StudyID.
>>>>>>>>>>>>>>>>>>>>>>>> So the StudyID i am
>>>>>>>>>>>>>>>>>>>>>>>> >>> looking for is not stored in the database?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> The StudyUID is stored in the DicomArchiveID
>>>>>>>>>>>>>>>>>>>>>>>> field of the
>>>>>>>>>>>>>>>>>>>>>>>> >>> tarchive table. It can also be found in the
>>>>>>>>>>>>>>>>>>>>>>>> metadata field but it is mixed
>>>>>>>>>>>>>>>>>>>>>>>> >>> with many other information.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Is StudyUID stored somewhere at the tables? At
>>>>>>>>>>>>>>>>>>>>>>>> the tarchive table,
>>>>>>>>>>>>>>>>>>>>>>>> >>> specifically at the AcquisitonMetadata column i
>>>>>>>>>>>>>>>>>>>>>>>> found something called
>>>>>>>>>>>>>>>>>>>>>>>> >>> 'Unique Study ID" in its context, but that must
>>>>>>>>>>>>>>>>>>>>>>>> be the Study Instance UID.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Your observation is correct. A little
>>>>>>>>>>>>>>>>>>>>>>>> explanation below.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> MINC files get inserted into the MRI violation
>>>>>>>>>>>>>>>>>>>>>>>> tables if:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>    - the scan type could not be identified (not
>>>>>>>>>>>>>>>>>>>>>>>> matching an entry in
>>>>>>>>>>>>>>>>>>>>>>>> >>>    the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>>> >>>    - one parameter of the scan type is out of
>>>>>>>>>>>>>>>>>>>>>>>> the expected range
>>>>>>>>>>>>>>>>>>>>>>>> >>>    present in the mri_protocol_checks (extra
>>>>>>>>>>>>>>>>>>>>>>>> filtering in case you need to be
>>>>>>>>>>>>>>>>>>>>>>>> >>>    stricker on some parameters not present in
>>>>>>>>>>>>>>>>>>>>>>>> the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>>> >>>    - if the CandID and PSCID do not match
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> The following cases do not get in the MRI
>>>>>>>>>>>>>>>>>>>>>>>> violation tables as it happens
>>>>>>>>>>>>>>>>>>>>>>>> >>> before the conversion of the DICOM to MINC
>>>>>>>>>>>>>>>>>>>>>>>> files and only MINC files
>>>>>>>>>>>>>>>>>>>>>>>> >>> violations are logged there:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>    - "No single DICOM" (since no valid DICOM
>>>>>>>>>>>>>>>>>>>>>>>> could be found to convert
>>>>>>>>>>>>>>>>>>>>>>>> >>>    to MINC)
>>>>>>>>>>>>>>>>>>>>>>>> >>>    - "Study already inserted" (duplicate
>>>>>>>>>>>>>>>>>>>>>>>> StudyUID) since this error
>>>>>>>>>>>>>>>>>>>>>>>> >>>    happens at the dicomTar.pl level (way before
>>>>>>>>>>>>>>>>>>>>>>>> conversion into MINC files)
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad everything is working out!!
>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> the mri passed, for some reason it consumed
>>>>>>>>>>>>>>>>>>>>>>>> 5.12GB of ram. Now about the
>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations, dicoms are triggered to be
>>>>>>>>>>>>>>>>>>>>>>>> inserted there only if there is
>>>>>>>>>>>>>>>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general for
>>>>>>>>>>>>>>>>>>>>>>>> its header parameter?
>>>>>>>>>>>>>>>>>>>>>>>> >>> Because i don't see the cases of 'No single
>>>>>>>>>>>>>>>>>>>>>>>> dicom" or with the 2 studyiuid
>>>>>>>>>>>>>>>>>>>>>>>> >>> to be there.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Sorry to hear you are having issues with the
>>>>>>>>>>>>>>>>>>>>>>>> memory. I think most of our
>>>>>>>>>>>>>>>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you
>>>>>>>>>>>>>>>>>>>>>>>> should be fine.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> about that dicom that had that insertion error
>>>>>>>>>>>>>>>>>>>>>>>> it's about 30mb and when
>>>>>>>>>>>>>>>>>>>>>>>> >>> it is being processed the ram is being
>>>>>>>>>>>>>>>>>>>>>>>> drastically increased from 2gb to
>>>>>>>>>>>>>>>>>>>>>>>> >>> 3.28 and then the whole virtual machine is
>>>>>>>>>>>>>>>>>>>>>>>> frozen. What is the recommended
>>>>>>>>>>>>>>>>>>>>>>>> >>> size of ram for using Loris?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to see that the StudyUID problem was fixed!
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> For the delete script issue, if you are
>>>>>>>>>>>>>>>>>>>>>>>> absolutely certain that no
>>>>>>>>>>>>>>>>>>>>>>>> >>> processes are run for that uploadID, you can
>>>>>>>>>>>>>>>>>>>>>>>> update the mri_upload table
>>>>>>>>>>>>>>>>>>>>>>>> >>> and set the column Inserting to 0 instead of 1
>>>>>>>>>>>>>>>>>>>>>>>> for that uploadID. It
>>>>>>>>>>>>>>>>>>>>>>>> >>> looks like for some reason the scripts did not
>>>>>>>>>>>>>>>>>>>>>>>> update this field when it
>>>>>>>>>>>>>>>>>>>>>>>> >>> stopped the insertion. Not sure why that would
>>>>>>>>>>>>>>>>>>>>>>>> be the case though.
>>>>>>>>>>>>>>>>>>>>>>>> >>> Note: only do that update if you are certain
>>>>>>>>>>>>>>>>>>>>>>>> that there is no processing
>>>>>>>>>>>>>>>>>>>>>>>> >>> happening.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> about the Dicoms i reported that didn't have a
>>>>>>>>>>>>>>>>>>>>>>>> StudyID they actually do
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> I thought that this might be a permission
>>>>>>>>>>>>>>>>>>>>>>>> because "w" was missing at the
>>>>>>>>>>>>>>>>>>>>>>>> >>> group. After using chmod -R 775 only 102809579
>>>>>>>>>>>>>>>>>>>>>>>> passed, but with no mnic
>>>>>>>>>>>>>>>>>>>>>>>> >>> files. Also now i have this error
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox
>>>>>>>>>>>>>>>>>>>>>>>> :/data/loris/bin/mri/tools$
>>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore
>>>>>>>>>>>>>>>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is
>>>>>>>>>>>>>>>>>>>>>>>> currently processing it.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> How can solve this?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Here is our auto dicom uploading python script:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> To give you a brief idea:
>>>>>>>>>>>>>>>>>>>>>>>> >>> Per folder it will:
>>>>>>>>>>>>>>>>>>>>>>>> >>> 1) Delete all the .bak files
>>>>>>>>>>>>>>>>>>>>>>>> >>> 2) Locate .dcm files and update the Patient
>>>>>>>>>>>>>>>>>>>>>>>> header
>>>>>>>>>>>>>>>>>>>>>>>> >>> 3) Furthermore we are interesting in finding
>>>>>>>>>>>>>>>>>>>>>>>> TR_min, TR_max, TE_min,
>>>>>>>>>>>>>>>>>>>>>>>> >>> TE_max parameters of T1 protocol and do an
>>>>>>>>>>>>>>>>>>>>>>>> update at the mri_protocol table
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205
>>>>>>>>>>>>>>>>>>>>>>>> >>> For some reason some files are missing
>>>>>>>>>>>>>>>>>>>>>>>> SeriesDescription/ProtocolName
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> In total i have 7 folders
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> 3/7 passed
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Also about the first patient with DC0000 had a
>>>>>>>>>>>>>>>>>>>>>>>> violation "T1 AXIAL SE
>>>>>>>>>>>>>>>>>>>>>>>> >>> GADO", but my script didn't output a TE of 17
>>>>>>>>>>>>>>>>>>>>>>>> nowhere and i find that weird
>>>>>>>>>>>>>>>>>>>>>>>> >>> since Loris detects the SeriesDescription.
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Now about the 4/7 that didn't passed
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> 102327840 and 102809579 outputs "The target
>>>>>>>>>>>>>>>>>>>>>>>> directory does not contain a
>>>>>>>>>>>>>>>>>>>>>>>> >>> single DICOM file.", therefore they are missing
>>>>>>>>>>>>>>>>>>>>>>>> their StudyUID
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it with
>>>>>>>>>>>>>>>>>>>>>>>> data from multiple
>>>>>>>>>>>>>>>>>>>>>>>> >>> studies."
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> and 102761034 "No data could be converted into
>>>>>>>>>>>>>>>>>>>>>>>> valid MINC files.
>>>>>>>>>>>>>>>>>>>>>>>> >>> localizer, scout will not be considered!" What
>>>>>>>>>>>>>>>>>>>>>>>> is this?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> If i wanted to force the insertion of
>>>>>>>>>>>>>>>>>>>>>>>> 102327840, 102809579 and 102506134
>>>>>>>>>>>>>>>>>>>>>>>> >>> can i just pass a flag parameter to
>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl? or
>>>>>>>>>>>>>>>>>>>>>>>> >>> modify imaging_upload_file.pl?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> PS
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> To diagnose a folder search the name of the
>>>>>>>>>>>>>>>>>>>>>>>> folder at dicom_output.txt.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear about your progress.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, the script you used to delete imaging data
>>>>>>>>>>>>>>>>>>>>>>>> is fully documented here
>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>> >>> -- let us know if you didn't find the answers
>>>>>>>>>>>>>>>>>>>>>>>> you were looking for there.
>>>>>>>>>>>>>>>>>>>>>>>> >>> (Is it possible the null row in *mri_scanner*
>>>>>>>>>>>>>>>>>>>>>>>> seen in your database
>>>>>>>>>>>>>>>>>>>>>>>> >>> management software is a visual placeholder for
>>>>>>>>>>>>>>>>>>>>>>>> you as the user?  I'm not
>>>>>>>>>>>>>>>>>>>>>>>> >>> sure why a scanner would ever be registered
>>>>>>>>>>>>>>>>>>>>>>>> with ID='0' as your screenshot
>>>>>>>>>>>>>>>>>>>>>>>> >>> showed.)
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> I fixed it with this
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> I tried to create a new candidate using the
>>>>>>>>>>>>>>>>>>>>>>>> API, is there something
>>>>>>>>>>>>>>>>>>>>>>>> >>> wrong with the structure? why did i receive a
>>>>>>>>>>>>>>>>>>>>>>>> 500 internal error? In the
>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-error log it state that there is
>>>>>>>>>>>>>>>>>>>>>>>> something wrong with token, but i
>>>>>>>>>>>>>>>>>>>>>>>> >>> verfied that the type of the token is a string.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error]
>>>>>>>>>>>>>>>>>>>>>>>> [pid 4535] [client
>>>>>>>>>>>>>>>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error:  Uncaught
>>>>>>>>>>>>>>>>>>>>>>>> TypeError: Argument 1
>>>>>>>>>>>>>>>>>>>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate()
>>>>>>>>>>>>>>>>>>>>>>>> must be of the type string,
>>>>>>>>>>>>>>>>>>>>>>>> >>> null given, called in
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and
>>>>>>>>>>>>>>>>>>>>>>>> >>> defined in
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
>>>>>>>>>>>>>>>>>>>>>>>> >>> trace:\n#0
>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
>>>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):
>>>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
>>>>>>>>>>>>>>>>>>>>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST',
>>>>>>>>>>>>>>>>>>>>>>>> Array)\n#5 {main}\n  thrown in
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Is there a way also to delete candidates? Just
>>>>>>>>>>>>>>>>>>>>>>>> to let you know what i
>>>>>>>>>>>>>>>>>>>>>>>> >>> did to clear candidates, because maybe i may
>>>>>>>>>>>>>>>>>>>>>>>> have missed dependencies.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> First i deleted all their uploads
>>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc (
>>>>>>>>>>>>>>>>>>>>>>>> is there a way to omit
>>>>>>>>>>>>>>>>>>>>>>>> >>> the backup file ? )
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Afterwards i had some scanner candidates, so i
>>>>>>>>>>>>>>>>>>>>>>>> deleted all the entries
>>>>>>>>>>>>>>>>>>>>>>>> >>> from mri_scanner except that i couldn't delete
>>>>>>>>>>>>>>>>>>>>>>>> this entry with the 0 ID.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Lastly i deleted the session and then the
>>>>>>>>>>>>>>>>>>>>>>>> candidate table.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> We recommend that you use our existing tools
>>>>>>>>>>>>>>>>>>>>>>>> for creating new candidates
>>>>>>>>>>>>>>>>>>>>>>>> >>> - either the LORIS API or if you are using a
>>>>>>>>>>>>>>>>>>>>>>>> PHP script, by calling the Candidate
>>>>>>>>>>>>>>>>>>>>>>>> >>> class's createNew()
>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200
>>>>>>>>>>>>>>>>>>>>>>>> >function.
>>>>>>>>>>>>>>>>>>>>>>>> >>> These will create the necessary records for
>>>>>>>>>>>>>>>>>>>>>>>> you.  (It's not recommended to
>>>>>>>>>>>>>>>>>>>>>>>> >>> make direct modifications to mysql database
>>>>>>>>>>>>>>>>>>>>>>>> tables in your script, if I
>>>>>>>>>>>>>>>>>>>>>>>> >>> understand you.)
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> The CandID should be a randomized 6 digit
>>>>>>>>>>>>>>>>>>>>>>>> randomized ID, and there are
>>>>>>>>>>>>>>>>>>>>>>>> >>> multiple reasons for this.
>>>>>>>>>>>>>>>>>>>>>>>> >>> You can use the PSCID for project-specific IDs
>>>>>>>>>>>>>>>>>>>>>>>> and the External ID field
>>>>>>>>>>>>>>>>>>>>>>>> >>> in the candidate table can also be used for any
>>>>>>>>>>>>>>>>>>>>>>>> values you like.
>>>>>>>>>>>>>>>>>>>>>>>> >>> Additionally, any number of custom IDs can be
>>>>>>>>>>>>>>>>>>>>>>>> added in parallel - these
>>>>>>>>>>>>>>>>>>>>>>>> >>> are entered/visible in the Candidate
>>>>>>>>>>>>>>>>>>>>>>>> Information module and added in the
>>>>>>>>>>>>>>>>>>>>>>>> >>> back-end as candidate parameters.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> We are building a script that will auto insert
>>>>>>>>>>>>>>>>>>>>>>>> the candidates based on
>>>>>>>>>>>>>>>>>>>>>>>> >>> their ExternalID. We would like to know
>>>>>>>>>>>>>>>>>>>>>>>> whethere when we are creating a new
>>>>>>>>>>>>>>>>>>>>>>>> >>> profile in the candidate table, if we also have
>>>>>>>>>>>>>>>>>>>>>>>> to insert a new record at
>>>>>>>>>>>>>>>>>>>>>>>> >>> another table? Furthermore is there a problem
>>>>>>>>>>>>>>>>>>>>>>>> that in our case CandID won't
>>>>>>>>>>>>>>>>>>>>>>>> >>> be a 6digit? ( should we start it from 100000?)
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> That would normally be the case but the numeric
>>>>>>>>>>>>>>>>>>>>>>>> part of the PSCID get
>>>>>>>>>>>>>>>>>>>>>>>> >>> paded with 0 on the left.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Ex. for sequential ID made of center ID of
>>>>>>>>>>>>>>>>>>>>>>>> `ABC` plus 4 numerical char
>>>>>>>>>>>>>>>>>>>>>>>> >>> with a min value of 1, the sequence would be:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0001
>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0002
>>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0010
>>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> thus sorting them ascending will always get the
>>>>>>>>>>>>>>>>>>>>>>>> latest value generated
>>>>>>>>>>>>>>>>>>>>>>>> >>> as the max value.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15
>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>> melanie.legault2 at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> I see, although the PSCID value is
>>>>>>>>>>>>>>>>>>>>>>>> varchar(255), it must be stored
>>>>>>>>>>>>>>>>>>>>>>>> >>> within a specific length of characters.
>>>>>>>>>>>>>>>>>>>>>>>> Otherwise if we were to sort
>>>>>>>>>>>>>>>>>>>>>>>> >>> strings with different lengths the result would
>>>>>>>>>>>>>>>>>>>>>>>> not be sorted correctly (
>>>>>>>>>>>>>>>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1,
>>>>>>>>>>>>>>>>>>>>>>>> 10, 11, 2 ).
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hello Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> There is no `last value` stored anywhere.
>>>>>>>>>>>>>>>>>>>>>>>> >>> The code simply look for the PSCID with the max
>>>>>>>>>>>>>>>>>>>>>>>> value and increase that
>>>>>>>>>>>>>>>>>>>>>>>> >>> value by 1 in order to generate the next PSCID.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this info help.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie Legault | Software developer | Faculty
>>>>>>>>>>>>>>>>>>>>>>>> of Medicine | McGill
>>>>>>>>>>>>>>>>>>>>>>>> >>> University
>>>>>>>>>>>>>>>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf
>>>>>>>>>>>>>>>>>>>>>>>> of Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43
>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> how does Loris determine the next available
>>>>>>>>>>>>>>>>>>>>>>>> PSCID value for a new
>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate?
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization
>>>>>>>>>>>>>>>>>>>>>>>> >>> e.x in the default case the PSCID is
>>>>>>>>>>>>>>>>>>>>>>>> sequential, but where do we store the
>>>>>>>>>>>>>>>>>>>>>>>> >>> last value for the sequential sequence?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> the parameters in the mri_protocol you have
>>>>>>>>>>>>>>>>>>>>>>>> assigned are global
>>>>>>>>>>>>>>>>>>>>>>>> >>> standard? or were assigned after trial and
>>>>>>>>>>>>>>>>>>>>>>>> error?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Given you have done the initial setup of your
>>>>>>>>>>>>>>>>>>>>>>>> tables to match your
>>>>>>>>>>>>>>>>>>>>>>>> >>> intended protocol/parameters according to
>>>>>>>>>>>>>>>>>>>>>>>> instructions --
>>>>>>>>>>>>>>>>>>>>>>>> >>> the Troubleshooting guide documentation
>>>>>>>>>>>>>>>>>>>>>>>> recommends
>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes
>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>> >>> re-running the pipeline (and first deleting
>>>>>>>>>>>>>>>>>>>>>>>> prior uploads).
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> *if i were to change their status to resolve
>>>>>>>>>>>>>>>>>>>>>>>> what would happen?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> I noticed that i can view the mnics at the
>>>>>>>>>>>>>>>>>>>>>>>> brainbrowser from the
>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations page ( those mnics are stored at
>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/trashbin/
>>>>>>>>>>>>>>>>>>>>>>>> >>> if i were to click their issue to resolve what
>>>>>>>>>>>>>>>>>>>>>>>> would happend? would they
>>>>>>>>>>>>>>>>>>>>>>>> >>> appear in the dicom_archive view too? ).
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> The defaut values of the schema exists in my
>>>>>>>>>>>>>>>>>>>>>>>> local database. If i adjust
>>>>>>>>>>>>>>>>>>>>>>>> >>> the default values of TR_min and TE_min the
>>>>>>>>>>>>>>>>>>>>>>>> mincs will be uploaded?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Is it possible that you haven't set up your
>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table ?   (and
>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_scan_type table too, for additional types
>>>>>>>>>>>>>>>>>>>>>>>> of scans)
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Like the psc table, this is a pre-requisite for
>>>>>>>>>>>>>>>>>>>>>>>> the Imaging insertion
>>>>>>>>>>>>>>>>>>>>>>>> >>> setup : See the install/setup documentation :
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> To add new rows, just use MySQL insert
>>>>>>>>>>>>>>>>>>>>>>>> statements.  You can adapt the
>>>>>>>>>>>>>>>>>>>>>>>> >>> insert statements which load the default table
>>>>>>>>>>>>>>>>>>>>>>>> values --> e.g. Here on
>>>>>>>>>>>>>>>>>>>>>>>> >>> GitHub :
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>>>>>>>>>>>>>>>>>>>>>>> >>> (see also the mri_scan_type table)
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> I see that i can edit the values but not how to
>>>>>>>>>>>>>>>>>>>>>>>> insert new rows.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> If i choose Inserted with flag then will the
>>>>>>>>>>>>>>>>>>>>>>>> minc be inserted?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear that *dcmodify* worked correctly.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> For the MRI Violations module, the screenshot
>>>>>>>>>>>>>>>>>>>>>>>> is enough.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> It says "could not identify scan type", which
>>>>>>>>>>>>>>>>>>>>>>>> we knew already.  Did you
>>>>>>>>>>>>>>>>>>>>>>>> >>> click on the link on those words?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> It will take you to the next page of the
>>>>>>>>>>>>>>>>>>>>>>>> module, showing for each scan
>>>>>>>>>>>>>>>>>>>>>>>> >>> what the scan parameters were, and will also
>>>>>>>>>>>>>>>>>>>>>>>> show for comparison what's
>>>>>>>>>>>>>>>>>>>>>>>> >>> stored in your *mri_protocol* table.
>>>>>>>>>>>>>>>>>>>>>>>> >>> Compare these values to find which parameter
>>>>>>>>>>>>>>>>>>>>>>>> was not correct according
>>>>>>>>>>>>>>>>>>>>>>>> >>> to your *mri_protocol* table scan type
>>>>>>>>>>>>>>>>>>>>>>>> definitions.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> You may end up broadening your mri_protocol
>>>>>>>>>>>>>>>>>>>>>>>> value ranges (e.g. TR, TE)
>>>>>>>>>>>>>>>>>>>>>>>> >>> for scans.
>>>>>>>>>>>>>>>>>>>>>>>> >>> This can be done in the front-end, by editing
>>>>>>>>>>>>>>>>>>>>>>>> the database table
>>>>>>>>>>>>>>>>>>>>>>>> >>> directly in the same subpage of the MRI
>>>>>>>>>>>>>>>>>>>>>>>> Violations module.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> The MRI Violations module features are
>>>>>>>>>>>>>>>>>>>>>>>> explained in more detail in the
>>>>>>>>>>>>>>>>>>>>>>>> >>> Help text for this module inside LORIS (click
>>>>>>>>>>>>>>>>>>>>>>>> the  ["?"] icon in the menu
>>>>>>>>>>>>>>>>>>>>>>>> >>> bar.)
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide
>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>> >>> :  no MINCs inserted- violated scans
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> looks like my previous email's attachment
>>>>>>>>>>>>>>>>>>>>>>>> wasn't delivered due to
>>>>>>>>>>>>>>>>>>>>>>>> >>> security reasons, i uploaded my file at google
>>>>>>>>>>>>>>>>>>>>>>>> drive
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> From Dicat's view seems that dcmodify worked in
>>>>>>>>>>>>>>>>>>>>>>>> both cases
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> For the mri_violations i attached the .html
>>>>>>>>>>>>>>>>>>>>>>>> output from webbrowser, so
>>>>>>>>>>>>>>>>>>>>>>>> >>> that you can check the filelds easier.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios --
>>>>>>>>>>>>>>>>>>>>>>>> >>> Great, sounds like more progress.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> About the dcmodify command -- I'm not sure why
>>>>>>>>>>>>>>>>>>>>>>>> you're getting an Endian
>>>>>>>>>>>>>>>>>>>>>>>> >>> warning.  (it's a warning not an error,
>>>>>>>>>>>>>>>>>>>>>>>> correct?)
>>>>>>>>>>>>>>>>>>>>>>>> >>> To clarify -- Were the DICOM headers
>>>>>>>>>>>>>>>>>>>>>>>> (PatientName) all successfully
>>>>>>>>>>>>>>>>>>>>>>>> >>> relabelled, after the command ran?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> You can use also our DICAT tool (
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/DICAT) to
>>>>>>>>>>>>>>>>>>>>>>>> >>> verify and/or update local DICOM headers --
>>>>>>>>>>>>>>>>>>>>>>>> though your dcmodify command is
>>>>>>>>>>>>>>>>>>>>>>>> >>> a great and fast solution for bulk header
>>>>>>>>>>>>>>>>>>>>>>>> updates.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> If you're concerned about fields being changed
>>>>>>>>>>>>>>>>>>>>>>>> (e.g. "(2001,105f)" from
>>>>>>>>>>>>>>>>>>>>>>>> >>> the warning message)  - you can also dcmdump a
>>>>>>>>>>>>>>>>>>>>>>>> DICOM slice before and look
>>>>>>>>>>>>>>>>>>>>>>>> >>> at these fields specifically.
>>>>>>>>>>>>>>>>>>>>>>>> >>> It's also not a bad "sanity check" to backup
>>>>>>>>>>>>>>>>>>>>>>>> your DICOMS before/after
>>>>>>>>>>>>>>>>>>>>>>>> >>> running dcmodify, and use dcmdump on each
>>>>>>>>>>>>>>>>>>>>>>>> version to diff the outputs --
>>>>>>>>>>>>>>>>>>>>>>>> >>> this will pinpoint what changed.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Re the protocol violation --
>>>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol not recognized or
>>>>>>>>>>>>>>>>>>>>>>>> >>> unknown :   this means your scans did not match
>>>>>>>>>>>>>>>>>>>>>>>> what is stored in your
>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_protocol table.
>>>>>>>>>>>>>>>>>>>>>>>> >>> Check the MRI Violations front-end module --
>>>>>>>>>>>>>>>>>>>>>>>> can you see why they didn't
>>>>>>>>>>>>>>>>>>>>>>>> >>> match?
>>>>>>>>>>>>>>>>>>>>>>>> >>> Send us an example, in addition to the contents
>>>>>>>>>>>>>>>>>>>>>>>> of the mri_protocol
>>>>>>>>>>>>>>>>>>>>>>>> >>> table, if you can't find the source of the
>>>>>>>>>>>>>>>>>>>>>>>> mismatch.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>  Here is the psc table
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> I created 2 candidates profiles through the
>>>>>>>>>>>>>>>>>>>>>>>> interface
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> then runned dcmodify command to a dicom file
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1"
>>>>>>>>>>>>>>>>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> and got those warning: is this okay?
>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify at another Dicom didn't show warnings.
>>>>>>>>>>>>>>>>>>>>>>>> Below you can see the
>>>>>>>>>>>>>>>>>>>>>>>> >>> execution for the second dicom. Mnics could not
>>>>>>>>>>>>>>>>>>>>>>>> be inserted due to
>>>>>>>>>>>>>>>>>>>>>>>> >>> AcquisitionProtocol being unknown.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Running now the following command:
>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>> >>> imaging_upload_file.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 12
>>>>>>>>>>>>>>>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>  find -path
>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX'
>>>>>>>>>>>>>>>>>>>>>>>> >>> -delete
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database
>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -verbose
>>>>>>>>>>>>>>>>>>>>>>>> >>>  Source: /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>> >>> Target: /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Testing for database connectivity.
>>>>>>>>>>>>>>>>>>>>>>>> >>> Database is available.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> You will archive the dir :
>>>>>>>>>>>>>>>>>>>>>>>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> You are creating a tar with the following
>>>>>>>>>>>>>>>>>>>>>>>> command:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> tar -cf
>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> getting md5sums and gzipping!!
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :
>>>>>>>>>>>>>>>>>>>>>>>> 127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :    Linux
>>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>>> 2019-09-06 18:36:50
>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814
>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f
>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e
>>>>>>>>>>>>>>>>>>>>>>>> >>>  DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Removing temporary files from target location
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Done adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation
>>>>>>>>>>>>>>>>>>>>>>>> >>> -profile prod
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>>>>>>>>>>>>>>>>>>>>>>> >>> -uploadID 12 -verbose
>>>>>>>>>>>>>>>>>>>>>>>> >>>  md5sum
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>> >>> Set centerID = 1
>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Number of MINC files that will be considered
>>>>>>>>>>>>>>>>>>>>>>>> for inserting into the
>>>>>>>>>>>>>>>>>>>>>>>> >>> database: 2
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file
>>>>>>>>>>>>>>>>>>>>>>>> is
>>>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file
>>>>>>>>>>>>>>>>>>>>>>>> is
>>>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>> cat
>>>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Acquisition protocol is unknown
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>   --> The minc file cannot be registered since
>>>>>>>>>>>>>>>>>>>>>>>> the AcquisitionProtocol
>>>>>>>>>>>>>>>>>>>>>>>> >>> is unknown
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Sure -- you can delete imaging datasets with
>>>>>>>>>>>>>>>>>>>>>>>> the *delete_imaging_upload*
>>>>>>>>>>>>>>>>>>>>>>>> >>> script --
>>>>>>>>>>>>>>>>>>>>>>>> >>> details here:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> What's in your *psc* table?  (Is it properly
>>>>>>>>>>>>>>>>>>>>>>>> populated? This is a
>>>>>>>>>>>>>>>>>>>>>>>> >>> pre-requisite to loading imaging data.
>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database
>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>>> >>> The foreign key constraint error on the
>>>>>>>>>>>>>>>>>>>>>>>> candidate record is curious.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> There are also a few options for creating
>>>>>>>>>>>>>>>>>>>>>>>> candidates when inserting
>>>>>>>>>>>>>>>>>>>>>>>> >>> imaging data:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then
>>>>>>>>>>>>>>>>>>>>>>>> DICOM insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> a. via the LORIS API -- Create the candidates
>>>>>>>>>>>>>>>>>>>>>>>> (and visits, optionally I
>>>>>>>>>>>>>>>>>>>>>>>> >>> think)
>>>>>>>>>>>>>>>>>>>>>>>> >>> How to:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>>>>>>>>>>>>>>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by
>>>>>>>>>>>>>>>>>>>>>>>> LORIS.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Then as a second step:
>>>>>>>>>>>>>>>>>>>>>>>> >>> b. Use the imaging insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets
>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>> >>> to load your DICOMs.
>>>>>>>>>>>>>>>>>>>>>>>> >>> You will want to first ensure that the
>>>>>>>>>>>>>>>>>>>>>>>> PatientName header in the DICOMs
>>>>>>>>>>>>>>>>>>>>>>>> >>> as well as tar package are correctly labelled
>>>>>>>>>>>>>>>>>>>>>>>> with PSCID_DCCID_VisitLabel
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets:
>>>>>>>>>>>>>>>>>>>>>>>> >>> How to :
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options when
>>>>>>>>>>>>>>>>>>>>>>>> running the bids_import script,
>>>>>>>>>>>>>>>>>>>>>>>> >>> to automatically create your candidates and
>>>>>>>>>>>>>>>>>>>>>>>> sessions.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> How do i delete a Study? And everytime do i
>>>>>>>>>>>>>>>>>>>>>>>> have to create a new
>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate to get DCCID and a PSCID?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> *First execution:*
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod <
>>>>>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match
>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update
>>>>>>>>>>>>>>>>>>>>>>>> a child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`,
>>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_candidate_1`
>>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES
>>>>>>>>>>>>>>>>>>>>>>>> `psc` (`CenterID`)) at
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060.
>>>>>>>>>>>>>>>>>>>>>>>> >>> ERROR: Failed to insert record in table
>>>>>>>>>>>>>>>>>>>>>>>> mri_scanner:
>>>>>>>>>>>>>>>>>>>>>>>> >>> The following database commands failed:
>>>>>>>>>>>>>>>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';
>>>>>>>>>>>>>>>>>>>>>>>> >>> SET
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
>>>>>>>>>>>>>>>>>>>>>>>> >>> Medical Systems';
>>>>>>>>>>>>>>>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>>>>>>>>>>>>>>>>>>>>>>> >>> Error obtained:Cannot add or update a child
>>>>>>>>>>>>>>>>>>>>>>>> row: a foreign key
>>>>>>>>>>>>>>>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`,
>>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_mri_scanner_1`
>>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate`
>>>>>>>>>>>>>>>>>>>>>>>> (`CandID`)) (error code 1452)
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>  ERROR: The validation has failed. Either
>>>>>>>>>>>>>>>>>>>>>>>> re-run the validation again
>>>>>>>>>>>>>>>>>>>>>>>> >>> and fix the problem. Or re-run
>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader.pl using -force to force the
>>>>>>>>>>>>>>>>>>>>>>>> >>> execution.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> The tarchiveLoader.pl insertion script has
>>>>>>>>>>>>>>>>>>>>>>>> failed.
>>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> *And second execution: *
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod <
>>>>>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match
>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> PROBLEM:
>>>>>>>>>>>>>>>>>>>>>>>> >>> The user 'lorisadmin' has already inserted this
>>>>>>>>>>>>>>>>>>>>>>>> study.
>>>>>>>>>>>>>>>>>>>>>>>> >>> The unique study ID is
>>>>>>>>>>>>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
>>>>>>>>>>>>>>>>>>>>>>>> >>> This is the information retained from the first
>>>>>>>>>>>>>>>>>>>>>>>> time the study was
>>>>>>>>>>>>>>>>>>>>>>>> >>> inserted:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy
>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :
>>>>>>>>>>>>>>>>>>>>>>>> 127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :    Linux
>>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>>> 2019-09-04 18:33:05
>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d
>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec
>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053
>>>>>>>>>>>>>>>>>>>>>>>> >>>  DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Last update of record:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> The dicomTar.pl execution has failed.
>>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Ok, this sounds like good progress.  Let us
>>>>>>>>>>>>>>>>>>>>>>>> know when you next encounter
>>>>>>>>>>>>>>>>>>>>>>>> >>> issues as you progress through the Imaging
>>>>>>>>>>>>>>>>>>>>>>>> Install/Setup docs
>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>>> >.
>>>>>>>>>>>>>>>>>>>>>>>> >>> I'll look into how we can better handle the
>>>>>>>>>>>>>>>>>>>>>>>> incoming/ directory next
>>>>>>>>>>>>>>>>>>>>>>>> >>> time.
>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is
>>>>>>>>>>>>>>>>>>>>>>>> >>> populated correctly except its port is  'port'
>>>>>>>>>>>>>>>>>>>>>>>>   : ''. Also i have tested
>>>>>>>>>>>>>>>>>>>>>>>> >>> that i can connect to MySQL with lorisuser.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> I executed the script again, because the only
>>>>>>>>>>>>>>>>>>>>>>>> error i had previously was
>>>>>>>>>>>>>>>>>>>>>>>> >>> that the /data/incoming folder didn't exist and
>>>>>>>>>>>>>>>>>>>>>>>> there are no errors
>>>>>>>>>>>>>>>>>>>>>>>> >>> reported back except of warnings <<mysql:
>>>>>>>>>>>>>>>>>>>>>>>> [Warning] Using a password on the
>>>>>>>>>>>>>>>>>>>>>>>> >>> command line interface can be insecure>>.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> It's possible -- if the script was unable to
>>>>>>>>>>>>>>>>>>>>>>>> connect to the database
>>>>>>>>>>>>>>>>>>>>>>>> >>> during its execution (e.g. typo in the
>>>>>>>>>>>>>>>>>>>>>>>> password), that would explain the
>>>>>>>>>>>>>>>>>>>>>>>> >>> underpopulated Image path and Loris-MRI code
>>>>>>>>>>>>>>>>>>>>>>>> path you saw in the Config
>>>>>>>>>>>>>>>>>>>>>>>> >>> module.
>>>>>>>>>>>>>>>>>>>>>>>> >>> It's hard to tell without seeing the output
>>>>>>>>>>>>>>>>>>>>>>>> from your script run -- Did
>>>>>>>>>>>>>>>>>>>>>>>> >>> you see a sign of any such error?
>>>>>>>>>>>>>>>>>>>>>>>> >>> The Config fields are populated by the
>>>>>>>>>>>>>>>>>>>>>>>> imaging_install.sh script (starting
>>>>>>>>>>>>>>>>>>>>>>>> >>> at line 222
>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222
>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> For example, check if the database connection
>>>>>>>>>>>>>>>>>>>>>>>> information was populated
>>>>>>>>>>>>>>>>>>>>>>>> >>> accurately in
>>>>>>>>>>>>>>>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> If you are referring to the imaging_install.sh
>>>>>>>>>>>>>>>>>>>>>>>> here is an image with the
>>>>>>>>>>>>>>>>>>>>>>>> >>> configurations i typed. Maybe the problem is
>>>>>>>>>>>>>>>>>>>>>>>> somewhere at the last part
>>>>>>>>>>>>>>>>>>>>>>>> >>> which asks to configure as much as possible
>>>>>>>>>>>>>>>>>>>>>>>> automatically?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear your LORIS core install is up and
>>>>>>>>>>>>>>>>>>>>>>>> working and all the
>>>>>>>>>>>>>>>>>>>>>>>> >>> front-end pages are loading.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$
>>>>>>>>>>>>>>>>>>>>>>>> chmod 775 project
>>>>>>>>>>>>>>>>>>>>>>>> >>> > and the web interface worked.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, it's important that project/ have 775
>>>>>>>>>>>>>>>>>>>>>>>> permissions and that
>>>>>>>>>>>>>>>>>>>>>>>> >>> lorisadmin be part of the sudoers group, per
>>>>>>>>>>>>>>>>>>>>>>>> step 1 in the install
>>>>>>>>>>>>>>>>>>>>>>>> >>> Readme <
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris#install-steps>.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image
>>>>>>>>>>>>>>>>>>>>>>>> should change LORIS to
>>>>>>>>>>>>>>>>>>>>>>>> >>> loris, right?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> These imaging paths will be updated during your
>>>>>>>>>>>>>>>>>>>>>>>> imaging installation
>>>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup> by
>>>>>>>>>>>>>>>>>>>>>>>> an automated script --
>>>>>>>>>>>>>>>>>>>>>>>> >>> you do not need to set them manually via the
>>>>>>>>>>>>>>>>>>>>>>>> Config module.
>>>>>>>>>>>>>>>>>>>>>>>> >>> Please continue to follow the Setup Guide
>>>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup> for
>>>>>>>>>>>>>>>>>>>>>>>> detailed steps to follow.
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image
>>>>>>>>>>>>>>>>>>>>>>>> should change LORIS to loris,
>>>>>>>>>>>>>>>>>>>>>>>> >>> right?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> i used
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x
>>>>>>>>>>>>>>>>>>>>>>>> | sudo -E bash -
>>>>>>>>>>>>>>>>>>>>>>>> >>> sudo apt-get install -y nodejs
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> you had suggested in the past, make worked and
>>>>>>>>>>>>>>>>>>>>>>>> now i can see all the
>>>>>>>>>>>>>>>>>>>>>>>> >>> contents in the web-interface, but i don't need
>>>>>>>>>>>>>>>>>>>>>>>> make install?
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>> -------------- next part --------------
>>>>>>>>>>>>>>>>>>>>>>>> An HTML attachment was scrubbed...
>>>>>>>>>>>>>>>>>>>>>>>> URL: <
>>>>>>>>>>>>>>>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html
>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16
>>>>>>>>>>>>>>>>>>>>>>>> *****************************************
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
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From lingyun.ma at mcin.ca  Thu Jan 30 10:35:25 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Thu, 30 Jan 2020 10:35:25 -0500
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAKHj7uRpA-8kzkoEnAk7JBNLP7v4cmK4zW-gMutHESiFGj7xjw@mail.gmail.com>
References: <mailman.1851.1573565332.16403.loris-dev@bic.mni.mcgill.ca>
 <CAEfMBom1HCWLo4NWgt5XG4625tCBfRT_Z_HepvtT_Er2LKbJoA@mail.gmail.com>
 <CAKHj7uS1AdMDjnacouTvxZgziYVgp5NNUeOuMkpDyrTskGTh-Q@mail.gmail.com>
 <CALbt7NDej8FGUUS6_oKbK5Fp-FnwsVz9AgZ6ZcJEZhmoKZmv8w@mail.gmail.com>
 <CAKHj7uSx-qqcXHZsWsZmSJ7sC1DgF+XapT5Y1+QdoVic37_DDg@mail.gmail.com>
 <CAMkiY3fQBGDGeNO8EHxwYAgbhTggNSQ+AVuCfdraDXwULMjjUg@mail.gmail.com>
 <CAKHj7uT5xXi=pOPdH=W9BroSphMHdTszdgW+GxuES=8wZox9eQ@mail.gmail.com>
 <CAMkiY3eUouxaRVdC4wH+vdjeQ=q_Nx8bcDNzcWgD_OgN77m3mw@mail.gmail.com>
 <CAKHj7uSxu4+tm+=x4+qJ1sAbrjmxG2H7LovDb7-2KMnyYQhrgg@mail.gmail.com>
 <CAMkiY3fdPZec2jx-cc2Zq37j3ekmTu_o819yBUv-bC7M98bkVw@mail.gmail.com>
 <CAKHj7uSZHozpuQ_YwGmy6wQ4tm43vJa556V0o2+JGDVsYaqN4g@mail.gmail.com>
 <CAMkiY3dge=x93bQDv0fHGMcrX0PA8Z_imLb_zSTh=nTrx5weFg@mail.gmail.com>
 <CAKHj7uR81gCkjvccMxwMA08dGSEgyTLJBJ+pZPkoUQDtGP_hFA@mail.gmail.com>
 <CAMkiY3fGhvExZ-JOvxeHe7dJQPvtPAHx3oJuiMVX7f1JgF1GAg@mail.gmail.com>
 <CAKHj7uRExO98Yyn9_07aw44wbh0bCL9_C1VFTAURKsxQLUuAeQ@mail.gmail.com>
 <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>
 <CAKHj7uRueb5fgh4VVCAyaq8tC9WM4gJ7k6Q=dxsqWzFgDqPfVQ@mail.gmail.com>
 <CAMkiY3d-Vt=3gQqwJ+GSRSacbLp2QxrB0g-_C7ONd8j_g1ipoQ@mail.gmail.com>
 <CAKHj7uQt9=nokz5g1zBuBx1-rJ8q7qKOuNVkQugC9wfvNFcjVA@mail.gmail.com>
 <CAMkiY3cAuQfT_5iMzYoF2BXVceu_vgz4eCq2sAtoyse+zUYeSg@mail.gmail.com>
 <CAMkiY3dq1O3V8+r4tTAWQ8N=rVFg=DNY-UPeMqbec+MSayj=Cg@mail.gmail.com>
 <CAKHj7uSEegvE1apPBGVyHmjyVzF+YxJjDMg0b+hDE4_-ON+dYw@mail.gmail.com>
 <CAKHj7uRx1NT7CycFq65uFpgPiOVwvT-jtK1NJX6_3rrLNFwdbA@mail.gmail.com>
 <CAMkiY3dAnkLdc4N=REmeCpX2qBfsQf=wRb=YtHtt20f8adXFyw@mail.gmail.com>
 <CAKHj7uRpA-8kzkoEnAk7JBNLP7v4cmK4zW-gMutHESiFGj7xjw@mail.gmail.com>
Message-ID: <CAMpvQ9hNLxz9SZsJwWec_yQ3R4KGhnqv3CDaSPOB1exPsO5AJA@mail.gmail.com>

Hi Sotirios,

By curiosity, I just looked at the error message, "Use of uninitialized
value $_ in pattern match (m//) at /data/loris/bin/mri/
batch_uploads_imageuploader.pl line 144." clearly means that there is no
match, but 144 line has no such code related with $_ in recent versions of
the batch_uploads_imageuploader.pl. There is something in the line 165 for
a few recent versions.

As to "xargs: file: No such file or directory", it could be due to a
command unable to find anything using the directory provided as the message
suggested.

In both cases, I feel that it could be helpful if you provide more details
such as which Loris_MRI version you are running, what is the exact command
line you are using to help supporters to understand.

Thanks.

Best regards,
Ling Ma
Consultant

On Wed, Jan 29, 2020 at 6:57 PM Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:

