From ioannis at berkeley.edu  Thu Feb  6 19:07:59 2020
From: ioannis at berkeley.edu (Ioannis Pappas)
Date: Thu, 6 Feb 2020 16:07:59 -0800
Subject: [Loris-dev] blank page after login
Message-ID: <CAH3c6xJ36EPmYY69hyUOw8rjmi7_=-ztfd4Jizw-ixhvst3KCw@mail.gmail.com>

Hi loris support.

I hope you are well. I would like to report a problem with respect to
signing in to the loris front-end. Despite signing in normally a month ago,
we are now getting a "blank" white page after logging in.

Below are the logs from /var/log/httpd/loris-error.log:

[Thu Feb 06 14:36:20.838065 2020] [php7:notice] [pid 7015] [client
10.0.2.4:55302] PHP Notice:  Undefined variable: isStudySite in
/srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php on line 130,
referer: http://loris/
[Thu Feb 06 14:36:20.838108 2020] [php7:warn] [pid 7015] [client
10.0.2.4:55302] PHP Warning:  in_array() expects parameter 2 to be array,
null given in
/srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php on line 130,
referer: http://loris/
[Thu Feb 06 14:36:20.838469 2020] [php7:error] [pid 7015] [client
10.0.2.4:55302] PHP Fatal error:  Uncaught TypeError: explode() expects
parameter 2 to be string, null given in
/srv/www/loris/php/libraries/User.class.inc:272\nStack trace:\n#0
/srv/www/loris/php/libraries/User.class.inc(272): explode(';', NULL)\n#1
/srv/www/loris/modules/dashboard/php/dashboard.class.inc(40):
User->getSiteNames()\n#2
/srv/www/loris/php/libraries/NDB_Form.class.inc(188):
LORIS\\dashboard\\Dashboard->setup()\n#3
/srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php(171):
NDB_Form->handle(Object(Zend\\Diactoros\\ServerRequest))\n#4
/srv/www/loris/src/Middleware/PageDecorationMiddleware.php(49):
LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest),
Object(LORIS\\dashboard\\Dashboard))\n#5
/srv/www/loris/php/libraries/NDB_Page.class.inc(659):
LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest),
Object(LORIS\\dashboard\\Dashboard))\n#6
/srv/www/loris/php/libraries/Module.class.inc(341):
NDB_Page->process(Object(Zend\\Diactoros\\ServerRequest),
Object(LORIS\\dashboar in /srv/www/loris/php/libraries/User.class.inc on
line 272, referer: http://loris/

We would appreciate any help with this.

Best wishes,
Ioannis
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From rida.abou-haidar at mcin.ca  Thu Feb  6 19:26:06 2020
From: rida.abou-haidar at mcin.ca (Rida Abou-Haidar)
Date: Thu, 6 Feb 2020 19:26:06 -0500
Subject: [Loris-dev] blank page after login
In-Reply-To: <CAH3c6xJ36EPmYY69hyUOw8rjmi7_=-ztfd4Jizw-ixhvst3KCw@mail.gmail.com>
References: <CAH3c6xJ36EPmYY69hyUOw8rjmi7_=-ztfd4Jizw-ixhvst3KCw@mail.gmail.com>
Message-ID: <CABbkjAir2n8qY6UpNdVBucPwixagPtu5cT5rUwHuKq6-qUstng@mail.gmail.com>

Hi Ioannis,

Could you tell us which version of LORIS you are currently using and your
PHP and MySQL versions as well please?

Did you recently upgrade any of those? what might have caused a difference
from last month to this month ?

Best,
Rida Abou-Haidar
Software Developer
Montreal Neurological Institute
McGill University
rida.abou-haidar at mcin.ca


On Thu, Feb 6, 2020 at 7:08 PM Ioannis Pappas <ioannis at berkeley.edu> wrote:

> Hi loris support.
>
> I hope you are well. I would like to report a problem with respect to
> signing in to the loris front-end. Despite signing in normally a month ago,
> we are now getting a "blank" white page after logging in.
>
> Below are the logs from /var/log/httpd/loris-error.log:
>
> [Thu Feb 06 14:36:20.838065 2020] [php7:notice] [pid 7015] [client
> 10.0.2.4:55302] PHP Notice:  Undefined variable: isStudySite in
> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php on line 130,
> referer: http://loris/
> [Thu Feb 06 14:36:20.838108 2020] [php7:warn] [pid 7015] [client
> 10.0.2.4:55302] PHP Warning:  in_array() expects parameter 2 to be array,
> null given in
> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php on line 130,
> referer: http://loris/
> [Thu Feb 06 14:36:20.838469 2020] [php7:error] [pid 7015] [client
> 10.0.2.4:55302] PHP Fatal error:  Uncaught TypeError: explode() expects
> parameter 2 to be string, null given in
> /srv/www/loris/php/libraries/User.class.inc:272\nStack trace:\n#0
> /srv/www/loris/php/libraries/User.class.inc(272): explode(';', NULL)\n#1
> /srv/www/loris/modules/dashboard/php/dashboard.class.inc(40):
> User->getSiteNames()\n#2
> /srv/www/loris/php/libraries/NDB_Form.class.inc(188):
> LORIS\\dashboard\\Dashboard->setup()\n#3
> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php(171):
> NDB_Form->handle(Object(Zend\\Diactoros\\ServerRequest))\n#4
> /srv/www/loris/src/Middleware/PageDecorationMiddleware.php(49):
> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest),
> Object(LORIS\\dashboard\\Dashboard))\n#5
> /srv/www/loris/php/libraries/NDB_Page.class.inc(659):
> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest),
> Object(LORIS\\dashboard\\Dashboard))\n#6
> /srv/www/loris/php/libraries/Module.class.inc(341):
> NDB_Page->process(Object(Zend\\Diactoros\\ServerRequest),
> Object(LORIS\\dashboar in /srv/www/loris/php/libraries/User.class.inc on
> line 272, referer: http://loris/
>
> We would appreciate any help with this.
>
> Best wishes,
> Ioannis
> _______________________________________________
> 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 Feb  6 19:49:30 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Thu, 6 Feb 2020 19:49:30 -0500
Subject: [Loris-dev] blank page after login
In-Reply-To: <CABbkjAir2n8qY6UpNdVBucPwixagPtu5cT5rUwHuKq6-qUstng@mail.gmail.com>
References: <CAH3c6xJ36EPmYY69hyUOw8rjmi7_=-ztfd4Jizw-ixhvst3KCw@mail.gmail.com>
 <CABbkjAir2n8qY6UpNdVBucPwixagPtu5cT5rUwHuKq6-qUstng@mail.gmail.com>
Message-ID: <CAMpvQ9jNA7B2v=6FC8zTpG3K16gbBfs8ROyQEJXGd8QUMvPDGA@mail.gmail.com>

Hi Ioannis,

I just guess that you are using version 21. also guess that the reason
could be that you have no psc associated with the user, you need to check
tables* psc, user_psc_rel* to see if the user has a psc record.

Best regards,
Ling Ma
Consultant

On Thu, Feb 6, 2020 at 7:26 PM Rida Abou-Haidar <rida.abou-haidar at mcin.ca>
wrote:

> Hi Ioannis,
>
> Could you tell us which version of LORIS you are currently using and your
> PHP and MySQL versions as well please?
>
> Did you recently upgrade any of those? what might have caused a difference
> from last month to this month ?
>
> Best,
> Rida Abou-Haidar
> Software Developer
> Montreal Neurological Institute
> McGill University
> rida.abou-haidar at mcin.ca
>
>
> On Thu, Feb 6, 2020 at 7:08 PM Ioannis Pappas <ioannis at berkeley.edu>
> wrote:
>
>> Hi loris support.
>>
>> I hope you are well. I would like to report a problem with respect to
>> signing in to the loris front-end. Despite signing in normally a month ago,
>> we are now getting a "blank" white page after logging in.
>>
>> Below are the logs from /var/log/httpd/loris-error.log:
>>
>> [Thu Feb 06 14:36:20.838065 2020] [php7:notice] [pid 7015] [client
>> 10.0.2.4:55302] PHP Notice:  Undefined variable: isStudySite in
>> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php on line 130,
>> referer: http://loris/
>> [Thu Feb 06 14:36:20.838108 2020] [php7:warn] [pid 7015] [client
>> 10.0.2.4:55302] PHP Warning:  in_array() expects parameter 2 to be
>> array, null given in
>> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php on line 130,
>> referer: http://loris/
>> [Thu Feb 06 14:36:20.838469 2020] [php7:error] [pid 7015] [client
>> 10.0.2.4:55302] PHP Fatal error:  Uncaught TypeError: explode() expects
>> parameter 2 to be string, null given in
>> /srv/www/loris/php/libraries/User.class.inc:272\nStack trace:\n#0
>> /srv/www/loris/php/libraries/User.class.inc(272): explode(';', NULL)\n#1
>> /srv/www/loris/modules/dashboard/php/dashboard.class.inc(40):
>> User->getSiteNames()\n#2
>> /srv/www/loris/php/libraries/NDB_Form.class.inc(188):
>> LORIS\\dashboard\\Dashboard->setup()\n#3
>> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php(171):
>> NDB_Form->handle(Object(Zend\\Diactoros\\ServerRequest))\n#4
>> /srv/www/loris/src/Middleware/PageDecorationMiddleware.php(49):
>> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest),
>> Object(LORIS\\dashboard\\Dashboard))\n#5
>> /srv/www/loris/php/libraries/NDB_Page.class.inc(659):
>> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest),
>> Object(LORIS\\dashboard\\Dashboard))\n#6
>> /srv/www/loris/php/libraries/Module.class.inc(341):
>> NDB_Page->process(Object(Zend\\Diactoros\\ServerRequest),
>> Object(LORIS\\dashboar in /srv/www/loris/php/libraries/User.class.inc on
>> line 272, referer: http://loris/
>>
>> We would appreciate any help with this.
>>
>> Best wishes,
>> Ioannis
>> _______________________________________________
>> 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 ioannis at berkeley.edu  Thu Feb  6 20:08:24 2020
From: ioannis at berkeley.edu (Ioannis Pappas)
Date: Thu, 6 Feb 2020 17:08:24 -0800
Subject: [Loris-dev] blank page after login
In-Reply-To: <CAMpvQ9jNA7B2v=6FC8zTpG3K16gbBfs8ROyQEJXGd8QUMvPDGA@mail.gmail.com>
References: <CAH3c6xJ36EPmYY69hyUOw8rjmi7_=-ztfd4Jizw-ixhvst3KCw@mail.gmail.com>
 <CABbkjAir2n8qY6UpNdVBucPwixagPtu5cT5rUwHuKq6-qUstng@mail.gmail.com>
 <CAMpvQ9jNA7B2v=6FC8zTpG3K16gbBfs8ROyQEJXGd8QUMvPDGA@mail.gmail.com>
Message-ID: <CAH3c6xLvwNRBQc5SzEPBc2YF29X+KNZuXgjb8wVwozwWiQsfug@mail.gmail.com>