> Hi Cecile,
>
> it seems that xargs is already installed in our docker container.
>
> [image: image.png]
>
>
> ???? ???, 29 ??? 2020 ???? 7:59 ?.?., ?/? Cecile Madjar <
> cecile.madjar at mcin.ca> ??????:
>
>> Hi Sotirios,
>>
>> It looks like xargs is not installed in your docker environment.
>>
>> This is being used by the following command in dicomTar.pl (and a few
>> other places but that is the one causing the error at the moment):
>>
>> $cmd = "cd " . $dcm_source . "; find -type f -name '.*' | *xargs* rm -f";
>>
>> So you need to install xargs in your docker for the command to run.
>>
>> Hope this helps,
>>
>> C?cile
>> On Wed, Jan 29, 2020 at 10:35 AM Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> wrote:
>>
>>> Hello,
>>>
>>> We are making a dockerized version of Loris 21 and when we execute the
>>> batch_uploads_imageuploader.pl we get an error about xargs. What could
>>> be the casue?
>>>
>>> Use of uninitialized value $_ in pattern match (m//) at
>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>>> Running now the following command: /data/loris/data//uploadNeuroDB/
>>> imaging_upload_file.pl -profile prod -upload_id 13
>>> /data/incoming/DCC0007_854380_V1.tar.gz -verbose
>>>
>>>  find -path \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml -name '__MACOSX'
>>> -delete
>>> xargs: file: No such file or directory
>>>
>>> dicomTar.pl \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml
>>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>>>  Source: /data/tmp/ImagingUpload-15-31-U_O5ml
>>> Target: /data/loris/data/tarchive
>>>
>>> Thanks
>>>
>>> ???? ???, 10 ??? 2019 ???? 7:21 ?.?., ?/? Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> ??????:
>>>
>>>> Hi,
>>>>
>>>> i opened an issue and looked up for the values of Volume they suggested
>>>> https://github.com/BIC-MNI/minc-toolkit-v2/issues/95. The only
>>>> attributes associated with it i saw are [0x00089206] and [0x00089207]
>>>>
>>>> [image: image.png]
>>>>
>>>> I looked up for the file that was being viewed fine in the BrainBrowser
>>>> and saw that it had that attribute empty so i used this command because i
>>>> couldn't find a way to modify the attribute via pydicom
>>>>
>>>> dcmodify -ma "(0008,9206)=" *.dcm
>>>>
>>>> and that command reported the warning about the Endian Syntax. I also
>>>> used the corresponding command for 9207 and got the message "Tag not found'
>>>>
>>>> Lastly I tried to upload some dicoms and now i am getting the SNR and i
>>>> can view them fine. I believe now that all of them will pass successfully,
>>>> i will report back later.
>>>>
>>>> Thanks,
>>>>
>>>> Sotirios
>>>>
>>>> ???? ???, 9 ??? 2019 ???? 8:10 ?.?., ?/? Cecile Madjar <
>>>> cecile.madjar at mcin.ca> ??????:
>>>>
>>>>> Hi Sotirios,
>>>>>
>>>>> The issue you are having is a indeed a dcm2mnc issue. The converter
>>>>> does not seem to work on your dataset for some reason. Unfortunately, there
>>>>> is not much we can do on our front to fix this...
>>>>>
>>>>> I would recommend creating an issue on the MINC tools repository
>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> so they can fix
>>>>> your problem.
>>>>>
>>>>> Very sorry that you are having that problem.
>>>>>
>>>>> Best,
>>>>>
>>>>> C?cile
>>>>>
>>>>> On Wed, Dec 4, 2019 at 8:59 AM Cecile Madjar <cecile.madjar at mcin.ca>
>>>>> wrote:
>>>>>
>>>>>> Hi Sotirios,
>>>>>>
>>>>>> Could you please share a dataset with us that produces the error you
>>>>>> get and the weird display in BrainBrowser? You could use the same SFTP
>>>>>> credential that Nicolas gave you.
>>>>>>
>>>>>> The message errors you got from imaging_install.sh are probably due
>>>>>> to the fact that you reran the install script and it tried to reinstall
>>>>>> something that was already there. I would not worry about it. FYI, the only
>>>>>> thing you needed to do was to update the MINC tools path in the environment
>>>>>> file as you did after re-running imaging_install.sh and source the
>>>>>> environment file.
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> C?cile
>>>>>>
>>>>>> On Wed, Dec 4, 2019 at 8:03 AM Sotirios Nikoloutsopoulos <
>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>
>>>>>>>  Hi Cecile,
>>>>>>>
>>>>>>> We used minctool 1.9.7 and we still get this error
>>>>>>>
>>>>>>> <<Restructuring...
>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>> Default GSL error handler invoked.
>>>>>>> noise_estimate --snr /data/loris/data>>
>>>>>>>
>>>>>>
>>>>>>> One dicom folder hadn't that error and is being viewed fine in the
>>>>>>> BrainBrowser of Loris.
>>>>>>>
>>>>>>
>>>>>>> When i used dpkg to the 1.9.17 the installation reported fine
>>>>>>> <<Unpacking minc-toolkit-v2 (1.9.17) over (1.9.16) ...>>
>>>>>>>
>>>>>>> and then i used source /opt/minc/1.9.17/minc-toolkit-config.sh
>>>>>>>
>>>>>>> and aftewards runned bash ./imaging_install.sh just to be sure.
>>>>>>>
>>>>>>> We also had to modify /data/loris/bin/mri/environment because it
>>>>>>> still pointed to the old version.
>>>>>>>
>>>>>>> What i found strange is this during the run of imaging_install.sh
>>>>>>>
>>>>>>> <<already using interpreter
>>>>>>> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/bin/python3
>>>>>>> Please use the *system* python to run this script
>>>>>>> Traceback (most recent call last):
>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>>>>>> 2632, in <module>
>>>>>>>     main()
>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>>>>>> 870, in main
>>>>>>>     symlink=options.symlink,
>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>>>>>> 1156, in create_environment
>>>>>>>     install_python(home_dir, lib_dir, inc_dir, bin_dir,
>>>>>>> site_packages=site_packages, clear=clear, symlink=symlink)
>>>>>>>   File
>>>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>>>> line 357, in abspath
>>>>>>>     if not isabs(path):
>>>>>>>   File
>>>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>>>> line 64, in isabs
>>>>>>>     return s.startswith(sep)
>>>>>>> AttributeError: 'NoneType' object has no attribute 'startswith'
>>>>>>> Installing the Python libraries into the loris-mri virtualenv...
>>>>>>> Requirement already satisfied: mysqlclient in
>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (1.4.4)
>>>>>>> Requirement already satisfied: mysql-connector in
>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (2.2.9)
>>>>>>> Requirement already satisfied: pybids in
>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (0.9.4)
>>>>>>> Requirement already satisfied: nibabel>=2.1 in ./python_virtua>>
>>>>>>>
>>>>>>> So should i open an issue for that error? or is there something else
>>>>>>> to try?
>>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>> Sotirios
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ???? ???, 3 ??? 2019 ???? 10:39 ?.?., ?/? Cecile Madjar <
>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>
>>>>>>>> Hi Sotirios,
>>>>>>>>
>>>>>>>> Does the pic screenshot in the imaging browser module also shows 1
>>>>>>>> slice? If so, that would mean there was an issue with the dcm2mnc
>>>>>>>> conversion. Once again, installing the latest version of the MINC tools
>>>>>>>> should help but if this issue persists I would recommend creating an issue
>>>>>>>> for that too on their repository
>>>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> (if not
>>>>>>>> already reported there, there are a few known issue reported).
>>>>>>>>
>>>>>>>> Other viewer for MINCs are register and Display (both part of the
>>>>>>>> MINC tools). For NIfTI, you have FSLeye, MRICron and probably many other
>>>>>>>> viewers that exists.
>>>>>>>>
>>>>>>>> Hope this helps,
>>>>>>>>
>>>>>>>> C?cile
>>>>>>>>
>>>>>>>> On Tue, Dec 3, 2019 at 3:26 PM Sotirios Nikoloutsopoulos <
>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi Cecile,
>>>>>>>>>
>>>>>>>>> Yes, Nifti files are mandatory for our work. From what we saw at a
>>>>>>>>> 3rd vm we setted up, the nifti files are being created ( i haven't verified
>>>>>>>>> if that is the case at the 2nd vm ). I will install the latest version and
>>>>>>>>> will report back, but do you know any nifti/minc viewer? because the
>>>>>>>>> Brainbrowser of Loris does not output them well, it's like it is loading
>>>>>>>>> only 1 slice and we would like to verify it with another tool too. We
>>>>>>>>> verified that the dcmconv command didn't affect the quality of
>>>>>>>>> the .dcm files.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> Sotirios
>>>>>>>>>
>>>>>>>>> ???? ???, 2 ??? 2019 ???? 6:59 ?.?., ?/? Cecile Madjar <
>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>
>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>
>>>>>>>>>> It looks like for some reason your binary mnc2nii is not working
>>>>>>>>>> and reports that error. Do you want to create NIfTI files or are you happy
>>>>>>>>>> with just the MINC files?
>>>>>>>>>>
>>>>>>>>>> If you don't need the NIfTI files, then maybe you can set the
>>>>>>>>>> Config setting "NIfTI file creation" to No instead of Yes and
>>>>>>>>>> this error will not appear anymore.
>>>>>>>>>>
>>>>>>>>>> If you need the NIfTI files to be created, then I would
>>>>>>>>>> recommend installing the latest version of the MINC tools (1.9.17). They
>>>>>>>>>> can be found there:
>>>>>>>>>>
>>>>>>>>>>    - pre-built packages:
>>>>>>>>>>    https://packages.bic.mni.mcgill.ca/minc-toolkit/
>>>>>>>>>>    - from the source code with installation instructions in the
>>>>>>>>>>    README: https://github.com/BIC-MNI/minc-toolkit-v2
>>>>>>>>>>
>>>>>>>>>> If the problem persists by using the latest release of MINC
>>>>>>>>>> tools, then create an issue on Github for the MINC developers
>>>>>>>>>> here <https://github.com/BIC-MNI/minc-toolkit-v2/issues>.
>>>>>>>>>>
>>>>>>>>>> Hope this helps,
>>>>>>>>>>
>>>>>>>>>> C?cile
>>>>>>>>>>
>>>>>>>>>> On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>
>>>>>>>>>>> Thanks to Nicholas i was able to create all the mincs images.
>>>>>>>>>>> The problem was that the files were in Little-Endian-Implicit transfer
>>>>>>>>>>> syntax and i had to convert them Little-Endian-Explicit transfer syntax
>>>>>>>>>>> with this command
>>>>>>>>>>>
>>>>>>>>>>> find <root_of_my_DICOM_files_directory> -type f | xargs -i
>>>>>>>>>>> dcmconv --write-xfer-little {} {}
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Looking back at our mails i saw that Little-Endian error had
>>>>>>>>>>> occurred when i used dcmodify, but i switcthed to using pydicom instead.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> In the output i see an error sometimes about "gsl:
>>>>>>>>>>> bessel_I0.c:216: ERROR: overflow". Is this okay?
>>>>>>>>>>>
>>>>>>>>>>> Restructuring...
>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>> noise_estimate --snr
>>>>>>>>>>> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
>>>>>>>>>>> SNR is:
>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>>
>>>>>>>>>>> Sotirios
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>
>>>>>>>>>>>> Thank you for the details!
>>>>>>>>>>>>
>>>>>>>>>>>> A few things to try:
>>>>>>>>>>>>
>>>>>>>>>>>>    - modify the TMPDIR to be on your /data directory where
>>>>>>>>>>>>    there might be more space to do processing (could create a /data/tmp where
>>>>>>>>>>>>    the temporary files would be created)
>>>>>>>>>>>>    - how many files are there for that upload in
>>>>>>>>>>>>    tarchive_files? Are they different from the ones showing the warning
>>>>>>>>>>>>    message?
>>>>>>>>>>>>       - FYI: query to get that: SELECT tf.* FROM
>>>>>>>>>>>>       tarchive_files tf JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your
>>>>>>>>>>>>       uploadID> (the output of that query would be very
>>>>>>>>>>>>       useful if you can provide it)
>>>>>>>>>>>>       - how many series are there for that upload in
>>>>>>>>>>>>    tarchive_series?
>>>>>>>>>>>>    - FYI: query to get that: SELECT ts.* FROM tarchive_series
>>>>>>>>>>>>       ts JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your uploadID> (the
>>>>>>>>>>>>       output of that query would be very useful if you can provide it)
>>>>>>>>>>>>    - things are failing when the scripts try running the
>>>>>>>>>>>>    following command: find
>>>>>>>>>>>>    /tmp/TarLoad-23-43-ccugaa/ImagingUpload-23-43-6JCOTO -type f  |
>>>>>>>>>>>>    /data/loris/bin/mri/dicom-archive/get_dicom_info.pl
>>>>>>>>>>>>    -studyuid -series -echo -image -file  -attvalue 0018 0024 -series_descr
>>>>>>>>>>>>    -stdin | sort -n -k1 -k2 -k7 -k3 -k6 -k4  | cut -f 5 | dcm2mnc -dname ''
>>>>>>>>>>>>    -stdin -clobber -usecoordinates /tmp/TarLoad-23-43-ccugaa
>>>>>>>>>>>>       - clearly the problems come from get_dicom_info.pl but I
>>>>>>>>>>>>       cannot pinpoint the error yet. I will ask around and get back to you
>>>>>>>>>>>>
>>>>>>>>>>>> If I cannot figure it out remotely, is there a way to have a
>>>>>>>>>>>> call using zoom? This way you could share your screen with me and run the
>>>>>>>>>>>> debugger on that script and hopefully we can figure out what is going on
>>>>>>>>>>>> with those datasets?
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks!
>>>>>>>>>>>>
>>>>>>>>>>>> C?cile
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Nov 26, 2019 at 5:17 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>
>>>>>>>>>>>>> In both my virtual machines
>>>>>>>>>>>>> export TMPDIR=/tmp
>>>>>>>>>>>>>
>>>>>>>>>>>>> In both vm also with dcm2mnc i get this output. Just to verify
>>>>>>>>>>>>> that this passed in my 1st vm and produced mincs.
>>>>>>>>>>>>>
>>>>>>>>>>>>> I attached the spool as a csv.
>>>>>>>>>>>>>
>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>
>>>>>>>>>>>>> And also one difference i found was this in the Loris-mri code
>>>>>>>>>>>>> ( left 1st workable vm, right 2nd vm that has to be fixed, although i
>>>>>>>>>>>>> changed it seems to be independent of the uninitialized value $_ )
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> that is puzzling... A few additional questions:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>    - what is the bash variable TMPDIR set to on the
>>>>>>>>>>>>>>    environment file?
>>>>>>>>>>>>>>    - could you try running separately dcm2mnc on the DICOM
>>>>>>>>>>>>>>    folder to see if that works?
>>>>>>>>>>>>>>    - could you send us the detailed log from the
>>>>>>>>>>>>>>    notification spool table (SELECT * FROM notification_spool WHERE
>>>>>>>>>>>>>>    UploadID=<your uploadID>) and send it back to us? Maybe there are some
>>>>>>>>>>>>>>    additional clues that could help figuring out what is going on.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thank you!
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Tue, Nov 26, 2019 at 10:12 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I checked for the StudyInstacueUID at the files with "The
>>>>>>>>>>>>>>> target directory does not contain a single DICOM file"" and their attribute
>>>>>>>>>>>>>>> has a value.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Regarding the scouter and localizer, i modified the settings
>>>>>>>>>>>>>>> in the imaging pipeline and now i don't get that error message, but still
>>>>>>>>>>>>>>> it doesn't create the mnics.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> The errors i am getting are ( uninitialized value $_ is not
>>>>>>>>>>>>>>> important? because i haven't got comments about that )
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>> Running now the following command:
>>>>>>>>>>>>>>> /data/loris/data//uploadNeuroDB/imaging_upload_file.pl
>>>>>>>>>>>>>>> -profile prod -upload_id 134 /data/incoming/DCC0025_118008_V1.tar.gz
>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> and
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Number of MINC files that will be considered for inserting
>>>>>>>>>>>>>>> into the database: 0
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> No data could be converted into valid MINC files.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> The tarchiveLoader.pl insertion script has failed.
>>>>>>>>>>>>>>> Use of uninitialized value $mail_user in concatenation (.)
>>>>>>>>>>>>>>> or string at /data/loris/bin/mri/
>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 250.
>>>>>>>>>>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 251.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> OK. So the issue I mentioned should not be a problem for
>>>>>>>>>>>>>>>> you.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Is the StudyInstanceUID DICOM header set in your images? If
>>>>>>>>>>>>>>>> it is not set, then you would end up with the error message "The target
>>>>>>>>>>>>>>>> directory does not contain a single DICOM file". So maybe this is the issue
>>>>>>>>>>>>>>>> you are having with those datasets?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Regarding not excluding series descriptions, you can
>>>>>>>>>>>>>>>> configure that in the Config module under the Imaging Pipeline section.
>>>>>>>>>>>>>>>> Simply remove all entries for the "Series description to exclude from
>>>>>>>>>>>>>>>> imaging insertion" setting.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Mon, Nov 25, 2019 at 9:58 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> We are using this version
>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/archive/v21.0.0.zip. Is it
>>>>>>>>>>>>>>>>> possible to insert low resolution now?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, <
>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Which version of LORIS-MRI are you using?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> There was a bug that got resolved in 20.2 in
>>>>>>>>>>>>>>>>>> get_dicom_info.pl. Basically, if a DICOM did not have
>>>>>>>>>>>>>>>>>> the (0020,0032) header, get_dicom_info.pl considered
>>>>>>>>>>>>>>>>>> that the file was not a DICOM, which was a mistake. This got fixed in
>>>>>>>>>>>>>>>>>> version 20.2 of LORIS-MRI. Hopefully this is the issue you are encountering.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> About scout and localizer, they are a type of short and
>>>>>>>>>>>>>>>>>> low resolution sequence that is used by the tech but is of no interest
>>>>>>>>>>>>>>>>>> scientifically, which is why we tend to no insert them.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios Nikoloutsopoulos
>>>>>>>>>>>>>>>>>> <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> i executed the find command and the output i got per
>>>>>>>>>>>>>>>>>>> folder was "DICOM medical imaging data. Maybe there is something wrong with
>>>>>>>>>>>>>>>>>>> the find command in the warning that it is unable to check if the file is a
>>>>>>>>>>>>>>>>>>> dicom file? Also when i use get_dicom_info.pl i don't
>>>>>>>>>>>>>>>>>>> get any output data. Finally i don't understand what scout or localizer is
>>>>>>>>>>>>>>>>>>> ( something like if and only if a file fails then the whole session is
>>>>>>>>>>>>>>>>>>> invalid? ).
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I took a closer look to the
>>>>>>>>>>>>>>>>>>>> batch_uploader_multiple_output.txt file you sent. It looks like there are
>>>>>>>>>>>>>>>>>>>> different reasons for failure depending on the DICOM folder uploaded.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>    - For 465466 DCC0000 V1; 727195 DCC0004 V1 and
>>>>>>>>>>>>>>>>>>>>    684908 DCC0007 V1: it looks like there is no file of type DICOM in the
>>>>>>>>>>>>>>>>>>>>    folder. Have you checked to see if that is indeed the case? Maybe you can
>>>>>>>>>>>>>>>>>>>>    try running the following command on that folder to see what are the types
>>>>>>>>>>>>>>>>>>>>    of the files? If it does not return at least one DICOM medical imaging data
>>>>>>>>>>>>>>>>>>>>    file, then that is why you get the error message from the pipeline:
>>>>>>>>>>>>>>>>>>>>       -
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>       find <my_dicom_archive_root_folder> -type f | xargs -i file {}|cut -d: -f2|sort|uniq
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>       - For 864173 DCC0001 V1: it looks like there are
>>>>>>>>>>>>>>>>>>>>    two different DICOM studies within the same folder. You will need to split
>>>>>>>>>>>>>>>>>>>>    that study in two based on the StudyUID field as the insertion pipeline
>>>>>>>>>>>>>>>>>>>>    does not allow for more than one StudyUID per upload.
>>>>>>>>>>>>>>>>>>>>    - For 890807 DCC0002 V1; 637025 DCC0005 V1 and
>>>>>>>>>>>>>>>>>>>>    239975 DCC0006 V1: it looks like the dcm2mnc command did not produce any
>>>>>>>>>>>>>>>>>>>>    MINC files. Can you check in the DICOM archive what are the series present
>>>>>>>>>>>>>>>>>>>>    in the tarchive for that visit? Maybe only a scout or localizer was
>>>>>>>>>>>>>>>>>>>>    acquired for that session, hence the no valid MINC files (scout and
>>>>>>>>>>>>>>>>>>>>    localizer being skipped for the conversion)
>>>>>>>>>>>>>>>>>>>>    - For 397410 DCC0003 V1: it looks like everything
>>>>>>>>>>>>>>>>>>>>    went well for this one.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> One script that is called by our pipeline is called
>>>>>>>>>>>>>>>>>>>> get_dicom_info.pl and this does all kind of checks on
>>>>>>>>>>>>>>>>>>>> the DICOM files (it is being called when running the dcm2mnc conversion).
>>>>>>>>>>>>>>>>>>>> You could run it independently on your folder if needed.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Since one of the study got in, it does not look like
>>>>>>>>>>>>>>>>>>>> you are having a problem with the setup. It seems more likely to be a
>>>>>>>>>>>>>>>>>>>> problem with the data themselves.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hope this helps.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> In my first vm i am able to create the minc files and
>>>>>>>>>>>>>>>>>>>>> view them at the mri browser (except of candidate 102761034 ), meanwhile
>>>>>>>>>>>>>>>>>>>>> the same files gives warnings at the 2nd vm. The output  of the batch
>>>>>>>>>>>>>>>>>>>>> upload can be seen in the file attached.
>>>>>>>>>>>>>>>>>>>>> Also a colleague of us has built a pre-validation tool
>>>>>>>>>>>>>>>>>>>>> for dicom
>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/
>>>>>>>>>>>>>>>>>>>>> which had found all the files that Loris gave as warning . Basically I
>>>>>>>>>>>>>>>>>>>>> confirmed that the total amount of files per dicom was the same amount as
>>>>>>>>>>>>>>>>>>>>> stated in Loris and checked some filenames given from warning to confirm
>>>>>>>>>>>>>>>>>>>>> that they match with our tool. But that was months ago and my colleague had
>>>>>>>>>>>>>>>>>>>>> changed some parameters for MIP and now our tool doesn't find all the
>>>>>>>>>>>>>>>>>>>>> invalid files, that's why i asked for the dicom header specification of
>>>>>>>>>>>>>>>>>>>>> Loris. In a discussion we had he mentioned that he doesn't check for some
>>>>>>>>>>>>>>>>>>>>> tags e.x. orientation. Lastly to mention that in my first vm i didn't use
>>>>>>>>>>>>>>>>>>>>> our tool to remove invalid dcm files.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>> Can you provide us with some fresh particulars of the
>>>>>>>>>>>>>>>>>>>>>> current issue and we'll take it from there?
>>>>>>>>>>>>>>>>>>>>>> Yang's team has built these scripts which can
>>>>>>>>>>>>>>>>>>>>>> definitely serve as a model for your pre-validation of your DICOM
>>>>>>>>>>>>>>>>>>>>>> collections.
>>>>>>>>>>>>>>>>>>>>>> cheers,
>>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> HI Yang,
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> We make use of pydicom library too. Now about the
>>>>>>>>>>>>>>>>>>>>>>> validate.py i see that you check if some attributes are missing such as
>>>>>>>>>>>>>>>>>>>>>>> PatientID, PatientName which all of our files contains that info. Maybe i
>>>>>>>>>>>>>>>>>>>>>>> have missed something on the setup of my other virtual machine ( although
>>>>>>>>>>>>>>>>>>>>>>> one dicom passed on the new vm successfully, the others that were inserted
>>>>>>>>>>>>>>>>>>>>>>> correctly on my old vm fails on the new one ), i think that i had asked
>>>>>>>>>>>>>>>>>>>>>>> about this error "Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>> line 144." but i don't remember the solution.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding <
>>>>>>>>>>>>>>>>>>>>>>> it at cnbp.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Hey, Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Christine from the LORIS team mentioned you had
>>>>>>>>>>>>>>>>>>>>>>>> some issue with DICOM.  I am a fellow developer for an external project
>>>>>>>>>>>>>>>>>>>>>>>> using LORIS, kind of just like you. We had to implement DICOM upload as
>>>>>>>>>>>>>>>>>>>>>>>> well but more as a fully automated pipeline actually.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> While we were building CNBP, we had coded up some
>>>>>>>>>>>>>>>>>>>>>>>> minor Python functions to check DICOM integrity (and simple validations)
>>>>>>>>>>>>>>>>>>>>>>>> and you might be able to gain some inspiration from it and help you with
>>>>>>>>>>>>>>>>>>>>>>>> your cause. For more comprehensive solution, PyDICOM (
>>>>>>>>>>>>>>>>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#)  seems
>>>>>>>>>>>>>>>>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks
>>>>>>>>>>>>>>>>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can
>>>>>>>>>>>>>>>>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty
>>>>>>>>>>>>>>>>>>>>>>>> rough around the edges but hopefully point you in the right direcitons
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Yang Ding, PhD.
>>>>>>>>>>>>>>>>>>>>>>>> Canadian Neonatal Brain Platform Architect
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM <
>>>>>>>>>>>>>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Send Loris-dev mailing list submissions to
>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> To subscribe or unsubscribe via the World Wide
>>>>>>>>>>>>>>>>>>>>>>>>> Web, visit
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>> or, via email, send a message with subject or body
>>>>>>>>>>>>>>>>>>>>>>>>> 'help' to
>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-request at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> You can reach the person managing the list at
>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-owner at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> When replying, please edit your Subject line so it
>>>>>>>>>>>>>>>>>>>>>>>>> is more specific
>>>>>>>>>>>>>>>>>>>>>>>>> than "Re: Contents of Loris-dev digest..."
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Today's Topics:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>    1. Re: Import mri - scripts (Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos)
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Message: 1
>>>>>>>>>>>>>>>>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200
>>>>>>>>>>>>>>>>>>>>>>>>> From: Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>> To: Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>>>> Message-ID:
>>>>>>>>>>>>>>>>>>>>>>>>>         <CAKHj7uST=
>>>>>>>>>>>>>>>>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com
>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Could we send you a link with 10 anonymized dicom
>>>>>>>>>>>>>>>>>>>>>>>>> files to diagnose the
>>>>>>>>>>>>>>>>>>>>>>>>> warnings we get?
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> > Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>> > We were wondering whether Loris has a tool to
>>>>>>>>>>>>>>>>>>>>>>>>> check if there are problems
>>>>>>>>>>>>>>>>>>>>>>>>> > with the dcm files, before trying to upload
>>>>>>>>>>>>>>>>>>>>>>>>> them. Something that could
>>>>>>>>>>>>>>>>>>>>>>>>> > provide the same results provided in the
>>>>>>>>>>>>>>>>>>>>>>>>> warning_output, this is the
>>>>>>>>>>>>>>>>>>>>>>>>> > summary from the mri_upload at the front-page.
>>>>>>>>>>>>>>>>>>>>>>>>> Also which attributes of the
>>>>>>>>>>>>>>>>>>>>>>>>> > dcm header would trigger a warning? is there a
>>>>>>>>>>>>>>>>>>>>>>>>> dcm file header
>>>>>>>>>>>>>>>>>>>>>>>>> > specification for Loris?
>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>> > Thanks
>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>> > Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> > sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp
>>>>>>>>>>>>>>>>>>>>>>>>> function it worked,but i
>>>>>>>>>>>>>>>>>>>>>>>>> >> thought that something else was causing the 2nd
>>>>>>>>>>>>>>>>>>>>>>>>> issue.
>>>>>>>>>>>>>>>>>>>>>>>>> >> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours
>>>>>>>>>>>>>>>>>>>>>>>>> Boucher, Mr, <
>>>>>>>>>>>>>>>>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> The first error occurs because the
>>>>>>>>>>>>>>>>>>>>>>>>> QCFirstChangeTime and columns are of
>>>>>>>>>>>>>>>>>>>>>>>>> >>> type `unsigned integer` and not `datatime`.
>>>>>>>>>>>>>>>>>>>>>>>>> You should be using
>>>>>>>>>>>>>>>>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW().
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> The second error occurs because the trigger
>>>>>>>>>>>>>>>>>>>>>>>>> triggers a rollback of the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> insert statement in the files table.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> See mysql documentation for trigger error
>>>>>>>>>>>>>>>>>>>>>>>>> handling.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> An error during either a BEFORE or AFTER
>>>>>>>>>>>>>>>>>>>>>>>>> trigger results in failure of
>>>>>>>>>>>>>>>>>>>>>>>>> >>> the entire statement that caused trigger
>>>>>>>>>>>>>>>>>>>>>>>>> invocation.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you for sharing that. I hope it helps.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Xavier
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on
>>>>>>>>>>>>>>>>>>>>>>>>> behalf of Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> When mincs are inserted their corresponding
>>>>>>>>>>>>>>>>>>>>>>>>> rows at the file table are
>>>>>>>>>>>>>>>>>>>>>>>>> >>> inserted too
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> i would like to insert their rows at
>>>>>>>>>>>>>>>>>>>>>>>>> file_qcstatus as well, because i
>>>>>>>>>>>>>>>>>>>>>>>>> >>> don't want manually to label them as passed
>>>>>>>>>>>>>>>>>>>>>>>>> throught the interface
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> That is the trigger i wrote
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER
>>>>>>>>>>>>>>>>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER
>>>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW
>>>>>>>>>>>>>>>>>>>>>>>>> >>> BEGIN
>>>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT INTO files_qcstatus
>>>>>>>>>>>>>>>>>>>>>>>>> >>> SET FileID = NEW.FileID,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>      SeriesUID = NEW.SeriesUID,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>      EchoTime = NEW.EchoTime,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCStatus = "Pass",
>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCFirstChangeTime = NOW(),
>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCLastChangeTime = NOW();
>>>>>>>>>>>>>>>>>>>>>>>>> >>> END
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> although it contains some errors
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range value
>>>>>>>>>>>>>>>>>>>>>>>>> for column
>>>>>>>>>>>>>>>>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update
>>>>>>>>>>>>>>>>>>>>>>>>> a child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails
>>>>>>>>>>>>>>>>>>>>>>>>> (`LORIS`.`parameter_file`, CONSTRAINT
>>>>>>>>>>>>>>>>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`)
>>>>>>>>>>>>>>>>>>>>>>>>> REFERENCES `files` (`FileID`))
>>>>>>>>>>>>>>>>>>>>>>>>> >>> at
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> In the mri_upload table, there is a TarchiveID
>>>>>>>>>>>>>>>>>>>>>>>>> column associated with
>>>>>>>>>>>>>>>>>>>>>>>>> >>> the MRI upload you inserted. When this value
>>>>>>>>>>>>>>>>>>>>>>>>> is NULL, it means no DICOMs
>>>>>>>>>>>>>>>>>>>>>>>>> >>> were inserted into the tarchive tables. At the
>>>>>>>>>>>>>>>>>>>>>>>>> end of the insertion of the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> DICOMs in the tarchive tables, this value is
>>>>>>>>>>>>>>>>>>>>>>>>> updated with the correct
>>>>>>>>>>>>>>>>>>>>>>>>> >>> TarchiveID associated with the upload.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Could this correspond to what you want to do?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Regarding the files_qcstatus, this table is
>>>>>>>>>>>>>>>>>>>>>>>>> only linked to the files
>>>>>>>>>>>>>>>>>>>>>>>>> >>> table (hence, the MINC files). You could
>>>>>>>>>>>>>>>>>>>>>>>>> always create a new table for
>>>>>>>>>>>>>>>>>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive
>>>>>>>>>>>>>>>>>>>>>>>>> table?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> i would like whenever a dicom is imported to
>>>>>>>>>>>>>>>>>>>>>>>>> mark all their
>>>>>>>>>>>>>>>>>>>>>>>>> >>> coressponding qc_status to "pass". I was
>>>>>>>>>>>>>>>>>>>>>>>>> thinking of creating a trigger for
>>>>>>>>>>>>>>>>>>>>>>>>> >>> that, but which tables do i need to add
>>>>>>>>>>>>>>>>>>>>>>>>> entries to? So far from what i see
>>>>>>>>>>>>>>>>>>>>>>>>> >>> i need to add entres at  the table "files"
>>>>>>>>>>>>>>>>>>>>>>>>> whenever an insertion happens to
>>>>>>>>>>>>>>>>>>>>>>>>> >>> files_qcstatus.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Oh, sorry i should have asked for StudyID, at
>>>>>>>>>>>>>>>>>>>>>>>>> the beginning of my email
>>>>>>>>>>>>>>>>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID).
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> that's the Study Instance UID, not the
>>>>>>>>>>>>>>>>>>>>>>>>> StudyID. So the StudyID i am
>>>>>>>>>>>>>>>>>>>>>>>>> >>> looking for is not stored in the database?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> The StudyUID is stored in the DicomArchiveID
>>>>>>>>>>>>>>>>>>>>>>>>> field of the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> tarchive table. It can also be found in the
>>>>>>>>>>>>>>>>>>>>>>>>> metadata field but it is mixed
>>>>>>>>>>>>>>>>>>>>>>>>> >>> with many other information.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is StudyUID stored somewhere at the tables? At
>>>>>>>>>>>>>>>>>>>>>>>>> the tarchive table,
>>>>>>>>>>>>>>>>>>>>>>>>> >>> specifically at the AcquisitonMetadata column
>>>>>>>>>>>>>>>>>>>>>>>>> i found something called
>>>>>>>>>>>>>>>>>>>>>>>>> >>> 'Unique Study ID" in its context, but that
>>>>>>>>>>>>>>>>>>>>>>>>> must be the Study Instance UID.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Your observation is correct. A little
>>>>>>>>>>>>>>>>>>>>>>>>> explanation below.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> MINC files get inserted into the MRI violation
>>>>>>>>>>>>>>>>>>>>>>>>> tables if:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - the scan type could not be identified
>>>>>>>>>>>>>>>>>>>>>>>>> (not matching an entry in
>>>>>>>>>>>>>>>>>>>>>>>>> >>>    the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - one parameter of the scan type is out of
>>>>>>>>>>>>>>>>>>>>>>>>> the expected range
>>>>>>>>>>>>>>>>>>>>>>>>> >>>    present in the mri_protocol_checks (extra
>>>>>>>>>>>>>>>>>>>>>>>>> filtering in case you need to be
>>>>>>>>>>>>>>>>>>>>>>>>> >>>    stricker on some parameters not present in
>>>>>>>>>>>>>>>>>>>>>>>>> the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - if the CandID and PSCID do not match
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> The following cases do not get in the MRI
>>>>>>>>>>>>>>>>>>>>>>>>> violation tables as it happens
>>>>>>>>>>>>>>>>>>>>>>>>> >>> before the conversion of the DICOM to MINC
>>>>>>>>>>>>>>>>>>>>>>>>> files and only MINC files
>>>>>>>>>>>>>>>>>>>>>>>>> >>> violations are logged there:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - "No single DICOM" (since no valid DICOM
>>>>>>>>>>>>>>>>>>>>>>>>> could be found to convert
>>>>>>>>>>>>>>>>>>>>>>>>> >>>    to MINC)
>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - "Study already inserted" (duplicate
>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID) since this error
>>>>>>>>>>>>>>>>>>>>>>>>> >>>    happens at the dicomTar.pl level (way
>>>>>>>>>>>>>>>>>>>>>>>>> before conversion into MINC files)
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad everything is working out!!
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> the mri passed, for some reason it consumed
>>>>>>>>>>>>>>>>>>>>>>>>> 5.12GB of ram. Now about the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations, dicoms are triggered to be
>>>>>>>>>>>>>>>>>>>>>>>>> inserted there only if there is
>>>>>>>>>>>>>>>>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general for
>>>>>>>>>>>>>>>>>>>>>>>>> its header parameter?
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Because i don't see the cases of 'No single
>>>>>>>>>>>>>>>>>>>>>>>>> dicom" or with the 2 studyiuid
>>>>>>>>>>>>>>>>>>>>>>>>> >>> to be there.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sorry to hear you are having issues with the
>>>>>>>>>>>>>>>>>>>>>>>>> memory. I think most of our
>>>>>>>>>>>>>>>>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you
>>>>>>>>>>>>>>>>>>>>>>>>> should be fine.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> about that dicom that had that insertion error
>>>>>>>>>>>>>>>>>>>>>>>>> it's about 30mb and when
>>>>>>>>>>>>>>>>>>>>>>>>> >>> it is being processed the ram is being
>>>>>>>>>>>>>>>>>>>>>>>>> drastically increased from 2gb to
>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3.28 and then the whole virtual machine is
>>>>>>>>>>>>>>>>>>>>>>>>> frozen. What is the recommended
>>>>>>>>>>>>>>>>>>>>>>>>> >>> size of ram for using Loris?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to see that the StudyUID problem was
>>>>>>>>>>>>>>>>>>>>>>>>> fixed!
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the delete script issue, if you are
>>>>>>>>>>>>>>>>>>>>>>>>> absolutely certain that no
>>>>>>>>>>>>>>>>>>>>>>>>> >>> processes are run for that uploadID, you can
>>>>>>>>>>>>>>>>>>>>>>>>> update the mri_upload table
>>>>>>>>>>>>>>>>>>>>>>>>> >>> and set the column Inserting to 0 instead of 1
>>>>>>>>>>>>>>>>>>>>>>>>> for that uploadID. It
>>>>>>>>>>>>>>>>>>>>>>>>> >>> looks like for some reason the scripts did not
>>>>>>>>>>>>>>>>>>>>>>>>> update this field when it
>>>>>>>>>>>>>>>>>>>>>>>>> >>> stopped the insertion. Not sure why that would
>>>>>>>>>>>>>>>>>>>>>>>>> be the case though.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Note: only do that update if you are certain
>>>>>>>>>>>>>>>>>>>>>>>>> that there is no processing
>>>>>>>>>>>>>>>>>>>>>>>>> >>> happening.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> about the Dicoms i reported that didn't have a
>>>>>>>>>>>>>>>>>>>>>>>>> StudyID they actually do
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> I thought that this might be a permission
>>>>>>>>>>>>>>>>>>>>>>>>> because "w" was missing at the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> group. After using chmod -R 775 only 102809579
>>>>>>>>>>>>>>>>>>>>>>>>> passed, but with no mnic
>>>>>>>>>>>>>>>>>>>>>>>>> >>> files. Also now i have this error
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox
>>>>>>>>>>>>>>>>>>>>>>>>> :/data/loris/bin/mri/tools$
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34
>>>>>>>>>>>>>>>>>>>>>>>>> -ignore
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is
>>>>>>>>>>>>>>>>>>>>>>>>> currently processing it.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> How can solve this?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Here is our auto dicom uploading python script:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> To give you a brief idea:
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Per folder it will:
>>>>>>>>>>>>>>>>>>>>>>>>> >>> 1) Delete all the .bak files
>>>>>>>>>>>>>>>>>>>>>>>>> >>> 2) Locate .dcm files and update the Patient
>>>>>>>>>>>>>>>>>>>>>>>>> header
>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3) Furthermore we are interesting in finding
>>>>>>>>>>>>>>>>>>>>>>>>> TR_min, TR_max, TE_min,
>>>>>>>>>>>>>>>>>>>>>>>>> >>> TE_max parameters of T1 protocol and do an
>>>>>>>>>>>>>>>>>>>>>>>>> update at the mri_protocol table
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205
>>>>>>>>>>>>>>>>>>>>>>>>> >>> For some reason some files are missing
>>>>>>>>>>>>>>>>>>>>>>>>> SeriesDescription/ProtocolName
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> In total i have 7 folders
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3/7 passed
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Also about the first patient with DC0000 had a
>>>>>>>>>>>>>>>>>>>>>>>>> violation "T1 AXIAL SE
>>>>>>>>>>>>>>>>>>>>>>>>> >>> GADO", but my script didn't output a TE of 17
>>>>>>>>>>>>>>>>>>>>>>>>> nowhere and i find that weird
>>>>>>>>>>>>>>>>>>>>>>>>> >>> since Loris detects the SeriesDescription.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Now about the 4/7 that didn't passed
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> 102327840 and 102809579 outputs "The target
>>>>>>>>>>>>>>>>>>>>>>>>> directory does not contain a
>>>>>>>>>>>>>>>>>>>>>>>>> >>> single DICOM file.", therefore they are
>>>>>>>>>>>>>>>>>>>>>>>>> missing their StudyUID
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it
>>>>>>>>>>>>>>>>>>>>>>>>> with data from multiple
>>>>>>>>>>>>>>>>>>>>>>>>> >>> studies."
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> and 102761034 "No data could be converted into
>>>>>>>>>>>>>>>>>>>>>>>>> valid MINC files.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> localizer, scout will not be considered!" What
>>>>>>>>>>>>>>>>>>>>>>>>> is this?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> If i wanted to force the insertion of
>>>>>>>>>>>>>>>>>>>>>>>>> 102327840, 102809579 and 102506134
>>>>>>>>>>>>>>>>>>>>>>>>> >>> can i just pass a flag parameter to
>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl? or
>>>>>>>>>>>>>>>>>>>>>>>>> >>> modify imaging_upload_file.pl?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> PS
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> To diagnose a folder search the name of the
>>>>>>>>>>>>>>>>>>>>>>>>> folder at dicom_output.txt.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear about your progress.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, the script you used to delete imaging
>>>>>>>>>>>>>>>>>>>>>>>>> data is fully documented here
>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- let us know if you didn't find the answers
>>>>>>>>>>>>>>>>>>>>>>>>> you were looking for there.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> (Is it possible the null row in *mri_scanner*
>>>>>>>>>>>>>>>>>>>>>>>>> seen in your database
>>>>>>>>>>>>>>>>>>>>>>>>> >>> management software is a visual placeholder
>>>>>>>>>>>>>>>>>>>>>>>>> for you as the user?  I'm not
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sure why a scanner would ever be registered
>>>>>>>>>>>>>>>>>>>>>>>>> with ID='0' as your screenshot
>>>>>>>>>>>>>>>>>>>>>>>>> >>> showed.)
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> I fixed it with this
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> I tried to create a new candidate using the
>>>>>>>>>>>>>>>>>>>>>>>>> API, is there something
>>>>>>>>>>>>>>>>>>>>>>>>> >>> wrong with the structure? why did i receive a
>>>>>>>>>>>>>>>>>>>>>>>>> 500 internal error? In the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-error log it state that there is
>>>>>>>>>>>>>>>>>>>>>>>>> something wrong with token, but i
>>>>>>>>>>>>>>>>>>>>>>>>> >>> verfied that the type of the token is a string.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error]
>>>>>>>>>>>>>>>>>>>>>>>>> [pid 4535] [client
>>>>>>>>>>>>>>>>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error:  Uncaught
>>>>>>>>>>>>>>>>>>>>>>>>> TypeError: Argument 1
>>>>>>>>>>>>>>>>>>>>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate()
>>>>>>>>>>>>>>>>>>>>>>>>> must be of the type string,
>>>>>>>>>>>>>>>>>>>>>>>>> >>> null given, called in
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and
>>>>>>>>>>>>>>>>>>>>>>>>> >>> defined in
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
>>>>>>>>>>>>>>>>>>>>>>>>> >>> trace:\n#0
>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
>>>>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):
>>>>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> NDB_Client->initialize('/var/www/loris/...')\n#3
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST',
>>>>>>>>>>>>>>>>>>>>>>>>> Array)\n#5 {main}\n  thrown in
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is there a way also to delete candidates? Just
>>>>>>>>>>>>>>>>>>>>>>>>> to let you know what i
>>>>>>>>>>>>>>>>>>>>>>>>> >>> did to clear candidates, because maybe i may
>>>>>>>>>>>>>>>>>>>>>>>>> have missed dependencies.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> First i deleted all their uploads
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc (
>>>>>>>>>>>>>>>>>>>>>>>>> is there a way to omit
>>>>>>>>>>>>>>>>>>>>>>>>> >>> the backup file ? )
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Afterwards i had some scanner candidates, so i
>>>>>>>>>>>>>>>>>>>>>>>>> deleted all the entries
>>>>>>>>>>>>>>>>>>>>>>>>> >>> from mri_scanner except that i couldn't delete
>>>>>>>>>>>>>>>>>>>>>>>>> this entry with the 0 ID.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Lastly i deleted the session and then the
>>>>>>>>>>>>>>>>>>>>>>>>> candidate table.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> We recommend that you use our existing tools
>>>>>>>>>>>>>>>>>>>>>>>>> for creating new candidates
>>>>>>>>>>>>>>>>>>>>>>>>> >>> - either the LORIS API or if you are using a
>>>>>>>>>>>>>>>>>>>>>>>>> PHP script, by calling the Candidate
>>>>>>>>>>>>>>>>>>>>>>>>> >>> class's createNew()
>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200
>>>>>>>>>>>>>>>>>>>>>>>>> >function.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> These will create the necessary records for
>>>>>>>>>>>>>>>>>>>>>>>>> you.  (It's not recommended to
>>>>>>>>>>>>>>>>>>>>>>>>> >>> make direct modifications to mysql database
>>>>>>>>>>>>>>>>>>>>>>>>> tables in your script, if I
>>>>>>>>>>>>>>>>>>>>>>>>> >>> understand you.)
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> The CandID should be a randomized 6 digit
>>>>>>>>>>>>>>>>>>>>>>>>> randomized ID, and there are
>>>>>>>>>>>>>>>>>>>>>>>>> >>> multiple reasons for this.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> You can use the PSCID for project-specific IDs
>>>>>>>>>>>>>>>>>>>>>>>>> and the External ID field
>>>>>>>>>>>>>>>>>>>>>>>>> >>> in the candidate table can also be used for
>>>>>>>>>>>>>>>>>>>>>>>>> any values you like.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Additionally, any number of custom IDs can be
>>>>>>>>>>>>>>>>>>>>>>>>> added in parallel - these
>>>>>>>>>>>>>>>>>>>>>>>>> >>> are entered/visible in the Candidate
>>>>>>>>>>>>>>>>>>>>>>>>> Information module and added in the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> back-end as candidate parameters.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> We are building a script that will auto insert
>>>>>>>>>>>>>>>>>>>>>>>>> the candidates based on
>>>>>>>>>>>>>>>>>>>>>>>>> >>> their ExternalID. We would like to know
>>>>>>>>>>>>>>>>>>>>>>>>> whethere when we are creating a new
>>>>>>>>>>>>>>>>>>>>>>>>> >>> profile in the candidate table, if we also
>>>>>>>>>>>>>>>>>>>>>>>>> have to insert a new record at
>>>>>>>>>>>>>>>>>>>>>>>>> >>> another table? Furthermore is there a problem
>>>>>>>>>>>>>>>>>>>>>>>>> that in our case CandID won't
>>>>>>>>>>>>>>>>>>>>>>>>> >>> be a 6digit? ( should we start it from 100000?)
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> That would normally be the case but the
>>>>>>>>>>>>>>>>>>>>>>>>> numeric part of the PSCID get
>>>>>>>>>>>>>>>>>>>>>>>>> >>> paded with 0 on the left.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ex. for sequential ID made of center ID of
>>>>>>>>>>>>>>>>>>>>>>>>> `ABC` plus 4 numerical char
>>>>>>>>>>>>>>>>>>>>>>>>> >>> with a min value of 1, the sequence would be:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0001
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0002
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0010
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> thus sorting them ascending will always get
>>>>>>>>>>>>>>>>>>>>>>>>> the latest value generated
>>>>>>>>>>>>>>>>>>>>>>>>> >>> as the max value.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>> melanie.legault2 at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> I see, although the PSCID value is
>>>>>>>>>>>>>>>>>>>>>>>>> varchar(255), it must be stored
>>>>>>>>>>>>>>>>>>>>>>>>> >>> within a specific length of characters.
>>>>>>>>>>>>>>>>>>>>>>>>> Otherwise if we were to sort
>>>>>>>>>>>>>>>>>>>>>>>>> >>> strings with different lengths the result
>>>>>>>>>>>>>>>>>>>>>>>>> would not be sorted correctly (
>>>>>>>>>>>>>>>>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1,
>>>>>>>>>>>>>>>>>>>>>>>>> 10, 11, 2 ).
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hello Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> There is no `last value` stored anywhere.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> The code simply look for the PSCID with the
>>>>>>>>>>>>>>>>>>>>>>>>> max value and increase that
>>>>>>>>>>>>>>>>>>>>>>>>> >>> value by 1 in order to generate the next PSCID.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this info help.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie Legault | Software developer | Faculty
>>>>>>>>>>>>>>>>>>>>>>>>> of Medicine | McGill
>>>>>>>>>>>>>>>>>>>>>>>>> >>> University
>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on
>>>>>>>>>>>>>>>>>>>>>>>>> behalf of Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> how does Loris determine the next available
>>>>>>>>>>>>>>>>>>>>>>>>> PSCID value for a new
>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate?
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization
>>>>>>>>>>>>>>>>>>>>>>>>> >>> e.x in the default case the PSCID is
>>>>>>>>>>>>>>>>>>>>>>>>> sequential, but where do we store the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> last value for the sequential sequence?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> the parameters in the mri_protocol you have
>>>>>>>>>>>>>>>>>>>>>>>>> assigned are global
>>>>>>>>>>>>>>>>>>>>>>>>> >>> standard? or were assigned after trial and
>>>>>>>>>>>>>>>>>>>>>>>>> error?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Given you have done the initial setup of your
>>>>>>>>>>>>>>>>>>>>>>>>> tables to match your
>>>>>>>>>>>>>>>>>>>>>>>>> >>> intended protocol/parameters according to
>>>>>>>>>>>>>>>>>>>>>>>>> instructions --
>>>>>>>>>>>>>>>>>>>>>>>>> >>> the Troubleshooting guide documentation
>>>>>>>>>>>>>>>>>>>>>>>>> recommends
>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes
>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>> >>> re-running the pipeline (and first deleting
>>>>>>>>>>>>>>>>>>>>>>>>> prior uploads).
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *if i were to change their status to resolve
>>>>>>>>>>>>>>>>>>>>>>>>> what would happen?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> I noticed that i can view the mnics at the
>>>>>>>>>>>>>>>>>>>>>>>>> brainbrowser from the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations page ( those mnics are stored
>>>>>>>>>>>>>>>>>>>>>>>>> at /data/loris/data/trashbin/
>>>>>>>>>>>>>>>>>>>>>>>>> >>> if i were to click their issue to resolve what
>>>>>>>>>>>>>>>>>>>>>>>>> would happend? would they
>>>>>>>>>>>>>>>>>>>>>>>>> >>> appear in the dicom_archive view too? ).
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> The defaut values of the schema exists in my
>>>>>>>>>>>>>>>>>>>>>>>>> local database. If i adjust
>>>>>>>>>>>>>>>>>>>>>>>>> >>> the default values of TR_min and TE_min the
>>>>>>>>>>>>>>>>>>>>>>>>> mincs will be uploaded?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is it possible that you haven't set up your
>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table ?   (and
>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_scan_type table too, for additional types
>>>>>>>>>>>>>>>>>>>>>>>>> of scans)
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Like the psc table, this is a pre-requisite
>>>>>>>>>>>>>>>>>>>>>>>>> for the Imaging insertion
>>>>>>>>>>>>>>>>>>>>>>>>> >>> setup : See the install/setup documentation :
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> To add new rows, just use MySQL insert
>>>>>>>>>>>>>>>>>>>>>>>>> statements.  You can adapt the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> insert statements which load the default table
>>>>>>>>>>>>>>>>>>>>>>>>> values --> e.g. Here on
>>>>>>>>>>>>>>>>>>>>>>>>> >>> GitHub :
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>>>>>>>>>>>>>>>>>>>>>>>> >>> (see also the mri_scan_type table)
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> I see that i can edit the values but not how
>>>>>>>>>>>>>>>>>>>>>>>>> to insert new rows.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> If i choose Inserted with flag then will the
>>>>>>>>>>>>>>>>>>>>>>>>> minc be inserted?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear that *dcmodify* worked correctly.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the MRI Violations module, the screenshot
>>>>>>>>>>>>>>>>>>>>>>>>> is enough.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> It says "could not identify scan type", which
>>>>>>>>>>>>>>>>>>>>>>>>> we knew already.  Did you
>>>>>>>>>>>>>>>>>>>>>>>>> >>> click on the link on those words?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> It will take you to the next page of the
>>>>>>>>>>>>>>>>>>>>>>>>> module, showing for each scan
>>>>>>>>>>>>>>>>>>>>>>>>> >>> what the scan parameters were, and will also
>>>>>>>>>>>>>>>>>>>>>>>>> show for comparison what's
>>>>>>>>>>>>>>>>>>>>>>>>> >>> stored in your *mri_protocol* table.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Compare these values to find which parameter
>>>>>>>>>>>>>>>>>>>>>>>>> was not correct according
>>>>>>>>>>>>>>>>>>>>>>>>> >>> to your *mri_protocol* table scan type
>>>>>>>>>>>>>>>>>>>>>>>>> definitions.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> You may end up broadening your mri_protocol
>>>>>>>>>>>>>>>>>>>>>>>>> value ranges (e.g. TR, TE)
>>>>>>>>>>>>>>>>>>>>>>>>> >>> for scans.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> This can be done in the front-end, by editing
>>>>>>>>>>>>>>>>>>>>>>>>> the database table
>>>>>>>>>>>>>>>>>>>>>>>>> >>> directly in the same subpage of the MRI
>>>>>>>>>>>>>>>>>>>>>>>>> Violations module.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> The MRI Violations module features are
>>>>>>>>>>>>>>>>>>>>>>>>> explained in more detail in the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Help text for this module inside LORIS (click
>>>>>>>>>>>>>>>>>>>>>>>>> the  ["?"] icon in the menu
>>>>>>>>>>>>>>>>>>>>>>>>> >>> bar.)
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide
>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>> >>> :  no MINCs inserted- violated scans
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> looks like my previous email's attachment
>>>>>>>>>>>>>>>>>>>>>>>>> wasn't delivered due to
>>>>>>>>>>>>>>>>>>>>>>>>> >>> security reasons, i uploaded my file at google
>>>>>>>>>>>>>>>>>>>>>>>>> drive
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> From Dicat's view seems that dcmodify worked
>>>>>>>>>>>>>>>>>>>>>>>>> in both cases
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the mri_violations i attached the .html
>>>>>>>>>>>>>>>>>>>>>>>>> output from webbrowser, so
>>>>>>>>>>>>>>>>>>>>>>>>> >>> that you can check the filelds easier.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios --
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Great, sounds like more progress.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> About the dcmodify command -- I'm not sure why
>>>>>>>>>>>>>>>>>>>>>>>>> you're getting an Endian
>>>>>>>>>>>>>>>>>>>>>>>>> >>> warning.  (it's a warning not an error,
>>>>>>>>>>>>>>>>>>>>>>>>> correct?)
>>>>>>>>>>>>>>>>>>>>>>>>> >>> To clarify -- Were the DICOM headers
>>>>>>>>>>>>>>>>>>>>>>>>> (PatientName) all successfully
>>>>>>>>>>>>>>>>>>>>>>>>> >>> relabelled, after the command ran?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> You can use also our DICAT tool (
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/DICAT) to
>>>>>>>>>>>>>>>>>>>>>>>>> >>> verify and/or update local DICOM headers --
>>>>>>>>>>>>>>>>>>>>>>>>> though your dcmodify command is
>>>>>>>>>>>>>>>>>>>>>>>>> >>> a great and fast solution for bulk header
>>>>>>>>>>>>>>>>>>>>>>>>> updates.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> If you're concerned about fields being changed
>>>>>>>>>>>>>>>>>>>>>>>>> (e.g. "(2001,105f)" from
>>>>>>>>>>>>>>>>>>>>>>>>> >>> the warning message)  - you can also dcmdump a
>>>>>>>>>>>>>>>>>>>>>>>>> DICOM slice before and look
>>>>>>>>>>>>>>>>>>>>>>>>> >>> at these fields specifically.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's also not a bad "sanity check" to backup
>>>>>>>>>>>>>>>>>>>>>>>>> your DICOMS before/after
>>>>>>>>>>>>>>>>>>>>>>>>> >>> running dcmodify, and use dcmdump on each
>>>>>>>>>>>>>>>>>>>>>>>>> version to diff the outputs --
>>>>>>>>>>>>>>>>>>>>>>>>> >>> this will pinpoint what changed.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Re the protocol violation --
>>>>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol not recognized or
>>>>>>>>>>>>>>>>>>>>>>>>> >>> unknown :   this means your scans did not
>>>>>>>>>>>>>>>>>>>>>>>>> match what is stored in your
>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_protocol table.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Check the MRI Violations front-end module --
>>>>>>>>>>>>>>>>>>>>>>>>> can you see why they didn't
>>>>>>>>>>>>>>>>>>>>>>>>> >>> match?
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Send us an example, in addition to the
>>>>>>>>>>>>>>>>>>>>>>>>> contents of the mri_protocol
>>>>>>>>>>>>>>>>>>>>>>>>> >>> table, if you can't find the source of the
>>>>>>>>>>>>>>>>>>>>>>>>> mismatch.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  Here is the psc table
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> I created 2 candidates profiles through the
>>>>>>>>>>>>>>>>>>>>>>>>> interface
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> then runned dcmodify command to a dicom file
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1"
>>>>>>>>>>>>>>>>>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> and got those warning: is this okay?
>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify at another Dicom didn't show
>>>>>>>>>>>>>>>>>>>>>>>>> warnings. Below you can see the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> execution for the second dicom. Mnics could
>>>>>>>>>>>>>>>>>>>>>>>>> not be inserted due to
>>>>>>>>>>>>>>>>>>>>>>>>> >>> AcquisitionProtocol being unknown.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Running now the following command:
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>> >>> imaging_upload_file.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 12
>>>>>>>>>>>>>>>>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  find -path
>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX'
>>>>>>>>>>>>>>>>>>>>>>>>> >>> -delete
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> dicomTar.pl
>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database
>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -verbose
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  Source: /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Target: /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Testing for database connectivity.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Database is available.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> You will archive the dir :
>>>>>>>>>>>>>>>>>>>>>>>>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> You are creating a tar with the following
>>>>>>>>>>>>>>>>>>>>>>>>> command:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> tar -cf
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> getting md5sums and gzipping!!
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :
>>>>>>>>>>>>>>>>>>>>>>>>> 127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :    Linux
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>>>> 2019-09-06 18:36:50
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Removing temporary files from target location
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Done adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation
>>>>>>>>>>>>>>>>>>>>>>>>> >>> -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>>>>>>>>>>>>>>>>>>>>>>>> >>> -uploadID 12 -verbose
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  md5sum
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Set centerID = 1
>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Number of MINC files that will be considered
>>>>>>>>>>>>>>>>>>>>>>>>> for inserting into the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> database: 2
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file
>>>>>>>>>>>>>>>>>>>>>>>>> is
>>>>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file
>>>>>>>>>>>>>>>>>>>>>>>>> is
>>>>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>> cat
>>>>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Acquisition protocol is unknown
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>   --> The minc file cannot be registered since
>>>>>>>>>>>>>>>>>>>>>>>>> the AcquisitionProtocol
>>>>>>>>>>>>>>>>>>>>>>>>> >>> is unknown
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sure -- you can delete imaging datasets with
>>>>>>>>>>>>>>>>>>>>>>>>> the *delete_imaging_upload*
>>>>>>>>>>>>>>>>>>>>>>>>> >>> script --
>>>>>>>>>>>>>>>>>>>>>>>>> >>> details here:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> What's in your *psc* table?  (Is it properly
>>>>>>>>>>>>>>>>>>>>>>>>> populated? This is a
>>>>>>>>>>>>>>>>>>>>>>>>> >>> pre-requisite to loading imaging data.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database
>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>>>> >>> The foreign key constraint error on the
>>>>>>>>>>>>>>>>>>>>>>>>> candidate record is curious.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> There are also a few options for creating
>>>>>>>>>>>>>>>>>>>>>>>>> candidates when inserting
>>>>>>>>>>>>>>>>>>>>>>>>> >>> imaging data:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then
>>>>>>>>>>>>>>>>>>>>>>>>> DICOM insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> a. via the LORIS API -- Create the candidates
>>>>>>>>>>>>>>>>>>>>>>>>> (and visits, optionally I
>>>>>>>>>>>>>>>>>>>>>>>>> >>> think)
>>>>>>>>>>>>>>>>>>>>>>>>> >>> How to:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by
>>>>>>>>>>>>>>>>>>>>>>>>> LORIS.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Then as a second step:
>>>>>>>>>>>>>>>>>>>>>>>>> >>> b. Use the imaging insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets
>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>> >>> to load your DICOMs.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> You will want to first ensure that the
>>>>>>>>>>>>>>>>>>>>>>>>> PatientName header in the DICOMs
>>>>>>>>>>>>>>>>>>>>>>>>> >>> as well as tar package are correctly labelled
>>>>>>>>>>>>>>>>>>>>>>>>> with PSCID_DCCID_VisitLabel
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets:
>>>>>>>>>>>>>>>>>>>>>>>>> >>> How to :
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options when
>>>>>>>>>>>>>>>>>>>>>>>>> running the bids_import script,
>>>>>>>>>>>>>>>>>>>>>>>>> >>> to automatically create your candidates and
>>>>>>>>>>>>>>>>>>>>>>>>> sessions.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> How do i delete a Study? And everytime do i
>>>>>>>>>>>>>>>>>>>>>>>>> have to create a new
>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate to get DCCID and a PSCID?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *First execution:*
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>> < ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match
>>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update
>>>>>>>>>>>>>>>>>>>>>>>>> a child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`,
>>>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_candidate_1`
>>>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`)
>>>>>>>>>>>>>>>>>>>>>>>>> REFERENCES `psc` (`CenterID`)) at
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ERROR: Failed to insert record in table
>>>>>>>>>>>>>>>>>>>>>>>>> mri_scanner:
>>>>>>>>>>>>>>>>>>>>>>>>> >>> The following database commands failed:
>>>>>>>>>>>>>>>>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';
>>>>>>>>>>>>>>>>>>>>>>>>> >>> SET
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Medical Systems';
>>>>>>>>>>>>>>>>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Error obtained:Cannot add or update a child
>>>>>>>>>>>>>>>>>>>>>>>>> row: a foreign key
>>>>>>>>>>>>>>>>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`,
>>>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_mri_scanner_1`
>>>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate`
>>>>>>>>>>>>>>>>>>>>>>>>> (`CandID`)) (error code 1452)
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ERROR: The validation has failed. Either
>>>>>>>>>>>>>>>>>>>>>>>>> re-run the validation again
>>>>>>>>>>>>>>>>>>>>>>>>> >>> and fix the problem. Or re-run
>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader.pl using -force to force the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> execution.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> The tarchiveLoader.pl insertion script has
>>>>>>>>>>>>>>>>>>>>>>>>> failed.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory
>>>>>>>>>>>>>>>>>>>>>>>>> at ./
>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> *And second execution: *
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>> < ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match
>>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> PROBLEM:
>>>>>>>>>>>>>>>>>>>>>>>>> >>> The user 'lorisadmin' has already inserted
>>>>>>>>>>>>>>>>>>>>>>>>> this study.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> The unique study ID is
>>>>>>>>>>>>>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> This is the information retained from the
>>>>>>>>>>>>>>>>>>>>>>>>> first time the study was
>>>>>>>>>>>>>>>>>>>>>>>>> >>> inserted:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :
>>>>>>>>>>>>>>>>>>>>>>>>> 127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :    Linux
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>>>> 2019-09-04 18:33:05
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053
>>>>>>>>>>>>>>>>>>>>>>>>> >>>  DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Last update of record:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> The dicomTar.pl execution has failed.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory
>>>>>>>>>>>>>>>>>>>>>>>>> at ./
>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ok, this sounds like good progress.  Let us
>>>>>>>>>>>>>>>>>>>>>>>>> know when you next encounter
>>>>>>>>>>>>>>>>>>>>>>>>> >>> issues as you progress through the Imaging
>>>>>>>>>>>>>>>>>>>>>>>>> Install/Setup docs
>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>>>> >.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> I'll look into how we can better handle the
>>>>>>>>>>>>>>>>>>>>>>>>> incoming/ directory next
>>>>>>>>>>>>>>>>>>>>>>>>> >>> time.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is
>>>>>>>>>>>>>>>>>>>>>>>>> >>> populated correctly except its port is
>>>>>>>>>>>>>>>>>>>>>>>>> 'port'    : ''. Also i have tested
>>>>>>>>>>>>>>>>>>>>>>>>> >>> that i can connect to MySQL with lorisuser.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> I executed the script again, because the only
>>>>>>>>>>>>>>>>>>>>>>>>> error i had previously was
>>>>>>>>>>>>>>>>>>>>>>>>> >>> that the /data/incoming folder didn't exist
>>>>>>>>>>>>>>>>>>>>>>>>> and there are no errors
>>>>>>>>>>>>>>>>>>>>>>>>> >>> reported back except of warnings <<mysql:
>>>>>>>>>>>>>>>>>>>>>>>>> [Warning] Using a password on the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> command line interface can be insecure>>.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's possible -- if the script was unable to
>>>>>>>>>>>>>>>>>>>>>>>>> connect to the database
>>>>>>>>>>>>>>>>>>>>>>>>> >>> during its execution (e.g. typo in the
>>>>>>>>>>>>>>>>>>>>>>>>> password), that would explain the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> underpopulated Image path and Loris-MRI code
>>>>>>>>>>>>>>>>>>>>>>>>> path you saw in the Config
>>>>>>>>>>>>>>>>>>>>>>>>> >>> module.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's hard to tell without seeing the output
>>>>>>>>>>>>>>>>>>>>>>>>> from your script run -- Did
>>>>>>>>>>>>>>>>>>>>>>>>> >>> you see a sign of any such error?
>>>>>>>>>>>>>>>>>>>>>>>>> >>> The Config fields are populated by the
>>>>>>>>>>>>>>>>>>>>>>>>> imaging_install.sh script (starting
>>>>>>>>>>>>>>>>>>>>>>>>> >>> at line 222
>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222
>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> For example, check if the database connection
>>>>>>>>>>>>>>>>>>>>>>>>> information was populated
>>>>>>>>>>>>>>>>>>>>>>>>> >>> accurately in
>>>>>>>>>>>>>>>>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> If you are referring to the imaging_install.sh
>>>>>>>>>>>>>>>>>>>>>>>>> here is an image with the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> configurations i typed. Maybe the problem is
>>>>>>>>>>>>>>>>>>>>>>>>> somewhere at the last part
>>>>>>>>>>>>>>>>>>>>>>>>> >>> which asks to configure as much as possible
>>>>>>>>>>>>>>>>>>>>>>>>> automatically?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear your LORIS core install is up and
>>>>>>>>>>>>>>>>>>>>>>>>> working and all the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> front-end pages are loading.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$
>>>>>>>>>>>>>>>>>>>>>>>>> chmod 775 project
>>>>>>>>>>>>>>>>>>>>>>>>> >>> > and the web interface worked.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, it's important that project/ have 775
>>>>>>>>>>>>>>>>>>>>>>>>> permissions and that
>>>>>>>>>>>>>>>>>>>>>>>>> >>> lorisadmin be part of the sudoers group, per
>>>>>>>>>>>>>>>>>>>>>>>>> step 1 in the install
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Readme <
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris#install-steps>.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image
>>>>>>>>>>>>>>>>>>>>>>>>> should change LORIS to
>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris, right?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> These imaging paths will be updated during
>>>>>>>>>>>>>>>>>>>>>>>>> your imaging installation
>>>>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup> by
>>>>>>>>>>>>>>>>>>>>>>>>> an automated script --
>>>>>>>>>>>>>>>>>>>>>>>>> >>> you do not need to set them manually via the
>>>>>>>>>>>>>>>>>>>>>>>>> Config module.
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Please continue to follow the Setup Guide
>>>>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup>
>>>>>>>>>>>>>>>>>>>>>>>>> for detailed steps to follow.
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image
>>>>>>>>>>>>>>>>>>>>>>>>> should change LORIS to loris,
>>>>>>>>>>>>>>>>>>>>>>>>> >>> right?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> i used
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x
>>>>>>>>>>>>>>>>>>>>>>>>> | sudo -E bash -
>>>>>>>>>>>>>>>>>>>>>>>>> >>> sudo apt-get install -y nodejs
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> you had suggested in the past, make worked and
>>>>>>>>>>>>>>>>>>>>>>>>> now i can see all the
>>>>>>>>>>>>>>>>>>>>>>>>> >>> contents in the web-interface, but i don't
>>>>>>>>>>>>>>>>>>>>>>>>> need make install?
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>> -------------- next part --------------
>>>>>>>>>>>>>>>>>>>>>>>>> An HTML attachment was scrubbed...
>>>>>>>>>>>>>>>>>>>>>>>>> URL: <
>>>>>>>>>>>>>>>>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html
>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16
>>>>>>>>>>>>>>>>>>>>>>>>> *****************************************
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
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From lingyun.ma at mcin.ca  Thu Jan 30 11:21:52 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Thu, 30 Jan 2020 11:21:52 -0500
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAMpvQ9hNLxz9SZsJwWec_yQ3R4KGhnqv3CDaSPOB1exPsO5AJA@mail.gmail.com>
References: <mailman.1851.1573565332.16403.loris-dev@bic.mni.mcgill.ca>
 <CAEfMBom1HCWLo4NWgt5XG4625tCBfRT_Z_HepvtT_Er2LKbJoA@mail.gmail.com>
 <CAKHj7uS1AdMDjnacouTvxZgziYVgp5NNUeOuMkpDyrTskGTh-Q@mail.gmail.com>
 <CALbt7NDej8FGUUS6_oKbK5Fp-FnwsVz9AgZ6ZcJEZhmoKZmv8w@mail.gmail.com>
 <CAKHj7uSx-qqcXHZsWsZmSJ7sC1DgF+XapT5Y1+QdoVic37_DDg@mail.gmail.com>
 <CAMkiY3fQBGDGeNO8EHxwYAgbhTggNSQ+AVuCfdraDXwULMjjUg@mail.gmail.com>
 <CAKHj7uT5xXi=pOPdH=W9BroSphMHdTszdgW+GxuES=8wZox9eQ@mail.gmail.com>
 <CAMkiY3eUouxaRVdC4wH+vdjeQ=q_Nx8bcDNzcWgD_OgN77m3mw@mail.gmail.com>
 <CAKHj7uSxu4+tm+=x4+qJ1sAbrjmxG2H7LovDb7-2KMnyYQhrgg@mail.gmail.com>
 <CAMkiY3fdPZec2jx-cc2Zq37j3ekmTu_o819yBUv-bC7M98bkVw@mail.gmail.com>
 <CAKHj7uSZHozpuQ_YwGmy6wQ4tm43vJa556V0o2+JGDVsYaqN4g@mail.gmail.com>
 <CAMkiY3dge=x93bQDv0fHGMcrX0PA8Z_imLb_zSTh=nTrx5weFg@mail.gmail.com>
 <CAKHj7uR81gCkjvccMxwMA08dGSEgyTLJBJ+pZPkoUQDtGP_hFA@mail.gmail.com>
 <CAMkiY3fGhvExZ-JOvxeHe7dJQPvtPAHx3oJuiMVX7f1JgF1GAg@mail.gmail.com>
 <CAKHj7uRExO98Yyn9_07aw44wbh0bCL9_C1VFTAURKsxQLUuAeQ@mail.gmail.com>
 <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>
 <CAKHj7uRueb5fgh4VVCAyaq8tC9WM4gJ7k6Q=dxsqWzFgDqPfVQ@mail.gmail.com>
 <CAMkiY3d-Vt=3gQqwJ+GSRSacbLp2QxrB0g-_C7ONd8j_g1ipoQ@mail.gmail.com>
 <CAKHj7uQt9=nokz5g1zBuBx1-rJ8q7qKOuNVkQugC9wfvNFcjVA@mail.gmail.com>
 <CAMkiY3cAuQfT_5iMzYoF2BXVceu_vgz4eCq2sAtoyse+zUYeSg@mail.gmail.com>
 <CAMkiY3dq1O3V8+r4tTAWQ8N=rVFg=DNY-UPeMqbec+MSayj=Cg@mail.gmail.com>
 <CAKHj7uSEegvE1apPBGVyHmjyVzF+YxJjDMg0b+hDE4_-ON+dYw@mail.gmail.com>
 <CAKHj7uRx1NT7CycFq65uFpgPiOVwvT-jtK1NJX6_3rrLNFwdbA@mail.gmail.com>
 <CAMkiY3dAnkLdc4N=REmeCpX2qBfsQf=wRb=YtHtt20f8adXFyw@mail.gmail.com>
 <CAKHj7uRpA-8kzkoEnAk7JBNLP7v4cmK4zW-gMutHESiFGj7xjw@mail.gmail.com>
 <CAMpvQ9hNLxz9SZsJwWec_yQ3R4KGhnqv3CDaSPOB1exPsO5AJA@mail.gmail.com>
Message-ID: <CAMpvQ9gTQUGvmd7E8_Mnk7sd8HtX4NHvLCfWZ0-hEi9aJuu_nw@mail.gmail.com>

Oh, I just found that you are using Loris-mri 21.0, as I stated in the
previous email, the "$_" could not find any matches, so your command might
not be correctly entered.

On Thu, Jan 30, 2020 at 10:35 AM Ling Ma <lingyun.ma at mcin.ca> wrote:

> Hi Sotirios,
>
> By curiosity, I just looked at the error message, "Use of uninitialized
> value $_ in pattern match (m//) at /data/loris/bin/mri/
> batch_uploads_imageuploader.pl line 144." clearly means that there is no
> match, but 144 line has no such code related with $_ in recent versions of
> the batch_uploads_imageuploader.pl. There is something in the line 165
> for a few recent versions.
>
> As to "xargs: file: No such file or directory", it could be due to a
> command unable to find anything using the directory provided as the message
> suggested.
>
> In both cases, I feel that it could be helpful if you provide more details
> such as which Loris_MRI version you are running, what is the exact command
> line you are using to help supporters to understand.
>
> Thanks.
>
> Best regards,
> Ling Ma
> Consultant
>
> On Wed, Jan 29, 2020 at 6:57 PM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> Hi Cecile,
>>
>> it seems that xargs is already installed in our docker container.
>>
>> [image: image.png]
>>
>>
>> ???? ???, 29 ??? 2020 ???? 7:59 ?.?., ?/? Cecile Madjar <
>> cecile.madjar at mcin.ca> ??????:
>>
>>> Hi Sotirios,
>>>
>>> It looks like xargs is not installed in your docker environment.
>>>
>>> This is being used by the following command in dicomTar.pl (and a few
>>> other places but that is the one causing the error at the moment):
>>>
>>> $cmd = "cd " . $dcm_source . "; find -type f -name '.*' | *xargs* rm
>>> -f";
>>>
>>> So you need to install xargs in your docker for the command to run.
>>>
>>> Hope this helps,
>>>
>>> C?cile
>>> On Wed, Jan 29, 2020 at 10:35 AM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>>> Hello,
>>>>
>>>> We are making a dockerized version of Loris 21 and when we execute the
>>>> batch_uploads_imageuploader.pl we get an error about xargs. What could
>>>> be the casue?
>>>>
>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>>>> Running now the following command: /data/loris/data//uploadNeuroDB/
>>>> imaging_upload_file.pl -profile prod -upload_id 13
>>>> /data/incoming/DCC0007_854380_V1.tar.gz -verbose
>>>>
>>>>  find -path \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml -name '__MACOSX'
>>>> -delete
>>>> xargs: file: No such file or directory
>>>>
>>>> dicomTar.pl \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml
>>>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>>>>  Source: /data/tmp/ImagingUpload-15-31-U_O5ml
>>>> Target: /data/loris/data/tarchive
>>>>
>>>> Thanks
>>>>
>>>> ???? ???, 10 ??? 2019 ???? 7:21 ?.?., ?/? Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> ??????:
>>>>
>>>>> Hi,
>>>>>
>>>>> i opened an issue and looked up for the values of Volume they
>>>>> suggested https://github.com/BIC-MNI/minc-toolkit-v2/issues/95. The
>>>>> only attributes associated with it i saw are [0x00089206] and [0x00089207]
>>>>>
>>>>> [image: image.png]
>>>>>
>>>>> I looked up for the file that was being viewed fine in the
>>>>> BrainBrowser and saw that it had that attribute empty so i used this
>>>>> command because i couldn't find a way to modify the attribute via pydicom
>>>>>
>>>>> dcmodify -ma "(0008,9206)=" *.dcm
>>>>>
>>>>> and that command reported the warning about the Endian Syntax. I also
>>>>> used the corresponding command for 9207 and got the message "Tag not found'
>>>>>
>>>>> Lastly I tried to upload some dicoms and now i am getting the SNR and
>>>>> i can view them fine. I believe now that all of them will pass
>>>>> successfully, i will report back later.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Sotirios
>>>>>
>>>>> ???? ???, 9 ??? 2019 ???? 8:10 ?.?., ?/? Cecile Madjar <
>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>
>>>>>> Hi Sotirios,
>>>>>>
>>>>>> The issue you are having is a indeed a dcm2mnc issue. The converter
>>>>>> does not seem to work on your dataset for some reason. Unfortunately, there
>>>>>> is not much we can do on our front to fix this...
>>>>>>
>>>>>> I would recommend creating an issue on the MINC tools repository
>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> so they can fix
>>>>>> your problem.
>>>>>>
>>>>>> Very sorry that you are having that problem.
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> C?cile
>>>>>>
>>>>>> On Wed, Dec 4, 2019 at 8:59 AM Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Sotirios,
>>>>>>>
>>>>>>> Could you please share a dataset with us that produces the error you
>>>>>>> get and the weird display in BrainBrowser? You could use the same SFTP
>>>>>>> credential that Nicolas gave you.
>>>>>>>
>>>>>>> The message errors you got from imaging_install.sh are probably due
>>>>>>> to the fact that you reran the install script and it tried to reinstall
>>>>>>> something that was already there. I would not worry about it. FYI, the only
>>>>>>> thing you needed to do was to update the MINC tools path in the environment
>>>>>>> file as you did after re-running imaging_install.sh and source the
>>>>>>> environment file.
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> C?cile
>>>>>>>
>>>>>>> On Wed, Dec 4, 2019 at 8:03 AM Sotirios Nikoloutsopoulos <
>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>
>>>>>>>>  Hi Cecile,
>>>>>>>>
>>>>>>>> We used minctool 1.9.7 and we still get this error
>>>>>>>>
>>>>>>>> <<Restructuring...
>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>> Default GSL error handler invoked.
>>>>>>>> noise_estimate --snr /data/loris/data>>
>>>>>>>>
>>>>>>>
>>>>>>>> One dicom folder hadn't that error and is being viewed fine in the
>>>>>>>> BrainBrowser of Loris.
>>>>>>>>
>>>>>>>
>>>>>>>> When i used dpkg to the 1.9.17 the installation reported fine
>>>>>>>> <<Unpacking minc-toolkit-v2 (1.9.17) over (1.9.16) ...>>
>>>>>>>>
>>>>>>>> and then i used source /opt/minc/1.9.17/minc-toolkit-config.sh
>>>>>>>>
>>>>>>>> and aftewards runned bash ./imaging_install.sh just to be sure.
>>>>>>>>
>>>>>>>> We also had to modify /data/loris/bin/mri/environment because it
>>>>>>>> still pointed to the old version.
>>>>>>>>
>>>>>>>> What i found strange is this during the run of imaging_install.sh
>>>>>>>>
>>>>>>>> <<already using interpreter
>>>>>>>> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/bin/python3
>>>>>>>> Please use the *system* python to run this script
>>>>>>>> Traceback (most recent call last):
>>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>>>>>>> 2632, in <module>
>>>>>>>>     main()
>>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>>>>>>> 870, in main
>>>>>>>>     symlink=options.symlink,
>>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>>>>>>> 1156, in create_environment
>>>>>>>>     install_python(home_dir, lib_dir, inc_dir, bin_dir,
>>>>>>>> site_packages=site_packages, clear=clear, symlink=symlink)
>>>>>>>>   File
>>>>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>>>>> line 357, in abspath
>>>>>>>>     if not isabs(path):
>>>>>>>>   File
>>>>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>>>>> line 64, in isabs
>>>>>>>>     return s.startswith(sep)
>>>>>>>> AttributeError: 'NoneType' object has no attribute 'startswith'
>>>>>>>> Installing the Python libraries into the loris-mri virtualenv...
>>>>>>>> Requirement already satisfied: mysqlclient in
>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (1.4.4)
>>>>>>>> Requirement already satisfied: mysql-connector in
>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (2.2.9)
>>>>>>>> Requirement already satisfied: pybids in
>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (0.9.4)
>>>>>>>> Requirement already satisfied: nibabel>=2.1 in ./python_virtua>>
>>>>>>>>
>>>>>>>> So should i open an issue for that error? or is there something
>>>>>>>> else to try?
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>>
>>>>>>>> Sotirios
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ???? ???, 3 ??? 2019 ???? 10:39 ?.?., ?/? Cecile Madjar <
>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>
>>>>>>>>> Hi Sotirios,
>>>>>>>>>
>>>>>>>>> Does the pic screenshot in the imaging browser module also shows 1
>>>>>>>>> slice? If so, that would mean there was an issue with the dcm2mnc
>>>>>>>>> conversion. Once again, installing the latest version of the MINC tools
>>>>>>>>> should help but if this issue persists I would recommend creating an issue
>>>>>>>>> for that too on their repository
>>>>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> (if not
>>>>>>>>> already reported there, there are a few known issue reported).
>>>>>>>>>
>>>>>>>>> Other viewer for MINCs are register and Display (both part of the
>>>>>>>>> MINC tools). For NIfTI, you have FSLeye, MRICron and probably many other
>>>>>>>>> viewers that exists.
>>>>>>>>>
>>>>>>>>> Hope this helps,
>>>>>>>>>
>>>>>>>>> C?cile
>>>>>>>>>
>>>>>>>>> On Tue, Dec 3, 2019 at 3:26 PM Sotirios Nikoloutsopoulos <
>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Cecile,
>>>>>>>>>>
>>>>>>>>>> Yes, Nifti files are mandatory for our work. From what we saw at
>>>>>>>>>> a 3rd vm we setted up, the nifti files are being created ( i haven't
>>>>>>>>>> verified if that is the case at the 2nd vm ). I will install the latest
>>>>>>>>>> version and will report back, but do you know any nifti/minc viewer?
>>>>>>>>>> because the Brainbrowser of Loris does not output them well, it's like it
>>>>>>>>>> is loading only 1 slice and we would like to verify it with another tool
>>>>>>>>>> too. We verified that the dcmconv command didn't affect the
>>>>>>>>>> quality of the .dcm files.
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> Sotirios
>>>>>>>>>>
>>>>>>>>>> ???? ???, 2 ??? 2019 ???? 6:59 ?.?., ?/? Cecile Madjar <
>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> It looks like for some reason your binary mnc2nii is not working
>>>>>>>>>>> and reports that error. Do you want to create NIfTI files or are you happy
>>>>>>>>>>> with just the MINC files?
>>>>>>>>>>>
>>>>>>>>>>> If you don't need the NIfTI files, then maybe you can set the
>>>>>>>>>>> Config setting "NIfTI file creation" to No instead of Yes and
>>>>>>>>>>> this error will not appear anymore.
>>>>>>>>>>>
>>>>>>>>>>> If you need the NIfTI files to be created, then I would
>>>>>>>>>>> recommend installing the latest version of the MINC tools (1.9.17). They
>>>>>>>>>>> can be found there:
>>>>>>>>>>>
>>>>>>>>>>>    - pre-built packages:
>>>>>>>>>>>    https://packages.bic.mni.mcgill.ca/minc-toolkit/
>>>>>>>>>>>    - from the source code with installation instructions in the
>>>>>>>>>>>    README: https://github.com/BIC-MNI/minc-toolkit-v2
>>>>>>>>>>>
>>>>>>>>>>> If the problem persists by using the latest release of MINC
>>>>>>>>>>> tools, then create an issue on Github for the MINC developers
>>>>>>>>>>> here <https://github.com/BIC-MNI/minc-toolkit-v2/issues>.
>>>>>>>>>>>
>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>
>>>>>>>>>>> C?cile
>>>>>>>>>>>
>>>>>>>>>>> On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks to Nicholas i was able to create all the mincs images.
>>>>>>>>>>>> The problem was that the files were in Little-Endian-Implicit transfer
>>>>>>>>>>>> syntax and i had to convert them Little-Endian-Explicit transfer syntax
>>>>>>>>>>>> with this command
>>>>>>>>>>>>
>>>>>>>>>>>> find <root_of_my_DICOM_files_directory> -type f | xargs -i
>>>>>>>>>>>> dcmconv --write-xfer-little {} {}
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Looking back at our mails i saw that Little-Endian error had
>>>>>>>>>>>> occurred when i used dcmodify, but i switcthed to using pydicom instead.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> In the output i see an error sometimes about "gsl:
>>>>>>>>>>>> bessel_I0.c:216: ERROR: overflow". Is this okay?
>>>>>>>>>>>>
>>>>>>>>>>>> Restructuring...
>>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>>> noise_estimate --snr
>>>>>>>>>>>> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
>>>>>>>>>>>> SNR is:
>>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>
>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you for the details!
>>>>>>>>>>>>>
>>>>>>>>>>>>> A few things to try:
>>>>>>>>>>>>>
>>>>>>>>>>>>>    - modify the TMPDIR to be on your /data directory where
>>>>>>>>>>>>>    there might be more space to do processing (could create a /data/tmp where
>>>>>>>>>>>>>    the temporary files would be created)
>>>>>>>>>>>>>    - how many files are there for that upload in
>>>>>>>>>>>>>    tarchive_files? Are they different from the ones showing the warning
>>>>>>>>>>>>>    message?
>>>>>>>>>>>>>       - FYI: query to get that: SELECT tf.* FROM
>>>>>>>>>>>>>       tarchive_files tf JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your
>>>>>>>>>>>>>       uploadID> (the output of that query would be very
>>>>>>>>>>>>>       useful if you can provide it)
>>>>>>>>>>>>>       - how many series are there for that upload in
>>>>>>>>>>>>>    tarchive_series?
>>>>>>>>>>>>>    - FYI: query to get that: SELECT ts.* FROM tarchive_series
>>>>>>>>>>>>>       ts JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your uploadID> (the
>>>>>>>>>>>>>       output of that query would be very useful if you can provide it)
>>>>>>>>>>>>>    - things are failing when the scripts try running the
>>>>>>>>>>>>>    following command: find
>>>>>>>>>>>>>    /tmp/TarLoad-23-43-ccugaa/ImagingUpload-23-43-6JCOTO -type f  |
>>>>>>>>>>>>>    /data/loris/bin/mri/dicom-archive/get_dicom_info.pl
>>>>>>>>>>>>>    -studyuid -series -echo -image -file  -attvalue 0018 0024 -series_descr
>>>>>>>>>>>>>    -stdin | sort -n -k1 -k2 -k7 -k3 -k6 -k4  | cut -f 5 | dcm2mnc -dname ''
>>>>>>>>>>>>>    -stdin -clobber -usecoordinates /tmp/TarLoad-23-43-ccugaa
>>>>>>>>>>>>>       - clearly the problems come from get_dicom_info.pl but
>>>>>>>>>>>>>       I cannot pinpoint the error yet. I will ask around and get back to you
>>>>>>>>>>>>>
>>>>>>>>>>>>> If I cannot figure it out remotely, is there a way to have a
>>>>>>>>>>>>> call using zoom? This way you could share your screen with me and run the
>>>>>>>>>>>>> debugger on that script and hopefully we can figure out what is going on
>>>>>>>>>>>>> with those datasets?
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks!
>>>>>>>>>>>>>
>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, Nov 26, 2019 at 5:17 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> In both my virtual machines
>>>>>>>>>>>>>> export TMPDIR=/tmp
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> In both vm also with dcm2mnc i get this output. Just to
>>>>>>>>>>>>>> verify that this passed in my 1st vm and produced mincs.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I attached the spool as a csv.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> And also one difference i found was this in the Loris-mri
>>>>>>>>>>>>>> code ( left 1st workable vm, right 2nd vm that has to be fixed, although i
>>>>>>>>>>>>>> changed it seems to be independent of the uninitialized value $_ )
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> that is puzzling... A few additional questions:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>    - what is the bash variable TMPDIR set to on the
>>>>>>>>>>>>>>>    environment file?
>>>>>>>>>>>>>>>    - could you try running separately dcm2mnc on the DICOM
>>>>>>>>>>>>>>>    folder to see if that works?
>>>>>>>>>>>>>>>    - could you send us the detailed log from the
>>>>>>>>>>>>>>>    notification spool table (SELECT * FROM notification_spool WHERE
>>>>>>>>>>>>>>>    UploadID=<your uploadID>) and send it back to us? Maybe there are some
>>>>>>>>>>>>>>>    additional clues that could help figuring out what is going on.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thank you!
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Tue, Nov 26, 2019 at 10:12 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I checked for the StudyInstacueUID at the files with "The
>>>>>>>>>>>>>>>> target directory does not contain a single DICOM file"" and their attribute
>>>>>>>>>>>>>>>> has a value.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Regarding the scouter and localizer, i modified the
>>>>>>>>>>>>>>>> settings in the imaging pipeline and now i don't get that error message,
>>>>>>>>>>>>>>>> but still it doesn't create the mnics.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> The errors i am getting are ( uninitialized value $_ is not
>>>>>>>>>>>>>>>> important? because i haven't got comments about that )
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line
>>>>>>>>>>>>>>>> 144.
>>>>>>>>>>>>>>>> Running now the following command:
>>>>>>>>>>>>>>>> /data/loris/data//uploadNeuroDB/imaging_upload_file.pl
>>>>>>>>>>>>>>>> -profile prod -upload_id 134 /data/incoming/DCC0025_118008_V1.tar.gz
>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> and
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Number of MINC files that will be considered for inserting
>>>>>>>>>>>>>>>> into the database: 0
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> No data could be converted into valid MINC files.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> The tarchiveLoader.pl insertion script has failed.
>>>>>>>>>>>>>>>> Use of uninitialized value $mail_user in concatenation (.)
>>>>>>>>>>>>>>>> or string at /data/loris/bin/mri/
>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line
>>>>>>>>>>>>>>>> 249.
>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 250.
>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 251.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> OK. So the issue I mentioned should not be a problem for
>>>>>>>>>>>>>>>>> you.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Is the StudyInstanceUID DICOM header set in your images?
>>>>>>>>>>>>>>>>> If it is not set, then you would end up with the error message "The target
>>>>>>>>>>>>>>>>> directory does not contain a single DICOM file". So maybe this is the issue
>>>>>>>>>>>>>>>>> you are having with those datasets?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Regarding not excluding series descriptions, you can
>>>>>>>>>>>>>>>>> configure that in the Config module under the Imaging Pipeline section.
>>>>>>>>>>>>>>>>> Simply remove all entries for the "Series description to exclude from
>>>>>>>>>>>>>>>>> imaging insertion" setting.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Mon, Nov 25, 2019 at 9:58 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> We are using this version
>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/archive/v21.0.0.zip. Is it
>>>>>>>>>>>>>>>>>> possible to insert low resolution now?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, <
>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Which version of LORIS-MRI are you using?
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> There was a bug that got resolved in 20.2 in
>>>>>>>>>>>>>>>>>>> get_dicom_info.pl. Basically, if a DICOM did not have
>>>>>>>>>>>>>>>>>>> the (0020,0032) header, get_dicom_info.pl considered
>>>>>>>>>>>>>>>>>>> that the file was not a DICOM, which was a mistake. This got fixed in
>>>>>>>>>>>>>>>>>>> version 20.2 of LORIS-MRI. Hopefully this is the issue you are encountering.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> About scout and localizer, they are a type of short and
>>>>>>>>>>>>>>>>>>> low resolution sequence that is used by the tech but is of no interest
>>>>>>>>>>>>>>>>>>> scientifically, which is why we tend to no insert them.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios
>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> i executed the find command and the output i got per
>>>>>>>>>>>>>>>>>>>> folder was "DICOM medical imaging data. Maybe there is something wrong with
>>>>>>>>>>>>>>>>>>>> the find command in the warning that it is unable to check if the file is a
>>>>>>>>>>>>>>>>>>>> dicom file? Also when i use get_dicom_info.pl i don't
>>>>>>>>>>>>>>>>>>>> get any output data. Finally i don't understand what scout or localizer is
>>>>>>>>>>>>>>>>>>>> ( something like if and only if a file fails then the whole session is
>>>>>>>>>>>>>>>>>>>> invalid? ).
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar
>>>>>>>>>>>>>>>>>>>> <cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> I took a closer look to the
>>>>>>>>>>>>>>>>>>>>> batch_uploader_multiple_output.txt file you sent. It looks like there are
>>>>>>>>>>>>>>>>>>>>> different reasons for failure depending on the DICOM folder uploaded.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>    - For 465466 DCC0000 V1; 727195 DCC0004 V1 and
>>>>>>>>>>>>>>>>>>>>>    684908 DCC0007 V1: it looks like there is no file of type DICOM in the
>>>>>>>>>>>>>>>>>>>>>    folder. Have you checked to see if that is indeed the case? Maybe you can
>>>>>>>>>>>>>>>>>>>>>    try running the following command on that folder to see what are the types
>>>>>>>>>>>>>>>>>>>>>    of the files? If it does not return at least one DICOM medical imaging data
>>>>>>>>>>>>>>>>>>>>>    file, then that is why you get the error message from the pipeline:
>>>>>>>>>>>>>>>>>>>>>       -
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>       find <my_dicom_archive_root_folder> -type f | xargs -i file {}|cut -d: -f2|sort|uniq
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>       - For 864173 DCC0001 V1: it looks like there
>>>>>>>>>>>>>>>>>>>>>    are two different DICOM studies within the same folder. You will need to
>>>>>>>>>>>>>>>>>>>>>    split that study in two based on the StudyUID field as the insertion
>>>>>>>>>>>>>>>>>>>>>    pipeline does not allow for more than one StudyUID per upload.
>>>>>>>>>>>>>>>>>>>>>    - For 890807 DCC0002 V1; 637025 DCC0005 V1 and
>>>>>>>>>>>>>>>>>>>>>    239975 DCC0006 V1: it looks like the dcm2mnc command did not produce any
>>>>>>>>>>>>>>>>>>>>>    MINC files. Can you check in the DICOM archive what are the series present
>>>>>>>>>>>>>>>>>>>>>    in the tarchive for that visit? Maybe only a scout or localizer was
>>>>>>>>>>>>>>>>>>>>>    acquired for that session, hence the no valid MINC files (scout and
>>>>>>>>>>>>>>>>>>>>>    localizer being skipped for the conversion)
>>>>>>>>>>>>>>>>>>>>>    - For 397410 DCC0003 V1: it looks like everything
>>>>>>>>>>>>>>>>>>>>>    went well for this one.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> One script that is called by our pipeline is called
>>>>>>>>>>>>>>>>>>>>> get_dicom_info.pl and this does all kind of checks on
>>>>>>>>>>>>>>>>>>>>> the DICOM files (it is being called when running the dcm2mnc conversion).
>>>>>>>>>>>>>>>>>>>>> You could run it independently on your folder if needed.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Since one of the study got in, it does not look like
>>>>>>>>>>>>>>>>>>>>> you are having a problem with the setup. It seems more likely to be a
>>>>>>>>>>>>>>>>>>>>> problem with the data themselves.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Hope this helps.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios
>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> In my first vm i am able to create the minc files and
>>>>>>>>>>>>>>>>>>>>>> view them at the mri browser (except of candidate 102761034 ), meanwhile
>>>>>>>>>>>>>>>>>>>>>> the same files gives warnings at the 2nd vm. The output  of the batch
>>>>>>>>>>>>>>>>>>>>>> upload can be seen in the file attached.
>>>>>>>>>>>>>>>>>>>>>> Also a colleague of us has built a pre-validation
>>>>>>>>>>>>>>>>>>>>>> tool for dicom
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/
>>>>>>>>>>>>>>>>>>>>>> which had found all the files that Loris gave as warning . Basically I
>>>>>>>>>>>>>>>>>>>>>> confirmed that the total amount of files per dicom was the same amount as
>>>>>>>>>>>>>>>>>>>>>> stated in Loris and checked some filenames given from warning to confirm
>>>>>>>>>>>>>>>>>>>>>> that they match with our tool. But that was months ago and my colleague had
>>>>>>>>>>>>>>>>>>>>>> changed some parameters for MIP and now our tool doesn't find all the
>>>>>>>>>>>>>>>>>>>>>> invalid files, that's why i asked for the dicom header specification of
>>>>>>>>>>>>>>>>>>>>>> Loris. In a discussion we had he mentioned that he doesn't check for some
>>>>>>>>>>>>>>>>>>>>>> tags e.x. orientation. Lastly to mention that in my first vm i didn't use
>>>>>>>>>>>>>>>>>>>>>> our tool to remove invalid dcm files.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>> Can you provide us with some fresh particulars of
>>>>>>>>>>>>>>>>>>>>>>> the current issue and we'll take it from there?
>>>>>>>>>>>>>>>>>>>>>>> Yang's team has built these scripts which can
>>>>>>>>>>>>>>>>>>>>>>> definitely serve as a model for your pre-validation of your DICOM
>>>>>>>>>>>>>>>>>>>>>>> collections.
>>>>>>>>>>>>>>>>>>>>>>> cheers,
>>>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> HI Yang,
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> We make use of pydicom library too. Now about the
>>>>>>>>>>>>>>>>>>>>>>>> validate.py i see that you check if some attributes are missing such as
>>>>>>>>>>>>>>>>>>>>>>>> PatientID, PatientName which all of our files contains that info. Maybe i
>>>>>>>>>>>>>>>>>>>>>>>> have missed something on the setup of my other virtual machine ( although
>>>>>>>>>>>>>>>>>>>>>>>> one dicom passed on the new vm successfully, the others that were inserted
>>>>>>>>>>>>>>>>>>>>>>>> correctly on my old vm fails on the new one ), i think that i had asked
>>>>>>>>>>>>>>>>>>>>>>>> about this error "Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>> line 144." but i don't remember the solution.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding
>>>>>>>>>>>>>>>>>>>>>>>> <it at cnbp.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Hey, Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Christine from the LORIS team mentioned you had
>>>>>>>>>>>>>>>>>>>>>>>>> some issue with DICOM.  I am a fellow developer for an external project
>>>>>>>>>>>>>>>>>>>>>>>>> using LORIS, kind of just like you. We had to implement DICOM upload as
>>>>>>>>>>>>>>>>>>>>>>>>> well but more as a fully automated pipeline actually.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> While we were building CNBP, we had coded up some
>>>>>>>>>>>>>>>>>>>>>>>>> minor Python functions to check DICOM integrity (and simple validations)
>>>>>>>>>>>>>>>>>>>>>>>>> and you might be able to gain some inspiration from it and help you with
>>>>>>>>>>>>>>>>>>>>>>>>> your cause. For more comprehensive solution, PyDICOM (
>>>>>>>>>>>>>>>>>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#)  seems
>>>>>>>>>>>>>>>>>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks
>>>>>>>>>>>>>>>>>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can
>>>>>>>>>>>>>>>>>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty
>>>>>>>>>>>>>>>>>>>>>>>>> rough around the edges but hopefully point you in the right direcitons
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Yang Ding, PhD.
>>>>>>>>>>>>>>>>>>>>>>>>> Canadian Neonatal Brain Platform Architect
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM <
>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Send Loris-dev mailing list submissions to
>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> To subscribe or unsubscribe via the World Wide
>>>>>>>>>>>>>>>>>>>>>>>>>> Web, visit
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>> or, via email, send a message with subject or
>>>>>>>>>>>>>>>>>>>>>>>>>> body 'help' to
>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-request at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> You can reach the person managing the list at
>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-owner at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> When replying, please edit your Subject line so
>>>>>>>>>>>>>>>>>>>>>>>>>> it is more specific
>>>>>>>>>>>>>>>>>>>>>>>>>> than "Re: Contents of Loris-dev digest..."
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Today's Topics:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>    1. Re: Import mri - scripts (Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos)
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Message: 1
>>>>>>>>>>>>>>>>>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200
>>>>>>>>>>>>>>>>>>>>>>>>>> From: Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>> To: Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>>>>> Message-ID:
>>>>>>>>>>>>>>>>>>>>>>>>>>         <CAKHj7uST=
>>>>>>>>>>>>>>>>>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com
>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Could we send you a link with 10 anonymized dicom
>>>>>>>>>>>>>>>>>>>>>>>>>> files to diagnose the
>>>>>>>>>>>>>>>>>>>>>>>>>> warnings we get?
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> > Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>> > We were wondering whether Loris has a tool to
>>>>>>>>>>>>>>>>>>>>>>>>>> check if there are problems
>>>>>>>>>>>>>>>>>>>>>>>>>> > with the dcm files, before trying to upload
>>>>>>>>>>>>>>>>>>>>>>>>>> them. Something that could
>>>>>>>>>>>>>>>>>>>>>>>>>> > provide the same results provided in the
>>>>>>>>>>>>>>>>>>>>>>>>>> warning_output, this is the
>>>>>>>>>>>>>>>>>>>>>>>>>> > summary from the mri_upload at the front-page.
>>>>>>>>>>>>>>>>>>>>>>>>>> Also which attributes of the
>>>>>>>>>>>>>>>>>>>>>>>>>> > dcm header would trigger a warning? is there a
>>>>>>>>>>>>>>>>>>>>>>>>>> dcm file header
>>>>>>>>>>>>>>>>>>>>>>>>>> > specification for Loris?
>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>> > Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>> > Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> > sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp
>>>>>>>>>>>>>>>>>>>>>>>>>> function it worked,but i
>>>>>>>>>>>>>>>>>>>>>>>>>> >> thought that something else was causing the
>>>>>>>>>>>>>>>>>>>>>>>>>> 2nd issue.
>>>>>>>>>>>>>>>>>>>>>>>>>> >> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours
>>>>>>>>>>>>>>>>>>>>>>>>>> Boucher, Mr, <
>>>>>>>>>>>>>>>>>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The first error occurs because the
>>>>>>>>>>>>>>>>>>>>>>>>>> QCFirstChangeTime and columns are of
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> type `unsigned integer` and not `datatime`.
>>>>>>>>>>>>>>>>>>>>>>>>>> You should be using
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW().
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The second error occurs because the trigger
>>>>>>>>>>>>>>>>>>>>>>>>>> triggers a rollback of the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> insert statement in the files table.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> See mysql documentation for trigger error
>>>>>>>>>>>>>>>>>>>>>>>>>> handling.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> An error during either a BEFORE or AFTER
>>>>>>>>>>>>>>>>>>>>>>>>>> trigger results in failure of
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the entire statement that caused trigger
>>>>>>>>>>>>>>>>>>>>>>>>>> invocation.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you for sharing that. I hope it helps.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Xavier
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on
>>>>>>>>>>>>>>>>>>>>>>>>>> behalf of Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> When mincs are inserted their corresponding
>>>>>>>>>>>>>>>>>>>>>>>>>> rows at the file table are
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> inserted too
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i would like to insert their rows at
>>>>>>>>>>>>>>>>>>>>>>>>>> file_qcstatus as well, because i
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> don't want manually to label them as passed
>>>>>>>>>>>>>>>>>>>>>>>>>> throught the interface
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> That is the trigger i wrote
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER
>>>>>>>>>>>>>>>>>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> BEGIN
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT INTO files_qcstatus
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SET FileID = NEW.FileID,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      SeriesUID = NEW.SeriesUID,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      EchoTime = NEW.EchoTime,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCStatus = "Pass",
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCFirstChangeTime = NOW(),
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCLastChangeTime = NOW();
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> END
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> although it contains some errors
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range value
>>>>>>>>>>>>>>>>>>>>>>>>>> for column
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or
>>>>>>>>>>>>>>>>>>>>>>>>>> update a child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails
>>>>>>>>>>>>>>>>>>>>>>>>>> (`LORIS`.`parameter_file`, CONSTRAINT
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`)
>>>>>>>>>>>>>>>>>>>>>>>>>> REFERENCES `files` (`FileID`))
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> In the mri_upload table, there is a
>>>>>>>>>>>>>>>>>>>>>>>>>> TarchiveID column associated with
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the MRI upload you inserted. When this value
>>>>>>>>>>>>>>>>>>>>>>>>>> is NULL, it means no DICOMs
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> were inserted into the tarchive tables. At
>>>>>>>>>>>>>>>>>>>>>>>>>> the end of the insertion of the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DICOMs in the tarchive tables, this value is
>>>>>>>>>>>>>>>>>>>>>>>>>> updated with the correct
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> TarchiveID associated with the upload.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Could this correspond to what you want to do?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Regarding the files_qcstatus, this table is
>>>>>>>>>>>>>>>>>>>>>>>>>> only linked to the files
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> table (hence, the MINC files). You could
>>>>>>>>>>>>>>>>>>>>>>>>>> always create a new table for
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive
>>>>>>>>>>>>>>>>>>>>>>>>>> table?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i would like whenever a dicom is imported to
>>>>>>>>>>>>>>>>>>>>>>>>>> mark all their
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> coressponding qc_status to "pass". I was
>>>>>>>>>>>>>>>>>>>>>>>>>> thinking of creating a trigger for
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that, but which tables do i need to add
>>>>>>>>>>>>>>>>>>>>>>>>>> entries to? So far from what i see
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i need to add entres at  the table "files"
>>>>>>>>>>>>>>>>>>>>>>>>>> whenever an insertion happens to
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> files_qcstatus.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Oh, sorry i should have asked for StudyID, at
>>>>>>>>>>>>>>>>>>>>>>>>>> the beginning of my email
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID).
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that's the Study Instance UID, not the
>>>>>>>>>>>>>>>>>>>>>>>>>> StudyID. So the StudyID i am
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looking for is not stored in the database?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The StudyUID is stored in the DicomArchiveID
>>>>>>>>>>>>>>>>>>>>>>>>>> field of the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> tarchive table. It can also be found in the
>>>>>>>>>>>>>>>>>>>>>>>>>> metadata field but it is mixed
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> with many other information.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is StudyUID stored somewhere at the tables?
>>>>>>>>>>>>>>>>>>>>>>>>>> At the tarchive table,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> specifically at the AcquisitonMetadata column
>>>>>>>>>>>>>>>>>>>>>>>>>> i found something called
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 'Unique Study ID" in its context, but that
>>>>>>>>>>>>>>>>>>>>>>>>>> must be the Study Instance UID.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Your observation is correct. A little
>>>>>>>>>>>>>>>>>>>>>>>>>> explanation below.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> MINC files get inserted into the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>> violation tables if:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - the scan type could not be identified
>>>>>>>>>>>>>>>>>>>>>>>>>> (not matching an entry in
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - one parameter of the scan type is out of
>>>>>>>>>>>>>>>>>>>>>>>>>> the expected range
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    present in the mri_protocol_checks (extra
>>>>>>>>>>>>>>>>>>>>>>>>>> filtering in case you need to be
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    stricker on some parameters not present in
>>>>>>>>>>>>>>>>>>>>>>>>>> the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - if the CandID and PSCID do not match
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The following cases do not get in the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>> violation tables as it happens
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> before the conversion of the DICOM to MINC
>>>>>>>>>>>>>>>>>>>>>>>>>> files and only MINC files
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> violations are logged there:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - "No single DICOM" (since no valid DICOM
>>>>>>>>>>>>>>>>>>>>>>>>>> could be found to convert
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    to MINC)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - "Study already inserted" (duplicate
>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID) since this error
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    happens at the dicomTar.pl level (way
>>>>>>>>>>>>>>>>>>>>>>>>>> before conversion into MINC files)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad everything is working out!!
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the mri passed, for some reason it consumed
>>>>>>>>>>>>>>>>>>>>>>>>>> 5.12GB of ram. Now about the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations, dicoms are triggered to be
>>>>>>>>>>>>>>>>>>>>>>>>>> inserted there only if there is
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general
>>>>>>>>>>>>>>>>>>>>>>>>>> for its header parameter?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Because i don't see the cases of 'No single
>>>>>>>>>>>>>>>>>>>>>>>>>> dicom" or with the 2 studyiuid
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to be there.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sorry to hear you are having issues with the
>>>>>>>>>>>>>>>>>>>>>>>>>> memory. I think most of our
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB
>>>>>>>>>>>>>>>>>>>>>>>>>> you should be fine.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> about that dicom that had that insertion
>>>>>>>>>>>>>>>>>>>>>>>>>> error it's about 30mb and when
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> it is being processed the ram is being
>>>>>>>>>>>>>>>>>>>>>>>>>> drastically increased from 2gb to
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3.28 and then the whole virtual machine is
>>>>>>>>>>>>>>>>>>>>>>>>>> frozen. What is the recommended
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> size of ram for using Loris?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to see that the StudyUID problem was
>>>>>>>>>>>>>>>>>>>>>>>>>> fixed!
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the delete script issue, if you are
>>>>>>>>>>>>>>>>>>>>>>>>>> absolutely certain that no
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> processes are run for that uploadID, you can
>>>>>>>>>>>>>>>>>>>>>>>>>> update the mri_upload table
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and set the column Inserting to 0 instead of
>>>>>>>>>>>>>>>>>>>>>>>>>> 1 for that uploadID. It
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looks like for some reason the scripts did
>>>>>>>>>>>>>>>>>>>>>>>>>> not update this field when it
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> stopped the insertion. Not sure why that
>>>>>>>>>>>>>>>>>>>>>>>>>> would be the case though.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Note: only do that update if you are certain
>>>>>>>>>>>>>>>>>>>>>>>>>> that there is no processing
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> happening.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> about the Dicoms i reported that didn't have
>>>>>>>>>>>>>>>>>>>>>>>>>> a StudyID they actually do
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I thought that this might be a permission
>>>>>>>>>>>>>>>>>>>>>>>>>> because "w" was missing at the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> group. After using chmod -R 775 only
>>>>>>>>>>>>>>>>>>>>>>>>>> 102809579 passed, but with no mnic
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> files. Also now i have this error
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox
>>>>>>>>>>>>>>>>>>>>>>>>>> :/data/loris/bin/mri/tools$
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34
>>>>>>>>>>>>>>>>>>>>>>>>>> -ignore
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is
>>>>>>>>>>>>>>>>>>>>>>>>>> currently processing it.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How can solve this?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Here is our auto dicom uploading python
>>>>>>>>>>>>>>>>>>>>>>>>>> script:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To give you a brief idea:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Per folder it will:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 1) Delete all the .bak files
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 2) Locate .dcm files and update the Patient
>>>>>>>>>>>>>>>>>>>>>>>>>> header
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3) Furthermore we are interesting in finding
>>>>>>>>>>>>>>>>>>>>>>>>>> TR_min, TR_max, TE_min,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> TE_max parameters of T1 protocol and do an
>>>>>>>>>>>>>>>>>>>>>>>>>> update at the mri_protocol table
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For some reason some files are missing
>>>>>>>>>>>>>>>>>>>>>>>>>> SeriesDescription/ProtocolName
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> In total i have 7 folders
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3/7 passed
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Also about the first patient with DC0000 had
>>>>>>>>>>>>>>>>>>>>>>>>>> a violation "T1 AXIAL SE
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> GADO", but my script didn't output a TE of 17
>>>>>>>>>>>>>>>>>>>>>>>>>> nowhere and i find that weird
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> since Loris detects the SeriesDescription.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Now about the 4/7 that didn't passed
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 102327840 and 102809579 outputs "The target
>>>>>>>>>>>>>>>>>>>>>>>>>> directory does not contain a
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> single DICOM file.", therefore they are
>>>>>>>>>>>>>>>>>>>>>>>>>> missing their StudyUID
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it
>>>>>>>>>>>>>>>>>>>>>>>>>> with data from multiple
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> studies."
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and 102761034 "No data could be converted
>>>>>>>>>>>>>>>>>>>>>>>>>> into valid MINC files.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> localizer, scout will not be considered!"
>>>>>>>>>>>>>>>>>>>>>>>>>> What is this?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If i wanted to force the insertion of
>>>>>>>>>>>>>>>>>>>>>>>>>> 102327840, 102809579 and 102506134
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> can i just pass a flag parameter to
>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl? or
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> modify imaging_upload_file.pl?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PS
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To diagnose a folder search the name of the
>>>>>>>>>>>>>>>>>>>>>>>>>> folder at dicom_output.txt.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear about your progress.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, the script you used to delete imaging
>>>>>>>>>>>>>>>>>>>>>>>>>> data is fully documented here
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- let us know if you didn't find the answers
>>>>>>>>>>>>>>>>>>>>>>>>>> you were looking for there.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (Is it possible the null row in *mri_scanner*
>>>>>>>>>>>>>>>>>>>>>>>>>> seen in your database
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> management software is a visual placeholder
>>>>>>>>>>>>>>>>>>>>>>>>>> for you as the user?  I'm not
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sure why a scanner would ever be registered
>>>>>>>>>>>>>>>>>>>>>>>>>> with ID='0' as your screenshot
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> showed.)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I fixed it with this
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I tried to create a new candidate using the
>>>>>>>>>>>>>>>>>>>>>>>>>> API, is there something
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> wrong with the structure? why did i receive a
>>>>>>>>>>>>>>>>>>>>>>>>>> 500 internal error? In the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-error log it state that there is
>>>>>>>>>>>>>>>>>>>>>>>>>> something wrong with token, but i
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> verfied that the type of the token is a
>>>>>>>>>>>>>>>>>>>>>>>>>> string.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019]
>>>>>>>>>>>>>>>>>>>>>>>>>> [php7:error] [pid 4535] [client
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error:  Uncaught
>>>>>>>>>>>>>>>>>>>>>>>>>> TypeError: Argument 1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate()
>>>>>>>>>>>>>>>>>>>>>>>>>> must be of the type string,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> null given, called in
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> defined in
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> trace:\n#0
>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> NDB_Client->initialize('/var/www/loris/...')\n#3
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST',
>>>>>>>>>>>>>>>>>>>>>>>>>> Array)\n#5 {main}\n  thrown in
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is there a way also to delete candidates?
>>>>>>>>>>>>>>>>>>>>>>>>>> Just to let you know what i
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> did to clear candidates, because maybe i may
>>>>>>>>>>>>>>>>>>>>>>>>>> have missed dependencies.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> First i deleted all their uploads
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc
>>>>>>>>>>>>>>>>>>>>>>>>>> ( is there a way to omit
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the backup file ? )
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Afterwards i had some scanner candidates, so
>>>>>>>>>>>>>>>>>>>>>>>>>> i deleted all the entries
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> from mri_scanner except that i couldn't
>>>>>>>>>>>>>>>>>>>>>>>>>> delete this entry with the 0 ID.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Lastly i deleted the session and then the
>>>>>>>>>>>>>>>>>>>>>>>>>> candidate table.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> We recommend that you use our existing tools
>>>>>>>>>>>>>>>>>>>>>>>>>> for creating new candidates
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> - either the LORIS API or if you are using a
>>>>>>>>>>>>>>>>>>>>>>>>>> PHP script, by calling the Candidate
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> class's createNew()
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200
>>>>>>>>>>>>>>>>>>>>>>>>>> >function.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> These will create the necessary records for
>>>>>>>>>>>>>>>>>>>>>>>>>> you.  (It's not recommended to
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> make direct modifications to mysql database
>>>>>>>>>>>>>>>>>>>>>>>>>> tables in your script, if I
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> understand you.)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The CandID should be a randomized 6 digit
>>>>>>>>>>>>>>>>>>>>>>>>>> randomized ID, and there are
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> multiple reasons for this.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You can use the PSCID for project-specific
>>>>>>>>>>>>>>>>>>>>>>>>>> IDs and the External ID field
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> in the candidate table can also be used for
>>>>>>>>>>>>>>>>>>>>>>>>>> any values you like.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Additionally, any number of custom IDs can be
>>>>>>>>>>>>>>>>>>>>>>>>>> added in parallel - these
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> are entered/visible in the Candidate
>>>>>>>>>>>>>>>>>>>>>>>>>> Information module and added in the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> back-end as candidate parameters.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> We are building a script that will auto
>>>>>>>>>>>>>>>>>>>>>>>>>> insert the candidates based on
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> their ExternalID. We would like to know
>>>>>>>>>>>>>>>>>>>>>>>>>> whethere when we are creating a new
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> profile in the candidate table, if we also
>>>>>>>>>>>>>>>>>>>>>>>>>> have to insert a new record at
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> another table? Furthermore is there a problem
>>>>>>>>>>>>>>>>>>>>>>>>>> that in our case CandID won't
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> be a 6digit? ( should we start it from
>>>>>>>>>>>>>>>>>>>>>>>>>> 100000?)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> That would normally be the case but the
>>>>>>>>>>>>>>>>>>>>>>>>>> numeric part of the PSCID get
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> paded with 0 on the left.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ex. for sequential ID made of center ID of
>>>>>>>>>>>>>>>>>>>>>>>>>> `ABC` plus 4 numerical char
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> with a min value of 1, the sequence would be:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0001
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0002
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0010
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> thus sorting them ascending will always get
>>>>>>>>>>>>>>>>>>>>>>>>>> the latest value generated
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> as the max value.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>> melanie.legault2 at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I see, although the PSCID value is
>>>>>>>>>>>>>>>>>>>>>>>>>> varchar(255), it must be stored
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> within a specific length of characters.
>>>>>>>>>>>>>>>>>>>>>>>>>> Otherwise if we were to sort
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> strings with different lengths the result
>>>>>>>>>>>>>>>>>>>>>>>>>> would not be sorted correctly (
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1,
>>>>>>>>>>>>>>>>>>>>>>>>>> 10, 11, 2 ).
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hello Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> There is no `last value` stored anywhere.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The code simply look for the PSCID with the
>>>>>>>>>>>>>>>>>>>>>>>>>> max value and increase that
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> value by 1 in order to generate the next
>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this info help.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie Legault | Software developer |
>>>>>>>>>>>>>>>>>>>>>>>>>> Faculty of Medicine | McGill
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> University
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on
>>>>>>>>>>>>>>>>>>>>>>>>>> behalf of Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> how does Loris determine the next available
>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID value for a new
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate?
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> e.x in the default case the PSCID is
>>>>>>>>>>>>>>>>>>>>>>>>>> sequential, but where do we store the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> last value for the sequential sequence?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the parameters in the mri_protocol you have
>>>>>>>>>>>>>>>>>>>>>>>>>> assigned are global
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> standard? or were assigned after trial and
>>>>>>>>>>>>>>>>>>>>>>>>>> error?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Given you have done the initial setup of your
>>>>>>>>>>>>>>>>>>>>>>>>>> tables to match your
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> intended protocol/parameters according to
>>>>>>>>>>>>>>>>>>>>>>>>>> instructions --
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the Troubleshooting guide documentation
>>>>>>>>>>>>>>>>>>>>>>>>>> recommends
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes
>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> re-running the pipeline (and first deleting
>>>>>>>>>>>>>>>>>>>>>>>>>> prior uploads).
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *if i were to change their status to resolve
>>>>>>>>>>>>>>>>>>>>>>>>>> what would happen?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I noticed that i can view the mnics at the
>>>>>>>>>>>>>>>>>>>>>>>>>> brainbrowser from the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations page ( those mnics are stored
>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/loris/data/trashbin/
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> if i were to click their issue to resolve
>>>>>>>>>>>>>>>>>>>>>>>>>> what would happend? would they
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> appear in the dicom_archive view too? ).
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The defaut values of the schema exists in my
>>>>>>>>>>>>>>>>>>>>>>>>>> local database. If i adjust
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the default values of TR_min and TE_min the
>>>>>>>>>>>>>>>>>>>>>>>>>> mincs will be uploaded?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is it possible that you haven't set up your
>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table ?   (and
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_scan_type table too, for additional types
>>>>>>>>>>>>>>>>>>>>>>>>>> of scans)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Like the psc table, this is a pre-requisite
>>>>>>>>>>>>>>>>>>>>>>>>>> for the Imaging insertion
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> setup : See the install/setup documentation :
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To add new rows, just use MySQL insert
>>>>>>>>>>>>>>>>>>>>>>>>>> statements.  You can adapt the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> insert statements which load the default
>>>>>>>>>>>>>>>>>>>>>>>>>> table values --> e.g. Here on
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> GitHub :
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (see also the mri_scan_type table)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I see that i can edit the values but not how
>>>>>>>>>>>>>>>>>>>>>>>>>> to insert new rows.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If i choose Inserted with flag then will the
>>>>>>>>>>>>>>>>>>>>>>>>>> minc be inserted?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear that *dcmodify* worked correctly.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the MRI Violations module, the screenshot
>>>>>>>>>>>>>>>>>>>>>>>>>> is enough.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It says "could not identify scan type", which
>>>>>>>>>>>>>>>>>>>>>>>>>> we knew already.  Did you
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> click on the link on those words?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It will take you to the next page of the
>>>>>>>>>>>>>>>>>>>>>>>>>> module, showing for each scan
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> what the scan parameters were, and will also
>>>>>>>>>>>>>>>>>>>>>>>>>> show for comparison what's
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> stored in your *mri_protocol* table.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Compare these values to find which parameter
>>>>>>>>>>>>>>>>>>>>>>>>>> was not correct according
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to your *mri_protocol* table scan type
>>>>>>>>>>>>>>>>>>>>>>>>>> definitions.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You may end up broadening your mri_protocol
>>>>>>>>>>>>>>>>>>>>>>>>>> value ranges (e.g. TR, TE)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> for scans.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> This can be done in the front-end, by editing
>>>>>>>>>>>>>>>>>>>>>>>>>> the database table
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> directly in the same subpage of the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>> Violations module.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The MRI Violations module features are
>>>>>>>>>>>>>>>>>>>>>>>>>> explained in more detail in the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Help text for this module inside LORIS (click
>>>>>>>>>>>>>>>>>>>>>>>>>> the  ["?"] icon in the menu
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> bar.)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> :  no MINCs inserted- violated scans
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looks like my previous email's attachment
>>>>>>>>>>>>>>>>>>>>>>>>>> wasn't delivered due to
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> security reasons, i uploaded my file at
>>>>>>>>>>>>>>>>>>>>>>>>>> google drive
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> From Dicat's view seems that dcmodify worked
>>>>>>>>>>>>>>>>>>>>>>>>>> in both cases
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the mri_violations i attached the .html
>>>>>>>>>>>>>>>>>>>>>>>>>> output from webbrowser, so
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that you can check the filelds easier.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios --
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Great, sounds like more progress.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> About the dcmodify command -- I'm not sure
>>>>>>>>>>>>>>>>>>>>>>>>>> why you're getting an Endian
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> warning.  (it's a warning not an error,
>>>>>>>>>>>>>>>>>>>>>>>>>> correct?)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To clarify -- Were the DICOM headers
>>>>>>>>>>>>>>>>>>>>>>>>>> (PatientName) all successfully
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> relabelled, after the command ran?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You can use also our DICAT tool (
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/DICAT) to
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> verify and/or update local DICOM headers --
>>>>>>>>>>>>>>>>>>>>>>>>>> though your dcmodify command is
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a great and fast solution for bulk header
>>>>>>>>>>>>>>>>>>>>>>>>>> updates.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If you're concerned about fields being
>>>>>>>>>>>>>>>>>>>>>>>>>> changed (e.g. "(2001,105f)" from
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the warning message)  - you can also dcmdump
>>>>>>>>>>>>>>>>>>>>>>>>>> a DICOM slice before and look
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at these fields specifically.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's also not a bad "sanity check" to backup
>>>>>>>>>>>>>>>>>>>>>>>>>> your DICOMS before/after
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> running dcmodify, and use dcmdump on each
>>>>>>>>>>>>>>>>>>>>>>>>>> version to diff the outputs --
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> this will pinpoint what changed.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Re the protocol violation --
>>>>>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol not recognized or
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> unknown :   this means your scans did not
>>>>>>>>>>>>>>>>>>>>>>>>>> match what is stored in your
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_protocol table.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Check the MRI Violations front-end module --
>>>>>>>>>>>>>>>>>>>>>>>>>> can you see why they didn't
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> match?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Send us an example, in addition to the
>>>>>>>>>>>>>>>>>>>>>>>>>> contents of the mri_protocol
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> table, if you can't find the source of the
>>>>>>>>>>>>>>>>>>>>>>>>>> mismatch.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  Here is the psc table
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I created 2 candidates profiles through the
>>>>>>>>>>>>>>>>>>>>>>>>>> interface
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> then runned dcmodify command to a dicom file
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1"
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and got those warning: is this okay?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify at another Dicom didn't show
>>>>>>>>>>>>>>>>>>>>>>>>>> warnings. Below you can see the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> execution for the second dicom. Mnics could
>>>>>>>>>>>>>>>>>>>>>>>>>> not be inserted due to
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> AcquisitionProtocol being unknown.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Running now the following command:
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> imaging_upload_file.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 12
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  find -path
>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX'
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -delete
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dicomTar.pl
>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database
>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  Source: /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Target: /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Testing for database connectivity.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Database is available.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You will archive the dir :
>>>>>>>>>>>>>>>>>>>>>>>>>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You are creating a tar with the following
>>>>>>>>>>>>>>>>>>>>>>>>>> command:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> tar -cf
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> getting md5sums and gzipping!!
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :
>>>>>>>>>>>>>>>>>>>>>>>>>> 127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :    Linux
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>>>>> 2019-09-06 18:36:50
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Removing temporary files from target location
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Done adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -uploadID 12 -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  md5sum
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Set centerID = 1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Number of MINC files that will be considered
>>>>>>>>>>>>>>>>>>>>>>>>>> for inserting into the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> database: 2
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log
>>>>>>>>>>>>>>>>>>>>>>>>>> file is
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log
>>>>>>>>>>>>>>>>>>>>>>>>>> file is
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>> cat
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Acquisition protocol is unknown
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>   --> The minc file cannot be registered
>>>>>>>>>>>>>>>>>>>>>>>>>> since the AcquisitionProtocol
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> is unknown
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sure -- you can delete imaging datasets with
>>>>>>>>>>>>>>>>>>>>>>>>>> the *delete_imaging_upload*
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> script --
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> details here:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> What's in your *psc* table?  (Is it properly
>>>>>>>>>>>>>>>>>>>>>>>>>> populated? This is a
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> pre-requisite to loading imaging data.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database
>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The foreign key constraint error on the
>>>>>>>>>>>>>>>>>>>>>>>>>> candidate record is curious.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> There are also a few options for creating
>>>>>>>>>>>>>>>>>>>>>>>>>> candidates when inserting
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> imaging data:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then
>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a. via the LORIS API -- Create the candidates
>>>>>>>>>>>>>>>>>>>>>>>>>> (and visits, optionally I
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> think)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How to:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by
>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Then as a second step:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> b. Use the imaging insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets
>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to load your DICOMs.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You will want to first ensure that the
>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName header in the DICOMs
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> as well as tar package are correctly labelled
>>>>>>>>>>>>>>>>>>>>>>>>>> with PSCID_DCCID_VisitLabel
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How to :
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options when
>>>>>>>>>>>>>>>>>>>>>>>>>> running the bids_import script,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to automatically create your candidates and
>>>>>>>>>>>>>>>>>>>>>>>>>> sessions.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How do i delete a Study? And everytime do i
>>>>>>>>>>>>>>>>>>>>>>>>>> have to create a new
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate to get DCCID and a PSCID?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *First execution:*
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>> < ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern
>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or
>>>>>>>>>>>>>>>>>>>>>>>>>> update a child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`,
>>>>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_candidate_1`
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`)
>>>>>>>>>>>>>>>>>>>>>>>>>> REFERENCES `psc` (`CenterID`)) at
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ERROR: Failed to insert record in table
>>>>>>>>>>>>>>>>>>>>>>>>>> mri_scanner:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The following database commands failed:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SET
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Medical Systems';
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Error obtained:Cannot add or update a child
>>>>>>>>>>>>>>>>>>>>>>>>>> row: a foreign key
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`,
>>>>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_mri_scanner_1`
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate`
>>>>>>>>>>>>>>>>>>>>>>>>>> (`CandID`)) (error code 1452)
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ERROR: The validation has failed. Either
>>>>>>>>>>>>>>>>>>>>>>>>>> re-run the validation again
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and fix the problem. Or re-run
>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader.pl using -force to force the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> execution.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The tarchiveLoader.pl insertion script has
>>>>>>>>>>>>>>>>>>>>>>>>>> failed.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory
>>>>>>>>>>>>>>>>>>>>>>>>>> at ./
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *And second execution: *
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>> < ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern
>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PROBLEM:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The user 'lorisadmin' has already inserted
>>>>>>>>>>>>>>>>>>>>>>>>>> this study.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The unique study ID is
>>>>>>>>>>>>>>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> This is the information retained from the
>>>>>>>>>>>>>>>>>>>>>>>>>> first time the study was
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> inserted:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :
>>>>>>>>>>>>>>>>>>>>>>>>>> 127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :    Linux
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>>>>> 2019-09-04 18:33:05
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Last update of record:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The dicomTar.pl execution has failed.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory
>>>>>>>>>>>>>>>>>>>>>>>>>> at ./
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ok, this sounds like good progress.  Let us
>>>>>>>>>>>>>>>>>>>>>>>>>> know when you next encounter
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> issues as you progress through the Imaging
>>>>>>>>>>>>>>>>>>>>>>>>>> Install/Setup docs
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>>>>> >.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I'll look into how we can better handle the
>>>>>>>>>>>>>>>>>>>>>>>>>> incoming/ directory next
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> time.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> populated correctly except its port is
>>>>>>>>>>>>>>>>>>>>>>>>>> 'port'    : ''. Also i have tested
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that i can connect to MySQL with lorisuser.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I executed the script again, because the only
>>>>>>>>>>>>>>>>>>>>>>>>>> error i had previously was
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that the /data/incoming folder didn't exist
>>>>>>>>>>>>>>>>>>>>>>>>>> and there are no errors
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> reported back except of warnings <<mysql:
>>>>>>>>>>>>>>>>>>>>>>>>>> [Warning] Using a password on the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> command line interface can be insecure>>.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's possible -- if the script was unable to
>>>>>>>>>>>>>>>>>>>>>>>>>> connect to the database
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> during its execution (e.g. typo in the
>>>>>>>>>>>>>>>>>>>>>>>>>> password), that would explain the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> underpopulated Image path and Loris-MRI code
>>>>>>>>>>>>>>>>>>>>>>>>>> path you saw in the Config
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> module.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's hard to tell without seeing the output
>>>>>>>>>>>>>>>>>>>>>>>>>> from your script run -- Did
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you see a sign of any such error?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The Config fields are populated by the
>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_install.sh script (starting
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at line 222
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222
>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For example, check if the database connection
>>>>>>>>>>>>>>>>>>>>>>>>>> information was populated
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> accurately in
>>>>>>>>>>>>>>>>>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If you are referring to the
>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_install.sh here is an image with the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> configurations i typed. Maybe the problem is
>>>>>>>>>>>>>>>>>>>>>>>>>> somewhere at the last part
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> which asks to configure as much as possible
>>>>>>>>>>>>>>>>>>>>>>>>>> automatically?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear your LORIS core install is up
>>>>>>>>>>>>>>>>>>>>>>>>>> and working and all the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> front-end pages are loading.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$
>>>>>>>>>>>>>>>>>>>>>>>>>> chmod 775 project
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > and the web interface worked.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, it's important that project/ have 775
>>>>>>>>>>>>>>>>>>>>>>>>>> permissions and that
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> lorisadmin be part of the sudoers group, per
>>>>>>>>>>>>>>>>>>>>>>>>>> step 1 in the install
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Readme <
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris#install-steps>.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image
>>>>>>>>>>>>>>>>>>>>>>>>>> should change LORIS to
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris, right?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> These imaging paths will be updated during
>>>>>>>>>>>>>>>>>>>>>>>>>> your imaging installation
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup>
>>>>>>>>>>>>>>>>>>>>>>>>>> by an automated script --
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you do not need to set them manually via the
>>>>>>>>>>>>>>>>>>>>>>>>>> Config module.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Please continue to follow the Setup Guide
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup>
>>>>>>>>>>>>>>>>>>>>>>>>>> for detailed steps to follow.
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image
>>>>>>>>>>>>>>>>>>>>>>>>>> should change LORIS to loris,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> right?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i used
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x
>>>>>>>>>>>>>>>>>>>>>>>>>> | sudo -E bash -
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sudo apt-get install -y nodejs
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you had suggested in the past, make worked
>>>>>>>>>>>>>>>>>>>>>>>>>> and now i can see all the
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> contents in the web-interface, but i don't
>>>>>>>>>>>>>>>>>>>>>>>>>> need make install?
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>> -------------- next part --------------
>>>>>>>>>>>>>>>>>>>>>>>>>> An HTML attachment was scrubbed...
>>>>>>>>>>>>>>>>>>>>>>>>>> URL: <
>>>>>>>>>>>>>>>>>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html
>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16
>>>>>>>>>>>>>>>>>>>>>>>>>> *****************************************
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>> Loris-dev mailing list
>> Loris-dev at bic.mni.mcgill.ca
>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>
>
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From sotirisnik at gmail.com  Fri Jan 31 09:23:07 2020
From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos)
Date: Fri, 31 Jan 2020 16:23:07 +0200
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAMpvQ9gTQUGvmd7E8_Mnk7sd8HtX4NHvLCfWZ0-hEi9aJuu_nw@mail.gmail.com>
References: <mailman.1851.1573565332.16403.loris-dev@bic.mni.mcgill.ca>
 <CAEfMBom1HCWLo4NWgt5XG4625tCBfRT_Z_HepvtT_Er2LKbJoA@mail.gmail.com>
 <CAKHj7uS1AdMDjnacouTvxZgziYVgp5NNUeOuMkpDyrTskGTh-Q@mail.gmail.com>
 <CALbt7NDej8FGUUS6_oKbK5Fp-FnwsVz9AgZ6ZcJEZhmoKZmv8w@mail.gmail.com>
 <CAKHj7uSx-qqcXHZsWsZmSJ7sC1DgF+XapT5Y1+QdoVic37_DDg@mail.gmail.com>
 <CAMkiY3fQBGDGeNO8EHxwYAgbhTggNSQ+AVuCfdraDXwULMjjUg@mail.gmail.com>
 <CAKHj7uT5xXi=pOPdH=W9BroSphMHdTszdgW+GxuES=8wZox9eQ@mail.gmail.com>
 <CAMkiY3eUouxaRVdC4wH+vdjeQ=q_Nx8bcDNzcWgD_OgN77m3mw@mail.gmail.com>
 <CAKHj7uSxu4+tm+=x4+qJ1sAbrjmxG2H7LovDb7-2KMnyYQhrgg@mail.gmail.com>
 <CAMkiY3fdPZec2jx-cc2Zq37j3ekmTu_o819yBUv-bC7M98bkVw@mail.gmail.com>
 <CAKHj7uSZHozpuQ_YwGmy6wQ4tm43vJa556V0o2+JGDVsYaqN4g@mail.gmail.com>
 <CAMkiY3dge=x93bQDv0fHGMcrX0PA8Z_imLb_zSTh=nTrx5weFg@mail.gmail.com>
 <CAKHj7uR81gCkjvccMxwMA08dGSEgyTLJBJ+pZPkoUQDtGP_hFA@mail.gmail.com>
 <CAMkiY3fGhvExZ-JOvxeHe7dJQPvtPAHx3oJuiMVX7f1JgF1GAg@mail.gmail.com>
 <CAKHj7uRExO98Yyn9_07aw44wbh0bCL9_C1VFTAURKsxQLUuAeQ@mail.gmail.com>
 <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>
 <CAKHj7uRueb5fgh4VVCAyaq8tC9WM4gJ7k6Q=dxsqWzFgDqPfVQ@mail.gmail.com>
 <CAMkiY3d-Vt=3gQqwJ+GSRSacbLp2QxrB0g-_C7ONd8j_g1ipoQ@mail.gmail.com>
 <CAKHj7uQt9=nokz5g1zBuBx1-rJ8q7qKOuNVkQugC9wfvNFcjVA@mail.gmail.com>
 <CAMkiY3cAuQfT_5iMzYoF2BXVceu_vgz4eCq2sAtoyse+zUYeSg@mail.gmail.com>
 <CAMkiY3dq1O3V8+r4tTAWQ8N=rVFg=DNY-UPeMqbec+MSayj=Cg@mail.gmail.com>
 <CAKHj7uSEegvE1apPBGVyHmjyVzF+YxJjDMg0b+hDE4_-ON+dYw@mail.gmail.com>
 <CAKHj7uRx1NT7CycFq65uFpgPiOVwvT-jtK1NJX6_3rrLNFwdbA@mail.gmail.com>
 <CAMkiY3dAnkLdc4N=REmeCpX2qBfsQf=wRb=YtHtt20f8adXFyw@mail.gmail.com>
 <CAKHj7uRpA-8kzkoEnAk7JBNLP7v4cmK4zW-gMutHESiFGj7xjw@mail.gmail.com>
 <CAMpvQ9hNLxz9SZsJwWec_yQ3R4KGhnqv3CDaSPOB1exPsO5AJA@mail.gmail.com>
 <CAMpvQ9gTQUGvmd7E8_Mnk7sd8HtX4NHvLCfWZ0-hEi9aJuu_nw@mail.gmail.com>
Message-ID: <CAKHj7uSNm=OX8jaDJ0-TZZsBA8zm3Uv6yErBSy76EnwUWdpsig@mail.gmail.com>

Hi Ling,

Yes it's Loris-mri 21.0. One thought i had is that maybe i should define
root as linux user?
https://github.com/aueb-wim/LORIS-for-MIP/blob/master/docs/pics/loris_docker_imaging_install.png.
But i see no difference either when i execute it as lorisadmin.

Also here are the files we use
https://github.com/aueb-wim/LORIS-for-MIP/tree/master/mri_loris

And here is the complete output of the batch execution.

Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/
batch_uploads_imageuploader.pl line 144.
Running now the following command: /data/loris/data//uploadNeuroDB/
imaging_upload_file.pl -profile prod -upload_id 35
/data/incoming/DCC0000_956912_V1.tar.gz -verbose

 find -path \/data\/tmp\/ImagingUpload\-14\-15\-z2B0N3 -name '__MACOSX'
-delete
xargs: file: No such file or directory

dicomTar.pl \/data\/tmp\/ImagingUpload\-14\-15\-z2B0N3
\/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
 Source: /data/tmp/ImagingUpload-14-15-z2B0N3
Target: /data/loris/data/tarchive

Testing for database connectivity.
Database is available.

You will archive the dir : ImagingUpload-14-15-z2B0N3

You are creating a tar with the following command:

tar -cf /data/loris/data/tarchive/ImagingUpload-14-15-z2B0N3.tar
ImagingUpload-14-15-z2B0N3


getting md5sums and gzipping!!

* Taken from dir                   :    /data/tmp/ImagingUpload-14-15-z2B0N3
* Archive target location          :
 /data/loris/data/tarchive/DCM_2015-09-07_ImagingUpload-14-15-z2B0N3.tar
* Name of creating host            :    172.28.1.1
* Name of host OS                  :    Linux
* Created by user                  :    lorisadmin
* Archived on                      :    2020-01-31 14:15:04
* dicomSummary version             :    1
* dicomTar version                 :    1
* md5sum for DICOM tarball         :    fcaf54e9078705799b10e08c4d34bf70
 ImagingUpload-14-15-z2B0N3.tar
* md5sum for DICOM tarball gzipped :    52c96cd08d168e659b5c73cb77b4621b
 ImagingUpload-14-15-z2B0N3.tar.gz
* md5sum for complete archive      :    f5103ec688a5921a37d3c95cba8598e0
 DCM_2015-09-07_ImagingUpload-14-15-z2B0N3.tar

Adding archive info into database


Removing temporary files from target location


Done adding archive info into database

\/data\/loris\/data\//uploadNeuroDB/tarchiveLoader.pl -globLocation
-profile prod
\/data\/loris\/data\/tarchive\/\/DCM_2015\-09\-07_ImagingUpload\-14\-15\-z2B0N3\.tar
-uploadID 35 -verbose
 md5sum
/data/loris/data/tarchive/DCM_2015-09-07_ImagingUpload-14-15-z2B0N3.tar
PSCID is: DCC0000
 CandID id: 956912
 visit_label is: V1
PSCID is: DCC0000
 CandID id: 956912
 visit_label is: V1
candidate id 956912
Set centerID = 1
PSCID is: DCC0000
 CandID id: 956912
 visit_label is: V1
PSCID is: DCC0000
 CandID id: 956912
 visit_label is: V1
xargs: file: No such file or directory

Number of MINC files that will be considered for inserting into the
database: 0

No data could be converted into valid MINC files.

The tarchiveLoader.pl insertion script has failed.
Use of uninitialized value $mail_user in concatenation (.) or string at
/data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
Can't exec "mail": No such file or directory at /data/loris/bin/mri/
batch_uploads_imageuploader.pl line 249.
print() on closed filehandle MAIL at /data/loris/bin/mri/
batch_uploads_imageuploader.pl line 250.
print() on closed filehandle MAIL at /data/loris/bin/mri/
batch_uploads_imageuploader.pl line 251.

???? ???, 30 ??? 2020 ???? 6:22 ?.?., ?/? Ling Ma <lingyun.ma at mcin.ca>
??????:

> Oh, I just found that you are using Loris-mri 21.0, as I stated in the
> previous email, the "$_" could not find any matches, so your command might
> not be correctly entered.
>
> On Thu, Jan 30, 2020 at 10:35 AM Ling Ma <lingyun.ma at mcin.ca> wrote:
>
>> Hi Sotirios,
>>
>> By curiosity, I just looked at the error message, "Use of uninitialized
>> value $_ in pattern match (m//) at /data/loris/bin/mri/
>> batch_uploads_imageuploader.pl line 144." clearly means that there is no
>> match, but 144 line has no such code related with $_ in recent versions of
>> the batch_uploads_imageuploader.pl. There is something in the line 165
>> for a few recent versions.
>>
>> As to "xargs: file: No such file or directory", it could be due to a
>> command unable to find anything using the directory provided as the message
>> suggested.
>>
>> In both cases, I feel that it could be helpful if you provide more
>> details such as which Loris_MRI version you are running, what is the exact
>> command line you are using to help supporters to understand.
>>
>> Thanks.
>>
>> Best regards,
>> Ling Ma
>> Consultant
>>
>> On Wed, Jan 29, 2020 at 6:57 PM Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> wrote:
>>
>>> Hi Cecile,
>>>
>>> it seems that xargs is already installed in our docker container.
>>>
>>> [image: image.png]
>>>
>>>
>>> ???? ???, 29 ??? 2020 ???? 7:59 ?.?., ?/? Cecile Madjar <
>>> cecile.madjar at mcin.ca> ??????:
>>>
>>>> Hi Sotirios,
>>>>
>>>> It looks like xargs is not installed in your docker environment.
>>>>
>>>> This is being used by the following command in dicomTar.pl (and a few
>>>> other places but that is the one causing the error at the moment):
>>>>
>>>> $cmd = "cd " . $dcm_source . "; find -type f -name '.*' | *xargs* rm
>>>> -f";
>>>>
>>>> So you need to install xargs in your docker for the command to run.
>>>>
>>>> Hope this helps,
>>>>
>>>> C?cile
>>>> On Wed, Jan 29, 2020 at 10:35 AM Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> We are making a dockerized version of Loris 21 and when we execute the
>>>>> batch_uploads_imageuploader.pl we get an error about xargs. What
>>>>> could be the casue?
>>>>>
>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>>>>> Running now the following command: /data/loris/data//uploadNeuroDB/
>>>>> imaging_upload_file.pl -profile prod -upload_id 13
>>>>> /data/incoming/DCC0007_854380_V1.tar.gz -verbose
>>>>>
>>>>>  find -path \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml -name
>>>>> '__MACOSX' -delete
>>>>> xargs: file: No such file or directory
>>>>>
>>>>> dicomTar.pl \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml
>>>>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>>>>>  Source: /data/tmp/ImagingUpload-15-31-U_O5ml
>>>>> Target: /data/loris/data/tarchive
>>>>>
>>>>> Thanks
>>>>>
>>>>> ???? ???, 10 ??? 2019 ???? 7:21 ?.?., ?/? Sotirios Nikoloutsopoulos <
>>>>> sotirisnik at gmail.com> ??????:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> i opened an issue and looked up for the values of Volume they
>>>>>> suggested https://github.com/BIC-MNI/minc-toolkit-v2/issues/95. The
>>>>>> only attributes associated with it i saw are [0x00089206] and [0x00089207]
>>>>>>
>>>>>> [image: image.png]
>>>>>>
>>>>>> I looked up for the file that was being viewed fine in the
>>>>>> BrainBrowser and saw that it had that attribute empty so i used this
>>>>>> command because i couldn't find a way to modify the attribute via pydicom
>>>>>>
>>>>>> dcmodify -ma "(0008,9206)=" *.dcm
>>>>>>
>>>>>> and that command reported the warning about the Endian Syntax. I also
>>>>>> used the corresponding command for 9207 and got the message "Tag not found'
>>>>>>
>>>>>> Lastly I tried to upload some dicoms and now i am getting the SNR and
>>>>>> i can view them fine. I believe now that all of them will pass
>>>>>> successfully, i will report back later.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Sotirios
>>>>>>
>>>>>> ???? ???, 9 ??? 2019 ???? 8:10 ?.?., ?/? Cecile Madjar <
>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>
>>>>>>> Hi Sotirios,
>>>>>>>
>>>>>>> The issue you are having is a indeed a dcm2mnc issue. The converter
>>>>>>> does not seem to work on your dataset for some reason. Unfortunately, there
>>>>>>> is not much we can do on our front to fix this...
>>>>>>>
>>>>>>> I would recommend creating an issue on the MINC tools repository
>>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> so they can fix
>>>>>>> your problem.
>>>>>>>
>>>>>>> Very sorry that you are having that problem.
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> C?cile
>>>>>>>
>>>>>>> On Wed, Dec 4, 2019 at 8:59 AM Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi Sotirios,
>>>>>>>>
>>>>>>>> Could you please share a dataset with us that produces the error
>>>>>>>> you get and the weird display in BrainBrowser? You could use the same SFTP
>>>>>>>> credential that Nicolas gave you.
>>>>>>>>
>>>>>>>> The message errors you got from imaging_install.sh are probably due
>>>>>>>> to the fact that you reran the install script and it tried to reinstall
>>>>>>>> something that was already there. I would not worry about it. FYI, the only
>>>>>>>> thing you needed to do was to update the MINC tools path in the environment
>>>>>>>> file as you did after re-running imaging_install.sh and source the
>>>>>>>> environment file.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>>
>>>>>>>> C?cile
>>>>>>>>
>>>>>>>> On Wed, Dec 4, 2019 at 8:03 AM Sotirios Nikoloutsopoulos <
>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>
>>>>>>>>>  Hi Cecile,
>>>>>>>>>
>>>>>>>>> We used minctool 1.9.7 and we still get this error
>>>>>>>>>
>>>>>>>>> <<Restructuring...
>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>> noise_estimate --snr /data/loris/data>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>> One dicom folder hadn't that error and is being viewed fine in the
>>>>>>>>> BrainBrowser of Loris.
>>>>>>>>>
>>>>>>>>
>>>>>>>>> When i used dpkg to the 1.9.17 the installation reported fine
>>>>>>>>> <<Unpacking minc-toolkit-v2 (1.9.17) over (1.9.16) ...>>
>>>>>>>>>
>>>>>>>>> and then i used source /opt/minc/1.9.17/minc-toolkit-config.sh
>>>>>>>>>
>>>>>>>>> and aftewards runned bash ./imaging_install.sh just to be sure.
>>>>>>>>>
>>>>>>>>> We also had to modify /data/loris/bin/mri/environment because it
>>>>>>>>> still pointed to the old version.
>>>>>>>>>
>>>>>>>>> What i found strange is this during the run of imaging_install.sh
>>>>>>>>>
>>>>>>>>> <<already using interpreter
>>>>>>>>> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/bin/python3
>>>>>>>>> Please use the *system* python to run this script
>>>>>>>>> Traceback (most recent call last):
>>>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py",
>>>>>>>>> line 2632, in <module>
>>>>>>>>>     main()
>>>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py",
>>>>>>>>> line 870, in main
>>>>>>>>>     symlink=options.symlink,
>>>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py",
>>>>>>>>> line 1156, in create_environment
>>>>>>>>>     install_python(home_dir, lib_dir, inc_dir, bin_dir,
>>>>>>>>> site_packages=site_packages, clear=clear, symlink=symlink)
>>>>>>>>>   File
>>>>>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>>>>>> line 357, in abspath
>>>>>>>>>     if not isabs(path):
>>>>>>>>>   File
>>>>>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>>>>>> line 64, in isabs
>>>>>>>>>     return s.startswith(sep)
>>>>>>>>> AttributeError: 'NoneType' object has no attribute 'startswith'
>>>>>>>>> Installing the Python libraries into the loris-mri virtualenv...
>>>>>>>>> Requirement already satisfied: mysqlclient in
>>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (1.4.4)
>>>>>>>>> Requirement already satisfied: mysql-connector in
>>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (2.2.9)
>>>>>>>>> Requirement already satisfied: pybids in
>>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (0.9.4)
>>>>>>>>> Requirement already satisfied: nibabel>=2.1 in ./python_virtua>>
>>>>>>>>>
>>>>>>>>> So should i open an issue for that error? or is there something
>>>>>>>>> else to try?
>>>>>>>>>
>>>>>>>>> Thanks
>>>>>>>>>
>>>>>>>>> Sotirios
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ???? ???, 3 ??? 2019 ???? 10:39 ?.?., ?/? Cecile Madjar <
>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>
>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>
>>>>>>>>>> Does the pic screenshot in the imaging browser module also shows
>>>>>>>>>> 1 slice? If so, that would mean there was an issue with the dcm2mnc
>>>>>>>>>> conversion. Once again, installing the latest version of the MINC tools
>>>>>>>>>> should help but if this issue persists I would recommend creating an issue
>>>>>>>>>> for that too on their repository
>>>>>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> (if not
>>>>>>>>>> already reported there, there are a few known issue reported).
>>>>>>>>>>
>>>>>>>>>> Other viewer for MINCs are register and Display (both part of the
>>>>>>>>>> MINC tools). For NIfTI, you have FSLeye, MRICron and probably many other
>>>>>>>>>> viewers that exists.
>>>>>>>>>>
>>>>>>>>>> Hope this helps,
>>>>>>>>>>
>>>>>>>>>> C?cile
>>>>>>>>>>
>>>>>>>>>> On Tue, Dec 3, 2019 at 3:26 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>
>>>>>>>>>>> Yes, Nifti files are mandatory for our work. From what we saw at
>>>>>>>>>>> a 3rd vm we setted up, the nifti files are being created ( i haven't
>>>>>>>>>>> verified if that is the case at the 2nd vm ). I will install the latest
>>>>>>>>>>> version and will report back, but do you know any nifti/minc viewer?
>>>>>>>>>>> because the Brainbrowser of Loris does not output them well, it's like it
>>>>>>>>>>> is loading only 1 slice and we would like to verify it with another tool
>>>>>>>>>>> too. We verified that the dcmconv command didn't affect the
>>>>>>>>>>> quality of the .dcm files.
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>>
>>>>>>>>>>> Sotirios
>>>>>>>>>>>
>>>>>>>>>>> ???? ???, 2 ??? 2019 ???? 6:59 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>
>>>>>>>>>>>> It looks like for some reason your binary mnc2nii is not
>>>>>>>>>>>> working and reports that error. Do you want to create NIfTI files or are
>>>>>>>>>>>> you happy with just the MINC files?
>>>>>>>>>>>>
>>>>>>>>>>>> If you don't need the NIfTI files, then maybe you can set the
>>>>>>>>>>>> Config setting "NIfTI file creation" to No instead of Yes and
>>>>>>>>>>>> this error will not appear anymore.
>>>>>>>>>>>>
>>>>>>>>>>>> If you need the NIfTI files to be created, then I would
>>>>>>>>>>>> recommend installing the latest version of the MINC tools (1.9.17). They
>>>>>>>>>>>> can be found there:
>>>>>>>>>>>>
>>>>>>>>>>>>    - pre-built packages:
>>>>>>>>>>>>    https://packages.bic.mni.mcgill.ca/minc-toolkit/
>>>>>>>>>>>>    - from the source code with installation instructions in
>>>>>>>>>>>>    the README: https://github.com/BIC-MNI/minc-toolkit-v2
>>>>>>>>>>>>
>>>>>>>>>>>> If the problem persists by using the latest release of MINC
>>>>>>>>>>>> tools, then create an issue on Github for the MINC developers
>>>>>>>>>>>> here <https://github.com/BIC-MNI/minc-toolkit-v2/issues>.
>>>>>>>>>>>>
>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>
>>>>>>>>>>>> C?cile
>>>>>>>>>>>>
>>>>>>>>>>>> On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks to Nicholas i was able to create all the mincs images.
>>>>>>>>>>>>> The problem was that the files were in Little-Endian-Implicit transfer
>>>>>>>>>>>>> syntax and i had to convert them Little-Endian-Explicit transfer syntax
>>>>>>>>>>>>> with this command
>>>>>>>>>>>>>
>>>>>>>>>>>>> find <root_of_my_DICOM_files_directory> -type f | xargs -i
>>>>>>>>>>>>> dcmconv --write-xfer-little {} {}
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Looking back at our mails i saw that Little-Endian error had
>>>>>>>>>>>>> occurred when i used dcmodify, but i switcthed to using pydicom instead.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> In the output i see an error sometimes about "gsl:
>>>>>>>>>>>>> bessel_I0.c:216: ERROR: overflow". Is this okay?
>>>>>>>>>>>>>
>>>>>>>>>>>>> Restructuring...
>>>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>>>> noise_estimate --snr
>>>>>>>>>>>>> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
>>>>>>>>>>>>> SNR is:
>>>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thank you for the details!
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> A few things to try:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>    - modify the TMPDIR to be on your /data directory where
>>>>>>>>>>>>>>    there might be more space to do processing (could create a /data/tmp where
>>>>>>>>>>>>>>    the temporary files would be created)
>>>>>>>>>>>>>>    - how many files are there for that upload in
>>>>>>>>>>>>>>    tarchive_files? Are they different from the ones showing the warning
>>>>>>>>>>>>>>    message?
>>>>>>>>>>>>>>       - FYI: query to get that: SELECT tf.* FROM
>>>>>>>>>>>>>>       tarchive_files tf JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your
>>>>>>>>>>>>>>       uploadID> (the output of that query would be very
>>>>>>>>>>>>>>       useful if you can provide it)
>>>>>>>>>>>>>>       - how many series are there for that upload in
>>>>>>>>>>>>>>    tarchive_series?
>>>>>>>>>>>>>>    - FYI: query to get that: SELECT ts.* FROM
>>>>>>>>>>>>>>       tarchive_series ts JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your
>>>>>>>>>>>>>>       uploadID> (the output of that query would be very
>>>>>>>>>>>>>>       useful if you can provide it)
>>>>>>>>>>>>>>    - things are failing when the scripts try running the
>>>>>>>>>>>>>>    following command: find
>>>>>>>>>>>>>>    /tmp/TarLoad-23-43-ccugaa/ImagingUpload-23-43-6JCOTO -type f  |
>>>>>>>>>>>>>>    /data/loris/bin/mri/dicom-archive/get_dicom_info.pl
>>>>>>>>>>>>>>    -studyuid -series -echo -image -file  -attvalue 0018 0024 -series_descr
>>>>>>>>>>>>>>    -stdin | sort -n -k1 -k2 -k7 -k3 -k6 -k4  | cut -f 5 | dcm2mnc -dname ''
>>>>>>>>>>>>>>    -stdin -clobber -usecoordinates /tmp/TarLoad-23-43-ccugaa
>>>>>>>>>>>>>>       - clearly the problems come from get_dicom_info.pl but
>>>>>>>>>>>>>>       I cannot pinpoint the error yet. I will ask around and get back to you
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> If I cannot figure it out remotely, is there a way to have a
>>>>>>>>>>>>>> call using zoom? This way you could share your screen with me and run the
>>>>>>>>>>>>>> debugger on that script and hopefully we can figure out what is going on
>>>>>>>>>>>>>> with those datasets?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks!
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Tue, Nov 26, 2019 at 5:17 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> In both my virtual machines
>>>>>>>>>>>>>>> export TMPDIR=/tmp
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> In both vm also with dcm2mnc i get this output. Just to
>>>>>>>>>>>>>>> verify that this passed in my 1st vm and produced mincs.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I attached the spool as a csv.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> And also one difference i found was this in the Loris-mri
>>>>>>>>>>>>>>> code ( left 1st workable vm, right 2nd vm that has to be fixed, although i
>>>>>>>>>>>>>>> changed it seems to be independent of the uninitialized value $_ )
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> that is puzzling... A few additional questions:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>    - what is the bash variable TMPDIR set to on the
>>>>>>>>>>>>>>>>    environment file?
>>>>>>>>>>>>>>>>    - could you try running separately dcm2mnc on the DICOM
>>>>>>>>>>>>>>>>    folder to see if that works?
>>>>>>>>>>>>>>>>    - could you send us the detailed log from the
>>>>>>>>>>>>>>>>    notification spool table (SELECT * FROM notification_spool WHERE
>>>>>>>>>>>>>>>>    UploadID=<your uploadID>) and send it back to us? Maybe there are some
>>>>>>>>>>>>>>>>    additional clues that could help figuring out what is going on.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thank you!
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Tue, Nov 26, 2019 at 10:12 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I checked for the StudyInstacueUID at the files with "The
>>>>>>>>>>>>>>>>> target directory does not contain a single DICOM file"" and their attribute
>>>>>>>>>>>>>>>>> has a value.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Regarding the scouter and localizer, i modified the
>>>>>>>>>>>>>>>>> settings in the imaging pipeline and now i don't get that error message,
>>>>>>>>>>>>>>>>> but still it doesn't create the mnics.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> The errors i am getting are ( uninitialized value $_ is
>>>>>>>>>>>>>>>>> not important? because i haven't got comments about that )
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line
>>>>>>>>>>>>>>>>> 144.
>>>>>>>>>>>>>>>>> Running now the following command:
>>>>>>>>>>>>>>>>> /data/loris/data//uploadNeuroDB/imaging_upload_file.pl
>>>>>>>>>>>>>>>>> -profile prod -upload_id 134 /data/incoming/DCC0025_118008_V1.tar.gz
>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> and
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for inserting
>>>>>>>>>>>>>>>>> into the database: 0
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> No data could be converted into valid MINC files.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> The tarchiveLoader.pl insertion script has failed.
>>>>>>>>>>>>>>>>> Use of uninitialized value $mail_user in concatenation (.)
>>>>>>>>>>>>>>>>> or string at /data/loris/bin/mri/
>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line
>>>>>>>>>>>>>>>>> 249.
>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 250.
>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 251.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> OK. So the issue I mentioned should not be a problem for
>>>>>>>>>>>>>>>>>> you.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Is the StudyInstanceUID DICOM header set in your images?
>>>>>>>>>>>>>>>>>> If it is not set, then you would end up with the error message "The target
>>>>>>>>>>>>>>>>>> directory does not contain a single DICOM file". So maybe this is the issue
>>>>>>>>>>>>>>>>>> you are having with those datasets?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Regarding not excluding series descriptions, you can
>>>>>>>>>>>>>>>>>> configure that in the Config module under the Imaging Pipeline section.
>>>>>>>>>>>>>>>>>> Simply remove all entries for the "Series description to exclude from
>>>>>>>>>>>>>>>>>> imaging insertion" setting.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Mon, Nov 25, 2019 at 9:58 AM Sotirios Nikoloutsopoulos
>>>>>>>>>>>>>>>>>> <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> We are using this version
>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/archive/v21.0.0.zip. Is
>>>>>>>>>>>>>>>>>>> it possible to insert low resolution now?
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, <
>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> wrote:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Which version of LORIS-MRI are you using?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> There was a bug that got resolved in 20.2 in
>>>>>>>>>>>>>>>>>>>> get_dicom_info.pl. Basically, if a DICOM did not have
>>>>>>>>>>>>>>>>>>>> the (0020,0032) header, get_dicom_info.pl considered
>>>>>>>>>>>>>>>>>>>> that the file was not a DICOM, which was a mistake. This got fixed in
>>>>>>>>>>>>>>>>>>>> version 20.2 of LORIS-MRI. Hopefully this is the issue you are encountering.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> About scout and localizer, they are a type of short and
>>>>>>>>>>>>>>>>>>>> low resolution sequence that is used by the tech but is of no interest
>>>>>>>>>>>>>>>>>>>> scientifically, which is why we tend to no insert them.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> i executed the find command and the output i got per
>>>>>>>>>>>>>>>>>>>>> folder was "DICOM medical imaging data. Maybe there is something wrong with
>>>>>>>>>>>>>>>>>>>>> the find command in the warning that it is unable to check if the file is a
>>>>>>>>>>>>>>>>>>>>> dicom file? Also when i use get_dicom_info.pl i don't
>>>>>>>>>>>>>>>>>>>>> get any output data. Finally i don't understand what scout or localizer is
>>>>>>>>>>>>>>>>>>>>> ( something like if and only if a file fails then the whole session is
>>>>>>>>>>>>>>>>>>>>> invalid? ).
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>>>>> Madjar <cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> I took a closer look to the
>>>>>>>>>>>>>>>>>>>>>> batch_uploader_multiple_output.txt file you sent. It looks like there are
>>>>>>>>>>>>>>>>>>>>>> different reasons for failure depending on the DICOM folder uploaded.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>    - For 465466 DCC0000 V1; 727195 DCC0004 V1 and
>>>>>>>>>>>>>>>>>>>>>>    684908 DCC0007 V1: it looks like there is no file of type DICOM in the
>>>>>>>>>>>>>>>>>>>>>>    folder. Have you checked to see if that is indeed the case? Maybe you can
>>>>>>>>>>>>>>>>>>>>>>    try running the following command on that folder to see what are the types
>>>>>>>>>>>>>>>>>>>>>>    of the files? If it does not return at least one DICOM medical imaging data
>>>>>>>>>>>>>>>>>>>>>>    file, then that is why you get the error message from the pipeline:
>>>>>>>>>>>>>>>>>>>>>>       -
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>       find <my_dicom_archive_root_folder> -type f | xargs -i file {}|cut -d: -f2|sort|uniq
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>       - For 864173 DCC0001 V1: it looks like there
>>>>>>>>>>>>>>>>>>>>>>    are two different DICOM studies within the same folder. You will need to
>>>>>>>>>>>>>>>>>>>>>>    split that study in two based on the StudyUID field as the insertion
>>>>>>>>>>>>>>>>>>>>>>    pipeline does not allow for more than one StudyUID per upload.
>>>>>>>>>>>>>>>>>>>>>>    - For 890807 DCC0002 V1; 637025 DCC0005 V1 and
>>>>>>>>>>>>>>>>>>>>>>    239975 DCC0006 V1: it looks like the dcm2mnc command did not produce any
>>>>>>>>>>>>>>>>>>>>>>    MINC files. Can you check in the DICOM archive what are the series present
>>>>>>>>>>>>>>>>>>>>>>    in the tarchive for that visit? Maybe only a scout or localizer was
>>>>>>>>>>>>>>>>>>>>>>    acquired for that session, hence the no valid MINC files (scout and
>>>>>>>>>>>>>>>>>>>>>>    localizer being skipped for the conversion)
>>>>>>>>>>>>>>>>>>>>>>    - For 397410 DCC0003 V1: it looks like everything
>>>>>>>>>>>>>>>>>>>>>>    went well for this one.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> One script that is called by our pipeline is called
>>>>>>>>>>>>>>>>>>>>>> get_dicom_info.pl and this does all kind of checks
>>>>>>>>>>>>>>>>>>>>>> on the DICOM files (it is being called when running the dcm2mnc
>>>>>>>>>>>>>>>>>>>>>> conversion). You could run it independently on your folder if needed.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Since one of the study got in, it does not look like
>>>>>>>>>>>>>>>>>>>>>> you are having a problem with the setup. It seems more likely to be a
>>>>>>>>>>>>>>>>>>>>>> problem with the data themselves.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hope this helps.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> In my first vm i am able to create the minc files
>>>>>>>>>>>>>>>>>>>>>>> and view them at the mri browser (except of candidate 102761034 ),
>>>>>>>>>>>>>>>>>>>>>>> meanwhile the same files gives warnings at the 2nd vm. The output  of the
>>>>>>>>>>>>>>>>>>>>>>> batch upload can be seen in the file attached.
>>>>>>>>>>>>>>>>>>>>>>> Also a colleague of us has built a pre-validation
>>>>>>>>>>>>>>>>>>>>>>> tool for dicom
>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/
>>>>>>>>>>>>>>>>>>>>>>> which had found all the files that Loris gave as warning . Basically I
>>>>>>>>>>>>>>>>>>>>>>> confirmed that the total amount of files per dicom was the same amount as
>>>>>>>>>>>>>>>>>>>>>>> stated in Loris and checked some filenames given from warning to confirm
>>>>>>>>>>>>>>>>>>>>>>> that they match with our tool. But that was months ago and my colleague had
>>>>>>>>>>>>>>>>>>>>>>> changed some parameters for MIP and now our tool doesn't find all the
>>>>>>>>>>>>>>>>>>>>>>> invalid files, that's why i asked for the dicom header specification of
>>>>>>>>>>>>>>>>>>>>>>> Loris. In a discussion we had he mentioned that he doesn't check for some
>>>>>>>>>>>>>>>>>>>>>>> tags e.x. orientation. Lastly to mention that in my first vm i didn't use
>>>>>>>>>>>>>>>>>>>>>>> our tool to remove invalid dcm files.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> Can you provide us with some fresh particulars of
>>>>>>>>>>>>>>>>>>>>>>>> the current issue and we'll take it from there?
>>>>>>>>>>>>>>>>>>>>>>>> Yang's team has built these scripts which can
>>>>>>>>>>>>>>>>>>>>>>>> definitely serve as a model for your pre-validation of your DICOM
>>>>>>>>>>>>>>>>>>>>>>>> collections.
>>>>>>>>>>>>>>>>>>>>>>>> cheers,
>>>>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> HI Yang,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> We make use of pydicom library too. Now about the
>>>>>>>>>>>>>>>>>>>>>>>>> validate.py i see that you check if some attributes are missing such as
>>>>>>>>>>>>>>>>>>>>>>>>> PatientID, PatientName which all of our files contains that info. Maybe i
>>>>>>>>>>>>>>>>>>>>>>>>> have missed something on the setup of my other virtual machine ( although
>>>>>>>>>>>>>>>>>>>>>>>>> one dicom passed on the new vm successfully, the others that were inserted
>>>>>>>>>>>>>>>>>>>>>>>>> correctly on my old vm fails on the new one ), i think that i had asked
>>>>>>>>>>>>>>>>>>>>>>>>> about this error "Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>> line 144." but i don't remember the solution.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang
>>>>>>>>>>>>>>>>>>>>>>>>> Ding <it at cnbp.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Hey, Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Christine from the LORIS team mentioned you had
>>>>>>>>>>>>>>>>>>>>>>>>>> some issue with DICOM.  I am a fellow developer for an external project
>>>>>>>>>>>>>>>>>>>>>>>>>> using LORIS, kind of just like you. We had to implement DICOM upload as
>>>>>>>>>>>>>>>>>>>>>>>>>> well but more as a fully automated pipeline actually.
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> While we were building CNBP, we had coded up some
>>>>>>>>>>>>>>>>>>>>>>>>>> minor Python functions to check DICOM integrity (and simple validations)
>>>>>>>>>>>>>>>>>>>>>>>>>> and you might be able to gain some inspiration from it and help you with
>>>>>>>>>>>>>>>>>>>>>>>>>> your cause. For more comprehensive solution, PyDICOM (
>>>>>>>>>>>>>>>>>>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#)  seems
>>>>>>>>>>>>>>>>>>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks
>>>>>>>>>>>>>>>>>>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can
>>>>>>>>>>>>>>>>>>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty
>>>>>>>>>>>>>>>>>>>>>>>>>> rough around the edges but hopefully point you in the right direcitons
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Yang Ding, PhD.
>>>>>>>>>>>>>>>>>>>>>>>>>> Canadian Neonatal Brain Platform Architect
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM <
>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Send Loris-dev mailing list submissions to
>>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> To subscribe or unsubscribe via the World Wide
>>>>>>>>>>>>>>>>>>>>>>>>>>> Web, visit
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>> or, via email, send a message with subject or
>>>>>>>>>>>>>>>>>>>>>>>>>>> body 'help' to
>>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-request at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> You can reach the person managing the list at
>>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-owner at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> When replying, please edit your Subject line so
>>>>>>>>>>>>>>>>>>>>>>>>>>> it is more specific
>>>>>>>>>>>>>>>>>>>>>>>>>>> than "Re: Contents of Loris-dev digest..."
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Today's Topics:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>    1. Re: Import mri - scripts (Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos)
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Message: 1
>>>>>>>>>>>>>>>>>>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200
>>>>>>>>>>>>>>>>>>>>>>>>>>> From: Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>> To: Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>> Message-ID:
>>>>>>>>>>>>>>>>>>>>>>>>>>>         <CAKHj7uST=
>>>>>>>>>>>>>>>>>>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com
>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Could we send you a link with 10 anonymized
>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom files to diagnose the
>>>>>>>>>>>>>>>>>>>>>>>>>>> warnings we get?
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> > Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>> > We were wondering whether Loris has a tool to
>>>>>>>>>>>>>>>>>>>>>>>>>>> check if there are problems
>>>>>>>>>>>>>>>>>>>>>>>>>>> > with the dcm files, before trying to upload
>>>>>>>>>>>>>>>>>>>>>>>>>>> them. Something that could
>>>>>>>>>>>>>>>>>>>>>>>>>>> > provide the same results provided in the
>>>>>>>>>>>>>>>>>>>>>>>>>>> warning_output, this is the
>>>>>>>>>>>>>>>>>>>>>>>>>>> > summary from the mri_upload at the front-page.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Also which attributes of the
>>>>>>>>>>>>>>>>>>>>>>>>>>> > dcm header would trigger a warning? is there a
>>>>>>>>>>>>>>>>>>>>>>>>>>> dcm file header
>>>>>>>>>>>>>>>>>>>>>>>>>>> > specification for Loris?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>> > Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>> > Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> > sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp
>>>>>>>>>>>>>>>>>>>>>>>>>>> function it worked,but i
>>>>>>>>>>>>>>>>>>>>>>>>>>> >> thought that something else was causing the
>>>>>>>>>>>>>>>>>>>>>>>>>>> 2nd issue.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours
>>>>>>>>>>>>>>>>>>>>>>>>>>> Boucher, Mr, <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The first error occurs because the
>>>>>>>>>>>>>>>>>>>>>>>>>>> QCFirstChangeTime and columns are of
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> type `unsigned integer` and not `datatime`.
>>>>>>>>>>>>>>>>>>>>>>>>>>> You should be using
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW().
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The second error occurs because the trigger
>>>>>>>>>>>>>>>>>>>>>>>>>>> triggers a rollback of the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> insert statement in the files table.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> See mysql documentation for trigger error
>>>>>>>>>>>>>>>>>>>>>>>>>>> handling.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> An error during either a BEFORE or AFTER
>>>>>>>>>>>>>>>>>>>>>>>>>>> trigger results in failure of
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the entire statement that caused trigger
>>>>>>>>>>>>>>>>>>>>>>>>>>> invocation.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you for sharing that. I hope it helps.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Xavier
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on
>>>>>>>>>>>>>>>>>>>>>>>>>>> behalf of Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> When mincs are inserted their corresponding
>>>>>>>>>>>>>>>>>>>>>>>>>>> rows at the file table are
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> inserted too
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i would like to insert their rows at
>>>>>>>>>>>>>>>>>>>>>>>>>>> file_qcstatus as well, because i
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> don't want manually to label them as passed
>>>>>>>>>>>>>>>>>>>>>>>>>>> throught the interface
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> That is the trigger i wrote
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER
>>>>>>>>>>>>>>>>>>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> BEGIN
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT INTO files_qcstatus
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SET FileID = NEW.FileID,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      SeriesUID = NEW.SeriesUID,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      EchoTime = NEW.EchoTime,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCStatus = "Pass",
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCFirstChangeTime = NOW(),
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCLastChangeTime = NOW();
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> END
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> although it contains some errors
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range value
>>>>>>>>>>>>>>>>>>>>>>>>>>> for column
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or
>>>>>>>>>>>>>>>>>>>>>>>>>>> update a child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails
>>>>>>>>>>>>>>>>>>>>>>>>>>> (`LORIS`.`parameter_file`, CONSTRAINT
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`)
>>>>>>>>>>>>>>>>>>>>>>>>>>> REFERENCES `files` (`FileID`))
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> In the mri_upload table, there is a
>>>>>>>>>>>>>>>>>>>>>>>>>>> TarchiveID column associated with
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the MRI upload you inserted. When this value
>>>>>>>>>>>>>>>>>>>>>>>>>>> is NULL, it means no DICOMs
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> were inserted into the tarchive tables. At
>>>>>>>>>>>>>>>>>>>>>>>>>>> the end of the insertion of the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DICOMs in the tarchive tables, this value is
>>>>>>>>>>>>>>>>>>>>>>>>>>> updated with the correct
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> TarchiveID associated with the upload.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Could this correspond to what you want to do?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Regarding the files_qcstatus, this table is
>>>>>>>>>>>>>>>>>>>>>>>>>>> only linked to the files
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> table (hence, the MINC files). You could
>>>>>>>>>>>>>>>>>>>>>>>>>>> always create a new table for
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive
>>>>>>>>>>>>>>>>>>>>>>>>>>> table?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i would like whenever a dicom is imported to
>>>>>>>>>>>>>>>>>>>>>>>>>>> mark all their
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> coressponding qc_status to "pass". I was
>>>>>>>>>>>>>>>>>>>>>>>>>>> thinking of creating a trigger for
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that, but which tables do i need to add
>>>>>>>>>>>>>>>>>>>>>>>>>>> entries to? So far from what i see
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i need to add entres at  the table "files"
>>>>>>>>>>>>>>>>>>>>>>>>>>> whenever an insertion happens to
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> files_qcstatus.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Oh, sorry i should have asked for StudyID,
>>>>>>>>>>>>>>>>>>>>>>>>>>> at the beginning of my email
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID).
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that's the Study Instance UID, not the
>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyID. So the StudyID i am
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looking for is not stored in the database?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The StudyUID is stored in the DicomArchiveID
>>>>>>>>>>>>>>>>>>>>>>>>>>> field of the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> tarchive table. It can also be found in the
>>>>>>>>>>>>>>>>>>>>>>>>>>> metadata field but it is mixed
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> with many other information.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is StudyUID stored somewhere at the tables?
>>>>>>>>>>>>>>>>>>>>>>>>>>> At the tarchive table,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> specifically at the AcquisitonMetadata
>>>>>>>>>>>>>>>>>>>>>>>>>>> column i found something called
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 'Unique Study ID" in its context, but that
>>>>>>>>>>>>>>>>>>>>>>>>>>> must be the Study Instance UID.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Your observation is correct. A little
>>>>>>>>>>>>>>>>>>>>>>>>>>> explanation below.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> MINC files get inserted into the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>> violation tables if:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - the scan type could not be identified
>>>>>>>>>>>>>>>>>>>>>>>>>>> (not matching an entry in
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - one parameter of the scan type is out
>>>>>>>>>>>>>>>>>>>>>>>>>>> of the expected range
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    present in the mri_protocol_checks (extra
>>>>>>>>>>>>>>>>>>>>>>>>>>> filtering in case you need to be
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    stricker on some parameters not present
>>>>>>>>>>>>>>>>>>>>>>>>>>> in the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - if the CandID and PSCID do not match
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The following cases do not get in the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>> violation tables as it happens
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> before the conversion of the DICOM to MINC
>>>>>>>>>>>>>>>>>>>>>>>>>>> files and only MINC files
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> violations are logged there:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - "No single DICOM" (since no valid DICOM
>>>>>>>>>>>>>>>>>>>>>>>>>>> could be found to convert
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    to MINC)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - "Study already inserted" (duplicate
>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID) since this error
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    happens at the dicomTar.pl level (way
>>>>>>>>>>>>>>>>>>>>>>>>>>> before conversion into MINC files)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad everything is working out!!
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the mri passed, for some reason it consumed
>>>>>>>>>>>>>>>>>>>>>>>>>>> 5.12GB of ram. Now about the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations, dicoms are triggered to be
>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted there only if there is
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general
>>>>>>>>>>>>>>>>>>>>>>>>>>> for its header parameter?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Because i don't see the cases of 'No single
>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom" or with the 2 studyiuid
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to be there.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sorry to hear you are having issues with the
>>>>>>>>>>>>>>>>>>>>>>>>>>> memory. I think most of our
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB
>>>>>>>>>>>>>>>>>>>>>>>>>>> you should be fine.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> about that dicom that had that insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>> error it's about 30mb and when
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> it is being processed the ram is being
>>>>>>>>>>>>>>>>>>>>>>>>>>> drastically increased from 2gb to
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3.28 and then the whole virtual machine is
>>>>>>>>>>>>>>>>>>>>>>>>>>> frozen. What is the recommended
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> size of ram for using Loris?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to see that the StudyUID problem was
>>>>>>>>>>>>>>>>>>>>>>>>>>> fixed!
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the delete script issue, if you are
>>>>>>>>>>>>>>>>>>>>>>>>>>> absolutely certain that no
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> processes are run for that uploadID, you can
>>>>>>>>>>>>>>>>>>>>>>>>>>> update the mri_upload table
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and set the column Inserting to 0 instead of
>>>>>>>>>>>>>>>>>>>>>>>>>>> 1 for that uploadID. It
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looks like for some reason the scripts did
>>>>>>>>>>>>>>>>>>>>>>>>>>> not update this field when it
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> stopped the insertion. Not sure why that
>>>>>>>>>>>>>>>>>>>>>>>>>>> would be the case though.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Note: only do that update if you are certain
>>>>>>>>>>>>>>>>>>>>>>>>>>> that there is no processing
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> happening.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> about the Dicoms i reported that didn't have
>>>>>>>>>>>>>>>>>>>>>>>>>>> a StudyID they actually do
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I thought that this might be a permission
>>>>>>>>>>>>>>>>>>>>>>>>>>> because "w" was missing at the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> group. After using chmod -R 775 only
>>>>>>>>>>>>>>>>>>>>>>>>>>> 102809579 passed, but with no mnic
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> files. Also now i have this error
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox
>>>>>>>>>>>>>>>>>>>>>>>>>>> :/data/loris/bin/mri/tools$
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34
>>>>>>>>>>>>>>>>>>>>>>>>>>> -ignore
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is
>>>>>>>>>>>>>>>>>>>>>>>>>>> currently processing it.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How can solve this?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Here is our auto dicom uploading python
>>>>>>>>>>>>>>>>>>>>>>>>>>> script:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To give you a brief idea:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Per folder it will:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 1) Delete all the .bak files
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 2) Locate .dcm files and update the Patient
>>>>>>>>>>>>>>>>>>>>>>>>>>> header
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3) Furthermore we are interesting in finding
>>>>>>>>>>>>>>>>>>>>>>>>>>> TR_min, TR_max, TE_min,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> TE_max parameters of T1 protocol and do an
>>>>>>>>>>>>>>>>>>>>>>>>>>> update at the mri_protocol table
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For some reason some files are missing
>>>>>>>>>>>>>>>>>>>>>>>>>>> SeriesDescription/ProtocolName
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> In total i have 7 folders
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3/7 passed
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Also about the first patient with DC0000 had
>>>>>>>>>>>>>>>>>>>>>>>>>>> a violation "T1 AXIAL SE
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> GADO", but my script didn't output a TE of
>>>>>>>>>>>>>>>>>>>>>>>>>>> 17 nowhere and i find that weird
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> since Loris detects the SeriesDescription.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Now about the 4/7 that didn't passed
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 102327840 and 102809579 outputs "The target
>>>>>>>>>>>>>>>>>>>>>>>>>>> directory does not contain a
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> single DICOM file.", therefore they are
>>>>>>>>>>>>>>>>>>>>>>>>>>> missing their StudyUID
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it
>>>>>>>>>>>>>>>>>>>>>>>>>>> with data from multiple
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> studies."
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and 102761034 "No data could be converted
>>>>>>>>>>>>>>>>>>>>>>>>>>> into valid MINC files.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> localizer, scout will not be considered!"
>>>>>>>>>>>>>>>>>>>>>>>>>>> What is this?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If i wanted to force the insertion of
>>>>>>>>>>>>>>>>>>>>>>>>>>> 102327840, 102809579 and 102506134
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> can i just pass a flag parameter to
>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl? or
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> modify imaging_upload_file.pl?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PS
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To diagnose a folder search the name of the
>>>>>>>>>>>>>>>>>>>>>>>>>>> folder at dicom_output.txt.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear about your progress.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, the script you used to delete imaging
>>>>>>>>>>>>>>>>>>>>>>>>>>> data is fully documented here
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- let us know if you didn't find the
>>>>>>>>>>>>>>>>>>>>>>>>>>> answers you were looking for there.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (Is it possible the null row in
>>>>>>>>>>>>>>>>>>>>>>>>>>> *mri_scanner* seen in your database
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> management software is a visual placeholder
>>>>>>>>>>>>>>>>>>>>>>>>>>> for you as the user?  I'm not
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sure why a scanner would ever be registered
>>>>>>>>>>>>>>>>>>>>>>>>>>> with ID='0' as your screenshot
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> showed.)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I fixed it with this
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I tried to create a new candidate using the
>>>>>>>>>>>>>>>>>>>>>>>>>>> API, is there something
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> wrong with the structure? why did i receive
>>>>>>>>>>>>>>>>>>>>>>>>>>> a 500 internal error? In the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-error log it state that there is
>>>>>>>>>>>>>>>>>>>>>>>>>>> something wrong with token, but i
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> verfied that the type of the token is a
>>>>>>>>>>>>>>>>>>>>>>>>>>> string.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019]
>>>>>>>>>>>>>>>>>>>>>>>>>>> [php7:error] [pid 4535] [client
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error:  Uncaught
>>>>>>>>>>>>>>>>>>>>>>>>>>> TypeError: Argument 1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> passed to
>>>>>>>>>>>>>>>>>>>>>>>>>>> SinglePointLogin::JWTAuthenticate() must be of the type string,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> null given, called in
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> defined in
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> trace:\n#0
>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> NDB_Client->initialize('/var/www/loris/...')\n#3
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST',
>>>>>>>>>>>>>>>>>>>>>>>>>>> Array)\n#5 {main}\n  thrown in
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is there a way also to delete candidates?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Just to let you know what i
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> did to clear candidates, because maybe i may
>>>>>>>>>>>>>>>>>>>>>>>>>>> have missed dependencies.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> First i deleted all their uploads
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc
>>>>>>>>>>>>>>>>>>>>>>>>>>> ( is there a way to omit
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the backup file ? )
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Afterwards i had some scanner candidates, so
>>>>>>>>>>>>>>>>>>>>>>>>>>> i deleted all the entries
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> from mri_scanner except that i couldn't
>>>>>>>>>>>>>>>>>>>>>>>>>>> delete this entry with the 0 ID.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Lastly i deleted the session and then the
>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate table.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> We recommend that you use our existing tools
>>>>>>>>>>>>>>>>>>>>>>>>>>> for creating new candidates
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> - either the LORIS API or if you are using a
>>>>>>>>>>>>>>>>>>>>>>>>>>> PHP script, by calling the Candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> class's createNew()
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200
>>>>>>>>>>>>>>>>>>>>>>>>>>> >function.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> These will create the necessary records for
>>>>>>>>>>>>>>>>>>>>>>>>>>> you.  (It's not recommended to
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> make direct modifications to mysql database
>>>>>>>>>>>>>>>>>>>>>>>>>>> tables in your script, if I
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> understand you.)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The CandID should be a randomized 6 digit
>>>>>>>>>>>>>>>>>>>>>>>>>>> randomized ID, and there are
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> multiple reasons for this.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You can use the PSCID for project-specific
>>>>>>>>>>>>>>>>>>>>>>>>>>> IDs and the External ID field
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> in the candidate table can also be used for
>>>>>>>>>>>>>>>>>>>>>>>>>>> any values you like.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Additionally, any number of custom IDs can
>>>>>>>>>>>>>>>>>>>>>>>>>>> be added in parallel - these
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> are entered/visible in the Candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>> Information module and added in the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> back-end as candidate parameters.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> We are building a script that will auto
>>>>>>>>>>>>>>>>>>>>>>>>>>> insert the candidates based on
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> their ExternalID. We would like to know
>>>>>>>>>>>>>>>>>>>>>>>>>>> whethere when we are creating a new
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> profile in the candidate table, if we also
>>>>>>>>>>>>>>>>>>>>>>>>>>> have to insert a new record at
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> another table? Furthermore is there a
>>>>>>>>>>>>>>>>>>>>>>>>>>> problem that in our case CandID won't
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> be a 6digit? ( should we start it from
>>>>>>>>>>>>>>>>>>>>>>>>>>> 100000?)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> That would normally be the case but the
>>>>>>>>>>>>>>>>>>>>>>>>>>> numeric part of the PSCID get
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> paded with 0 on the left.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ex. for sequential ID made of center ID of
>>>>>>>>>>>>>>>>>>>>>>>>>>> `ABC` plus 4 numerical char
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> with a min value of 1, the sequence would be:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0002
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0010
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> thus sorting them ascending will always get
>>>>>>>>>>>>>>>>>>>>>>>>>>> the latest value generated
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> as the max value.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>>> melanie.legault2 at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I see, although the PSCID value is
>>>>>>>>>>>>>>>>>>>>>>>>>>> varchar(255), it must be stored
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> within a specific length of characters.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Otherwise if we were to sort
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> strings with different lengths the result
>>>>>>>>>>>>>>>>>>>>>>>>>>> would not be sorted correctly (
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1,
>>>>>>>>>>>>>>>>>>>>>>>>>>> 10, 11, 2 ).
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hello Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> There is no `last value` stored anywhere.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The code simply look for the PSCID with the
>>>>>>>>>>>>>>>>>>>>>>>>>>> max value and increase that
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> value by 1 in order to generate the next
>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this info help.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie Legault | Software developer |
>>>>>>>>>>>>>>>>>>>>>>>>>>> Faculty of Medicine | McGill
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> University
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on
>>>>>>>>>>>>>>>>>>>>>>>>>>> behalf of Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> how does Loris determine the next available
>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID value for a new
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate?
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> e.x in the default case the PSCID is
>>>>>>>>>>>>>>>>>>>>>>>>>>> sequential, but where do we store the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> last value for the sequential sequence?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the parameters in the mri_protocol you have
>>>>>>>>>>>>>>>>>>>>>>>>>>> assigned are global
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> standard? or were assigned after trial and
>>>>>>>>>>>>>>>>>>>>>>>>>>> error?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Given you have done the initial setup of
>>>>>>>>>>>>>>>>>>>>>>>>>>> your tables to match your
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> intended protocol/parameters according to
>>>>>>>>>>>>>>>>>>>>>>>>>>> instructions --
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the Troubleshooting guide documentation
>>>>>>>>>>>>>>>>>>>>>>>>>>> recommends
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes
>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> re-running the pipeline (and first deleting
>>>>>>>>>>>>>>>>>>>>>>>>>>> prior uploads).
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *if i were to change their status to resolve
>>>>>>>>>>>>>>>>>>>>>>>>>>> what would happen?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I noticed that i can view the mnics at the
>>>>>>>>>>>>>>>>>>>>>>>>>>> brainbrowser from the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations page ( those mnics are stored
>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/loris/data/trashbin/
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> if i were to click their issue to resolve
>>>>>>>>>>>>>>>>>>>>>>>>>>> what would happend? would they
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> appear in the dicom_archive view too? ).
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The defaut values of the schema exists in my
>>>>>>>>>>>>>>>>>>>>>>>>>>> local database. If i adjust
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the default values of TR_min and TE_min the
>>>>>>>>>>>>>>>>>>>>>>>>>>> mincs will be uploaded?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is it possible that you haven't set up your
>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table ?   (and
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_scan_type table too, for additional
>>>>>>>>>>>>>>>>>>>>>>>>>>> types of scans)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Like the psc table, this is a pre-requisite
>>>>>>>>>>>>>>>>>>>>>>>>>>> for the Imaging insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> setup : See the install/setup documentation :
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To add new rows, just use MySQL insert
>>>>>>>>>>>>>>>>>>>>>>>>>>> statements.  You can adapt the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> insert statements which load the default
>>>>>>>>>>>>>>>>>>>>>>>>>>> table values --> e.g. Here on
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> GitHub :
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (see also the mri_scan_type table)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I see that i can edit the values but not how
>>>>>>>>>>>>>>>>>>>>>>>>>>> to insert new rows.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If i choose Inserted with flag then will the
>>>>>>>>>>>>>>>>>>>>>>>>>>> minc be inserted?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear that *dcmodify* worked
>>>>>>>>>>>>>>>>>>>>>>>>>>> correctly.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the MRI Violations module, the
>>>>>>>>>>>>>>>>>>>>>>>>>>> screenshot is enough.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It says "could not identify scan type",
>>>>>>>>>>>>>>>>>>>>>>>>>>> which we knew already.  Did you
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> click on the link on those words?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It will take you to the next page of the
>>>>>>>>>>>>>>>>>>>>>>>>>>> module, showing for each scan
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> what the scan parameters were, and will also
>>>>>>>>>>>>>>>>>>>>>>>>>>> show for comparison what's
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> stored in your *mri_protocol* table.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Compare these values to find which parameter
>>>>>>>>>>>>>>>>>>>>>>>>>>> was not correct according
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to your *mri_protocol* table scan type
>>>>>>>>>>>>>>>>>>>>>>>>>>> definitions.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You may end up broadening your mri_protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>> value ranges (e.g. TR, TE)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> for scans.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> This can be done in the front-end, by
>>>>>>>>>>>>>>>>>>>>>>>>>>> editing the database table
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> directly in the same subpage of the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>> Violations module.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The MRI Violations module features are
>>>>>>>>>>>>>>>>>>>>>>>>>>> explained in more detail in the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Help text for this module inside LORIS
>>>>>>>>>>>>>>>>>>>>>>>>>>> (click the  ["?"] icon in the menu
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> bar.)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> :  no MINCs inserted- violated scans
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looks like my previous email's attachment
>>>>>>>>>>>>>>>>>>>>>>>>>>> wasn't delivered due to
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> security reasons, i uploaded my file at
>>>>>>>>>>>>>>>>>>>>>>>>>>> google drive
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> From Dicat's view seems that dcmodify worked
>>>>>>>>>>>>>>>>>>>>>>>>>>> in both cases
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the mri_violations i attached the .html
>>>>>>>>>>>>>>>>>>>>>>>>>>> output from webbrowser, so
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that you can check the filelds easier.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios --
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Great, sounds like more progress.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> About the dcmodify command -- I'm not sure
>>>>>>>>>>>>>>>>>>>>>>>>>>> why you're getting an Endian
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> warning.  (it's a warning not an error,
>>>>>>>>>>>>>>>>>>>>>>>>>>> correct?)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To clarify -- Were the DICOM headers
>>>>>>>>>>>>>>>>>>>>>>>>>>> (PatientName) all successfully
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> relabelled, after the command ran?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You can use also our DICAT tool (
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/DICAT) to
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> verify and/or update local DICOM headers --
>>>>>>>>>>>>>>>>>>>>>>>>>>> though your dcmodify command is
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a great and fast solution for bulk header
>>>>>>>>>>>>>>>>>>>>>>>>>>> updates.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If you're concerned about fields being
>>>>>>>>>>>>>>>>>>>>>>>>>>> changed (e.g. "(2001,105f)" from
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the warning message)  - you can also dcmdump
>>>>>>>>>>>>>>>>>>>>>>>>>>> a DICOM slice before and look
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at these fields specifically.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's also not a bad "sanity check" to backup
>>>>>>>>>>>>>>>>>>>>>>>>>>> your DICOMS before/after
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> running dcmodify, and use dcmdump on each
>>>>>>>>>>>>>>>>>>>>>>>>>>> version to diff the outputs --
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> this will pinpoint what changed.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Re the protocol violation --
>>>>>>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol not recognized or
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> unknown :   this means your scans did not
>>>>>>>>>>>>>>>>>>>>>>>>>>> match what is stored in your
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_protocol table.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Check the MRI Violations front-end module --
>>>>>>>>>>>>>>>>>>>>>>>>>>> can you see why they didn't
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> match?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Send us an example, in addition to the
>>>>>>>>>>>>>>>>>>>>>>>>>>> contents of the mri_protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> table, if you can't find the source of the
>>>>>>>>>>>>>>>>>>>>>>>>>>> mismatch.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  Here is the psc table
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I created 2 candidates profiles through the
>>>>>>>>>>>>>>>>>>>>>>>>>>> interface
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> then runned dcmodify command to a dicom file
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1"
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and got those warning: is this okay?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify at another Dicom didn't show
>>>>>>>>>>>>>>>>>>>>>>>>>>> warnings. Below you can see the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> execution for the second dicom. Mnics could
>>>>>>>>>>>>>>>>>>>>>>>>>>> not be inserted due to
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> AcquisitionProtocol being unknown.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Running now the following command:
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> imaging_upload_file.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 12
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  find -path
>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX'
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -delete
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dicomTar.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database
>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  Source: /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Target: /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Testing for database connectivity.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Database is available.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You will archive the dir :
>>>>>>>>>>>>>>>>>>>>>>>>>>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You are creating a tar with the following
>>>>>>>>>>>>>>>>>>>>>>>>>>> command:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> tar -cf
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> getting md5sums and gzipping!!
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :
>>>>>>>>>>>>>>>>>>>>>>>>>>> 127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :    Linux
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>>>>>> 2019-09-06 18:36:50
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Removing temporary files from target location
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Done adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -uploadID 12 -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  md5sum
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Set centerID = 1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Number of MINC files that will be considered
>>>>>>>>>>>>>>>>>>>>>>>>>>> for inserting into the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> database: 2
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log
>>>>>>>>>>>>>>>>>>>>>>>>>>> file is
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log
>>>>>>>>>>>>>>>>>>>>>>>>>>> file is
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>> cat
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Acquisition protocol is unknown
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>   --> The minc file cannot be registered
>>>>>>>>>>>>>>>>>>>>>>>>>>> since the AcquisitionProtocol
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> is unknown
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sure -- you can delete imaging datasets with
>>>>>>>>>>>>>>>>>>>>>>>>>>> the *delete_imaging_upload*
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> script --
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> details here:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> What's in your *psc* table?  (Is it properly
>>>>>>>>>>>>>>>>>>>>>>>>>>> populated? This is a
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> pre-requisite to loading imaging data.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database
>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The foreign key constraint error on the
>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate record is curious.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> There are also a few options for creating
>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates when inserting
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> imaging data:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then
>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a. via the LORIS API -- Create the
>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates (and visits, optionally I
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> think)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How to:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by
>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Then as a second step:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> b. Use the imaging insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets
>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to load your DICOMs.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You will want to first ensure that the
>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName header in the DICOMs
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> as well as tar package are correctly
>>>>>>>>>>>>>>>>>>>>>>>>>>> labelled with PSCID_DCCID_VisitLabel
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How to :
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options
>>>>>>>>>>>>>>>>>>>>>>>>>>> when running the bids_import script,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to automatically create your candidates and
>>>>>>>>>>>>>>>>>>>>>>>>>>> sessions.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How do i delete a Study? And everytime do i
>>>>>>>>>>>>>>>>>>>>>>>>>>> have to create a new
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate to get DCCID and a PSCID?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *First execution:*
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile
>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern
>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or
>>>>>>>>>>>>>>>>>>>>>>>>>>> update a child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`,
>>>>>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_candidate_1`
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`)
>>>>>>>>>>>>>>>>>>>>>>>>>>> REFERENCES `psc` (`CenterID`)) at
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ERROR: Failed to insert record in table
>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_scanner:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The following database commands failed:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SET
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Medical Systems';
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Error obtained:Cannot add or update a child
>>>>>>>>>>>>>>>>>>>>>>>>>>> row: a foreign key
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`,
>>>>>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_mri_scanner_1`
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES
>>>>>>>>>>>>>>>>>>>>>>>>>>> `candidate` (`CandID`)) (error code 1452)
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ERROR: The validation has failed. Either
>>>>>>>>>>>>>>>>>>>>>>>>>>> re-run the validation again
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and fix the problem. Or re-run
>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader.pl using -force to force the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> execution.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The tarchiveLoader.pl insertion script has
>>>>>>>>>>>>>>>>>>>>>>>>>>> failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory
>>>>>>>>>>>>>>>>>>>>>>>>>>> at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *And second execution: *
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile
>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern
>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PROBLEM:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The user 'lorisadmin' has already inserted
>>>>>>>>>>>>>>>>>>>>>>>>>>> this study.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The unique study ID is
>>>>>>>>>>>>>>>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> This is the information retained from the
>>>>>>>>>>>>>>>>>>>>>>>>>>> first time the study was
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> inserted:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :
>>>>>>>>>>>>>>>>>>>>>>>>>>> 127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :    Linux
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>>>>>> 2019-09-04 18:33:05
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Last update of record:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The dicomTar.pl execution has failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory
>>>>>>>>>>>>>>>>>>>>>>>>>>> at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ok, this sounds like good progress.  Let us
>>>>>>>>>>>>>>>>>>>>>>>>>>> know when you next encounter
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> issues as you progress through the Imaging
>>>>>>>>>>>>>>>>>>>>>>>>>>> Install/Setup docs
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>>>>>> >.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I'll look into how we can better handle the
>>>>>>>>>>>>>>>>>>>>>>>>>>> incoming/ directory next
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> time.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> populated correctly except its port is
>>>>>>>>>>>>>>>>>>>>>>>>>>> 'port'    : ''. Also i have tested
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that i can connect to MySQL with lorisuser.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I executed the script again, because the
>>>>>>>>>>>>>>>>>>>>>>>>>>> only error i had previously was
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that the /data/incoming folder didn't exist
>>>>>>>>>>>>>>>>>>>>>>>>>>> and there are no errors
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> reported back except of warnings <<mysql:
>>>>>>>>>>>>>>>>>>>>>>>>>>> [Warning] Using a password on the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> command line interface can be insecure>>.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's possible -- if the script was unable to
>>>>>>>>>>>>>>>>>>>>>>>>>>> connect to the database
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> during its execution (e.g. typo in the
>>>>>>>>>>>>>>>>>>>>>>>>>>> password), that would explain the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> underpopulated Image path and Loris-MRI code
>>>>>>>>>>>>>>>>>>>>>>>>>>> path you saw in the Config
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> module.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's hard to tell without seeing the output
>>>>>>>>>>>>>>>>>>>>>>>>>>> from your script run -- Did
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you see a sign of any such error?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The Config fields are populated by the
>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_install.sh script (starting
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at line 222
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222
>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For example, check if the database
>>>>>>>>>>>>>>>>>>>>>>>>>>> connection information was populated
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> accurately in
>>>>>>>>>>>>>>>>>>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If you are referring to the
>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_install.sh here is an image with the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> configurations i typed. Maybe the problem is
>>>>>>>>>>>>>>>>>>>>>>>>>>> somewhere at the last part
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> which asks to configure as much as possible
>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear your LORIS core install is up
>>>>>>>>>>>>>>>>>>>>>>>>>>> and working and all the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> front-end pages are loading.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$
>>>>>>>>>>>>>>>>>>>>>>>>>>> chmod 775 project
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > and the web interface worked.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, it's important that project/ have 775
>>>>>>>>>>>>>>>>>>>>>>>>>>> permissions and that
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> lorisadmin be part of the sudoers group, per
>>>>>>>>>>>>>>>>>>>>>>>>>>> step 1 in the install
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Readme <
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris#install-steps>.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image
>>>>>>>>>>>>>>>>>>>>>>>>>>> should change LORIS to
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris, right?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> These imaging paths will be updated during
>>>>>>>>>>>>>>>>>>>>>>>>>>> your imaging installation
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup>
>>>>>>>>>>>>>>>>>>>>>>>>>>> by an automated script --
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you do not need to set them manually via the
>>>>>>>>>>>>>>>>>>>>>>>>>>> Config module.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Please continue to follow the Setup Guide
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup>
>>>>>>>>>>>>>>>>>>>>>>>>>>> for detailed steps to follow.
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image
>>>>>>>>>>>>>>>>>>>>>>>>>>> should change LORIS to loris,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> right?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i used
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> curl -sL
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://deb.nodesource.com/setup_8.x | sudo -E
>>>>>>>>>>>>>>>>>>>>>>>>>>> bash -
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sudo apt-get install -y nodejs
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you had suggested in the past, make worked
>>>>>>>>>>>>>>>>>>>>>>>>>>> and now i can see all the
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> contents in the web-interface, but i don't
>>>>>>>>>>>>>>>>>>>>>>>>>>> need make install?
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> -------------- next part --------------
>>>>>>>>>>>>>>>>>>>>>>>>>>> An HTML attachment was scrubbed...
>>>>>>>>>>>>>>>>>>>>>>>>>>> URL: <
>>>>>>>>>>>>>>>>>>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html
>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16
>>>>>>>>>>>>>>>>>>>>>>>>>>> *****************************************
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>> Loris-dev mailing list
>>> Loris-dev at bic.mni.mcgill.ca
>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>
>>
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From cecile.madjar at mcin.ca  Fri Jan 31 09:38:44 2020
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Fri, 31 Jan 2020 09:38:44 -0500
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAKHj7uSNm=OX8jaDJ0-TZZsBA8zm3Uv6yErBSy76EnwUWdpsig@mail.gmail.com>
References: <mailman.1851.1573565332.16403.loris-dev@bic.mni.mcgill.ca>
 <CAEfMBom1HCWLo4NWgt5XG4625tCBfRT_Z_HepvtT_Er2LKbJoA@mail.gmail.com>
 <CAKHj7uS1AdMDjnacouTvxZgziYVgp5NNUeOuMkpDyrTskGTh-Q@mail.gmail.com>
 <CALbt7NDej8FGUUS6_oKbK5Fp-FnwsVz9AgZ6ZcJEZhmoKZmv8w@mail.gmail.com>
 <CAKHj7uSx-qqcXHZsWsZmSJ7sC1DgF+XapT5Y1+QdoVic37_DDg@mail.gmail.com>
 <CAMkiY3fQBGDGeNO8EHxwYAgbhTggNSQ+AVuCfdraDXwULMjjUg@mail.gmail.com>
 <CAKHj7uT5xXi=pOPdH=W9BroSphMHdTszdgW+GxuES=8wZox9eQ@mail.gmail.com>
 <CAMkiY3eUouxaRVdC4wH+vdjeQ=q_Nx8bcDNzcWgD_OgN77m3mw@mail.gmail.com>
 <CAKHj7uSxu4+tm+=x4+qJ1sAbrjmxG2H7LovDb7-2KMnyYQhrgg@mail.gmail.com>
 <CAMkiY3fdPZec2jx-cc2Zq37j3ekmTu_o819yBUv-bC7M98bkVw@mail.gmail.com>
 <CAKHj7uSZHozpuQ_YwGmy6wQ4tm43vJa556V0o2+JGDVsYaqN4g@mail.gmail.com>
 <CAMkiY3dge=x93bQDv0fHGMcrX0PA8Z_imLb_zSTh=nTrx5weFg@mail.gmail.com>
 <CAKHj7uR81gCkjvccMxwMA08dGSEgyTLJBJ+pZPkoUQDtGP_hFA@mail.gmail.com>
 <CAMkiY3fGhvExZ-JOvxeHe7dJQPvtPAHx3oJuiMVX7f1JgF1GAg@mail.gmail.com>
 <CAKHj7uRExO98Yyn9_07aw44wbh0bCL9_C1VFTAURKsxQLUuAeQ@mail.gmail.com>
 <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>
 <CAKHj7uRueb5fgh4VVCAyaq8tC9WM4gJ7k6Q=dxsqWzFgDqPfVQ@mail.gmail.com>
 <CAMkiY3d-Vt=3gQqwJ+GSRSacbLp2QxrB0g-_C7ONd8j_g1ipoQ@mail.gmail.com>
 <CAKHj7uQt9=nokz5g1zBuBx1-rJ8q7qKOuNVkQugC9wfvNFcjVA@mail.gmail.com>
 <CAMkiY3cAuQfT_5iMzYoF2BXVceu_vgz4eCq2sAtoyse+zUYeSg@mail.gmail.com>
 <CAMkiY3dq1O3V8+r4tTAWQ8N=rVFg=DNY-UPeMqbec+MSayj=Cg@mail.gmail.com>
 <CAKHj7uSEegvE1apPBGVyHmjyVzF+YxJjDMg0b+hDE4_-ON+dYw@mail.gmail.com>
 <CAKHj7uRx1NT7CycFq65uFpgPiOVwvT-jtK1NJX6_3rrLNFwdbA@mail.gmail.com>
 <CAMkiY3dAnkLdc4N=REmeCpX2qBfsQf=wRb=YtHtt20f8adXFyw@mail.gmail.com>
 <CAKHj7uRpA-8kzkoEnAk7JBNLP7v4cmK4zW-gMutHESiFGj7xjw@mail.gmail.com>
 <CAMpvQ9hNLxz9SZsJwWec_yQ3R4KGhnqv3CDaSPOB1exPsO5AJA@mail.gmail.com>
 <CAMpvQ9gTQUGvmd7E8_Mnk7sd8HtX4NHvLCfWZ0-hEi9aJuu_nw@mail.gmail.com>
 <CAKHj7uSNm=OX8jaDJ0-TZZsBA8zm3Uv6yErBSy76EnwUWdpsig@mail.gmail.com>
Message-ID: <CAMkiY3dGcQDPCfr9BDOUY3NEgoskTkU7D99FrkvmqPagKtAROQ@mail.gmail.com>

Hi Sotirios,

Actually, is it possible that 'file' is not installed on your VM. I misread
the error in my earlier email and it might be crashing in MRI.pm at line
1523 of your code. In that line, 'file' is used to determine if the file is
a DICOM, if not, it will show a warning and not count the file as a DICOM.
So in the end, none of your files are considered DICOM files and when it
comes to convert the list of DICOMs, there is nothing to convert, hence the
number of MINC file = 0.

Anyway, I have a feeling this might be the issue you are having.

Let me know how it goes,

C?cile

On Fri, Jan 31, 2020 at 9:23 AM Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:

> Hi Ling,
>
> Yes it's Loris-mri 21.0. One thought i had is that maybe i should define
> root as linux user?
> https://github.com/aueb-wim/LORIS-for-MIP/blob/master/docs/pics/loris_docker_imaging_install.png.
> But i see no difference either when i execute it as lorisadmin.
>
> Also here are the files we use
> https://github.com/aueb-wim/LORIS-for-MIP/tree/master/mri_loris
>
> And here is the complete output of the batch execution.
>
> Use of uninitialized value $_ in pattern match (m//) at
> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
> Running now the following command: /data/loris/data//uploadNeuroDB/
> imaging_upload_file.pl -profile prod -upload_id 35
> /data/incoming/DCC0000_956912_V1.tar.gz -verbose
>
>  find -path \/data\/tmp\/ImagingUpload\-14\-15\-z2B0N3 -name '__MACOSX'
> -delete
> xargs: file: No such file or directory
>
> dicomTar.pl \/data\/tmp\/ImagingUpload\-14\-15\-z2B0N3
> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>  Source: /data/tmp/ImagingUpload-14-15-z2B0N3
> Target: /data/loris/data/tarchive
>
> Testing for database connectivity.
> Database is available.
>
> You will archive the dir : ImagingUpload-14-15-z2B0N3
>
> You are creating a tar with the following command:
>
> tar -cf /data/loris/data/tarchive/ImagingUpload-14-15-z2B0N3.tar
> ImagingUpload-14-15-z2B0N3
>
>
> getting md5sums and gzipping!!
>
> * Taken from dir                   :
>  /data/tmp/ImagingUpload-14-15-z2B0N3
> * Archive target location          :
>  /data/loris/data/tarchive/DCM_2015-09-07_ImagingUpload-14-15-z2B0N3.tar
> * Name of creating host            :    172.28.1.1
> * Name of host OS                  :    Linux
> * Created by user                  :    lorisadmin
> * Archived on                      :    2020-01-31 14:15:04
> * dicomSummary version             :    1
> * dicomTar version                 :    1
> * md5sum for DICOM tarball         :    fcaf54e9078705799b10e08c4d34bf70
>  ImagingUpload-14-15-z2B0N3.tar
> * md5sum for DICOM tarball gzipped :    52c96cd08d168e659b5c73cb77b4621b
>  ImagingUpload-14-15-z2B0N3.tar.gz
> * md5sum for complete archive      :    f5103ec688a5921a37d3c95cba8598e0
>  DCM_2015-09-07_ImagingUpload-14-15-z2B0N3.tar
>
> Adding archive info into database
>
>
> Removing temporary files from target location
>
>
> Done adding archive info into database
>
> \/data\/loris\/data\//uploadNeuroDB/tarchiveLoader.pl -globLocation
> -profile prod
> \/data\/loris\/data\/tarchive\/\/DCM_2015\-09\-07_ImagingUpload\-14\-15\-z2B0N3\.tar
> -uploadID 35 -verbose
>  md5sum
> /data/loris/data/tarchive/DCM_2015-09-07_ImagingUpload-14-15-z2B0N3.tar
> PSCID is: DCC0000
>  CandID id: 956912
>  visit_label is: V1
> PSCID is: DCC0000
>  CandID id: 956912
>  visit_label is: V1
> candidate id 956912
> Set centerID = 1
> PSCID is: DCC0000
>  CandID id: 956912
>  visit_label is: V1
> PSCID is: DCC0000
>  CandID id: 956912
>  visit_label is: V1
> xargs: file: No such file or directory
>
> Number of MINC files that will be considered for inserting into the
> database: 0
>
> No data could be converted into valid MINC files.
>
> The tarchiveLoader.pl insertion script has failed.
> Use of uninitialized value $mail_user in concatenation (.) or string at
> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
> Can't exec "mail": No such file or directory at /data/loris/bin/mri/
> batch_uploads_imageuploader.pl line 249.
> print() on closed filehandle MAIL at /data/loris/bin/mri/
> batch_uploads_imageuploader.pl line 250.
> print() on closed filehandle MAIL at /data/loris/bin/mri/
> batch_uploads_imageuploader.pl line 251.
>
> ???? ???, 30 ??? 2020 ???? 6:22 ?.?., ?/? Ling Ma <lingyun.ma at mcin.ca>
> ??????:
>
>> Oh, I just found that you are using Loris-mri 21.0, as I stated in the
>> previous email, the "$_" could not find any matches, so your command might
>> not be correctly entered.
>>
>> On Thu, Jan 30, 2020 at 10:35 AM Ling Ma <lingyun.ma at mcin.ca> wrote:
>>
>>> Hi Sotirios,
>>>
>>> By curiosity, I just looked at the error message, "Use of uninitialized
>>> value $_ in pattern match (m//) at /data/loris/bin/mri/
>>> batch_uploads_imageuploader.pl line 144." clearly means that there is
>>> no match, but 144 line has no such code related with $_ in recent versions
>>> of the batch_uploads_imageuploader.pl. There is something in the line
>>> 165 for a few recent versions.
>>>
>>> As to "xargs: file: No such file or directory", it could be due to a
>>> command unable to find anything using the directory provided as the message
>>> suggested.
>>>
>>> In both cases, I feel that it could be helpful if you provide more
>>> details such as which Loris_MRI version you are running, what is the exact
>>> command line you are using to help supporters to understand.
>>>
>>> Thanks.
>>>
>>> Best regards,
>>> Ling Ma
>>> Consultant
>>>
>>> On Wed, Jan 29, 2020 at 6:57 PM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>>> Hi Cecile,
>>>>
>>>> it seems that xargs is already installed in our docker container.
>>>>
>>>> [image: image.png]
>>>>
>>>>
>>>> ???? ???, 29 ??? 2020 ???? 7:59 ?.?., ?/? Cecile Madjar <
>>>> cecile.madjar at mcin.ca> ??????:
>>>>
>>>>> Hi Sotirios,
>>>>>
>>>>> It looks like xargs is not installed in your docker environment.
>>>>>
>>>>> This is being used by the following command in dicomTar.pl (and a few
>>>>> other places but that is the one causing the error at the moment):
>>>>>
>>>>> $cmd = "cd " . $dcm_source . "; find -type f -name '.*' | *xargs* rm
>>>>> -f";
>>>>>
>>>>> So you need to install xargs in your docker for the command to run.
>>>>>
>>>>> Hope this helps,
>>>>>
>>>>> C?cile
>>>>> On Wed, Jan 29, 2020 at 10:35 AM Sotirios Nikoloutsopoulos <
>>>>> sotirisnik at gmail.com> wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> We are making a dockerized version of Loris 21 and when we execute
>>>>>> the batch_uploads_imageuploader.pl we get an error about xargs. What
>>>>>> could be the casue?
>>>>>>
>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>>>>>> Running now the following command: /data/loris/data//uploadNeuroDB/
>>>>>> imaging_upload_file.pl -profile prod -upload_id 13
>>>>>> /data/incoming/DCC0007_854380_V1.tar.gz -verbose
>>>>>>
>>>>>>  find -path \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml -name
>>>>>> '__MACOSX' -delete
>>>>>> xargs: file: No such file or directory
>>>>>>
>>>>>> dicomTar.pl \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml
>>>>>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>>>>>>  Source: /data/tmp/ImagingUpload-15-31-U_O5ml
>>>>>> Target: /data/loris/data/tarchive
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> ???? ???, 10 ??? 2019 ???? 7:21 ?.?., ?/? Sotirios Nikoloutsopoulos <
>>>>>> sotirisnik at gmail.com> ??????:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> i opened an issue and looked up for the values of Volume they
>>>>>>> suggested https://github.com/BIC-MNI/minc-toolkit-v2/issues/95. The
>>>>>>> only attributes associated with it i saw are [0x00089206] and [0x00089207]
>>>>>>>
>>>>>>> [image: image.png]
>>>>>>>
>>>>>>> I looked up for the file that was being viewed fine in the
>>>>>>> BrainBrowser and saw that it had that attribute empty so i used this
>>>>>>> command because i couldn't find a way to modify the attribute via pydicom
>>>>>>>
>>>>>>> dcmodify -ma "(0008,9206)=" *.dcm
>>>>>>>
>>>>>>> and that command reported the warning about the Endian Syntax. I
>>>>>>> also used the corresponding command for 9207 and got the message "Tag not
>>>>>>> found'
>>>>>>>
>>>>>>> Lastly I tried to upload some dicoms and now i am getting the SNR
>>>>>>> and i can view them fine. I believe now that all of them will pass
>>>>>>> successfully, i will report back later.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Sotirios
>>>>>>>
>>>>>>> ???? ???, 9 ??? 2019 ???? 8:10 ?.?., ?/? Cecile Madjar <
>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>
>>>>>>>> Hi Sotirios,
>>>>>>>>
>>>>>>>> The issue you are having is a indeed a dcm2mnc issue. The converter
>>>>>>>> does not seem to work on your dataset for some reason. Unfortunately, there
>>>>>>>> is not much we can do on our front to fix this...
>>>>>>>>
>>>>>>>> I would recommend creating an issue on the MINC tools repository
>>>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> so they can
>>>>>>>> fix your problem.
>>>>>>>>
>>>>>>>> Very sorry that you are having that problem.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>>
>>>>>>>> C?cile
>>>>>>>>
>>>>>>>> On Wed, Dec 4, 2019 at 8:59 AM Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Hi Sotirios,
>>>>>>>>>
>>>>>>>>> Could you please share a dataset with us that produces the error
>>>>>>>>> you get and the weird display in BrainBrowser? You could use the same SFTP
>>>>>>>>> credential that Nicolas gave you.
>>>>>>>>>
>>>>>>>>> The message errors you got from imaging_install.sh are probably
>>>>>>>>> due to the fact that you reran the install script and it tried to reinstall
>>>>>>>>> something that was already there. I would not worry about it. FYI, the only
>>>>>>>>> thing you needed to do was to update the MINC tools path in the environment
>>>>>>>>> file as you did after re-running imaging_install.sh and source the
>>>>>>>>> environment file.
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>>
>>>>>>>>> C?cile
>>>>>>>>>
>>>>>>>>> On Wed, Dec 4, 2019 at 8:03 AM Sotirios Nikoloutsopoulos <
>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>>  Hi Cecile,
>>>>>>>>>>
>>>>>>>>>> We used minctool 1.9.7 and we still get this error
>>>>>>>>>>
>>>>>>>>>> <<Restructuring...
>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>> noise_estimate --snr /data/loris/data>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> One dicom folder hadn't that error and is being viewed fine in
>>>>>>>>>> the BrainBrowser of Loris.
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> When i used dpkg to the 1.9.17 the installation reported fine
>>>>>>>>>> <<Unpacking minc-toolkit-v2 (1.9.17) over (1.9.16) ...>>
>>>>>>>>>>
>>>>>>>>>> and then i used source /opt/minc/1.9.17/minc-toolkit-config.sh
>>>>>>>>>>
>>>>>>>>>> and aftewards runned bash ./imaging_install.sh just to be sure.
>>>>>>>>>>
>>>>>>>>>> We also had to modify /data/loris/bin/mri/environment because it
>>>>>>>>>> still pointed to the old version.
>>>>>>>>>>
>>>>>>>>>> What i found strange is this during the run of imaging_install.sh
>>>>>>>>>>
>>>>>>>>>> <<already using interpreter
>>>>>>>>>> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/bin/python3
>>>>>>>>>> Please use the *system* python to run this script
>>>>>>>>>> Traceback (most recent call last):
>>>>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py",
>>>>>>>>>> line 2632, in <module>
>>>>>>>>>>     main()
>>>>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py",
>>>>>>>>>> line 870, in main
>>>>>>>>>>     symlink=options.symlink,
>>>>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py",
>>>>>>>>>> line 1156, in create_environment
>>>>>>>>>>     install_python(home_dir, lib_dir, inc_dir, bin_dir,
>>>>>>>>>> site_packages=site_packages, clear=clear, symlink=symlink)
>>>>>>>>>>   File
>>>>>>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>>>>>>> line 357, in abspath
>>>>>>>>>>     if not isabs(path):
>>>>>>>>>>   File
>>>>>>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>>>>>>> line 64, in isabs
>>>>>>>>>>     return s.startswith(sep)
>>>>>>>>>> AttributeError: 'NoneType' object has no attribute 'startswith'
>>>>>>>>>> Installing the Python libraries into the loris-mri virtualenv...
>>>>>>>>>> Requirement already satisfied: mysqlclient in
>>>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (1.4.4)
>>>>>>>>>> Requirement already satisfied: mysql-connector in
>>>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (2.2.9)
>>>>>>>>>> Requirement already satisfied: pybids in
>>>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (0.9.4)
>>>>>>>>>> Requirement already satisfied: nibabel>=2.1 in ./python_virtua>>
>>>>>>>>>>
>>>>>>>>>> So should i open an issue for that error? or is there something
>>>>>>>>>> else to try?
>>>>>>>>>>
>>>>>>>>>> Thanks
>>>>>>>>>>
>>>>>>>>>> Sotirios
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 10:39 ?.?., ?/? Cecile Madjar <
>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> Does the pic screenshot in the imaging browser module also shows
>>>>>>>>>>> 1 slice? If so, that would mean there was an issue with the dcm2mnc
>>>>>>>>>>> conversion. Once again, installing the latest version of the MINC tools
>>>>>>>>>>> should help but if this issue persists I would recommend creating an issue
>>>>>>>>>>> for that too on their repository
>>>>>>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> (if not
>>>>>>>>>>> already reported there, there are a few known issue reported).
>>>>>>>>>>>
>>>>>>>>>>> Other viewer for MINCs are register and Display (both part of
>>>>>>>>>>> the MINC tools). For NIfTI, you have FSLeye, MRICron and probably many
>>>>>>>>>>> other viewers that exists.
>>>>>>>>>>>
>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>
>>>>>>>>>>> C?cile
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Dec 3, 2019 at 3:26 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>
>>>>>>>>>>>> Yes, Nifti files are mandatory for our work. From what we saw
>>>>>>>>>>>> at a 3rd vm we setted up, the nifti files are being created ( i haven't
>>>>>>>>>>>> verified if that is the case at the 2nd vm ). I will install the latest
>>>>>>>>>>>> version and will report back, but do you know any nifti/minc viewer?
>>>>>>>>>>>> because the Brainbrowser of Loris does not output them well, it's like it
>>>>>>>>>>>> is loading only 1 slice and we would like to verify it with another tool
>>>>>>>>>>>> too. We verified that the dcmconv command didn't affect the
>>>>>>>>>>>> quality of the .dcm files.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>
>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>
>>>>>>>>>>>> ???? ???, 2 ??? 2019 ???? 6:59 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>
>>>>>>>>>>>>> It looks like for some reason your binary mnc2nii is not
>>>>>>>>>>>>> working and reports that error. Do you want to create NIfTI files or are
>>>>>>>>>>>>> you happy with just the MINC files?
>>>>>>>>>>>>>
>>>>>>>>>>>>> If you don't need the NIfTI files, then maybe you can set the
>>>>>>>>>>>>> Config setting "NIfTI file creation" to No instead of Yes and
>>>>>>>>>>>>> this error will not appear anymore.
>>>>>>>>>>>>>
>>>>>>>>>>>>> If you need the NIfTI files to be created, then I would
>>>>>>>>>>>>> recommend installing the latest version of the MINC tools (1.9.17). They
>>>>>>>>>>>>> can be found there:
>>>>>>>>>>>>>
>>>>>>>>>>>>>    - pre-built packages:
>>>>>>>>>>>>>    https://packages.bic.mni.mcgill.ca/minc-toolkit/
>>>>>>>>>>>>>    - from the source code with installation instructions in
>>>>>>>>>>>>>    the README: https://github.com/BIC-MNI/minc-toolkit-v2
>>>>>>>>>>>>>
>>>>>>>>>>>>> If the problem persists by using the latest release of MINC
>>>>>>>>>>>>> tools, then create an issue on Github for the MINC developers
>>>>>>>>>>>>> here <https://github.com/BIC-MNI/minc-toolkit-v2/issues>.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>
>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks to Nicholas i was able to create all the mincs images.
>>>>>>>>>>>>>> The problem was that the files were in Little-Endian-Implicit transfer
>>>>>>>>>>>>>> syntax and i had to convert them Little-Endian-Explicit transfer syntax
>>>>>>>>>>>>>> with this command
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> find <root_of_my_DICOM_files_directory> -type f | xargs -i
>>>>>>>>>>>>>> dcmconv --write-xfer-little {} {}
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Looking back at our mails i saw that Little-Endian error had
>>>>>>>>>>>>>> occurred when i used dcmodify, but i switcthed to using pydicom instead.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> In the output i see an error sometimes about "gsl:
>>>>>>>>>>>>>> bessel_I0.c:216: ERROR: overflow". Is this okay?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Restructuring...
>>>>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>>>>> noise_estimate --snr
>>>>>>>>>>>>>> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
>>>>>>>>>>>>>> SNR is:
>>>>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thank you for the details!
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> A few things to try:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>    - modify the TMPDIR to be on your /data directory where
>>>>>>>>>>>>>>>    there might be more space to do processing (could create a /data/tmp where
>>>>>>>>>>>>>>>    the temporary files would be created)
>>>>>>>>>>>>>>>    - how many files are there for that upload in
>>>>>>>>>>>>>>>    tarchive_files? Are they different from the ones showing the warning
>>>>>>>>>>>>>>>    message?
>>>>>>>>>>>>>>>       - FYI: query to get that: SELECT tf.* FROM
>>>>>>>>>>>>>>>       tarchive_files tf JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your
>>>>>>>>>>>>>>>       uploadID> (the output of that query would be very
>>>>>>>>>>>>>>>       useful if you can provide it)
>>>>>>>>>>>>>>>       - how many series are there for that upload in
>>>>>>>>>>>>>>>    tarchive_series?
>>>>>>>>>>>>>>>    - FYI: query to get that: SELECT ts.* FROM
>>>>>>>>>>>>>>>       tarchive_series ts JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your
>>>>>>>>>>>>>>>       uploadID> (the output of that query would be very
>>>>>>>>>>>>>>>       useful if you can provide it)
>>>>>>>>>>>>>>>    - things are failing when the scripts try running the
>>>>>>>>>>>>>>>    following command: find
>>>>>>>>>>>>>>>    /tmp/TarLoad-23-43-ccugaa/ImagingUpload-23-43-6JCOTO -type f  |
>>>>>>>>>>>>>>>    /data/loris/bin/mri/dicom-archive/get_dicom_info.pl
>>>>>>>>>>>>>>>    -studyuid -series -echo -image -file  -attvalue 0018 0024 -series_descr
>>>>>>>>>>>>>>>    -stdin | sort -n -k1 -k2 -k7 -k3 -k6 -k4  | cut -f 5 | dcm2mnc -dname ''
>>>>>>>>>>>>>>>    -stdin -clobber -usecoordinates /tmp/TarLoad-23-43-ccugaa
>>>>>>>>>>>>>>>       - clearly the problems come from get_dicom_info.pl
>>>>>>>>>>>>>>>       but I cannot pinpoint the error yet. I will ask around and get back to you
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> If I cannot figure it out remotely, is there a way to have a
>>>>>>>>>>>>>>> call using zoom? This way you could share your screen with me and run the
>>>>>>>>>>>>>>> debugger on that script and hopefully we can figure out what is going on
>>>>>>>>>>>>>>> with those datasets?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks!
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Tue, Nov 26, 2019 at 5:17 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> In both my virtual machines
>>>>>>>>>>>>>>>> export TMPDIR=/tmp
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> In both vm also with dcm2mnc i get this output. Just to
>>>>>>>>>>>>>>>> verify that this passed in my 1st vm and produced mincs.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I attached the spool as a csv.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> And also one difference i found was this in the Loris-mri
>>>>>>>>>>>>>>>> code ( left 1st workable vm, right 2nd vm that has to be fixed, although i
>>>>>>>>>>>>>>>> changed it seems to be independent of the uninitialized value $_ )
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> that is puzzling... A few additional questions:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>    - what is the bash variable TMPDIR set to on the
>>>>>>>>>>>>>>>>>    environment file?
>>>>>>>>>>>>>>>>>    - could you try running separately dcm2mnc on the
>>>>>>>>>>>>>>>>>    DICOM folder to see if that works?
>>>>>>>>>>>>>>>>>    - could you send us the detailed log from the
>>>>>>>>>>>>>>>>>    notification spool table (SELECT * FROM notification_spool WHERE
>>>>>>>>>>>>>>>>>    UploadID=<your uploadID>) and send it back to us? Maybe there are some
>>>>>>>>>>>>>>>>>    additional clues that could help figuring out what is going on.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thank you!
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Tue, Nov 26, 2019 at 10:12 AM Sotirios Nikoloutsopoulos
>>>>>>>>>>>>>>>>> <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> I checked for the StudyInstacueUID at the files with "The
>>>>>>>>>>>>>>>>>> target directory does not contain a single DICOM file"" and their attribute
>>>>>>>>>>>>>>>>>> has a value.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Regarding the scouter and localizer, i modified the
>>>>>>>>>>>>>>>>>> settings in the imaging pipeline and now i don't get that error message,
>>>>>>>>>>>>>>>>>> but still it doesn't create the mnics.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> The errors i am getting are ( uninitialized value $_ is
>>>>>>>>>>>>>>>>>> not important? because i haven't got comments about that )
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line
>>>>>>>>>>>>>>>>>> 144.
>>>>>>>>>>>>>>>>>> Running now the following command:
>>>>>>>>>>>>>>>>>> /data/loris/data//uploadNeuroDB/imaging_upload_file.pl
>>>>>>>>>>>>>>>>>> -profile prod -upload_id 134 /data/incoming/DCC0025_118008_V1.tar.gz
>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> and
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for
>>>>>>>>>>>>>>>>>> inserting into the database: 0
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> No data could be converted into valid MINC files.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> The tarchiveLoader.pl insertion script has failed.
>>>>>>>>>>>>>>>>>> Use of uninitialized value $mail_user in concatenation
>>>>>>>>>>>>>>>>>> (.) or string at /data/loris/bin/mri/
>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line
>>>>>>>>>>>>>>>>>> 249.
>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 250.
>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 251.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> OK. So the issue I mentioned should not be a problem for
>>>>>>>>>>>>>>>>>>> you.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Is the StudyInstanceUID DICOM header set in your images?
>>>>>>>>>>>>>>>>>>> If it is not set, then you would end up with the error message "The target
>>>>>>>>>>>>>>>>>>> directory does not contain a single DICOM file". So maybe this is the issue
>>>>>>>>>>>>>>>>>>> you are having with those datasets?
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Regarding not excluding series descriptions, you can
>>>>>>>>>>>>>>>>>>> configure that in the Config module under the Imaging Pipeline section.
>>>>>>>>>>>>>>>>>>> Simply remove all entries for the "Series description to exclude from
>>>>>>>>>>>>>>>>>>> imaging insertion" setting.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Mon, Nov 25, 2019 at 9:58 AM Sotirios
>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> We are using this version
>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/archive/v21.0.0.zip. Is
>>>>>>>>>>>>>>>>>>>> it possible to insert low resolution now?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, <
>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Which version of LORIS-MRI are you using?
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> There was a bug that got resolved in 20.2 in
>>>>>>>>>>>>>>>>>>>>> get_dicom_info.pl. Basically, if a DICOM did not have
>>>>>>>>>>>>>>>>>>>>> the (0020,0032) header, get_dicom_info.pl considered
>>>>>>>>>>>>>>>>>>>>> that the file was not a DICOM, which was a mistake. This got fixed in
>>>>>>>>>>>>>>>>>>>>> version 20.2 of LORIS-MRI. Hopefully this is the issue you are encountering.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> About scout and localizer, they are a type of short
>>>>>>>>>>>>>>>>>>>>> and low resolution sequence that is used by the tech but is of no interest
>>>>>>>>>>>>>>>>>>>>> scientifically, which is why we tend to no insert them.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios
>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> i executed the find command and the output i got per
>>>>>>>>>>>>>>>>>>>>>> folder was "DICOM medical imaging data. Maybe there is something wrong with
>>>>>>>>>>>>>>>>>>>>>> the find command in the warning that it is unable to check if the file is a
>>>>>>>>>>>>>>>>>>>>>> dicom file? Also when i use get_dicom_info.pl i
>>>>>>>>>>>>>>>>>>>>>> don't get any output data. Finally i don't understand what scout or
>>>>>>>>>>>>>>>>>>>>>> localizer is ( something like if and only if a file fails then the whole
>>>>>>>>>>>>>>>>>>>>>> session is invalid? ).
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>>>>>> Madjar <cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> I took a closer look to the
>>>>>>>>>>>>>>>>>>>>>>> batch_uploader_multiple_output.txt file you sent. It looks like there are
>>>>>>>>>>>>>>>>>>>>>>> different reasons for failure depending on the DICOM folder uploaded.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>    - For 465466 DCC0000 V1; 727195 DCC0004 V1 and
>>>>>>>>>>>>>>>>>>>>>>>    684908 DCC0007 V1: it looks like there is no file of type DICOM in the
>>>>>>>>>>>>>>>>>>>>>>>    folder. Have you checked to see if that is indeed the case? Maybe you can
>>>>>>>>>>>>>>>>>>>>>>>    try running the following command on that folder to see what are the types
>>>>>>>>>>>>>>>>>>>>>>>    of the files? If it does not return at least one DICOM medical imaging data
>>>>>>>>>>>>>>>>>>>>>>>    file, then that is why you get the error message from the pipeline:
>>>>>>>>>>>>>>>>>>>>>>>       -
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>       find <my_dicom_archive_root_folder> -type f | xargs -i file {}|cut -d: -f2|sort|uniq
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>       - For 864173 DCC0001 V1: it looks like there
>>>>>>>>>>>>>>>>>>>>>>>    are two different DICOM studies within the same folder. You will need to
>>>>>>>>>>>>>>>>>>>>>>>    split that study in two based on the StudyUID field as the insertion
>>>>>>>>>>>>>>>>>>>>>>>    pipeline does not allow for more than one StudyUID per upload.
>>>>>>>>>>>>>>>>>>>>>>>    - For 890807 DCC0002 V1; 637025 DCC0005 V1 and
>>>>>>>>>>>>>>>>>>>>>>>    239975 DCC0006 V1: it looks like the dcm2mnc command did not produce any
>>>>>>>>>>>>>>>>>>>>>>>    MINC files. Can you check in the DICOM archive what are the series present
>>>>>>>>>>>>>>>>>>>>>>>    in the tarchive for that visit? Maybe only a scout or localizer was
>>>>>>>>>>>>>>>>>>>>>>>    acquired for that session, hence the no valid MINC files (scout and
>>>>>>>>>>>>>>>>>>>>>>>    localizer being skipped for the conversion)
>>>>>>>>>>>>>>>>>>>>>>>    - For 397410 DCC0003 V1: it looks like
>>>>>>>>>>>>>>>>>>>>>>>    everything went well for this one.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> One script that is called by our pipeline is called
>>>>>>>>>>>>>>>>>>>>>>> get_dicom_info.pl and this does all kind of checks
>>>>>>>>>>>>>>>>>>>>>>> on the DICOM files (it is being called when running the dcm2mnc
>>>>>>>>>>>>>>>>>>>>>>> conversion). You could run it independently on your folder if needed.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Since one of the study got in, it does not look like
>>>>>>>>>>>>>>>>>>>>>>> you are having a problem with the setup. It seems more likely to be a
>>>>>>>>>>>>>>>>>>>>>>> problem with the data themselves.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hope this helps.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> In my first vm i am able to create the minc files
>>>>>>>>>>>>>>>>>>>>>>>> and view them at the mri browser (except of candidate 102761034 ),
>>>>>>>>>>>>>>>>>>>>>>>> meanwhile the same files gives warnings at the 2nd vm. The output  of the
>>>>>>>>>>>>>>>>>>>>>>>> batch upload can be seen in the file attached.
>>>>>>>>>>>>>>>>>>>>>>>> Also a colleague of us has built a pre-validation
>>>>>>>>>>>>>>>>>>>>>>>> tool for dicom
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/
>>>>>>>>>>>>>>>>>>>>>>>> which had found all the files that Loris gave as warning . Basically I
>>>>>>>>>>>>>>>>>>>>>>>> confirmed that the total amount of files per dicom was the same amount as
>>>>>>>>>>>>>>>>>>>>>>>> stated in Loris and checked some filenames given from warning to confirm
>>>>>>>>>>>>>>>>>>>>>>>> that they match with our tool. But that was months ago and my colleague had
>>>>>>>>>>>>>>>>>>>>>>>> changed some parameters for MIP and now our tool doesn't find all the
>>>>>>>>>>>>>>>>>>>>>>>> invalid files, that's why i asked for the dicom header specification of
>>>>>>>>>>>>>>>>>>>>>>>> Loris. In a discussion we had he mentioned that he doesn't check for some
>>>>>>>>>>>>>>>>>>>>>>>> tags e.x. orientation. Lastly to mention that in my first vm i didn't use
>>>>>>>>>>>>>>>>>>>>>>>> our tool to remove invalid dcm files.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> Can you provide us with some fresh particulars of
>>>>>>>>>>>>>>>>>>>>>>>>> the current issue and we'll take it from there?
>>>>>>>>>>>>>>>>>>>>>>>>> Yang's team has built these scripts which can
>>>>>>>>>>>>>>>>>>>>>>>>> definitely serve as a model for your pre-validation of your DICOM
>>>>>>>>>>>>>>>>>>>>>>>>> collections.
>>>>>>>>>>>>>>>>>>>>>>>>> cheers,
>>>>>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> HI Yang,
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> We make use of pydicom library too. Now about the
>>>>>>>>>>>>>>>>>>>>>>>>>> validate.py i see that you check if some attributes are missing such as
>>>>>>>>>>>>>>>>>>>>>>>>>> PatientID, PatientName which all of our files contains that info. Maybe i
>>>>>>>>>>>>>>>>>>>>>>>>>> have missed something on the setup of my other virtual machine ( although
>>>>>>>>>>>>>>>>>>>>>>>>>> one dicom passed on the new vm successfully, the others that were inserted
>>>>>>>>>>>>>>>>>>>>>>>>>> correctly on my old vm fails on the new one ), i think that i had asked
>>>>>>>>>>>>>>>>>>>>>>>>>> about this error "Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/
>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 144." but i
>>>>>>>>>>>>>>>>>>>>>>>>>> don't remember the solution.
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang
>>>>>>>>>>>>>>>>>>>>>>>>>> Ding <it at cnbp.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Hey, Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine from the LORIS team mentioned you had
>>>>>>>>>>>>>>>>>>>>>>>>>>> some issue with DICOM.  I am a fellow developer for an external project
>>>>>>>>>>>>>>>>>>>>>>>>>>> using LORIS, kind of just like you. We had to implement DICOM upload as
>>>>>>>>>>>>>>>>>>>>>>>>>>> well but more as a fully automated pipeline actually.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> While we were building CNBP, we had coded up
>>>>>>>>>>>>>>>>>>>>>>>>>>> some minor Python functions to check DICOM integrity (and simple
>>>>>>>>>>>>>>>>>>>>>>>>>>> validations) and you might be able to gain some inspiration from it and
>>>>>>>>>>>>>>>>>>>>>>>>>>> help you with your cause. For more comprehensive solution, PyDICOM (
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#)  seems
>>>>>>>>>>>>>>>>>>>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks
>>>>>>>>>>>>>>>>>>>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can
>>>>>>>>>>>>>>>>>>>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty
>>>>>>>>>>>>>>>>>>>>>>>>>>> rough around the edges but hopefully point you in the right direcitons
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Yang Ding, PhD.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Canadian Neonatal Brain Platform Architect
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM <
>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Send Loris-dev mailing list submissions to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> To subscribe or unsubscribe via the World Wide
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Web, visit
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>> or, via email, send a message with subject or
>>>>>>>>>>>>>>>>>>>>>>>>>>>> body 'help' to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-request at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> You can reach the person managing the list at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-owner at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> When replying, please edit your Subject line so
>>>>>>>>>>>>>>>>>>>>>>>>>>>> it is more specific
>>>>>>>>>>>>>>>>>>>>>>>>>>>> than "Re: Contents of Loris-dev digest..."
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Today's Topics:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>    1. Re: Import mri - scripts (Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Message: 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200
>>>>>>>>>>>>>>>>>>>>>>>>>>>> From: Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> To: Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Message-ID:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>         <CAKHj7uST=
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could we send you a link with 10 anonymized
>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom files to diagnose the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> warnings we get?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>> > We were wondering whether Loris has a tool to
>>>>>>>>>>>>>>>>>>>>>>>>>>>> check if there are problems
>>>>>>>>>>>>>>>>>>>>>>>>>>>> > with the dcm files, before trying to upload
>>>>>>>>>>>>>>>>>>>>>>>>>>>> them. Something that could
>>>>>>>>>>>>>>>>>>>>>>>>>>>> > provide the same results provided in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> warning_output, this is the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> > summary from the mri_upload at the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-page. Also which attributes of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> > dcm header would trigger a warning? is there
>>>>>>>>>>>>>>>>>>>>>>>>>>>> a dcm file header
>>>>>>>>>>>>>>>>>>>>>>>>>>>> > specification for Loris?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> > sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp
>>>>>>>>>>>>>>>>>>>>>>>>>>>> function it worked,but i
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> thought that something else was causing the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2nd issue.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Boucher, Mr, <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The first error occurs because the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> QCFirstChangeTime and columns are of
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> type `unsigned integer` and not `datatime`.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> You should be using
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW().
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The second error occurs because the trigger
>>>>>>>>>>>>>>>>>>>>>>>>>>>> triggers a rollback of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> insert statement in the files table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> See mysql documentation for trigger error
>>>>>>>>>>>>>>>>>>>>>>>>>>>> handling.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> An error during either a BEFORE or AFTER
>>>>>>>>>>>>>>>>>>>>>>>>>>>> trigger results in failure of
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the entire statement that caused trigger
>>>>>>>>>>>>>>>>>>>>>>>>>>>> invocation.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you for sharing that. I hope it helps.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Xavier
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on
>>>>>>>>>>>>>>>>>>>>>>>>>>>> behalf of Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> When mincs are inserted their corresponding
>>>>>>>>>>>>>>>>>>>>>>>>>>>> rows at the file table are
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> inserted too
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i would like to insert their rows at
>>>>>>>>>>>>>>>>>>>>>>>>>>>> file_qcstatus as well, because i
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> don't want manually to label them as passed
>>>>>>>>>>>>>>>>>>>>>>>>>>>> throught the interface
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> That is the trigger i wrote
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER
>>>>>>>>>>>>>>>>>>>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> BEGIN
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT INTO files_qcstatus
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SET FileID = NEW.FileID,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      SeriesUID = NEW.SeriesUID,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      EchoTime = NEW.EchoTime,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCStatus = "Pass",
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCFirstChangeTime = NOW(),
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCLastChangeTime = NOW();
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> END
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> although it contains some errors
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range
>>>>>>>>>>>>>>>>>>>>>>>>>>>> value for column
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or
>>>>>>>>>>>>>>>>>>>>>>>>>>>> update a child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails
>>>>>>>>>>>>>>>>>>>>>>>>>>>> (`LORIS`.`parameter_file`, CONSTRAINT
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY
>>>>>>>>>>>>>>>>>>>>>>>>>>>> (`FileID`) REFERENCES `files` (`FileID`))
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> In the mri_upload table, there is a
>>>>>>>>>>>>>>>>>>>>>>>>>>>> TarchiveID column associated with
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the MRI upload you inserted. When this
>>>>>>>>>>>>>>>>>>>>>>>>>>>> value is NULL, it means no DICOMs
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> were inserted into the tarchive tables. At
>>>>>>>>>>>>>>>>>>>>>>>>>>>> the end of the insertion of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DICOMs in the tarchive tables, this value
>>>>>>>>>>>>>>>>>>>>>>>>>>>> is updated with the correct
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> TarchiveID associated with the upload.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Could this correspond to what you want to
>>>>>>>>>>>>>>>>>>>>>>>>>>>> do?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Regarding the files_qcstatus, this table is
>>>>>>>>>>>>>>>>>>>>>>>>>>>> only linked to the files
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> table (hence, the MINC files). You could
>>>>>>>>>>>>>>>>>>>>>>>>>>>> always create a new table for
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive
>>>>>>>>>>>>>>>>>>>>>>>>>>>> table?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i would like whenever a dicom is imported
>>>>>>>>>>>>>>>>>>>>>>>>>>>> to mark all their
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> coressponding qc_status to "pass". I was
>>>>>>>>>>>>>>>>>>>>>>>>>>>> thinking of creating a trigger for
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that, but which tables do i need to add
>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries to? So far from what i see
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i need to add entres at  the table "files"
>>>>>>>>>>>>>>>>>>>>>>>>>>>> whenever an insertion happens to
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> files_qcstatus.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Oh, sorry i should have asked for StudyID,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> at the beginning of my email
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID).
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that's the Study Instance UID, not the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyID. So the StudyID i am
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looking for is not stored in the database?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The StudyUID is stored in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> DicomArchiveID field of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> tarchive table. It can also be found in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> metadata field but it is mixed
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> with many other information.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is StudyUID stored somewhere at the tables?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the tarchive table,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> specifically at the AcquisitonMetadata
>>>>>>>>>>>>>>>>>>>>>>>>>>>> column i found something called
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 'Unique Study ID" in its context, but that
>>>>>>>>>>>>>>>>>>>>>>>>>>>> must be the Study Instance UID.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Your observation is correct. A little
>>>>>>>>>>>>>>>>>>>>>>>>>>>> explanation below.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> MINC files get inserted into the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>> violation tables if:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - the scan type could not be identified
>>>>>>>>>>>>>>>>>>>>>>>>>>>> (not matching an entry in
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - one parameter of the scan type is out
>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the expected range
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    present in the mri_protocol_checks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> (extra filtering in case you need to be
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    stricker on some parameters not present
>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - if the CandID and PSCID do not match
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The following cases do not get in the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>> violation tables as it happens
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> before the conversion of the DICOM to MINC
>>>>>>>>>>>>>>>>>>>>>>>>>>>> files and only MINC files
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> violations are logged there:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - "No single DICOM" (since no valid
>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM could be found to convert
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    to MINC)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - "Study already inserted" (duplicate
>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID) since this error
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    happens at the dicomTar.pl level (way
>>>>>>>>>>>>>>>>>>>>>>>>>>>> before conversion into MINC files)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad everything is working out!!
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the mri passed, for some reason it consumed
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 5.12GB of ram. Now about the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations, dicoms are triggered to be
>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted there only if there is
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general
>>>>>>>>>>>>>>>>>>>>>>>>>>>> for its header parameter?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Because i don't see the cases of 'No single
>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom" or with the 2 studyiuid
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to be there.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sorry to hear you are having issues with
>>>>>>>>>>>>>>>>>>>>>>>>>>>> the memory. I think most of our
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB
>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should be fine.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> about that dicom that had that insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>> error it's about 30mb and when
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> it is being processed the ram is being
>>>>>>>>>>>>>>>>>>>>>>>>>>>> drastically increased from 2gb to
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3.28 and then the whole virtual machine is
>>>>>>>>>>>>>>>>>>>>>>>>>>>> frozen. What is the recommended
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> size of ram for using Loris?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to see that the StudyUID problem was
>>>>>>>>>>>>>>>>>>>>>>>>>>>> fixed!
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the delete script issue, if you are
>>>>>>>>>>>>>>>>>>>>>>>>>>>> absolutely certain that no
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> processes are run for that uploadID, you
>>>>>>>>>>>>>>>>>>>>>>>>>>>> can update the mri_upload table
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and set the column Inserting to 0 instead
>>>>>>>>>>>>>>>>>>>>>>>>>>>> of 1 for that uploadID. It
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looks like for some reason the scripts did
>>>>>>>>>>>>>>>>>>>>>>>>>>>> not update this field when it
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> stopped the insertion. Not sure why that
>>>>>>>>>>>>>>>>>>>>>>>>>>>> would be the case though.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Note: only do that update if you are
>>>>>>>>>>>>>>>>>>>>>>>>>>>> certain that there is no processing
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> happening.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> about the Dicoms i reported that didn't
>>>>>>>>>>>>>>>>>>>>>>>>>>>> have a StudyID they actually do
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I thought that this might be a permission
>>>>>>>>>>>>>>>>>>>>>>>>>>>> because "w" was missing at the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> group. After using chmod -R 775 only
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 102809579 passed, but with no mnic
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> files. Also now i have this error
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox
>>>>>>>>>>>>>>>>>>>>>>>>>>>> :/data/loris/bin/mri/tools$
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34
>>>>>>>>>>>>>>>>>>>>>>>>>>>> -ignore
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>>> is currently processing it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How can solve this?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Here is our auto dicom uploading python
>>>>>>>>>>>>>>>>>>>>>>>>>>>> script:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To give you a brief idea:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Per folder it will:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 1) Delete all the .bak files
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 2) Locate .dcm files and update the Patient
>>>>>>>>>>>>>>>>>>>>>>>>>>>> header
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3) Furthermore we are interesting in
>>>>>>>>>>>>>>>>>>>>>>>>>>>> finding TR_min, TR_max, TE_min,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> TE_max parameters of T1 protocol and do an
>>>>>>>>>>>>>>>>>>>>>>>>>>>> update at the mri_protocol table
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For some reason some files are missing
>>>>>>>>>>>>>>>>>>>>>>>>>>>> SeriesDescription/ProtocolName
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> In total i have 7 folders
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3/7 passed
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Also about the first patient with DC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>> had a violation "T1 AXIAL SE
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> GADO", but my script didn't output a TE of
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 17 nowhere and i find that weird
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> since Loris detects the SeriesDescription.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Now about the 4/7 that didn't passed
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 102327840 and 102809579 outputs "The target
>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory does not contain a
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> single DICOM file.", therefore they are
>>>>>>>>>>>>>>>>>>>>>>>>>>>> missing their StudyUID
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it
>>>>>>>>>>>>>>>>>>>>>>>>>>>> with data from multiple
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> studies."
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and 102761034 "No data could be converted
>>>>>>>>>>>>>>>>>>>>>>>>>>>> into valid MINC files.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> localizer, scout will not be considered!"
>>>>>>>>>>>>>>>>>>>>>>>>>>>> What is this?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If i wanted to force the insertion of
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 102327840, 102809579 and 102506134
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> can i just pass a flag parameter to
>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl? or
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> modify imaging_upload_file.pl?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PS
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To diagnose a folder search the name of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> folder at dicom_output.txt.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear about your progress.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, the script you used to delete imaging
>>>>>>>>>>>>>>>>>>>>>>>>>>>> data is fully documented here
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- let us know if you didn't find the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> answers you were looking for there.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (Is it possible the null row in
>>>>>>>>>>>>>>>>>>>>>>>>>>>> *mri_scanner* seen in your database
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> management software is a visual placeholder
>>>>>>>>>>>>>>>>>>>>>>>>>>>> for you as the user?  I'm not
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sure why a scanner would ever be registered
>>>>>>>>>>>>>>>>>>>>>>>>>>>> with ID='0' as your screenshot
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> showed.)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I fixed it with this
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I tried to create a new candidate using the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> API, is there something
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> wrong with the structure? why did i receive
>>>>>>>>>>>>>>>>>>>>>>>>>>>> a 500 internal error? In the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-error log it state that there is
>>>>>>>>>>>>>>>>>>>>>>>>>>>> something wrong with token, but i
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> verfied that the type of the token is a
>>>>>>>>>>>>>>>>>>>>>>>>>>>> string.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> [php7:error] [pid 4535] [client
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Uncaught TypeError: Argument 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> passed to
>>>>>>>>>>>>>>>>>>>>>>>>>>>> SinglePointLogin::JWTAuthenticate() must be of the type string,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> null given, called in
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> defined in
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> trace:\n#0
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> NDB_Client->initialize('/var/www/loris/...')\n#3
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST',
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Array)\n#5 {main}\n  thrown in
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is there a way also to delete candidates?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Just to let you know what i
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> did to clear candidates, because maybe i
>>>>>>>>>>>>>>>>>>>>>>>>>>>> may have missed dependencies.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> First i deleted all their uploads
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13
>>>>>>>>>>>>>>>>>>>>>>>>>>>> etc ( is there a way to omit
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the backup file ? )
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Afterwards i had some scanner candidates,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> so i deleted all the entries
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> from mri_scanner except that i couldn't
>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete this entry with the 0 ID.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Lastly i deleted the session and then the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> We recommend that you use our existing
>>>>>>>>>>>>>>>>>>>>>>>>>>>> tools for creating new candidates
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> - either the LORIS API or if you are using
>>>>>>>>>>>>>>>>>>>>>>>>>>>> a PHP script, by calling the Candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> class's createNew()
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >function.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> These will create the necessary records for
>>>>>>>>>>>>>>>>>>>>>>>>>>>> you.  (It's not recommended to
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> make direct modifications to mysql database
>>>>>>>>>>>>>>>>>>>>>>>>>>>> tables in your script, if I
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> understand you.)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The CandID should be a randomized 6 digit
>>>>>>>>>>>>>>>>>>>>>>>>>>>> randomized ID, and there are
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> multiple reasons for this.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You can use the PSCID for project-specific
>>>>>>>>>>>>>>>>>>>>>>>>>>>> IDs and the External ID field
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> in the candidate table can also be used for
>>>>>>>>>>>>>>>>>>>>>>>>>>>> any values you like.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Additionally, any number of custom IDs can
>>>>>>>>>>>>>>>>>>>>>>>>>>>> be added in parallel - these
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> are entered/visible in the Candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Information module and added in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> back-end as candidate parameters.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> We are building a script that will auto
>>>>>>>>>>>>>>>>>>>>>>>>>>>> insert the candidates based on
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> their ExternalID. We would like to know
>>>>>>>>>>>>>>>>>>>>>>>>>>>> whethere when we are creating a new
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> profile in the candidate table, if we also
>>>>>>>>>>>>>>>>>>>>>>>>>>>> have to insert a new record at
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> another table? Furthermore is there a
>>>>>>>>>>>>>>>>>>>>>>>>>>>> problem that in our case CandID won't
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> be a 6digit? ( should we start it from
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 100000?)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> That would normally be the case but the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> numeric part of the PSCID get
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> paded with 0 on the left.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ex. for sequential ID made of center ID of
>>>>>>>>>>>>>>>>>>>>>>>>>>>> `ABC` plus 4 numerical char
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> with a min value of 1, the sequence would
>>>>>>>>>>>>>>>>>>>>>>>>>>>> be:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0002
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0010
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> thus sorting them ascending will always get
>>>>>>>>>>>>>>>>>>>>>>>>>>>> the latest value generated
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> as the max value.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> melanie.legault2 at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I see, although the PSCID value is
>>>>>>>>>>>>>>>>>>>>>>>>>>>> varchar(255), it must be stored
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> within a specific length of characters.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Otherwise if we were to sort
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> strings with different lengths the result
>>>>>>>>>>>>>>>>>>>>>>>>>>>> would not be sorted correctly (
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1, 10, 11, 2 ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hello Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> There is no `last value` stored anywhere.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The code simply look for the PSCID with the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> max value and increase that
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> value by 1 in order to generate the next
>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this info help.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie Legault | Software developer |
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Faculty of Medicine | McGill
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> University
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on
>>>>>>>>>>>>>>>>>>>>>>>>>>>> behalf of Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> how does Loris determine the next available
>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID value for a new
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> e.x in the default case the PSCID is
>>>>>>>>>>>>>>>>>>>>>>>>>>>> sequential, but where do we store the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> last value for the sequential sequence?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the parameters in the mri_protocol you have
>>>>>>>>>>>>>>>>>>>>>>>>>>>> assigned are global
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> standard? or were assigned after trial and
>>>>>>>>>>>>>>>>>>>>>>>>>>>> error?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Given you have done the initial setup of
>>>>>>>>>>>>>>>>>>>>>>>>>>>> your tables to match your
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> intended protocol/parameters according to
>>>>>>>>>>>>>>>>>>>>>>>>>>>> instructions --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the Troubleshooting guide documentation
>>>>>>>>>>>>>>>>>>>>>>>>>>>> recommends
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> re-running the pipeline (and first deleting
>>>>>>>>>>>>>>>>>>>>>>>>>>>> prior uploads).
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *if i were to change their status to
>>>>>>>>>>>>>>>>>>>>>>>>>>>> resolve what would happen?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I noticed that i can view the mnics at the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> brainbrowser from the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations page ( those mnics are
>>>>>>>>>>>>>>>>>>>>>>>>>>>> stored at /data/loris/data/trashbin/
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> if i were to click their issue to resolve
>>>>>>>>>>>>>>>>>>>>>>>>>>>> what would happend? would they
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> appear in the dicom_archive view too? ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The defaut values of the schema exists in
>>>>>>>>>>>>>>>>>>>>>>>>>>>> my local database. If i adjust
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the default values of TR_min and TE_min the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> mincs will be uploaded?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is it possible that you haven't set up your
>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table ?   (and
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_scan_type table too, for additional
>>>>>>>>>>>>>>>>>>>>>>>>>>>> types of scans)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Like the psc table, this is a pre-requisite
>>>>>>>>>>>>>>>>>>>>>>>>>>>> for the Imaging insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> setup : See the install/setup documentation
>>>>>>>>>>>>>>>>>>>>>>>>>>>> :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To add new rows, just use MySQL insert
>>>>>>>>>>>>>>>>>>>>>>>>>>>> statements.  You can adapt the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> insert statements which load the default
>>>>>>>>>>>>>>>>>>>>>>>>>>>> table values --> e.g. Here on
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> GitHub :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (see also the mri_scan_type table)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I see that i can edit the values but not
>>>>>>>>>>>>>>>>>>>>>>>>>>>> how to insert new rows.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If i choose Inserted with flag then will
>>>>>>>>>>>>>>>>>>>>>>>>>>>> the minc be inserted?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear that *dcmodify* worked
>>>>>>>>>>>>>>>>>>>>>>>>>>>> correctly.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the MRI Violations module, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> screenshot is enough.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It says "could not identify scan type",
>>>>>>>>>>>>>>>>>>>>>>>>>>>> which we knew already.  Did you
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> click on the link on those words?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It will take you to the next page of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> module, showing for each scan
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> what the scan parameters were, and will
>>>>>>>>>>>>>>>>>>>>>>>>>>>> also show for comparison what's
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> stored in your *mri_protocol* table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Compare these values to find which
>>>>>>>>>>>>>>>>>>>>>>>>>>>> parameter was not correct according
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to your *mri_protocol* table scan type
>>>>>>>>>>>>>>>>>>>>>>>>>>>> definitions.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You may end up broadening your mri_protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>> value ranges (e.g. TR, TE)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> for scans.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> This can be done in the front-end, by
>>>>>>>>>>>>>>>>>>>>>>>>>>>> editing the database table
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> directly in the same subpage of the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Violations module.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The MRI Violations module features are
>>>>>>>>>>>>>>>>>>>>>>>>>>>> explained in more detail in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Help text for this module inside LORIS
>>>>>>>>>>>>>>>>>>>>>>>>>>>> (click the  ["?"] icon in the menu
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> bar.)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> :  no MINCs inserted- violated scans
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looks like my previous email's attachment
>>>>>>>>>>>>>>>>>>>>>>>>>>>> wasn't delivered due to
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> security reasons, i uploaded my file at
>>>>>>>>>>>>>>>>>>>>>>>>>>>> google drive
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> From Dicat's view seems that dcmodify
>>>>>>>>>>>>>>>>>>>>>>>>>>>> worked in both cases
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the mri_violations i attached the .html
>>>>>>>>>>>>>>>>>>>>>>>>>>>> output from webbrowser, so
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that you can check the filelds easier.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Great, sounds like more progress.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> About the dcmodify command -- I'm not sure
>>>>>>>>>>>>>>>>>>>>>>>>>>>> why you're getting an Endian
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> warning.  (it's a warning not an error,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> correct?)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To clarify -- Were the DICOM headers
>>>>>>>>>>>>>>>>>>>>>>>>>>>> (PatientName) all successfully
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> relabelled, after the command ran?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You can use also our DICAT tool (
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/DICAT) to
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> verify and/or update local DICOM headers --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> though your dcmodify command is
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a great and fast solution for bulk header
>>>>>>>>>>>>>>>>>>>>>>>>>>>> updates.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If you're concerned about fields being
>>>>>>>>>>>>>>>>>>>>>>>>>>>> changed (e.g. "(2001,105f)" from
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the warning message)  - you can also
>>>>>>>>>>>>>>>>>>>>>>>>>>>> dcmdump a DICOM slice before and look
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at these fields specifically.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's also not a bad "sanity check" to
>>>>>>>>>>>>>>>>>>>>>>>>>>>> backup your DICOMS before/after
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> running dcmodify, and use dcmdump on each
>>>>>>>>>>>>>>>>>>>>>>>>>>>> version to diff the outputs --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> this will pinpoint what changed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Re the protocol violation --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol not recognized or
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> unknown :   this means your scans did not
>>>>>>>>>>>>>>>>>>>>>>>>>>>> match what is stored in your
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_protocol table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Check the MRI Violations front-end module
>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- can you see why they didn't
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> match?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Send us an example, in addition to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> contents of the mri_protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> table, if you can't find the source of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> mismatch.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  Here is the psc table
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I created 2 candidates profiles through the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> interface
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> then runned dcmodify command to a dicom file
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1"
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and got those warning: is this okay?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and
>>>>>>>>>>>>>>>>>>>>>>>>>>>> undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify at another Dicom didn't show
>>>>>>>>>>>>>>>>>>>>>>>>>>>> warnings. Below you can see the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> execution for the second dicom. Mnics could
>>>>>>>>>>>>>>>>>>>>>>>>>>>> not be inserted due to
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> AcquisitionProtocol being unknown.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Running now the following command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> imaging_upload_file.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 12
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  find -path
>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX'
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dicomTar.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database
>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  Source: /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Target: /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Testing for database connectivity.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Database is available.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You will archive the dir :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You are creating a tar with the following
>>>>>>>>>>>>>>>>>>>>>>>>>>>> command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> tar -cf
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> getting md5sums and gzipping!!
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Linux
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2019-09-06 18:36:50
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Removing temporary files from target
>>>>>>>>>>>>>>>>>>>>>>>>>>>> location
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Done adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -uploadID 12 -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  md5sum
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Set centerID = 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Number of MINC files that will be
>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> database: 2
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log
>>>>>>>>>>>>>>>>>>>>>>>>>>>> file is
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log
>>>>>>>>>>>>>>>>>>>>>>>>>>>> file is
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>> cat
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Acquisition protocol is unknown
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>   --> The minc file cannot be registered
>>>>>>>>>>>>>>>>>>>>>>>>>>>> since the AcquisitionProtocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> is unknown
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sure -- you can delete imaging datasets
>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the *delete_imaging_upload*
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> script --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> details here:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> What's in your *psc* table?  (Is it
>>>>>>>>>>>>>>>>>>>>>>>>>>>> properly populated? This is a
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> pre-requisite to loading imaging data.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The foreign key constraint error on the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate record is curious.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> There are also a few options for creating
>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates when inserting
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> imaging data:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then
>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a. via the LORIS API -- Create the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates (and visits, optionally I
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> think)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How to:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by
>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Then as a second step:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> b. Use the imaging insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to load your DICOMs.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You will want to first ensure that the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName header in the DICOMs
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> as well as tar package are correctly
>>>>>>>>>>>>>>>>>>>>>>>>>>>> labelled with PSCID_DCCID_VisitLabel
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How to :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options
>>>>>>>>>>>>>>>>>>>>>>>>>>>> when running the bids_import script,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to automatically create your candidates and
>>>>>>>>>>>>>>>>>>>>>>>>>>>> sessions.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How do i delete a Study? And everytime do i
>>>>>>>>>>>>>>>>>>>>>>>>>>>> have to create a new
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate to get DCCID and a PSCID?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *First execution:*
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile
>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern
>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or
>>>>>>>>>>>>>>>>>>>>>>>>>>>> update a child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_candidate_1`
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> REFERENCES `psc` (`CenterID`)) at
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ERROR: Failed to insert record in table
>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_scanner:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The following database commands failed:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SET
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Medical Systems';
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Error obtained:Cannot add or update a child
>>>>>>>>>>>>>>>>>>>>>>>>>>>> row: a foreign key
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_mri_scanner_1`
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES
>>>>>>>>>>>>>>>>>>>>>>>>>>>> `candidate` (`CandID`)) (error code 1452)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ERROR: The validation has failed. Either
>>>>>>>>>>>>>>>>>>>>>>>>>>>> re-run the validation again
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and fix the problem. Or re-run
>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader.pl using -force to force the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> execution.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The tarchiveLoader.pl insertion script has
>>>>>>>>>>>>>>>>>>>>>>>>>>>> failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or
>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *And second execution: *
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile
>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern
>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PROBLEM:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The user 'lorisadmin' has already inserted
>>>>>>>>>>>>>>>>>>>>>>>>>>>> this study.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The unique study ID is
>>>>>>>>>>>>>>>>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> This is the information retained from the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> first time the study was
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> inserted:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Linux
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2019-09-04 18:33:05
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Last update of record:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The dicomTar.pl execution has failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or
>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ok, this sounds like good progress.  Let us
>>>>>>>>>>>>>>>>>>>>>>>>>>>> know when you next encounter
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> issues as you progress through the Imaging
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Install/Setup docs
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I'll look into how we can better handle the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> incoming/ directory next
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> time.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> populated correctly except its port is
>>>>>>>>>>>>>>>>>>>>>>>>>>>> 'port'    : ''. Also i have tested
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that i can connect to MySQL with lorisuser.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I executed the script again, because the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> only error i had previously was
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that the /data/incoming folder didn't exist
>>>>>>>>>>>>>>>>>>>>>>>>>>>> and there are no errors
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> reported back except of warnings <<mysql:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> [Warning] Using a password on the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> command line interface can be insecure>>.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's possible -- if the script was unable
>>>>>>>>>>>>>>>>>>>>>>>>>>>> to connect to the database
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> during its execution (e.g. typo in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> password), that would explain the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> underpopulated Image path and Loris-MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>> code path you saw in the Config
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> module.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's hard to tell without seeing the output
>>>>>>>>>>>>>>>>>>>>>>>>>>>> from your script run -- Did
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you see a sign of any such error?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The Config fields are populated by the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_install.sh script (starting
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at line 222
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For example, check if the database
>>>>>>>>>>>>>>>>>>>>>>>>>>>> connection information was populated
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> accurately in
>>>>>>>>>>>>>>>>>>>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If you are referring to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_install.sh here is an image with the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> configurations i typed. Maybe the problem
>>>>>>>>>>>>>>>>>>>>>>>>>>>> is somewhere at the last part
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> which asks to configure as much as possible
>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear your LORIS core install is up
>>>>>>>>>>>>>>>>>>>>>>>>>>>> and working and all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> front-end pages are loading.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$
>>>>>>>>>>>>>>>>>>>>>>>>>>>> chmod 775 project
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > and the web interface worked.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, it's important that project/ have 775
>>>>>>>>>>>>>>>>>>>>>>>>>>>> permissions and that
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> lorisadmin be part of the sudoers group,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> per step 1 in the install
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Readme <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris#install-steps>.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Image should change LORIS to
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris, right?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> These imaging paths will be updated during
>>>>>>>>>>>>>>>>>>>>>>>>>>>> your imaging installation
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> by an automated script --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you do not need to set them manually via
>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Config module.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Please continue to follow the Setup Guide
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> for detailed steps to follow.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image
>>>>>>>>>>>>>>>>>>>>>>>>>>>> should change LORIS to loris,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> right?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i used
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> curl -sL
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://deb.nodesource.com/setup_8.x | sudo -E
>>>>>>>>>>>>>>>>>>>>>>>>>>>> bash -
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sudo apt-get install -y nodejs
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you had suggested in the past, make worked
>>>>>>>>>>>>>>>>>>>>>>>>>>>> and now i can see all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> contents in the web-interface, but i don't
>>>>>>>>>>>>>>>>>>>>>>>>>>>> need make install?
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> -------------- next part --------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>> An HTML attachment was scrubbed...
>>>>>>>>>>>>>>>>>>>>>>>>>>>> URL: <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html
>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16
>>>>>>>>>>>>>>>>>>>>>>>>>>>> *****************************************
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>> Loris-dev mailing list
>>>> Loris-dev at bic.mni.mcgill.ca
>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>
>>>
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From sotirisnik at gmail.com  Fri Jan 31 10:25:30 2020
From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos)
Date: Fri, 31 Jan 2020 17:25:30 +0200
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAMkiY3dGcQDPCfr9BDOUY3NEgoskTkU7D99FrkvmqPagKtAROQ@mail.gmail.com>
References: <mailman.1851.1573565332.16403.loris-dev@bic.mni.mcgill.ca>
 <CAEfMBom1HCWLo4NWgt5XG4625tCBfRT_Z_HepvtT_Er2LKbJoA@mail.gmail.com>
 <CAKHj7uS1AdMDjnacouTvxZgziYVgp5NNUeOuMkpDyrTskGTh-Q@mail.gmail.com>
 <CALbt7NDej8FGUUS6_oKbK5Fp-FnwsVz9AgZ6ZcJEZhmoKZmv8w@mail.gmail.com>
 <CAKHj7uSx-qqcXHZsWsZmSJ7sC1DgF+XapT5Y1+QdoVic37_DDg@mail.gmail.com>
 <CAMkiY3fQBGDGeNO8EHxwYAgbhTggNSQ+AVuCfdraDXwULMjjUg@mail.gmail.com>
 <CAKHj7uT5xXi=pOPdH=W9BroSphMHdTszdgW+GxuES=8wZox9eQ@mail.gmail.com>
 <CAMkiY3eUouxaRVdC4wH+vdjeQ=q_Nx8bcDNzcWgD_OgN77m3mw@mail.gmail.com>
 <CAKHj7uSxu4+tm+=x4+qJ1sAbrjmxG2H7LovDb7-2KMnyYQhrgg@mail.gmail.com>
 <CAMkiY3fdPZec2jx-cc2Zq37j3ekmTu_o819yBUv-bC7M98bkVw@mail.gmail.com>
 <CAKHj7uSZHozpuQ_YwGmy6wQ4tm43vJa556V0o2+JGDVsYaqN4g@mail.gmail.com>
 <CAMkiY3dge=x93bQDv0fHGMcrX0PA8Z_imLb_zSTh=nTrx5weFg@mail.gmail.com>
 <CAKHj7uR81gCkjvccMxwMA08dGSEgyTLJBJ+pZPkoUQDtGP_hFA@mail.gmail.com>
 <CAMkiY3fGhvExZ-JOvxeHe7dJQPvtPAHx3oJuiMVX7f1JgF1GAg@mail.gmail.com>
 <CAKHj7uRExO98Yyn9_07aw44wbh0bCL9_C1VFTAURKsxQLUuAeQ@mail.gmail.com>
 <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>
 <CAKHj7uRueb5fgh4VVCAyaq8tC9WM4gJ7k6Q=dxsqWzFgDqPfVQ@mail.gmail.com>
 <CAMkiY3d-Vt=3gQqwJ+GSRSacbLp2QxrB0g-_C7ONd8j_g1ipoQ@mail.gmail.com>
 <CAKHj7uQt9=nokz5g1zBuBx1-rJ8q7qKOuNVkQugC9wfvNFcjVA@mail.gmail.com>
 <CAMkiY3cAuQfT_5iMzYoF2BXVceu_vgz4eCq2sAtoyse+zUYeSg@mail.gmail.com>
 <CAMkiY3dq1O3V8+r4tTAWQ8N=rVFg=DNY-UPeMqbec+MSayj=Cg@mail.gmail.com>
 <CAKHj7uSEegvE1apPBGVyHmjyVzF+YxJjDMg0b+hDE4_-ON+dYw@mail.gmail.com>
 <CAKHj7uRx1NT7CycFq65uFpgPiOVwvT-jtK1NJX6_3rrLNFwdbA@mail.gmail.com>
 <CAMkiY3dAnkLdc4N=REmeCpX2qBfsQf=wRb=YtHtt20f8adXFyw@mail.gmail.com>
 <CAKHj7uRpA-8kzkoEnAk7JBNLP7v4cmK4zW-gMutHESiFGj7xjw@mail.gmail.com>
 <CAMpvQ9hNLxz9SZsJwWec_yQ3R4KGhnqv3CDaSPOB1exPsO5AJA@mail.gmail.com>
 <CAMpvQ9gTQUGvmd7E8_Mnk7sd8HtX4NHvLCfWZ0-hEi9aJuu_nw@mail.gmail.com>
 <CAKHj7uSNm=OX8jaDJ0-TZZsBA8zm3Uv6yErBSy76EnwUWdpsig@mail.gmail.com>
 <CAMkiY3dGcQDPCfr9BDOUY3NEgoskTkU7D99FrkvmqPagKtAROQ@mail.gmail.com>
Message-ID: <CAKHj7uRBub=X8+qGSY0N5xCbn5t2PGeiP_QmmZ6fNQkWE=3sfg@mail.gmail.com>

Hi Cecile,

Indeed 'file' was missing and now it worked. I also wanted to ask about the
installdb.php if it is possible to automate the execution. I tried thse
commands with curl to execute the http queries for the forms. Although I
don't have the error1.html and error2.html files at the moment, their html
code showed that the execution was successful and the config.xml is being
created, but when I login it's like the css is not loading.

#first query
curl --data "formname=validaterootaccount" --data "dbhost=172.28.1.2"
--data "dbadminuser=root" --data "dbadminpassword=neopass" --data
"dbname=LORIS" http://localhost/installdb.php > error1.html
#second query
curl --data "formname=createmysqlaccount" --data "dbhost=172.28.1.2" --data
"dbadminuser=root" --data "dbadminpassword=neopass" --data "dbname=LORIS"
--data "lorismysqluser=lorisuser" --data "lorismysqlpassword=neopass"
--data "frontenduser=lorisuser" --data "frontendpassword=1234"
http://localhost/installdb.php > error2.html

If i normally execute installdb.php on the browser, there is no problem.

Thanks



???? ???, 31 ??? 2020 ???? 4:39 ?.?., ?/? Cecile Madjar <
cecile.madjar at mcin.ca> ??????:

> Hi Sotirios,
>
> Actually, is it possible that 'file' is not installed on your VM. I
> misread the error in my earlier email and it might be crashing in MRI.pm at
> line 1523 of your code. In that line, 'file' is used to determine if the
> file is a DICOM, if not, it will show a warning and not count the file as a
> DICOM. So in the end, none of your files are considered DICOM files and
> when it comes to convert the list of DICOMs, there is nothing to convert,
> hence the number of MINC file = 0.
>
> Anyway, I have a feeling this might be the issue you are having.
>
> Let me know how it goes,
>
> C?cile
>
> On Fri, Jan 31, 2020 at 9:23 AM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> Hi Ling,
>>
>> Yes it's Loris-mri 21.0. One thought i had is that maybe i should define
>> root as linux user?
>> https://github.com/aueb-wim/LORIS-for-MIP/blob/master/docs/pics/loris_docker_imaging_install.png.
>> But i see no difference either when i execute it as lorisadmin.
>>
>> Also here are the files we use
>> https://github.com/aueb-wim/LORIS-for-MIP/tree/master/mri_loris
>>
>> And here is the complete output of the batch execution.
>>
>> Use of uninitialized value $_ in pattern match (m//) at
>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>> Running now the following command: /data/loris/data//uploadNeuroDB/
>> imaging_upload_file.pl -profile prod -upload_id 35
>> /data/incoming/DCC0000_956912_V1.tar.gz -verbose
>>
>>  find -path \/data\/tmp\/ImagingUpload\-14\-15\-z2B0N3 -name '__MACOSX'
>> -delete
>> xargs: file: No such file or directory
>>
>> dicomTar.pl \/data\/tmp\/ImagingUpload\-14\-15\-z2B0N3
>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>>  Source: /data/tmp/ImagingUpload-14-15-z2B0N3
>> Target: /data/loris/data/tarchive
>>
>> Testing for database connectivity.
>> Database is available.
>>
>> You will archive the dir : ImagingUpload-14-15-z2B0N3
>>
>> You are creating a tar with the following command:
>>
>> tar -cf /data/loris/data/tarchive/ImagingUpload-14-15-z2B0N3.tar
>> ImagingUpload-14-15-z2B0N3
>>
>>
>> getting md5sums and gzipping!!
>>
>> * Taken from dir                   :
>>  /data/tmp/ImagingUpload-14-15-z2B0N3
>> * Archive target location          :
>>  /data/loris/data/tarchive/DCM_2015-09-07_ImagingUpload-14-15-z2B0N3.tar
>> * Name of creating host            :    172.28.1.1
>> * Name of host OS                  :    Linux
>> * Created by user                  :    lorisadmin
>> * Archived on                      :    2020-01-31 14:15:04
>> * dicomSummary version             :    1
>> * dicomTar version                 :    1
>> * md5sum for DICOM tarball         :    fcaf54e9078705799b10e08c4d34bf70
>>  ImagingUpload-14-15-z2B0N3.tar
>> * md5sum for DICOM tarball gzipped :    52c96cd08d168e659b5c73cb77b4621b
>>  ImagingUpload-14-15-z2B0N3.tar.gz
>> * md5sum for complete archive      :    f5103ec688a5921a37d3c95cba8598e0
>>  DCM_2015-09-07_ImagingUpload-14-15-z2B0N3.tar
>>
>> Adding archive info into database
>>
>>
>> Removing temporary files from target location
>>
>>
>> Done adding archive info into database
>>
>> \/data\/loris\/data\//uploadNeuroDB/tarchiveLoader.pl -globLocation
>> -profile prod
>> \/data\/loris\/data\/tarchive\/\/DCM_2015\-09\-07_ImagingUpload\-14\-15\-z2B0N3\.tar
>> -uploadID 35 -verbose
>>  md5sum
>> /data/loris/data/tarchive/DCM_2015-09-07_ImagingUpload-14-15-z2B0N3.tar
>> PSCID is: DCC0000
>>  CandID id: 956912
>>  visit_label is: V1
>> PSCID is: DCC0000
>>  CandID id: 956912
>>  visit_label is: V1
>> candidate id 956912
>> Set centerID = 1
>> PSCID is: DCC0000
>>  CandID id: 956912
>>  visit_label is: V1
>> PSCID is: DCC0000
>>  CandID id: 956912
>>  visit_label is: V1
>> xargs: file: No such file or directory
>>
>> Number of MINC files that will be considered for inserting into the
>> database: 0
>>
>> No data could be converted into valid MINC files.
>>
>> The tarchiveLoader.pl insertion script has failed.
>> Use of uninitialized value $mail_user in concatenation (.) or string at
>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
>> Can't exec "mail": No such file or directory at /data/loris/bin/mri/
>> batch_uploads_imageuploader.pl line 249.
>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>> batch_uploads_imageuploader.pl line 250.
>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>> batch_uploads_imageuploader.pl line 251.
>>
>> ???? ???, 30 ??? 2020 ???? 6:22 ?.?., ?/? Ling Ma <lingyun.ma at mcin.ca>
>> ??????:
>>
>>> Oh, I just found that you are using Loris-mri 21.0, as I stated in the
>>> previous email, the "$_" could not find any matches, so your command might
>>> not be correctly entered.
>>>
>>> On Thu, Jan 30, 2020 at 10:35 AM Ling Ma <lingyun.ma at mcin.ca> wrote:
>>>
>>>> Hi Sotirios,
>>>>
>>>> By curiosity, I just looked at the error message, "Use of
>>>> uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/
>>>> batch_uploads_imageuploader.pl line 144." clearly means that there is
>>>> no match, but 144 line has no such code related with $_ in recent versions
>>>> of the batch_uploads_imageuploader.pl. There is something in the line
>>>> 165 for a few recent versions.
>>>>
>>>> As to "xargs: file: No such file or directory", it could be due to a
>>>> command unable to find anything using the directory provided as the message
>>>> suggested.
>>>>
>>>> In both cases, I feel that it could be helpful if you provide more
>>>> details such as which Loris_MRI version you are running, what is the exact
>>>> command line you are using to help supporters to understand.
>>>>
>>>> Thanks.
>>>>
>>>> Best regards,
>>>> Ling Ma
>>>> Consultant
>>>>
>>>> On Wed, Jan 29, 2020 at 6:57 PM Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> wrote:
>>>>
>>>>> Hi Cecile,
>>>>>
>>>>> it seems that xargs is already installed in our docker container.
>>>>>
>>>>> [image: image.png]
>>>>>
>>>>>
>>>>> ???? ???, 29 ??? 2020 ???? 7:59 ?.?., ?/? Cecile Madjar <
>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>
>>>>>> Hi Sotirios,
>>>>>>
>>>>>> It looks like xargs is not installed in your docker environment.
>>>>>>
>>>>>> This is being used by the following command in dicomTar.pl (and a few
>>>>>> other places but that is the one causing the error at the moment):
>>>>>>
>>>>>> $cmd = "cd " . $dcm_source . "; find -type f -name '.*' | *xargs* rm
>>>>>> -f";
>>>>>>
>>>>>> So you need to install xargs in your docker for the command to run.
>>>>>>
>>>>>> Hope this helps,
>>>>>>
>>>>>> C?cile
>>>>>> On Wed, Jan 29, 2020 at 10:35 AM Sotirios Nikoloutsopoulos <
>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> We are making a dockerized version of Loris 21 and when we execute
>>>>>>> the batch_uploads_imageuploader.pl we get an error about xargs.
>>>>>>> What could be the casue?
>>>>>>>
>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>>>>>>> Running now the following command: /data/loris/data//uploadNeuroDB/
>>>>>>> imaging_upload_file.pl -profile prod -upload_id 13
>>>>>>> /data/incoming/DCC0007_854380_V1.tar.gz -verbose
>>>>>>>
>>>>>>>  find -path \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml -name
>>>>>>> '__MACOSX' -delete
>>>>>>> xargs: file: No such file or directory
>>>>>>>
>>>>>>> dicomTar.pl \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml
>>>>>>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>>>>>>>  Source: /data/tmp/ImagingUpload-15-31-U_O5ml
>>>>>>> Target: /data/loris/data/tarchive
>>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>> ???? ???, 10 ??? 2019 ???? 7:21 ?.?., ?/? Sotirios Nikoloutsopoulos <
>>>>>>> sotirisnik at gmail.com> ??????:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> i opened an issue and looked up for the values of Volume they
>>>>>>>> suggested https://github.com/BIC-MNI/minc-toolkit-v2/issues/95.
>>>>>>>> The only attributes associated with it i saw are [0x00089206] and
>>>>>>>> [0x00089207]
>>>>>>>>
>>>>>>>> [image: image.png]
>>>>>>>>
>>>>>>>> I looked up for the file that was being viewed fine in the
>>>>>>>> BrainBrowser and saw that it had that attribute empty so i used this
>>>>>>>> command because i couldn't find a way to modify the attribute via pydicom
>>>>>>>>
>>>>>>>> dcmodify -ma "(0008,9206)=" *.dcm
>>>>>>>>
>>>>>>>> and that command reported the warning about the Endian Syntax. I
>>>>>>>> also used the corresponding command for 9207 and got the message "Tag not
>>>>>>>> found'
>>>>>>>>
>>>>>>>> Lastly I tried to upload some dicoms and now i am getting the SNR
>>>>>>>> and i can view them fine. I believe now that all of them will pass
>>>>>>>> successfully, i will report back later.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Sotirios
>>>>>>>>
>>>>>>>> ???? ???, 9 ??? 2019 ???? 8:10 ?.?., ?/? Cecile Madjar <
>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>
>>>>>>>>> Hi Sotirios,
>>>>>>>>>
>>>>>>>>> The issue you are having is a indeed a dcm2mnc issue. The
>>>>>>>>> converter does not seem to work on your dataset for some reason.
>>>>>>>>> Unfortunately, there is not much we can do on our front to fix this...
>>>>>>>>>
>>>>>>>>> I would recommend creating an issue on the MINC tools repository
>>>>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> so they can
>>>>>>>>> fix your problem.
>>>>>>>>>
>>>>>>>>> Very sorry that you are having that problem.
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>>
>>>>>>>>> C?cile
>>>>>>>>>
>>>>>>>>> On Wed, Dec 4, 2019 at 8:59 AM Cecile Madjar <
>>>>>>>>> cecile.madjar at mcin.ca> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>
>>>>>>>>>> Could you please share a dataset with us that produces the error
>>>>>>>>>> you get and the weird display in BrainBrowser? You could use the same SFTP
>>>>>>>>>> credential that Nicolas gave you.
>>>>>>>>>>
>>>>>>>>>> The message errors you got from imaging_install.sh are probably
>>>>>>>>>> due to the fact that you reran the install script and it tried to reinstall
>>>>>>>>>> something that was already there. I would not worry about it. FYI, the only
>>>>>>>>>> thing you needed to do was to update the MINC tools path in the environment
>>>>>>>>>> file as you did after re-running imaging_install.sh and source the
>>>>>>>>>> environment file.
>>>>>>>>>>
>>>>>>>>>> Best,
>>>>>>>>>>
>>>>>>>>>> C?cile
>>>>>>>>>>
>>>>>>>>>> On Wed, Dec 4, 2019 at 8:03 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>>  Hi Cecile,
>>>>>>>>>>>
>>>>>>>>>>> We used minctool 1.9.7 and we still get this error
>>>>>>>>>>>
>>>>>>>>>>> <<Restructuring...
>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>> noise_estimate --snr /data/loris/data>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> One dicom folder hadn't that error and is being viewed fine in
>>>>>>>>>>> the BrainBrowser of Loris.
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> When i used dpkg to the 1.9.17 the installation reported fine
>>>>>>>>>>> <<Unpacking minc-toolkit-v2 (1.9.17) over (1.9.16) ...>>
>>>>>>>>>>>
>>>>>>>>>>> and then i used source /opt/minc/1.9.17/minc-toolkit-config.sh
>>>>>>>>>>>
>>>>>>>>>>> and aftewards runned bash ./imaging_install.sh just to be sure.
>>>>>>>>>>>
>>>>>>>>>>> We also had to modify /data/loris/bin/mri/environment because it
>>>>>>>>>>> still pointed to the old version.
>>>>>>>>>>>
>>>>>>>>>>> What i found strange is this during the run of imaging_install.sh
>>>>>>>>>>>
>>>>>>>>>>> <<already using interpreter
>>>>>>>>>>> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/bin/python3
>>>>>>>>>>> Please use the *system* python to run this script
>>>>>>>>>>> Traceback (most recent call last):
>>>>>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py",
>>>>>>>>>>> line 2632, in <module>
>>>>>>>>>>>     main()
>>>>>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py",
>>>>>>>>>>> line 870, in main
>>>>>>>>>>>     symlink=options.symlink,
>>>>>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py",
>>>>>>>>>>> line 1156, in create_environment
>>>>>>>>>>>     install_python(home_dir, lib_dir, inc_dir, bin_dir,
>>>>>>>>>>> site_packages=site_packages, clear=clear, symlink=symlink)
>>>>>>>>>>>   File
>>>>>>>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>>>>>>>> line 357, in abspath
>>>>>>>>>>>     if not isabs(path):
>>>>>>>>>>>   File
>>>>>>>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>>>>>>>> line 64, in isabs
>>>>>>>>>>>     return s.startswith(sep)
>>>>>>>>>>> AttributeError: 'NoneType' object has no attribute 'startswith'
>>>>>>>>>>> Installing the Python libraries into the loris-mri virtualenv...
>>>>>>>>>>> Requirement already satisfied: mysqlclient in
>>>>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (1.4.4)
>>>>>>>>>>> Requirement already satisfied: mysql-connector in
>>>>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (2.2.9)
>>>>>>>>>>> Requirement already satisfied: pybids in
>>>>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (0.9.4)
>>>>>>>>>>> Requirement already satisfied: nibabel>=2.1 in ./python_virtua>>
>>>>>>>>>>>
>>>>>>>>>>> So should i open an issue for that error? or is there something
>>>>>>>>>>> else to try?
>>>>>>>>>>>
>>>>>>>>>>> Thanks
>>>>>>>>>>>
>>>>>>>>>>> Sotirios
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 10:39 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>
>>>>>>>>>>>> Does the pic screenshot in the imaging browser module also
>>>>>>>>>>>> shows 1 slice? If so, that would mean there was an issue with the dcm2mnc
>>>>>>>>>>>> conversion. Once again, installing the latest version of the MINC tools
>>>>>>>>>>>> should help but if this issue persists I would recommend creating an issue
>>>>>>>>>>>> for that too on their repository
>>>>>>>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> (if not
>>>>>>>>>>>> already reported there, there are a few known issue reported).
>>>>>>>>>>>>
>>>>>>>>>>>> Other viewer for MINCs are register and Display (both part of
>>>>>>>>>>>> the MINC tools). For NIfTI, you have FSLeye, MRICron and probably many
>>>>>>>>>>>> other viewers that exists.
>>>>>>>>>>>>
>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>
>>>>>>>>>>>> C?cile
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Dec 3, 2019 at 3:26 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Yes, Nifti files are mandatory for our work. From what we saw
>>>>>>>>>>>>> at a 3rd vm we setted up, the nifti files are being created ( i haven't
>>>>>>>>>>>>> verified if that is the case at the 2nd vm ). I will install the latest
>>>>>>>>>>>>> version and will report back, but do you know any nifti/minc viewer?
>>>>>>>>>>>>> because the Brainbrowser of Loris does not output them well, it's like it
>>>>>>>>>>>>> is loading only 1 slice and we would like to verify it with another tool
>>>>>>>>>>>>> too. We verified that the dcmconv command didn't affect the
>>>>>>>>>>>>> quality of the .dcm files.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>
>>>>>>>>>>>>> ???? ???, 2 ??? 2019 ???? 6:59 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> It looks like for some reason your binary mnc2nii is not
>>>>>>>>>>>>>> working and reports that error. Do you want to create NIfTI files or are
>>>>>>>>>>>>>> you happy with just the MINC files?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> If you don't need the NIfTI files, then maybe you can set the
>>>>>>>>>>>>>> Config setting "NIfTI file creation" to No instead of Yes
>>>>>>>>>>>>>> and this error will not appear anymore.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> If you need the NIfTI files to be created, then I would
>>>>>>>>>>>>>> recommend installing the latest version of the MINC tools (1.9.17). They
>>>>>>>>>>>>>> can be found there:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>    - pre-built packages:
>>>>>>>>>>>>>>    https://packages.bic.mni.mcgill.ca/minc-toolkit/
>>>>>>>>>>>>>>    - from the source code with installation instructions in
>>>>>>>>>>>>>>    the README: https://github.com/BIC-MNI/minc-toolkit-v2
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> If the problem persists by using the latest release of MINC
>>>>>>>>>>>>>> tools, then create an issue on Github for the MINC developers
>>>>>>>>>>>>>> here <https://github.com/BIC-MNI/minc-toolkit-v2/issues>.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks to Nicholas i was able to create all the mincs
>>>>>>>>>>>>>>> images. The problem was that the files were in Little-Endian-Implicit
>>>>>>>>>>>>>>> transfer syntax and i had to convert them Little-Endian-Explicit transfer
>>>>>>>>>>>>>>> syntax with this command
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> find <root_of_my_DICOM_files_directory> -type f | xargs -i
>>>>>>>>>>>>>>> dcmconv --write-xfer-little {} {}
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Looking back at our mails i saw that Little-Endian error had
>>>>>>>>>>>>>>> occurred when i used dcmodify, but i switcthed to using pydicom instead.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> In the output i see an error sometimes about "gsl:
>>>>>>>>>>>>>>> bessel_I0.c:216: ERROR: overflow". Is this okay?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Restructuring...
>>>>>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>>>>>> noise_estimate --snr
>>>>>>>>>>>>>>> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
>>>>>>>>>>>>>>> SNR is:
>>>>>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thank you for the details!
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> A few things to try:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>    - modify the TMPDIR to be on your /data directory where
>>>>>>>>>>>>>>>>    there might be more space to do processing (could create a /data/tmp where
>>>>>>>>>>>>>>>>    the temporary files would be created)
>>>>>>>>>>>>>>>>    - how many files are there for that upload in
>>>>>>>>>>>>>>>>    tarchive_files? Are they different from the ones showing the warning
>>>>>>>>>>>>>>>>    message?
>>>>>>>>>>>>>>>>       - FYI: query to get that: SELECT tf.* FROM
>>>>>>>>>>>>>>>>       tarchive_files tf JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your
>>>>>>>>>>>>>>>>       uploadID> (the output of that query would be very
>>>>>>>>>>>>>>>>       useful if you can provide it)
>>>>>>>>>>>>>>>>       - how many series are there for that upload in
>>>>>>>>>>>>>>>>    tarchive_series?
>>>>>>>>>>>>>>>>    - FYI: query to get that: SELECT ts.* FROM
>>>>>>>>>>>>>>>>       tarchive_series ts JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your
>>>>>>>>>>>>>>>>       uploadID> (the output of that query would be very
>>>>>>>>>>>>>>>>       useful if you can provide it)
>>>>>>>>>>>>>>>>    - things are failing when the scripts try running the
>>>>>>>>>>>>>>>>    following command: find
>>>>>>>>>>>>>>>>    /tmp/TarLoad-23-43-ccugaa/ImagingUpload-23-43-6JCOTO -type f  |
>>>>>>>>>>>>>>>>    /data/loris/bin/mri/dicom-archive/get_dicom_info.pl
>>>>>>>>>>>>>>>>    -studyuid -series -echo -image -file  -attvalue 0018 0024 -series_descr
>>>>>>>>>>>>>>>>    -stdin | sort -n -k1 -k2 -k7 -k3 -k6 -k4  | cut -f 5 | dcm2mnc -dname ''
>>>>>>>>>>>>>>>>    -stdin -clobber -usecoordinates /tmp/TarLoad-23-43-ccugaa
>>>>>>>>>>>>>>>>       - clearly the problems come from get_dicom_info.pl
>>>>>>>>>>>>>>>>       but I cannot pinpoint the error yet. I will ask around and get back to you
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> If I cannot figure it out remotely, is there a way to have
>>>>>>>>>>>>>>>> a call using zoom? This way you could share your screen with me and run the
>>>>>>>>>>>>>>>> debugger on that script and hopefully we can figure out what is going on
>>>>>>>>>>>>>>>> with those datasets?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks!
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Tue, Nov 26, 2019 at 5:17 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> In both my virtual machines
>>>>>>>>>>>>>>>>> export TMPDIR=/tmp
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> In both vm also with dcm2mnc i get this output. Just to
>>>>>>>>>>>>>>>>> verify that this passed in my 1st vm and produced mincs.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I attached the spool as a csv.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> And also one difference i found was this in the Loris-mri
>>>>>>>>>>>>>>>>> code ( left 1st workable vm, right 2nd vm that has to be fixed, although i
>>>>>>>>>>>>>>>>> changed it seems to be independent of the uninitialized value $_ )
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> that is puzzling... A few additional questions:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>    - what is the bash variable TMPDIR set to on the
>>>>>>>>>>>>>>>>>>    environment file?
>>>>>>>>>>>>>>>>>>    - could you try running separately dcm2mnc on the
>>>>>>>>>>>>>>>>>>    DICOM folder to see if that works?
>>>>>>>>>>>>>>>>>>    - could you send us the detailed log from the
>>>>>>>>>>>>>>>>>>    notification spool table (SELECT * FROM notification_spool WHERE
>>>>>>>>>>>>>>>>>>    UploadID=<your uploadID>) and send it back to us? Maybe there are some
>>>>>>>>>>>>>>>>>>    additional clues that could help figuring out what is going on.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thank you!
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Tue, Nov 26, 2019 at 10:12 AM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> I checked for the StudyInstacueUID at the files with
>>>>>>>>>>>>>>>>>>> "The target directory does not contain a single DICOM file"" and their
>>>>>>>>>>>>>>>>>>> attribute has a value.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Regarding the scouter and localizer, i modified the
>>>>>>>>>>>>>>>>>>> settings in the imaging pipeline and now i don't get that error message,
>>>>>>>>>>>>>>>>>>> but still it doesn't create the mnics.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> The errors i am getting are ( uninitialized value $_ is
>>>>>>>>>>>>>>>>>>> not important? because i haven't got comments about that )
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line
>>>>>>>>>>>>>>>>>>> 144.
>>>>>>>>>>>>>>>>>>> Running now the following command:
>>>>>>>>>>>>>>>>>>> /data/loris/data//uploadNeuroDB/imaging_upload_file.pl
>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 134 /data/incoming/DCC0025_118008_V1.tar.gz
>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> and
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for
>>>>>>>>>>>>>>>>>>> inserting into the database: 0
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> No data could be converted into valid MINC files.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> The tarchiveLoader.pl insertion script has failed.
>>>>>>>>>>>>>>>>>>> Use of uninitialized value $mail_user in concatenation
>>>>>>>>>>>>>>>>>>> (.) or string at /data/loris/bin/mri/
>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line
>>>>>>>>>>>>>>>>>>> 249.
>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 250.
>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 251.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> OK. So the issue I mentioned should not be a problem
>>>>>>>>>>>>>>>>>>>> for you.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Is the StudyInstanceUID DICOM header set in your
>>>>>>>>>>>>>>>>>>>> images? If it is not set, then you would end up with the error message "The
>>>>>>>>>>>>>>>>>>>> target directory does not contain a single DICOM file". So maybe this is
>>>>>>>>>>>>>>>>>>>> the issue you are having with those datasets?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Regarding not excluding series descriptions, you can
>>>>>>>>>>>>>>>>>>>> configure that in the Config module under the Imaging Pipeline section.
>>>>>>>>>>>>>>>>>>>> Simply remove all entries for the "Series description to exclude from
>>>>>>>>>>>>>>>>>>>> imaging insertion" setting.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Mon, Nov 25, 2019 at 9:58 AM Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> We are using this version
>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/archive/v21.0.0.zip. Is
>>>>>>>>>>>>>>>>>>>>> it possible to insert low resolution now?
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, <
>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Which version of LORIS-MRI are you using?
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> There was a bug that got resolved in 20.2 in
>>>>>>>>>>>>>>>>>>>>>> get_dicom_info.pl. Basically, if a DICOM did not
>>>>>>>>>>>>>>>>>>>>>> have the (0020,0032) header, get_dicom_info.pl
>>>>>>>>>>>>>>>>>>>>>> considered that the file was not a DICOM, which was a mistake. This got
>>>>>>>>>>>>>>>>>>>>>> fixed in version 20.2 of LORIS-MRI. Hopefully this is the issue you are
>>>>>>>>>>>>>>>>>>>>>> encountering.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> About scout and localizer, they are a type of short
>>>>>>>>>>>>>>>>>>>>>> and low resolution sequence that is used by the tech but is of no interest
>>>>>>>>>>>>>>>>>>>>>> scientifically, which is why we tend to no insert them.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> i executed the find command and the output i got per
>>>>>>>>>>>>>>>>>>>>>>> folder was "DICOM medical imaging data. Maybe there is something wrong with
>>>>>>>>>>>>>>>>>>>>>>> the find command in the warning that it is unable to check if the file is a
>>>>>>>>>>>>>>>>>>>>>>> dicom file? Also when i use get_dicom_info.pl i
>>>>>>>>>>>>>>>>>>>>>>> don't get any output data. Finally i don't understand what scout or
>>>>>>>>>>>>>>>>>>>>>>> localizer is ( something like if and only if a file fails then the whole
>>>>>>>>>>>>>>>>>>>>>>> session is invalid? ).
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>>>>>>> Madjar <cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> I took a closer look to the
>>>>>>>>>>>>>>>>>>>>>>>> batch_uploader_multiple_output.txt file you sent. It looks like there are
>>>>>>>>>>>>>>>>>>>>>>>> different reasons for failure depending on the DICOM folder uploaded.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>    - For 465466 DCC0000 V1; 727195 DCC0004 V1 and
>>>>>>>>>>>>>>>>>>>>>>>>    684908 DCC0007 V1: it looks like there is no file of type DICOM in the
>>>>>>>>>>>>>>>>>>>>>>>>    folder. Have you checked to see if that is indeed the case? Maybe you can
>>>>>>>>>>>>>>>>>>>>>>>>    try running the following command on that folder to see what are the types
>>>>>>>>>>>>>>>>>>>>>>>>    of the files? If it does not return at least one DICOM medical imaging data
>>>>>>>>>>>>>>>>>>>>>>>>    file, then that is why you get the error message from the pipeline:
>>>>>>>>>>>>>>>>>>>>>>>>       -
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>       find <my_dicom_archive_root_folder> -type f | xargs -i file {}|cut -d: -f2|sort|uniq
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>       - For 864173 DCC0001 V1: it looks like there
>>>>>>>>>>>>>>>>>>>>>>>>    are two different DICOM studies within the same folder. You will need to
>>>>>>>>>>>>>>>>>>>>>>>>    split that study in two based on the StudyUID field as the insertion
>>>>>>>>>>>>>>>>>>>>>>>>    pipeline does not allow for more than one StudyUID per upload.
>>>>>>>>>>>>>>>>>>>>>>>>    - For 890807 DCC0002 V1; 637025 DCC0005 V1 and
>>>>>>>>>>>>>>>>>>>>>>>>    239975 DCC0006 V1: it looks like the dcm2mnc command did not produce any
>>>>>>>>>>>>>>>>>>>>>>>>    MINC files. Can you check in the DICOM archive what are the series present
>>>>>>>>>>>>>>>>>>>>>>>>    in the tarchive for that visit? Maybe only a scout or localizer was
>>>>>>>>>>>>>>>>>>>>>>>>    acquired for that session, hence the no valid MINC files (scout and
>>>>>>>>>>>>>>>>>>>>>>>>    localizer being skipped for the conversion)
>>>>>>>>>>>>>>>>>>>>>>>>    - For 397410 DCC0003 V1: it looks like
>>>>>>>>>>>>>>>>>>>>>>>>    everything went well for this one.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> One script that is called by our pipeline is called
>>>>>>>>>>>>>>>>>>>>>>>> get_dicom_info.pl and this does all kind of checks
>>>>>>>>>>>>>>>>>>>>>>>> on the DICOM files (it is being called when running the dcm2mnc
>>>>>>>>>>>>>>>>>>>>>>>> conversion). You could run it independently on your folder if needed.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Since one of the study got in, it does not look
>>>>>>>>>>>>>>>>>>>>>>>> like you are having a problem with the setup. It seems more likely to be a
>>>>>>>>>>>>>>>>>>>>>>>> problem with the data themselves.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> In my first vm i am able to create the minc files
>>>>>>>>>>>>>>>>>>>>>>>>> and view them at the mri browser (except of candidate 102761034 ),
>>>>>>>>>>>>>>>>>>>>>>>>> meanwhile the same files gives warnings at the 2nd vm. The output  of the
>>>>>>>>>>>>>>>>>>>>>>>>> batch upload can be seen in the file attached.
>>>>>>>>>>>>>>>>>>>>>>>>> Also a colleague of us has built a pre-validation
>>>>>>>>>>>>>>>>>>>>>>>>> tool for dicom
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/
>>>>>>>>>>>>>>>>>>>>>>>>> which had found all the files that Loris gave as warning . Basically I
>>>>>>>>>>>>>>>>>>>>>>>>> confirmed that the total amount of files per dicom was the same amount as
>>>>>>>>>>>>>>>>>>>>>>>>> stated in Loris and checked some filenames given from warning to confirm
>>>>>>>>>>>>>>>>>>>>>>>>> that they match with our tool. But that was months ago and my colleague had
>>>>>>>>>>>>>>>>>>>>>>>>> changed some parameters for MIP and now our tool doesn't find all the
>>>>>>>>>>>>>>>>>>>>>>>>> invalid files, that's why i asked for the dicom header specification of
>>>>>>>>>>>>>>>>>>>>>>>>> Loris. In a discussion we had he mentioned that he doesn't check for some
>>>>>>>>>>>>>>>>>>>>>>>>> tags e.x. orientation. Lastly to mention that in my first vm i didn't use
>>>>>>>>>>>>>>>>>>>>>>>>> our tool to remove invalid dcm files.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>> Can you provide us with some fresh particulars of
>>>>>>>>>>>>>>>>>>>>>>>>>> the current issue and we'll take it from there?
>>>>>>>>>>>>>>>>>>>>>>>>>> Yang's team has built these scripts which can
>>>>>>>>>>>>>>>>>>>>>>>>>> definitely serve as a model for your pre-validation of your DICOM
>>>>>>>>>>>>>>>>>>>>>>>>>> collections.
>>>>>>>>>>>>>>>>>>>>>>>>>> cheers,
>>>>>>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> HI Yang,
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> We make use of pydicom library too. Now about
>>>>>>>>>>>>>>>>>>>>>>>>>>> the validate.py i see that you check if some attributes are missing such as
>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientID, PatientName which all of our files contains that info. Maybe i
>>>>>>>>>>>>>>>>>>>>>>>>>>> have missed something on the setup of my other virtual machine ( although
>>>>>>>>>>>>>>>>>>>>>>>>>>> one dicom passed on the new vm successfully, the others that were inserted
>>>>>>>>>>>>>>>>>>>>>>>>>>> correctly on my old vm fails on the new one ), i think that i had asked
>>>>>>>>>>>>>>>>>>>>>>>>>>> about this error "Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/
>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 144." but i
>>>>>>>>>>>>>>>>>>>>>>>>>>> don't remember the solution.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang
>>>>>>>>>>>>>>>>>>>>>>>>>>> Ding <it at cnbp.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hey, Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine from the LORIS team mentioned you had
>>>>>>>>>>>>>>>>>>>>>>>>>>>> some issue with DICOM.  I am a fellow developer for an external project
>>>>>>>>>>>>>>>>>>>>>>>>>>>> using LORIS, kind of just like you. We had to implement DICOM upload as
>>>>>>>>>>>>>>>>>>>>>>>>>>>> well but more as a fully automated pipeline actually.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> While we were building CNBP, we had coded up
>>>>>>>>>>>>>>>>>>>>>>>>>>>> some minor Python functions to check DICOM integrity (and simple
>>>>>>>>>>>>>>>>>>>>>>>>>>>> validations) and you might be able to gain some inspiration from it and
>>>>>>>>>>>>>>>>>>>>>>>>>>>> help you with your cause. For more comprehensive solution, PyDICOM (
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#)  seems
>>>>>>>>>>>>>>>>>>>>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks
>>>>>>>>>>>>>>>>>>>>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can
>>>>>>>>>>>>>>>>>>>>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty
>>>>>>>>>>>>>>>>>>>>>>>>>>>> rough around the edges but hopefully point you in the right direcitons
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Yang Ding, PhD.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Canadian Neonatal Brain Platform Architect
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Send Loris-dev mailing list submissions to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To subscribe or unsubscribe via the World Wide
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Web, visit
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> or, via email, send a message with subject or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> body 'help' to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-request at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You can reach the person managing the list at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-owner at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When replying, please edit your Subject line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> so it is more specific
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> than "Re: Contents of Loris-dev digest..."
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Today's Topics:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>    1. Re: Import mri - scripts (Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Message: 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From: Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To: Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Message-ID:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         <CAKHj7uST=
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could we send you a link with 10 anonymized
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom files to diagnose the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> warnings we get?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > We were wondering whether Loris has a tool
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to check if there are problems
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > with the dcm files, before trying to upload
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> them. Something that could
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > provide the same results provided in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> warning_output, this is the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > summary from the mri_upload at the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-page. Also which attributes of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > dcm header would trigger a warning? is there
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a dcm file header
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > specification for Loris?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> function it worked,but i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> thought that something else was causing the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2nd issue.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Boucher, Mr, <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The first error occurs because the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> QCFirstChangeTime and columns are of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> type `unsigned integer` and not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> `datatime`. You should be using
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW().
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The second error occurs because the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> trigger triggers a rollback of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> insert statement in the files table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> See mysql documentation for trigger error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> handling.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> An error during either a BEFORE or AFTER
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> trigger results in failure of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the entire statement that caused trigger
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> invocation.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you for sharing that. I hope it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> helps.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Xavier
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> behalf of Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Cecile Madjar <cecile.madjar at mcin.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> When mincs are inserted their
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> corresponding rows at the file table are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> inserted too
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i would like to insert their rows at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file_qcstatus as well, because i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> don't want manually to label them as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> passed throught the interface
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> That is the trigger i wrote
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> BEGIN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT INTO files_qcstatus
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SET FileID = NEW.FileID,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      SeriesUID = NEW.SeriesUID,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      EchoTime = NEW.EchoTime,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCStatus = "Pass",
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCFirstChangeTime = NOW(),
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCLastChangeTime = NOW();
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> END
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> although it contains some errors
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> value for column
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update a child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (`LORIS`.`parameter_file`, CONSTRAINT
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (`FileID`) REFERENCES `files` (`FileID`))
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> In the mri_upload table, there is a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> TarchiveID column associated with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the MRI upload you inserted. When this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> value is NULL, it means no DICOMs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> were inserted into the tarchive tables. At
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the end of the insertion of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DICOMs in the tarchive tables, this value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is updated with the correct
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> TarchiveID associated with the upload.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Could this correspond to what you want to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> do?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Regarding the files_qcstatus, this table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is only linked to the files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> table (hence, the MINC files). You could
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> always create a new table for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i would like whenever a dicom is imported
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to mark all their
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> coressponding qc_status to "pass". I was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> thinking of creating a trigger for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that, but which tables do i need to add
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries to? So far from what i see
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i need to add entres at  the table "files"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> whenever an insertion happens to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> files_qcstatus.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Oh, sorry i should have asked for StudyID,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at the beginning of my email
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that's the Study Instance UID, not the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyID. So the StudyID i am
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looking for is not stored in the database?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The StudyUID is stored in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DicomArchiveID field of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> tarchive table. It can also be found in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the metadata field but it is mixed
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> with many other information.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is StudyUID stored somewhere at the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tables? At the tarchive table,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> specifically at the AcquisitonMetadata
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> column i found something called
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 'Unique Study ID" in its context, but that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> must be the Study Instance UID.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Your observation is correct. A little
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> explanation below.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> MINC files get inserted into the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> violation tables if:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - the scan type could not be identified
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (not matching an entry in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - one parameter of the scan type is out
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the expected range
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    present in the mri_protocol_checks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (extra filtering in case you need to be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    stricker on some parameters not present
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - if the CandID and PSCID do not match
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The following cases do not get in the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> violation tables as it happens
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> before the conversion of the DICOM to MINC
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files and only MINC files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> violations are logged there:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - "No single DICOM" (since no valid
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM could be found to convert
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    to MINC)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - "Study already inserted" (duplicate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID) since this error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    happens at the dicomTar.pl level (way
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> before conversion into MINC files)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad everything is working out!!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the mri passed, for some reason it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> consumed 5.12GB of ram. Now about the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations, dicoms are triggered to be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted there only if there is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for its header parameter?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Because i don't see the cases of 'No
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> single dicom" or with the 2 studyiuid
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to be there.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sorry to hear you are having issues with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the memory. I think most of our
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should be fine.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> about that dicom that had that insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error it's about 30mb and when
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> it is being processed the ram is being
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> drastically increased from 2gb to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3.28 and then the whole virtual machine is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> frozen. What is the recommended
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> size of ram for using Loris?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to see that the StudyUID problem was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fixed!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the delete script issue, if you are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> absolutely certain that no
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> processes are run for that uploadID, you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can update the mri_upload table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and set the column Inserting to 0 instead
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of 1 for that uploadID. It
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looks like for some reason the scripts did
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> not update this field when it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> stopped the insertion. Not sure why that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> would be the case though.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Note: only do that update if you are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> certain that there is no processing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> happening.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> about the Dicoms i reported that didn't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have a StudyID they actually do
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I thought that this might be a permission
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> because "w" was missing at the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> group. After using chmod -R 775 only
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 102809579 passed, but with no mnic
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> files. Also now i have this error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> :/data/loris/bin/mri/tools$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -ignore
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is currently processing it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How can solve this?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Here is our auto dicom uploading python
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To give you a brief idea:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Per folder it will:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 1) Delete all the .bak files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 2) Locate .dcm files and update the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Patient header
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3) Furthermore we are interesting in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> finding TR_min, TR_max, TE_min,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> TE_max parameters of T1 protocol and do an
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update at the mri_protocol table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For some reason some files are missing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SeriesDescription/ProtocolName
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> In total i have 7 folders
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3/7 passed
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Also about the first patient with DC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> had a violation "T1 AXIAL SE
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> GADO", but my script didn't output a TE of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 17 nowhere and i find that weird
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> since Loris detects the SeriesDescription.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Now about the 4/7 that didn't passed
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 102327840 and 102809579 outputs "The
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> target directory does not contain a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> single DICOM file.", therefore they are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> missing their StudyUID
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with data from multiple
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> studies."
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and 102761034 "No data could be converted
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into valid MINC files.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> localizer, scout will not be considered!"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What is this?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If i wanted to force the insertion of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 102327840, 102809579 and 102506134
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> can i just pass a flag parameter to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl? or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> modify imaging_upload_file.pl?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PS
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To diagnose a folder search the name of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the folder at dicom_output.txt.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear about your progress.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, the script you used to delete imaging
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> data is fully documented here
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- let us know if you didn't find the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> answers you were looking for there.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (Is it possible the null row in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> *mri_scanner* seen in your database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> management software is a visual
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> placeholder for you as the user?  I'm not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sure why a scanner would ever be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> registered with ID='0' as your screenshot
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> showed.)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I fixed it with this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I tried to create a new candidate using
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the API, is there something
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> wrong with the structure? why did i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> receive a 500 internal error? In the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-error log it state that there is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> something wrong with token, but i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> verfied that the type of the token is a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [php7:error] [pid 4535] [client
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Uncaught TypeError: Argument 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> passed to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SinglePointLogin::JWTAuthenticate() must be of the type string,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> null given, called in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> defined in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> trace:\n#0
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> NDB_Client->initialize('/var/www/loris/...')\n#3
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris\\API\\APIBase->__construct('POST')\n#4
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n  thrown in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is there a way also to delete candidates?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Just to let you know what i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> did to clear candidates, because maybe i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> may have missed dependencies.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> First i deleted all their uploads
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> etc ( is there a way to omit
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the backup file ? )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Afterwards i had some scanner candidates,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> so i deleted all the entries
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> from mri_scanner except that i couldn't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete this entry with the 0 ID.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Lastly i deleted the session and then the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> We recommend that you use our existing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tools for creating new candidates
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> - either the LORIS API or if you are using
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a PHP script, by calling the Candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> class's createNew()
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >function.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> These will create the necessary records
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for you.  (It's not recommended to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> make direct modifications to mysql
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database tables in your script, if I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> understand you.)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The CandID should be a randomized 6 digit
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> randomized ID, and there are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> multiple reasons for this.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You can use the PSCID for project-specific
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> IDs and the External ID field
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> in the candidate table can also be used
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for any values you like.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Additionally, any number of custom IDs can
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be added in parallel - these
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> are entered/visible in the Candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Information module and added in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> back-end as candidate parameters.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> We are building a script that will auto
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insert the candidates based on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> their ExternalID. We would like to know
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> whethere when we are creating a new
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> profile in the candidate table, if we also
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have to insert a new record at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> another table? Furthermore is there a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> problem that in our case CandID won't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> be a 6digit? ( should we start it from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 100000?)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> That would normally be the case but the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> numeric part of the PSCID get
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> paded with 0 on the left.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ex. for sequential ID made of center ID of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> `ABC` plus 4 numerical char
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> with a min value of 1, the sequence would
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0002
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0010
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> thus sorting them ascending will always
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> get the latest value generated
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> as the max value.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> melanie.legault2 at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I see, although the PSCID value is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> varchar(255), it must be stored
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> within a specific length of characters.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Otherwise if we were to sort
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> strings with different lengths the result
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> would not be sorted correctly (
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1, 10, 11, 2 ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hello Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> There is no `last value` stored anywhere.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The code simply look for the PSCID with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the max value and increase that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> value by 1 in order to generate the next
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this info help.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie Legault | Software developer |
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Faculty of Medicine | McGill
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> University
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> behalf of Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> how does Loris determine the next
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> available PSCID value for a new
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> e.x in the default case the PSCID is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sequential, but where do we store the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> last value for the sequential sequence?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the parameters in the mri_protocol you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have assigned are global
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> standard? or were assigned after trial and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Given you have done the initial setup of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your tables to match your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> intended protocol/parameters according to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> instructions --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the Troubleshooting guide documentation
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> recommends
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> re-running the pipeline (and first
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> deleting prior uploads).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *if i were to change their status to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> resolve what would happen?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I noticed that i can view the mnics at the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> brainbrowser from the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations page ( those mnics are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> stored at /data/loris/data/trashbin/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> if i were to click their issue to resolve
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what would happend? would they
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> appear in the dicom_archive view too? ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The defaut values of the schema exists in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my local database. If i adjust
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the default values of TR_min and TE_min
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the mincs will be uploaded?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is it possible that you haven't set up
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your mri_protocol table ?   (and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_scan_type table too, for additional
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> types of scans)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Like the psc table, this is a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pre-requisite for the Imaging insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> setup : See the install/setup
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> documentation :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To add new rows, just use MySQL insert
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> statements.  You can adapt the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> insert statements which load the default
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table values --> e.g. Here on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> GitHub :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (see also the mri_scan_type table)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I see that i can edit the values but not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> how to insert new rows.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If i choose Inserted with flag then will
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the minc be inserted?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear that *dcmodify* worked
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> correctly.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the MRI Violations module, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> screenshot is enough.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It says "could not identify scan type",
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> which we knew already.  Did you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> click on the link on those words?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It will take you to the next page of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module, showing for each scan
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> what the scan parameters were, and will
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also show for comparison what's
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> stored in your *mri_protocol* table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Compare these values to find which
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> parameter was not correct according
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to your *mri_protocol* table scan type
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> definitions.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You may end up broadening your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol value ranges (e.g. TR, TE)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> for scans.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> This can be done in the front-end, by
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> editing the database table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> directly in the same subpage of the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Violations module.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The MRI Violations module features are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> explained in more detail in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Help text for this module inside LORIS
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (click the  ["?"] icon in the menu
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> bar.)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> :  no MINCs inserted- violated scans
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looks like my previous email's attachment
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wasn't delivered due to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> security reasons, i uploaded my file at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> google drive
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> From Dicat's view seems that dcmodify
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> worked in both cases
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the mri_violations i attached the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .html output from webbrowser, so
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that you can check the filelds easier.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Great, sounds like more progress.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> About the dcmodify command -- I'm not sure
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> why you're getting an Endian
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> warning.  (it's a warning not an error,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> correct?)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To clarify -- Were the DICOM headers
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (PatientName) all successfully
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> relabelled, after the command ran?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You can use also our DICAT tool (
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/DICAT) to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> verify and/or update local DICOM headers
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- though your dcmodify command is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a great and fast solution for bulk header
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> updates.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If you're concerned about fields being
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> changed (e.g. "(2001,105f)" from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the warning message)  - you can also
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dcmdump a DICOM slice before and look
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at these fields specifically.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's also not a bad "sanity check" to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> backup your DICOMS before/after
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> running dcmodify, and use dcmdump on each
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> version to diff the outputs --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> this will pinpoint what changed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Re the protocol violation --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol not recognized or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> unknown :   this means your scans did not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match what is stored in your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_protocol table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Check the MRI Violations front-end module
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- can you see why they didn't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> match?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Send us an example, in addition to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> contents of the mri_protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> table, if you can't find the source of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mismatch.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  Here is the psc table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I created 2 candidates profiles through
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the interface
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> then runned dcmodify command to a dicom
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify -ma
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName="DCC0000_258024_V1"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and got those warning: is this okay?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify at another Dicom didn't show
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> warnings. Below you can see the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> execution for the second dicom. Mnics
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> could not be inserted due to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> AcquisitionProtocol being unknown.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Running now the following command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> imaging_upload_file.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 12
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  find -path
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dicomTar.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  Source: /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Target: /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Testing for database connectivity.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Database is available.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You will archive the dir :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You are creating a tar with the following
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> tar -cf
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> getting md5sums and gzipping!!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Linux
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2019-09-06 18:36:50
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Removing temporary files from target
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> location
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Done adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -uploadID 12 -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  md5sum
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Set centerID = 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Number of MINC files that will be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> database: 2
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cat
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Acquisition protocol is unknown
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>   --> The minc file cannot be registered
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> since the AcquisitionProtocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> is unknown
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sure -- you can delete imaging datasets
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the *delete_imaging_upload*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> script --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> details here:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> What's in your *psc* table?  (Is it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> properly populated? This is a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> pre-requisite to loading imaging data.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The foreign key constraint error on the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate record is curious.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> There are also a few options for creating
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates when inserting
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> imaging data:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a. via the LORIS API -- Create the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates (and visits, optionally I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> think)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How to:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> by LORIS.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Then as a second step:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> b. Use the imaging insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to load your DICOMs.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You will want to first ensure that the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName header in the DICOMs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> as well as tar package are correctly
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> labelled with PSCID_DCCID_VisitLabel
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How to :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when running the bids_import script,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to automatically create your candidates
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and sessions.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How do i delete a Study? And everytime do
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i have to create a new
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate to get DCCID and a PSCID?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *First execution:*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update a child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_candidate_1`
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> REFERENCES `psc` (`CenterID`)) at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ERROR: Failed to insert record in table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_scanner:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The following database commands failed:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SET
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Medical Systems';
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Error obtained:Cannot add or update a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> child row: a foreign key
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_mri_scanner_1`
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> `candidate` (`CandID`)) (error code 1452)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ERROR: The validation has failed. Either
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> re-run the validation again
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and fix the problem. Or re-run
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader.pl using -force to force the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> execution.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The tarchiveLoader.pl insertion script has
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *And second execution: *
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PROBLEM:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The user 'lorisadmin' has already inserted
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this study.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The unique study ID is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> This is the information retained from the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> first time the study was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> inserted:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Linux
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2019-09-04 18:33:05
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Last update of record:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The dicomTar.pl execution has failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ok, this sounds like good progress.  Let
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> us know when you next encounter
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> issues as you progress through the Imaging
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Install/Setup docs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I'll look into how we can better handle
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the incoming/ directory next
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> time.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> populated correctly except its port is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 'port'    : ''. Also i have tested
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that i can connect to MySQL with lorisuser.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I executed the script again, because the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> only error i had previously was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that the /data/incoming folder didn't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> exist and there are no errors
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> reported back except of warnings <<mysql:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [Warning] Using a password on the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> command line interface can be insecure>>.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's possible -- if the script was unable
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to connect to the database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> during its execution (e.g. typo in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> password), that would explain the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> underpopulated Image path and Loris-MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> code path you saw in the Config
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> module.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's hard to tell without seeing the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> output from your script run -- Did
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you see a sign of any such error?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The Config fields are populated by the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_install.sh script (starting
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at line 222
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For example, check if the database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> connection information was populated
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> accurately in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If you are referring to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_install.sh here is an image with the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> configurations i typed. Maybe the problem
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is somewhere at the last part
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> which asks to configure as much as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> possible automatically?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear your LORIS core install is up
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and working and all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> front-end pages are loading.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> chmod 775 project
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > and the web interface worked.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, it's important that project/ have 775
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> permissions and that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> lorisadmin be part of the sudoers group,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> per step 1 in the install
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Readme <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris#install-steps>.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Image should change LORIS to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris, right?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> These imaging paths will be updated during
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your imaging installation
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> by an automated script --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you do not need to set them manually via
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Config module.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Please continue to follow the Setup Guide
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for detailed steps to follow.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should change LORIS to loris,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> right?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i used
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> curl -sL
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://deb.nodesource.com/setup_8.x | sudo
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -E bash -
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sudo apt-get install -y nodejs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /0/#inbox/FMfcgxwGBmlrdRDRSFqvSfhPwxLQTrhM>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you had suggested in the past, make worked
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and now i can see all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> contents in the web-interface, but i don't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need make install?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -------------- next part --------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> An HTML attachment was scrubbed...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> URL: <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> *****************************************
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>> Loris-dev mailing list
>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>
>>>>
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From lingyun.ma at mcin.ca  Fri Jan 31 10:34:52 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Fri, 31 Jan 2020 10:34:52 -0500
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAKHj7uRBub=X8+qGSY0N5xCbn5t2PGeiP_QmmZ6fNQkWE=3sfg@mail.gmail.com>
References: <mailman.1851.1573565332.16403.loris-dev@bic.mni.mcgill.ca>
 <CAEfMBom1HCWLo4NWgt5XG4625tCBfRT_Z_HepvtT_Er2LKbJoA@mail.gmail.com>
 <CAKHj7uS1AdMDjnacouTvxZgziYVgp5NNUeOuMkpDyrTskGTh-Q@mail.gmail.com>
 <CALbt7NDej8FGUUS6_oKbK5Fp-FnwsVz9AgZ6ZcJEZhmoKZmv8w@mail.gmail.com>
 <CAKHj7uSx-qqcXHZsWsZmSJ7sC1DgF+XapT5Y1+QdoVic37_DDg@mail.gmail.com>
 <CAMkiY3fQBGDGeNO8EHxwYAgbhTggNSQ+AVuCfdraDXwULMjjUg@mail.gmail.com>
 <CAKHj7uT5xXi=pOPdH=W9BroSphMHdTszdgW+GxuES=8wZox9eQ@mail.gmail.com>
 <CAMkiY3eUouxaRVdC4wH+vdjeQ=q_Nx8bcDNzcWgD_OgN77m3mw@mail.gmail.com>
 <CAKHj7uSxu4+tm+=x4+qJ1sAbrjmxG2H7LovDb7-2KMnyYQhrgg@mail.gmail.com>
 <CAMkiY3fdPZec2jx-cc2Zq37j3ekmTu_o819yBUv-bC7M98bkVw@mail.gmail.com>
 <CAKHj7uSZHozpuQ_YwGmy6wQ4tm43vJa556V0o2+JGDVsYaqN4g@mail.gmail.com>
 <CAMkiY3dge=x93bQDv0fHGMcrX0PA8Z_imLb_zSTh=nTrx5weFg@mail.gmail.com>
 <CAKHj7uR81gCkjvccMxwMA08dGSEgyTLJBJ+pZPkoUQDtGP_hFA@mail.gmail.com>
 <CAMkiY3fGhvExZ-JOvxeHe7dJQPvtPAHx3oJuiMVX7f1JgF1GAg@mail.gmail.com>
 <CAKHj7uRExO98Yyn9_07aw44wbh0bCL9_C1VFTAURKsxQLUuAeQ@mail.gmail.com>
 <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>
 <CAKHj7uRueb5fgh4VVCAyaq8tC9WM4gJ7k6Q=dxsqWzFgDqPfVQ@mail.gmail.com>
 <CAMkiY3d-Vt=3gQqwJ+GSRSacbLp2QxrB0g-_C7ONd8j_g1ipoQ@mail.gmail.com>
 <CAKHj7uQt9=nokz5g1zBuBx1-rJ8q7qKOuNVkQugC9wfvNFcjVA@mail.gmail.com>
 <CAMkiY3cAuQfT_5iMzYoF2BXVceu_vgz4eCq2sAtoyse+zUYeSg@mail.gmail.com>
 <CAMkiY3dq1O3V8+r4tTAWQ8N=rVFg=DNY-UPeMqbec+MSayj=Cg@mail.gmail.com>
 <CAKHj7uSEegvE1apPBGVyHmjyVzF+YxJjDMg0b+hDE4_-ON+dYw@mail.gmail.com>
 <CAKHj7uRx1NT7CycFq65uFpgPiOVwvT-jtK1NJX6_3rrLNFwdbA@mail.gmail.com>
 <CAMkiY3dAnkLdc4N=REmeCpX2qBfsQf=wRb=YtHtt20f8adXFyw@mail.gmail.com>
 <CAKHj7uRpA-8kzkoEnAk7JBNLP7v4cmK4zW-gMutHESiFGj7xjw@mail.gmail.com>
 <CAMpvQ9hNLxz9SZsJwWec_yQ3R4KGhnqv3CDaSPOB1exPsO5AJA@mail.gmail.com>
 <CAMpvQ9gTQUGvmd7E8_Mnk7sd8HtX4NHvLCfWZ0-hEi9aJuu_nw@mail.gmail.com>
 <CAKHj7uSNm=OX8jaDJ0-TZZsBA8zm3Uv6yErBSy76EnwUWdpsig@mail.gmail.com>
 <CAMkiY3dGcQDPCfr9BDOUY3NEgoskTkU7D99FrkvmqPagKtAROQ@mail.gmail.com>
 <CAKHj7uRBub=X8+qGSY0N5xCbn5t2PGeiP_QmmZ6fNQkWE=3sfg@mail.gmail.com>
Message-ID: <CAMpvQ9ifuSdu9_v2mpCmvK3o7zMibq=cE7k32O7Kp_S8V_=5Cw@mail.gmail.com>

Hi Sotirios,

This is because you are runing the installdb from curl, whose host name is
not the one you used on the browser. You can modify Config table host and
url two configurations or possibly pass a good hostname to curl.

Ling

On Fri, Jan 31, 2020 at 10:25 AM Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:

> Hi Cecile,
>
> Indeed 'file' was missing and now it worked. I also wanted to ask about
> the installdb.php if it is possible to automate the execution. I tried thse
> commands with curl to execute the http queries for the forms. Although I
> don't have the error1.html and error2.html files at the moment, their html
> code showed that the execution was successful and the config.xml is being
> created, but when I login it's like the css is not loading.
>
> #first query
> curl --data "formname=validaterootaccount" --data "dbhost=172.28.1.2"
> --data "dbadminuser=root" --data "dbadminpassword=neopass" --data
> "dbname=LORIS" http://localhost/installdb.php > error1.html
> #second query
> curl --data "formname=createmysqlaccount" --data "dbhost=172.28.1.2"
> --data "dbadminuser=root" --data "dbadminpassword=neopass" --data
> "dbname=LORIS" --data "lorismysqluser=lorisuser" --data
> "lorismysqlpassword=neopass" --data "frontenduser=lorisuser" --data
> "frontendpassword=1234" http://localhost/installdb.php > error2.html
>
> If i normally execute installdb.php on the browser, there is no problem.
>
> Thanks
>
>
>
> ???? ???, 31 ??? 2020 ???? 4:39 ?.?., ?/? Cecile Madjar <
> cecile.madjar at mcin.ca> ??????:
>
>> Hi Sotirios,
>>
>> Actually, is it possible that 'file' is not installed on your VM. I
>> misread the error in my earlier email and it might be crashing in MRI.pm at
>> line 1523 of your code. In that line, 'file' is used to determine if the
>> file is a DICOM, if not, it will show a warning and not count the file as a
>> DICOM. So in the end, none of your files are considered DICOM files and
>> when it comes to convert the list of DICOMs, there is nothing to convert,
>> hence the number of MINC file = 0.
>>
>> Anyway, I have a feeling this might be the issue you are having.
>>
>> Let me know how it goes,
>>
>> C?cile
>>
>> On Fri, Jan 31, 2020 at 9:23 AM Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> wrote:
>>
>>> Hi Ling,
>>>
>>> Yes it's Loris-mri 21.0. One thought i had is that maybe i should define
>>> root as linux user?
>>> https://github.com/aueb-wim/LORIS-for-MIP/blob/master/docs/pics/loris_docker_imaging_install.png.
>>> But i see no difference either when i execute it as lorisadmin.
>>>
>>> Also here are the files we use
>>> https://github.com/aueb-wim/LORIS-for-MIP/tree/master/mri_loris
>>>
>>> And here is the complete output of the batch execution.
>>>
>>> Use of uninitialized value $_ in pattern match (m//) at
>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>>> Running now the following command: /data/loris/data//uploadNeuroDB/
>>> imaging_upload_file.pl -profile prod -upload_id 35
>>> /data/incoming/DCC0000_956912_V1.tar.gz -verbose
>>>
>>>  find -path \/data\/tmp\/ImagingUpload\-14\-15\-z2B0N3 -name '__MACOSX'
>>> -delete
>>> xargs: file: No such file or directory
>>>
>>> dicomTar.pl \/data\/tmp\/ImagingUpload\-14\-15\-z2B0N3
>>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>>>  Source: /data/tmp/ImagingUpload-14-15-z2B0N3
>>> Target: /data/loris/data/tarchive
>>>
>>> Testing for database connectivity.
>>> Database is available.
>>>
>>> You will archive the dir : ImagingUpload-14-15-z2B0N3
>>>
>>> You are creating a tar with the following command:
>>>
>>> tar -cf /data/loris/data/tarchive/ImagingUpload-14-15-z2B0N3.tar
>>> ImagingUpload-14-15-z2B0N3
>>>
>>>
>>> getting md5sums and gzipping!!
>>>
>>> * Taken from dir                   :
>>>  /data/tmp/ImagingUpload-14-15-z2B0N3
>>> * Archive target location          :
>>>  /data/loris/data/tarchive/DCM_2015-09-07_ImagingUpload-14-15-z2B0N3.tar
>>> * Name of creating host            :    172.28.1.1
>>> * Name of host OS                  :    Linux
>>> * Created by user                  :    lorisadmin
>>> * Archived on                      :    2020-01-31 14:15:04
>>> * dicomSummary version             :    1
>>> * dicomTar version                 :    1
>>> * md5sum for DICOM tarball         :    fcaf54e9078705799b10e08c4d34bf70
>>>  ImagingUpload-14-15-z2B0N3.tar
>>> * md5sum for DICOM tarball gzipped :    52c96cd08d168e659b5c73cb77b4621b
>>>  ImagingUpload-14-15-z2B0N3.tar.gz
>>> * md5sum for complete archive      :    f5103ec688a5921a37d3c95cba8598e0
>>>  DCM_2015-09-07_ImagingUpload-14-15-z2B0N3.tar
>>>
>>> Adding archive info into database
>>>
>>>
>>> Removing temporary files from target location
>>>
>>>
>>> Done adding archive info into database
>>>
>>> \/data\/loris\/data\//uploadNeuroDB/tarchiveLoader.pl -globLocation
>>> -profile prod
>>> \/data\/loris\/data\/tarchive\/\/DCM_2015\-09\-07_ImagingUpload\-14\-15\-z2B0N3\.tar
>>> -uploadID 35 -verbose
>>>  md5sum
>>> /data/loris/data/tarchive/DCM_2015-09-07_ImagingUpload-14-15-z2B0N3.tar
>>> PSCID is: DCC0000
>>>  CandID id: 956912
>>>  visit_label is: V1
>>> PSCID is: DCC0000
>>>  CandID id: 956912
>>>  visit_label is: V1
>>> candidate id 956912
>>> Set centerID = 1
>>> PSCID is: DCC0000
>>>  CandID id: 956912
>>>  visit_label is: V1
>>> PSCID is: DCC0000
>>>  CandID id: 956912
>>>  visit_label is: V1
>>> xargs: file: No such file or directory
>>>
>>> Number of MINC files that will be considered for inserting into the
>>> database: 0
>>>
>>> No data could be converted into valid MINC files.
>>>
>>> The tarchiveLoader.pl insertion script has failed.
>>> Use of uninitialized value $mail_user in concatenation (.) or string at
>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
>>> Can't exec "mail": No such file or directory at /data/loris/bin/mri/
>>> batch_uploads_imageuploader.pl line 249.
>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>> batch_uploads_imageuploader.pl line 250.
>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>> batch_uploads_imageuploader.pl line 251.
>>>
>>> ???? ???, 30 ??? 2020 ???? 6:22 ?.?., ?/? Ling Ma <lingyun.ma at mcin.ca>
>>> ??????:
>>>
>>>> Oh, I just found that you are using Loris-mri 21.0, as I stated in the
>>>> previous email, the "$_" could not find any matches, so your command might
>>>> not be correctly entered.
>>>>
>>>> On Thu, Jan 30, 2020 at 10:35 AM Ling Ma <lingyun.ma at mcin.ca> wrote:
>>>>
>>>>> Hi Sotirios,
>>>>>
>>>>> By curiosity, I just looked at the error message, "Use of
>>>>> uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/
>>>>> batch_uploads_imageuploader.pl line 144." clearly means that there is
>>>>> no match, but 144 line has no such code related with $_ in recent versions
>>>>> of the batch_uploads_imageuploader.pl. There is something in the line
>>>>> 165 for a few recent versions.
>>>>>
>>>>> As to "xargs: file: No such file or directory", it could be due to a
>>>>> command unable to find anything using the directory provided as the message
>>>>> suggested.
>>>>>
>>>>> In both cases, I feel that it could be helpful if you provide more
>>>>> details such as which Loris_MRI version you are running, what is the exact
>>>>> command line you are using to help supporters to understand.
>>>>>
>>>>> Thanks.
>>>>>
>>>>> Best regards,
>>>>> Ling Ma
>>>>> Consultant
>>>>>
>>>>> On Wed, Jan 29, 2020 at 6:57 PM Sotirios Nikoloutsopoulos <
>>>>> sotirisnik at gmail.com> wrote:
>>>>>
>>>>>> Hi Cecile,
>>>>>>
>>>>>> it seems that xargs is already installed in our docker container.
>>>>>>
>>>>>> [image: image.png]
>>>>>>
>>>>>>
>>>>>> ???? ???, 29 ??? 2020 ???? 7:59 ?.?., ?/? Cecile Madjar <
>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>
>>>>>>> Hi Sotirios,
>>>>>>>
>>>>>>> It looks like xargs is not installed in your docker environment.
>>>>>>>
>>>>>>> This is being used by the following command in dicomTar.pl (and a
>>>>>>> few other places but that is the one causing the error at the moment):
>>>>>>>
>>>>>>> $cmd = "cd " . $dcm_source . "; find -type f -name '.*' | *xargs*
>>>>>>> rm -f";
>>>>>>>
>>>>>>> So you need to install xargs in your docker for the command to run.
>>>>>>>
>>>>>>> Hope this helps,
>>>>>>>
>>>>>>> C?cile
>>>>>>> On Wed, Jan 29, 2020 at 10:35 AM Sotirios Nikoloutsopoulos <
>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> We are making a dockerized version of Loris 21 and when we execute
>>>>>>>> the batch_uploads_imageuploader.pl we get an error about xargs.
>>>>>>>> What could be the casue?
>>>>>>>>
>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>>>>>>>> Running now the following command: /data/loris/data//uploadNeuroDB/
>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 13
>>>>>>>> /data/incoming/DCC0007_854380_V1.tar.gz -verbose
>>>>>>>>
>>>>>>>>  find -path \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml -name
>>>>>>>> '__MACOSX' -delete
>>>>>>>> xargs: file: No such file or directory
>>>>>>>>
>>>>>>>> dicomTar.pl \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml
>>>>>>>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>>>>>>>>  Source: /data/tmp/ImagingUpload-15-31-U_O5ml
>>>>>>>> Target: /data/loris/data/tarchive
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>>
>>>>>>>> ???? ???, 10 ??? 2019 ???? 7:21 ?.?., ?/? Sotirios Nikoloutsopoulos
>>>>>>>> <sotirisnik at gmail.com> ??????:
>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> i opened an issue and looked up for the values of Volume they
>>>>>>>>> suggested https://github.com/BIC-MNI/minc-toolkit-v2/issues/95.
>>>>>>>>> The only attributes associated with it i saw are [0x00089206] and
>>>>>>>>> [0x00089207]
>>>>>>>>>
>>>>>>>>> [image: image.png]
>>>>>>>>>
>>>>>>>>> I looked up for the file that was being viewed fine in the
>>>>>>>>> BrainBrowser and saw that it had that attribute empty so i used this
>>>>>>>>> command because i couldn't find a way to modify the attribute via pydicom
>>>>>>>>>
>>>>>>>>> dcmodify -ma "(0008,9206)=" *.dcm
>>>>>>>>>
>>>>>>>>> and that command reported the warning about the Endian Syntax. I
>>>>>>>>> also used the corresponding command for 9207 and got the message "Tag not
>>>>>>>>> found'
>>>>>>>>>
>>>>>>>>> Lastly I tried to upload some dicoms and now i am getting the SNR
>>>>>>>>> and i can view them fine. I believe now that all of them will pass
>>>>>>>>> successfully, i will report back later.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> Sotirios
>>>>>>>>>
>>>>>>>>> ???? ???, 9 ??? 2019 ???? 8:10 ?.?., ?/? Cecile Madjar <
>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>
>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>
>>>>>>>>>> The issue you are having is a indeed a dcm2mnc issue. The
>>>>>>>>>> converter does not seem to work on your dataset for some reason.
>>>>>>>>>> Unfortunately, there is not much we can do on our front to fix this...
>>>>>>>>>>
>>>>>>>>>> I would recommend creating an issue on the MINC tools repository
>>>>>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> so they can
>>>>>>>>>> fix your problem.
>>>>>>>>>>
>>>>>>>>>> Very sorry that you are having that problem.
>>>>>>>>>>
>>>>>>>>>> Best,
>>>>>>>>>>
>>>>>>>>>> C?cile
>>>>>>>>>>
>>>>>>>>>> On Wed, Dec 4, 2019 at 8:59 AM Cecile Madjar <
>>>>>>>>>> cecile.madjar at mcin.ca> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> Could you please share a dataset with us that produces the error
>>>>>>>>>>> you get and the weird display in BrainBrowser? You could use the same SFTP
>>>>>>>>>>> credential that Nicolas gave you.
>>>>>>>>>>>
>>>>>>>>>>> The message errors you got from imaging_install.sh are probably
>>>>>>>>>>> due to the fact that you reran the install script and it tried to reinstall
>>>>>>>>>>> something that was already there. I would not worry about it. FYI, the only
>>>>>>>>>>> thing you needed to do was to update the MINC tools path in the environment
>>>>>>>>>>> file as you did after re-running imaging_install.sh and source the
>>>>>>>>>>> environment file.
>>>>>>>>>>>
>>>>>>>>>>> Best,
>>>>>>>>>>>
>>>>>>>>>>> C?cile
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Dec 4, 2019 at 8:03 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>>  Hi Cecile,
>>>>>>>>>>>>
>>>>>>>>>>>> We used minctool 1.9.7 and we still get this error
>>>>>>>>>>>>
>>>>>>>>>>>> <<Restructuring...
>>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>>> noise_estimate --snr /data/loris/data>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> One dicom folder hadn't that error and is being viewed fine in
>>>>>>>>>>>> the BrainBrowser of Loris.
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> When i used dpkg to the 1.9.17 the installation reported fine
>>>>>>>>>>>> <<Unpacking minc-toolkit-v2 (1.9.17) over (1.9.16) ...>>
>>>>>>>>>>>>
>>>>>>>>>>>> and then i used source /opt/minc/1.9.17/minc-toolkit-config.sh
>>>>>>>>>>>>
>>>>>>>>>>>> and aftewards runned bash ./imaging_install.sh just to be sure.
>>>>>>>>>>>>
>>>>>>>>>>>> We also had to modify /data/loris/bin/mri/environment because
>>>>>>>>>>>> it still pointed to the old version.
>>>>>>>>>>>>
>>>>>>>>>>>> What i found strange is this during the run of
>>>>>>>>>>>> imaging_install.sh
>>>>>>>>>>>>
>>>>>>>>>>>> <<already using interpreter
>>>>>>>>>>>> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/bin/python3
>>>>>>>>>>>> Please use the *system* python to run this script
>>>>>>>>>>>> Traceback (most recent call last):
>>>>>>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py",
>>>>>>>>>>>> line 2632, in <module>
>>>>>>>>>>>>     main()
>>>>>>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py",
>>>>>>>>>>>> line 870, in main
>>>>>>>>>>>>     symlink=options.symlink,
>>>>>>>>>>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py",
>>>>>>>>>>>> line 1156, in create_environment
>>>>>>>>>>>>     install_python(home_dir, lib_dir, inc_dir, bin_dir,
>>>>>>>>>>>> site_packages=site_packages, clear=clear, symlink=symlink)
>>>>>>>>>>>>   File
>>>>>>>>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>>>>>>>>> line 357, in abspath
>>>>>>>>>>>>     if not isabs(path):
>>>>>>>>>>>>   File
>>>>>>>>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>>>>>>>>> line 64, in isabs
>>>>>>>>>>>>     return s.startswith(sep)
>>>>>>>>>>>> AttributeError: 'NoneType' object has no attribute 'startswith'
>>>>>>>>>>>> Installing the Python libraries into the loris-mri virtualenv...
>>>>>>>>>>>> Requirement already satisfied: mysqlclient in
>>>>>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (1.4.4)
>>>>>>>>>>>> Requirement already satisfied: mysql-connector in
>>>>>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (2.2.9)
>>>>>>>>>>>> Requirement already satisfied: pybids in
>>>>>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (0.9.4)
>>>>>>>>>>>> Requirement already satisfied: nibabel>=2.1 in ./python_virtua>>
>>>>>>>>>>>>
>>>>>>>>>>>> So should i open an issue for that error? or is there something
>>>>>>>>>>>> else to try?
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks
>>>>>>>>>>>>
>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 10:39 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Does the pic screenshot in the imaging browser module also
>>>>>>>>>>>>> shows 1 slice? If so, that would mean there was an issue with the dcm2mnc
>>>>>>>>>>>>> conversion. Once again, installing the latest version of the MINC tools
>>>>>>>>>>>>> should help but if this issue persists I would recommend creating an issue
>>>>>>>>>>>>> for that too on their repository
>>>>>>>>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> (if not
>>>>>>>>>>>>> already reported there, there are a few known issue reported).
>>>>>>>>>>>>>
>>>>>>>>>>>>> Other viewer for MINCs are register and Display (both part of
>>>>>>>>>>>>> the MINC tools). For NIfTI, you have FSLeye, MRICron and probably many
>>>>>>>>>>>>> other viewers that exists.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>
>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, Dec 3, 2019 at 3:26 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Yes, Nifti files are mandatory for our work. From what we saw
>>>>>>>>>>>>>> at a 3rd vm we setted up, the nifti files are being created ( i haven't
>>>>>>>>>>>>>> verified if that is the case at the 2nd vm ). I will install the latest
>>>>>>>>>>>>>> version and will report back, but do you know any nifti/minc viewer?
>>>>>>>>>>>>>> because the Brainbrowser of Loris does not output them well, it's like it
>>>>>>>>>>>>>> is loading only 1 slice and we would like to verify it with another tool
>>>>>>>>>>>>>> too. We verified that the dcmconv command didn't affect the
>>>>>>>>>>>>>> quality of the .dcm files.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ???? ???, 2 ??? 2019 ???? 6:59 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> It looks like for some reason your binary mnc2nii is not
>>>>>>>>>>>>>>> working and reports that error. Do you want to create NIfTI files or are
>>>>>>>>>>>>>>> you happy with just the MINC files?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> If you don't need the NIfTI files, then maybe you can set
>>>>>>>>>>>>>>> the Config setting "NIfTI file creation" to No instead of
>>>>>>>>>>>>>>> Yes and this error will not appear anymore.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> If you need the NIfTI files to be created, then I would
>>>>>>>>>>>>>>> recommend installing the latest version of the MINC tools (1.9.17). They
>>>>>>>>>>>>>>> can be found there:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>    - pre-built packages:
>>>>>>>>>>>>>>>    https://packages.bic.mni.mcgill.ca/minc-toolkit/
>>>>>>>>>>>>>>>    - from the source code with installation instructions in
>>>>>>>>>>>>>>>    the README: https://github.com/BIC-MNI/minc-toolkit-v2
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> If the problem persists by using the latest release of MINC
>>>>>>>>>>>>>>> tools, then create an issue on Github for the MINC developers
>>>>>>>>>>>>>>> here <https://github.com/BIC-MNI/minc-toolkit-v2/issues>.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks to Nicholas i was able to create all the mincs
>>>>>>>>>>>>>>>> images. The problem was that the files were in Little-Endian-Implicit
>>>>>>>>>>>>>>>> transfer syntax and i had to convert them Little-Endian-Explicit transfer
>>>>>>>>>>>>>>>> syntax with this command
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> find <root_of_my_DICOM_files_directory> -type f | xargs -i
>>>>>>>>>>>>>>>> dcmconv --write-xfer-little {} {}
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Looking back at our mails i saw that Little-Endian error
>>>>>>>>>>>>>>>> had occurred when i used dcmodify, but i switcthed to using pydicom instead.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> In the output i see an error sometimes about "gsl:
>>>>>>>>>>>>>>>> bessel_I0.c:216: ERROR: overflow". Is this okay?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Restructuring...
>>>>>>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>>>>>>> noise_estimate --snr
>>>>>>>>>>>>>>>> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
>>>>>>>>>>>>>>>> SNR is:
>>>>>>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thank you for the details!
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> A few things to try:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>    - modify the TMPDIR to be on your /data directory
>>>>>>>>>>>>>>>>>    where there might be more space to do processing (could create a /data/tmp
>>>>>>>>>>>>>>>>>    where the temporary files would be created)
>>>>>>>>>>>>>>>>>    - how many files are there for that upload in
>>>>>>>>>>>>>>>>>    tarchive_files? Are they different from the ones showing the warning
>>>>>>>>>>>>>>>>>    message?
>>>>>>>>>>>>>>>>>       - FYI: query to get that: SELECT tf.* FROM
>>>>>>>>>>>>>>>>>       tarchive_files tf JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your
>>>>>>>>>>>>>>>>>       uploadID> (the output of that query would be very
>>>>>>>>>>>>>>>>>       useful if you can provide it)
>>>>>>>>>>>>>>>>>       - how many series are there for that upload in
>>>>>>>>>>>>>>>>>    tarchive_series?
>>>>>>>>>>>>>>>>>    - FYI: query to get that: SELECT ts.* FROM
>>>>>>>>>>>>>>>>>       tarchive_series ts JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your
>>>>>>>>>>>>>>>>>       uploadID> (the output of that query would be very
>>>>>>>>>>>>>>>>>       useful if you can provide it)
>>>>>>>>>>>>>>>>>    - things are failing when the scripts try running the
>>>>>>>>>>>>>>>>>    following command: find
>>>>>>>>>>>>>>>>>    /tmp/TarLoad-23-43-ccugaa/ImagingUpload-23-43-6JCOTO -type f  |
>>>>>>>>>>>>>>>>>    /data/loris/bin/mri/dicom-archive/get_dicom_info.pl
>>>>>>>>>>>>>>>>>    -studyuid -series -echo -image -file  -attvalue 0018 0024 -series_descr
>>>>>>>>>>>>>>>>>    -stdin | sort -n -k1 -k2 -k7 -k3 -k6 -k4  | cut -f 5 | dcm2mnc -dname ''
>>>>>>>>>>>>>>>>>    -stdin -clobber -usecoordinates /tmp/TarLoad-23-43-ccugaa
>>>>>>>>>>>>>>>>>       - clearly the problems come from get_dicom_info.pl
>>>>>>>>>>>>>>>>>       but I cannot pinpoint the error yet. I will ask around and get back to you
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> If I cannot figure it out remotely, is there a way to have
>>>>>>>>>>>>>>>>> a call using zoom? This way you could share your screen with me and run the
>>>>>>>>>>>>>>>>> debugger on that script and hopefully we can figure out what is going on
>>>>>>>>>>>>>>>>> with those datasets?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thanks!
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Tue, Nov 26, 2019 at 5:17 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> In both my virtual machines
>>>>>>>>>>>>>>>>>> export TMPDIR=/tmp
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> In both vm also with dcm2mnc i get this output. Just to
>>>>>>>>>>>>>>>>>> verify that this passed in my 1st vm and produced mincs.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> I attached the spool as a csv.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> And also one difference i found was this in the Loris-mri
>>>>>>>>>>>>>>>>>> code ( left 1st workable vm, right 2nd vm that has to be fixed, although i
>>>>>>>>>>>>>>>>>> changed it seems to be independent of the uninitialized value $_ )
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> that is puzzling... A few additional questions:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>    - what is the bash variable TMPDIR set to on the
>>>>>>>>>>>>>>>>>>>    environment file?
>>>>>>>>>>>>>>>>>>>    - could you try running separately dcm2mnc on the
>>>>>>>>>>>>>>>>>>>    DICOM folder to see if that works?
>>>>>>>>>>>>>>>>>>>    - could you send us the detailed log from the
>>>>>>>>>>>>>>>>>>>    notification spool table (SELECT * FROM notification_spool WHERE
>>>>>>>>>>>>>>>>>>>    UploadID=<your uploadID>) and send it back to us? Maybe there are some
>>>>>>>>>>>>>>>>>>>    additional clues that could help figuring out what is going on.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thank you!
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Tue, Nov 26, 2019 at 10:12 AM Sotirios
>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I checked for the StudyInstacueUID at the files with
>>>>>>>>>>>>>>>>>>>> "The target directory does not contain a single DICOM file"" and their
>>>>>>>>>>>>>>>>>>>> attribute has a value.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Regarding the scouter and localizer, i modified the
>>>>>>>>>>>>>>>>>>>> settings in the imaging pipeline and now i don't get that error message,
>>>>>>>>>>>>>>>>>>>> but still it doesn't create the mnics.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> The errors i am getting are ( uninitialized value $_ is
>>>>>>>>>>>>>>>>>>>> not important? because i haven't got comments about that )
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>> line 144.
>>>>>>>>>>>>>>>>>>>> Running now the following command:
>>>>>>>>>>>>>>>>>>>> /data/loris/data//uploadNeuroDB/imaging_upload_file.pl
>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 134 /data/incoming/DCC0025_118008_V1.tar.gz
>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> and
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for
>>>>>>>>>>>>>>>>>>>> inserting into the database: 0
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> No data could be converted into valid MINC files.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> The tarchiveLoader.pl insertion script has failed.
>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $mail_user in concatenation
>>>>>>>>>>>>>>>>>>>> (.) or string at /data/loris/bin/mri/
>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>> line 249.
>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>> line 250.
>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>> line 251.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar
>>>>>>>>>>>>>>>>>>>> <cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> OK. So the issue I mentioned should not be a problem
>>>>>>>>>>>>>>>>>>>>> for you.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Is the StudyInstanceUID DICOM header set in your
>>>>>>>>>>>>>>>>>>>>> images? If it is not set, then you would end up with the error message "The
>>>>>>>>>>>>>>>>>>>>> target directory does not contain a single DICOM file". So maybe this is
>>>>>>>>>>>>>>>>>>>>> the issue you are having with those datasets?
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Regarding not excluding series descriptions, you can
>>>>>>>>>>>>>>>>>>>>> configure that in the Config module under the Imaging Pipeline section.
>>>>>>>>>>>>>>>>>>>>> Simply remove all entries for the "Series description to exclude from
>>>>>>>>>>>>>>>>>>>>> imaging insertion" setting.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On Mon, Nov 25, 2019 at 9:58 AM Sotirios
>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> We are using this version
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/archive/v21.0.0.zip.
>>>>>>>>>>>>>>>>>>>>>> Is it possible to insert low resolution now?
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, <
>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Which version of LORIS-MRI are you using?
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> There was a bug that got resolved in 20.2 in
>>>>>>>>>>>>>>>>>>>>>>> get_dicom_info.pl. Basically, if a DICOM did not
>>>>>>>>>>>>>>>>>>>>>>> have the (0020,0032) header, get_dicom_info.pl
>>>>>>>>>>>>>>>>>>>>>>> considered that the file was not a DICOM, which was a mistake. This got
>>>>>>>>>>>>>>>>>>>>>>> fixed in version 20.2 of LORIS-MRI. Hopefully this is the issue you are
>>>>>>>>>>>>>>>>>>>>>>> encountering.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> About scout and localizer, they are a type of short
>>>>>>>>>>>>>>>>>>>>>>> and low resolution sequence that is used by the tech but is of no interest
>>>>>>>>>>>>>>>>>>>>>>> scientifically, which is why we tend to no insert them.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> i executed the find command and the output i got
>>>>>>>>>>>>>>>>>>>>>>>> per folder was "DICOM medical imaging data. Maybe there is something wrong
>>>>>>>>>>>>>>>>>>>>>>>> with the find command in the warning that it is unable to check if the file
>>>>>>>>>>>>>>>>>>>>>>>> is a dicom file? Also when i use get_dicom_info.pl
>>>>>>>>>>>>>>>>>>>>>>>> i don't get any output data. Finally i don't understand what scout or
>>>>>>>>>>>>>>>>>>>>>>>> localizer is ( something like if and only if a file fails then the whole
>>>>>>>>>>>>>>>>>>>>>>>> session is invalid? ).
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>>>>>>>> Madjar <cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> I took a closer look to the
>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploader_multiple_output.txt file you sent. It looks like there are
>>>>>>>>>>>>>>>>>>>>>>>>> different reasons for failure depending on the DICOM folder uploaded.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>    - For 465466 DCC0000 V1; 727195 DCC0004 V1 and
>>>>>>>>>>>>>>>>>>>>>>>>>    684908 DCC0007 V1: it looks like there is no file of type DICOM in the
>>>>>>>>>>>>>>>>>>>>>>>>>    folder. Have you checked to see if that is indeed the case? Maybe you can
>>>>>>>>>>>>>>>>>>>>>>>>>    try running the following command on that folder to see what are the types
>>>>>>>>>>>>>>>>>>>>>>>>>    of the files? If it does not return at least one DICOM medical imaging data
>>>>>>>>>>>>>>>>>>>>>>>>>    file, then that is why you get the error message from the pipeline:
>>>>>>>>>>>>>>>>>>>>>>>>>       -
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>       find <my_dicom_archive_root_folder> -type f | xargs -i file {}|cut -d: -f2|sort|uniq
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>       - For 864173 DCC0001 V1: it looks like
>>>>>>>>>>>>>>>>>>>>>>>>>    there are two different DICOM studies within the same folder. You will need
>>>>>>>>>>>>>>>>>>>>>>>>>    to split that study in two based on the StudyUID field as the insertion
>>>>>>>>>>>>>>>>>>>>>>>>>    pipeline does not allow for more than one StudyUID per upload.
>>>>>>>>>>>>>>>>>>>>>>>>>    - For 890807 DCC0002 V1; 637025 DCC0005 V1 and
>>>>>>>>>>>>>>>>>>>>>>>>>    239975 DCC0006 V1: it looks like the dcm2mnc command did not produce any
>>>>>>>>>>>>>>>>>>>>>>>>>    MINC files. Can you check in the DICOM archive what are the series present
>>>>>>>>>>>>>>>>>>>>>>>>>    in the tarchive for that visit? Maybe only a scout or localizer was
>>>>>>>>>>>>>>>>>>>>>>>>>    acquired for that session, hence the no valid MINC files (scout and
>>>>>>>>>>>>>>>>>>>>>>>>>    localizer being skipped for the conversion)
>>>>>>>>>>>>>>>>>>>>>>>>>    - For 397410 DCC0003 V1: it looks like
>>>>>>>>>>>>>>>>>>>>>>>>>    everything went well for this one.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> One script that is called by our pipeline is
>>>>>>>>>>>>>>>>>>>>>>>>> called get_dicom_info.pl and this does all kind
>>>>>>>>>>>>>>>>>>>>>>>>> of checks on the DICOM files (it is being called when running the dcm2mnc
>>>>>>>>>>>>>>>>>>>>>>>>> conversion). You could run it independently on your folder if needed.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Since one of the study got in, it does not look
>>>>>>>>>>>>>>>>>>>>>>>>> like you are having a problem with the setup. It seems more likely to be a
>>>>>>>>>>>>>>>>>>>>>>>>> problem with the data themselves.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> In my first vm i am able to create the minc files
>>>>>>>>>>>>>>>>>>>>>>>>>> and view them at the mri browser (except of candidate 102761034 ),
>>>>>>>>>>>>>>>>>>>>>>>>>> meanwhile the same files gives warnings at the 2nd vm. The output  of the
>>>>>>>>>>>>>>>>>>>>>>>>>> batch upload can be seen in the file attached.
>>>>>>>>>>>>>>>>>>>>>>>>>> Also a colleague of us has built a pre-validation
>>>>>>>>>>>>>>>>>>>>>>>>>> tool for dicom
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/
>>>>>>>>>>>>>>>>>>>>>>>>>> which had found all the files that Loris gave as warning . Basically I
>>>>>>>>>>>>>>>>>>>>>>>>>> confirmed that the total amount of files per dicom was the same amount as
>>>>>>>>>>>>>>>>>>>>>>>>>> stated in Loris and checked some filenames given from warning to confirm
>>>>>>>>>>>>>>>>>>>>>>>>>> that they match with our tool. But that was months ago and my colleague had
>>>>>>>>>>>>>>>>>>>>>>>>>> changed some parameters for MIP and now our tool doesn't find all the
>>>>>>>>>>>>>>>>>>>>>>>>>> invalid files, that's why i asked for the dicom header specification of
>>>>>>>>>>>>>>>>>>>>>>>>>> Loris. In a discussion we had he mentioned that he doesn't check for some
>>>>>>>>>>>>>>>>>>>>>>>>>> tags e.x. orientation. Lastly to mention that in my first vm i didn't use
>>>>>>>>>>>>>>>>>>>>>>>>>> our tool to remove invalid dcm files.
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you provide us with some fresh particulars
>>>>>>>>>>>>>>>>>>>>>>>>>>> of the current issue and we'll take it from there?
>>>>>>>>>>>>>>>>>>>>>>>>>>> Yang's team has built these scripts which can
>>>>>>>>>>>>>>>>>>>>>>>>>>> definitely serve as a model for your pre-validation of your DICOM
>>>>>>>>>>>>>>>>>>>>>>>>>>> collections.
>>>>>>>>>>>>>>>>>>>>>>>>>>> cheers,
>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> HI Yang,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> We make use of pydicom library too. Now about
>>>>>>>>>>>>>>>>>>>>>>>>>>>> the validate.py i see that you check if some attributes are missing such as
>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientID, PatientName which all of our files contains that info. Maybe i
>>>>>>>>>>>>>>>>>>>>>>>>>>>> have missed something on the setup of my other virtual machine ( although
>>>>>>>>>>>>>>>>>>>>>>>>>>>> one dicom passed on the new vm successfully, the others that were inserted
>>>>>>>>>>>>>>>>>>>>>>>>>>>> correctly on my old vm fails on the new one ), i think that i had asked
>>>>>>>>>>>>>>>>>>>>>>>>>>>> about this error "Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/
>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 144." but
>>>>>>>>>>>>>>>>>>>>>>>>>>>> i don't remember the solution.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ding <it at cnbp.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hey, Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine from the LORIS team mentioned you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> had some issue with DICOM.  I am a fellow developer for an external project
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using LORIS, kind of just like you. We had to implement DICOM upload as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> well but more as a fully automated pipeline actually.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> While we were building CNBP, we had coded up
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> some minor Python functions to check DICOM integrity (and simple
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> validations) and you might be able to gain some inspiration from it and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> help you with your cause. For more comprehensive solution, PyDICOM (
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#)  seems
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> rough around the edges but hopefully point you in the right direcitons
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Yang Ding, PhD.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Canadian Neonatal Brain Platform Architect
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Send Loris-dev mailing list submissions to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To subscribe or unsubscribe via the World
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Wide Web, visit
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> or, via email, send a message with subject or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> body 'help' to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-request at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You can reach the person managing the list at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-owner at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When replying, please edit your Subject line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> so it is more specific
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> than "Re: Contents of Loris-dev digest..."
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Today's Topics:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>    1. Re: Import mri - scripts (Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Message: 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From: Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To: Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Message-ID:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         <CAKHj7uST=
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could we send you a link with 10 anonymized
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom files to diagnose the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> warnings we get?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > We were wondering whether Loris has a tool
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to check if there are problems
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > with the dcm files, before trying to upload
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> them. Something that could
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > provide the same results provided in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> warning_output, this is the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > summary from the mri_upload at the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-page. Also which attributes of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > dcm header would trigger a warning? is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> there a dcm file header
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > specification for Loris?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> function it worked,but i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> thought that something else was causing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the 2nd issue.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Boucher, Mr, <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The first error occurs because the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> QCFirstChangeTime and columns are of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> type `unsigned integer` and not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> `datatime`. You should be using
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW().
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The second error occurs because the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> trigger triggers a rollback of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> insert statement in the files table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> See mysql documentation for trigger error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> handling.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> An error during either a BEFORE or AFTER
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> trigger results in failure of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the entire statement that caused trigger
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> invocation.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you for sharing that. I hope it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> helps.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Xavier
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> behalf of Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> When mincs are inserted their
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> corresponding rows at the file table are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> inserted too
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i would like to insert their rows at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file_qcstatus as well, because i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> don't want manually to label them as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> passed throught the interface
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> That is the trigger i wrote
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> BEGIN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT INTO files_qcstatus
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SET FileID = NEW.FileID,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      SeriesUID = NEW.SeriesUID,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      EchoTime = NEW.EchoTime,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCStatus = "Pass",
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCFirstChangeTime = NOW(),
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCLastChangeTime = NOW();
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> END
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> although it contains some errors
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> value for column
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update a child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (`LORIS`.`parameter_file`, CONSTRAINT
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (`FileID`) REFERENCES `files` (`FileID`))
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> In the mri_upload table, there is a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> TarchiveID column associated with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the MRI upload you inserted. When this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> value is NULL, it means no DICOMs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> were inserted into the tarchive tables.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the end of the insertion of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DICOMs in the tarchive tables, this value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is updated with the correct
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> TarchiveID associated with the upload.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Could this correspond to what you want to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> do?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Regarding the files_qcstatus, this table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is only linked to the files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> table (hence, the MINC files). You could
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> always create a new table for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dicom_qcstatus and link it to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive table?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i would like whenever a dicom is imported
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to mark all their
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> coressponding qc_status to "pass". I was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> thinking of creating a trigger for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that, but which tables do i need to add
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries to? So far from what i see
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i need to add entres at  the table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "files" whenever an insertion happens to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> files_qcstatus.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Oh, sorry i should have asked for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyID, at the beginning of my email
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that's the Study Instance UID, not the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyID. So the StudyID i am
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looking for is not stored in the database?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The StudyUID is stored in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DicomArchiveID field of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> tarchive table. It can also be found in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the metadata field but it is mixed
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> with many other information.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is StudyUID stored somewhere at the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tables? At the tarchive table,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> specifically at the AcquisitonMetadata
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> column i found something called
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 'Unique Study ID" in its context, but
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that must be the Study Instance UID.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Your observation is correct. A little
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> explanation below.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> MINC files get inserted into the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> violation tables if:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - the scan type could not be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identified (not matching an entry in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - one parameter of the scan type is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out of the expected range
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    present in the mri_protocol_checks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (extra filtering in case you need to be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    stricker on some parameters not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> present in the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - if the CandID and PSCID do not match
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The following cases do not get in the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> violation tables as it happens
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> before the conversion of the DICOM to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MINC files and only MINC files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> violations are logged there:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - "No single DICOM" (since no valid
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM could be found to convert
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    to MINC)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - "Study already inserted" (duplicate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID) since this error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    happens at the dicomTar.pl level (way
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> before conversion into MINC files)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad everything is working out!!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the mri passed, for some reason it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> consumed 5.12GB of ram. Now about the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations, dicoms are triggered to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be inserted there only if there is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> general for its header parameter?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Because i don't see the cases of 'No
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> single dicom" or with the 2 studyiuid
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to be there.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sorry to hear you are having issues with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the memory. I think most of our
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 4GB you should be fine.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> about that dicom that had that insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error it's about 30mb and when
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> it is being processed the ram is being
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> drastically increased from 2gb to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3.28 and then the whole virtual machine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is frozen. What is the recommended
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> size of ram for using Loris?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to see that the StudyUID problem was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fixed!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the delete script issue, if you are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> absolutely certain that no
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> processes are run for that uploadID, you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can update the mri_upload table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and set the column Inserting to 0 instead
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of 1 for that uploadID. It
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looks like for some reason the scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> did not update this field when it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> stopped the insertion. Not sure why that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> would be the case though.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Note: only do that update if you are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> certain that there is no processing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> happening.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> about the Dicoms i reported that didn't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have a StudyID they actually do
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I thought that this might be a permission
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> because "w" was missing at the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> group. After using chmod -R 775 only
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 102809579 passed, but with no mnic
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> files. Also now i have this error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> :/data/loris/bin/mri/tools$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -ignore
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is currently processing it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How can solve this?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Here is our auto dicom uploading python
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To give you a brief idea:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Per folder it will:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 1) Delete all the .bak files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 2) Locate .dcm files and update the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Patient header
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3) Furthermore we are interesting in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> finding TR_min, TR_max, TE_min,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> TE_max parameters of T1 protocol and do
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> an update at the mri_protocol table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For some reason some files are missing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SeriesDescription/ProtocolName
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> In total i have 7 folders
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3/7 passed
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Also about the first patient with DC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> had a violation "T1 AXIAL SE
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> GADO", but my script didn't output a TE
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of 17 nowhere and i find that weird
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> since Loris detects the SeriesDescription.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Now about the 4/7 that didn't passed
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 102327840 and 102809579 outputs "The
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> target directory does not contain a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> single DICOM file.", therefore they are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> missing their StudyUID
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it with data from multiple
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> studies."
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and 102761034 "No data could be converted
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into valid MINC files.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> localizer, scout will not be considered!"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What is this?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If i wanted to force the insertion of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 102327840, 102809579 and 102506134
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> can i just pass a flag parameter to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl? or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> modify imaging_upload_file.pl?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PS
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To diagnose a folder search the name of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the folder at dicom_output.txt.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear about your progress.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, the script you used to delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging data is fully documented here
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- let us know if you didn't find the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> answers you were looking for there.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (Is it possible the null row in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> *mri_scanner* seen in your database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> management software is a visual
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> placeholder for you as the user?  I'm not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sure why a scanner would ever be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> registered with ID='0' as your screenshot
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> showed.)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I fixed it with this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I tried to create a new candidate using
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the API, is there something
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> wrong with the structure? why did i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> receive a 500 internal error? In the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-error log it state that there is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> something wrong with token, but i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> verfied that the type of the token is a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [php7:error] [pid 4535] [client
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Uncaught TypeError: Argument 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> passed to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SinglePointLogin::JWTAuthenticate() must be of the type string,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> null given, called in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> defined in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> trace:\n#0
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SinglePointLogin->JWTAuthenticate(NULL)\n#1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> NDB_Client->initialize('/var/www/loris/...')\n#3
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris\\API\\APIBase->__construct('POST')\n#4
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n  thrown in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is there a way also to delete candidates?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Just to let you know what i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> did to clear candidates, because maybe i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> may have missed dependencies.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> First i deleted all their uploads
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> etc ( is there a way to omit
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the backup file ? )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Afterwards i had some scanner candidates,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> so i deleted all the entries
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> from mri_scanner except that i couldn't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete this entry with the 0 ID.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Lastly i deleted the session and then the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> We recommend that you use our existing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tools for creating new candidates
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> - either the LORIS API or if you are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using a PHP script, by calling the Candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> class's createNew()
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >function.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> These will create the necessary records
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for you.  (It's not recommended to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> make direct modifications to mysql
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database tables in your script, if I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> understand you.)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The CandID should be a randomized 6 digit
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> randomized ID, and there are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> multiple reasons for this.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You can use the PSCID for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> project-specific IDs and the External ID field
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> in the candidate table can also be used
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for any values you like.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Additionally, any number of custom IDs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can be added in parallel - these
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> are entered/visible in the Candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Information module and added in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> back-end as candidate parameters.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> We are building a script that will auto
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insert the candidates based on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> their ExternalID. We would like to know
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> whethere when we are creating a new
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> profile in the candidate table, if we
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also have to insert a new record at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> another table? Furthermore is there a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> problem that in our case CandID won't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> be a 6digit? ( should we start it from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 100000?)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> That would normally be the case but the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> numeric part of the PSCID get
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> paded with 0 on the left.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ex. for sequential ID made of center ID
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of `ABC` plus 4 numerical char
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> with a min value of 1, the sequence would
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0002
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0010
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> thus sorting them ascending will always
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> get the latest value generated
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> as the max value.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> melanie.legault2 at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I see, although the PSCID value is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> varchar(255), it must be stored
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> within a specific length of characters.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Otherwise if we were to sort
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> strings with different lengths the result
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> would not be sorted correctly (
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1, 10, 11, 2 ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hello Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> There is no `last value` stored anywhere.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The code simply look for the PSCID with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the max value and increase that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> value by 1 in order to generate the next
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this info help.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie Legault | Software developer |
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Faculty of Medicine | McGill
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> University
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> behalf of Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> how does Loris determine the next
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> available PSCID value for a new
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> e.x in the default case the PSCID is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sequential, but where do we store the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> last value for the sequential sequence?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the parameters in the mri_protocol you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have assigned are global
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> standard? or were assigned after trial
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and error?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Given you have done the initial setup of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your tables to match your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> intended protocol/parameters according to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> instructions --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the Troubleshooting guide documentation
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> recommends
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> re-running the pipeline (and first
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> deleting prior uploads).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *if i were to change their status to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> resolve what would happen?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I noticed that i can view the mnics at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the brainbrowser from the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations page ( those mnics are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> stored at /data/loris/data/trashbin/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> if i were to click their issue to resolve
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what would happend? would they
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> appear in the dicom_archive view too? ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The defaut values of the schema exists in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my local database. If i adjust
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the default values of TR_min and TE_min
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the mincs will be uploaded?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is it possible that you haven't set up
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your mri_protocol table ?   (and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_scan_type table too, for additional
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> types of scans)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Like the psc table, this is a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pre-requisite for the Imaging insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> setup : See the install/setup
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> documentation :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To add new rows, just use MySQL insert
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> statements.  You can adapt the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> insert statements which load the default
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table values --> e.g. Here on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> GitHub :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (see also the mri_scan_type table)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I see that i can edit the values but not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> how to insert new rows.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If i choose Inserted with flag then will
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the minc be inserted?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear that *dcmodify* worked
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> correctly.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the MRI Violations module, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> screenshot is enough.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It says "could not identify scan type",
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> which we knew already.  Did you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> click on the link on those words?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It will take you to the next page of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module, showing for each scan
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> what the scan parameters were, and will
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also show for comparison what's
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> stored in your *mri_protocol* table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Compare these values to find which
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> parameter was not correct according
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to your *mri_protocol* table scan type
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> definitions.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You may end up broadening your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol value ranges (e.g. TR, TE)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> for scans.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> This can be done in the front-end, by
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> editing the database table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> directly in the same subpage of the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Violations module.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The MRI Violations module features are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> explained in more detail in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Help text for this module inside LORIS
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (click the  ["?"] icon in the menu
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> bar.)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> :  no MINCs inserted- violated scans
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looks like my previous email's attachment
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wasn't delivered due to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> security reasons, i uploaded my file at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> google drive
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> From Dicat's view seems that dcmodify
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> worked in both cases
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the mri_violations i attached the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .html output from webbrowser, so
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that you can check the filelds easier.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Great, sounds like more progress.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> About the dcmodify command -- I'm not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sure why you're getting an Endian
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> warning.  (it's a warning not an error,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> correct?)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To clarify -- Were the DICOM headers
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (PatientName) all successfully
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> relabelled, after the command ran?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You can use also our DICAT tool (
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/DICAT) to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> verify and/or update local DICOM headers
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- though your dcmodify command is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a great and fast solution for bulk header
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> updates.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If you're concerned about fields being
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> changed (e.g. "(2001,105f)" from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the warning message)  - you can also
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dcmdump a DICOM slice before and look
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at these fields specifically.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's also not a bad "sanity check" to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> backup your DICOMS before/after
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> running dcmodify, and use dcmdump on each
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> version to diff the outputs --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> this will pinpoint what changed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Re the protocol violation --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol not recognized or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> unknown :   this means your scans did not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match what is stored in your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_protocol table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Check the MRI Violations front-end module
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- can you see why they didn't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> match?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Send us an example, in addition to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> contents of the mri_protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> table, if you can't find the source of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the mismatch.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  Here is the psc table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I created 2 candidates profiles through
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the interface
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> then runned dcmodify command to a dicom
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify -ma
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName="DCC0000_258024_V1"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and got those warning: is this okay?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify at another Dicom didn't show
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> warnings. Below you can see the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> execution for the second dicom. Mnics
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> could not be inserted due to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> AcquisitionProtocol being unknown.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Running now the following command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> imaging_upload_file.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 12
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  find -path
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dicomTar.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  Source: /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Target: /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Testing for database connectivity.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Database is available.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You will archive the dir :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You are creating a tar with the following
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> tar -cf
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> getting md5sums and gzipping!!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Linux
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2019-09-06 18:36:50
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Removing temporary files from target
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> location
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Done adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -uploadID 12 -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  md5sum
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Set centerID = 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Number of MINC files that will be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> database: 2
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cat
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Acquisition protocol is unknown
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>   --> The minc file cannot be registered
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> since the AcquisitionProtocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> is unknown
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sure -- you can delete imaging datasets
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the *delete_imaging_upload*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> script --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> details here:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> What's in your *psc* table?  (Is it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> properly populated? This is a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> pre-requisite to loading imaging data.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The foreign key constraint error on the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate record is curious.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> There are also a few options for creating
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates when inserting
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> imaging data:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> then DICOM insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a. via the LORIS API -- Create the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates (and visits, optionally I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> think)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How to:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> by LORIS.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Then as a second step:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> b. Use the imaging insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to load your DICOMs.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You will want to first ensure that the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName header in the DICOMs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> as well as tar package are correctly
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> labelled with PSCID_DCCID_VisitLabel
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How to :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when running the bids_import script,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to automatically create your candidates
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and sessions.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How do i delete a Study? And everytime do
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i have to create a new
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate to get DCCID and a PSCID?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *First execution:*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update a child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (`LORIS`.`candidate`, CONSTRAINT `FK_candidate_1`
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> REFERENCES `psc` (`CenterID`)) at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ERROR: Failed to insert record in table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_scanner:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The following database commands failed:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SET
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Medical Systems';
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Error obtained:Cannot add or update a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> child row: a foreign key
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CONSTRAINT `FK_mri_scanner_1`
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> `candidate` (`CandID`)) (error code 1452)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ERROR: The validation has failed. Either
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> re-run the validation again
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and fix the problem. Or re-run
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader.pl using -force to force the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> execution.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The tarchiveLoader.pl insertion script
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *And second execution: *
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PROBLEM:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The user 'lorisadmin' has already
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted this study.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The unique study ID is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> This is the information retained from the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> first time the study was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> inserted:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Linux
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2019-09-04 18:33:05
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Last update of record:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The dicomTar.pl execution has failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ok, this sounds like good progress.  Let
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> us know when you next encounter
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> issues as you progress through the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Imaging Install/Setup docs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I'll look into how we can better handle
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the incoming/ directory next
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> time.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> populated correctly except its port is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 'port'    : ''. Also i have tested
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that i can connect to MySQL with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisuser.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I executed the script again, because the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> only error i had previously was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that the /data/incoming folder didn't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> exist and there are no errors
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> reported back except of warnings <<mysql:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [Warning] Using a password on the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> command line interface can be insecure>>.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's possible -- if the script was unable
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to connect to the database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> during its execution (e.g. typo in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> password), that would explain the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> underpopulated Image path and Loris-MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> code path you saw in the Config
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> module.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's hard to tell without seeing the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> output from your script run -- Did
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you see a sign of any such error?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The Config fields are populated by the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_install.sh script (starting
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at line 222
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For example, check if the database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> connection information was populated
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> accurately in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If you are referring to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_install.sh here is an image with the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> configurations i typed. Maybe the problem
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is somewhere at the last part
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> which asks to configure as much as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> possible automatically?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear your LORIS core install is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> up and working and all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> front-end pages are loading.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> chmod 775 project
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > and the web interface worked.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, it's important that project/ have
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 775 permissions and that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> lorisadmin be part of the sudoers group,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> per step 1 in the install
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Readme <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris#install-steps>.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Image should change LORIS to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris, right?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> These imaging paths will be updated
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> during your imaging installation
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> by an automated script --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you do not need to set them manually via
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Config module.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Please continue to follow the Setup Guide
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for detailed steps to follow.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Image should change LORIS to loris,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> right?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i used
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> curl -sL
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://deb.nodesource.com/setup_8.x | sudo
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -E bash -
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sudo apt-get install -y nodejs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /0/#inbox/FMfcgxwGBmlrdRDRSFqvSfhPwxLQTrhM>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you had suggested in the past, make
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> worked and now i can see all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> contents in the web-interface, but i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> don't need make install?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -------------- next part --------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> An HTML attachment was scrubbed...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> URL: <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> *****************************************
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>> Loris-dev mailing list
>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>
>>>>>
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