Hi Ling and Rida.
Apologies for the late reply.

[ioannis at loris ~]$ rpm -q httpd
httpd-2.4.6-90.el7.centos.x86_64

Also

[ioannis at loris ~]$ mysql -V
mysql  Ver 15.1 Distrib 10.3.20-MariaDB, for Linux (x86_64) using readline
5.1

I think I have loris version 21. What's the best way for me to look at
the version?
These are my two tables:

MariaDB [loris_database]> SELECT * FROM psc;
+----------+----------+---------+---------+------+---------+------+--------+--------+----------+----------+-------+-----------+---------+------------+
| CenterID | Name     | PSCArea | Address | City | StateID | ZIP  | Phone1
| Phone2 | Contact1 | Contact2 | Alias | MRI_alias | Account | Study_site |
+----------+----------+---------+---------+------+---------+------+--------+--------+----------+----------+-------+-----------+---------+------------+
|        1 | MT | NULL    | NULL    | NULL |    NULL | NULL | NULL   | NULL
  | NULL     | NULL     | MT    | MT        | NULL    | Y          |
|        2 | BC | NULL    | NULL    | NULL |    NULL | NULL | NULL   | NULL
  | NULL     | NULL     | BR    | BR        | NULL    | Y          |
+----------+----------+---------+---------+------+---------+------+--------+--------+----------+----------+-------+-----------+---------+------------+
2 rows in set (0.028 sec)

MariaDB [loris_database]> SELECT * FROM user_psc_rel;
+--------+----------+
| UserID | CenterID |
+--------+----------+
|      2 |        1 |
+--------+----------+
1 row in set (0.000 sec)

I might have done something wrong here. The user is not associated with the
center id?
Best wishes,
Ioannis

On Thu, Feb 6, 2020 at 4:49 PM Ling Ma <lingyun.ma at mcin.ca> wrote:

> Hi Ioannis,
>
> I just guess that you are using version 21. also guess that the reason
> could be that you have no psc associated with the user, you need to check
> tables* psc, user_psc_rel* to see if the user has a psc record.
>
> Best regards,
> Ling Ma
> Consultant
>
> On Thu, Feb 6, 2020 at 7:26 PM Rida Abou-Haidar <rida.abou-haidar at mcin.ca>
> wrote:
>
>> Hi Ioannis,
>>
>> Could you tell us which version of LORIS you are currently using and your
>> PHP and MySQL versions as well please?
>>
>> Did you recently upgrade any of those? what might have caused a
>> difference from last month to this month ?
>>
>> Best,
>> Rida Abou-Haidar
>> Software Developer
>> Montreal Neurological Institute
>> McGill University
>> rida.abou-haidar at mcin.ca
>>
>>
>> On Thu, Feb 6, 2020 at 7:08 PM Ioannis Pappas <ioannis at berkeley.edu>
>> wrote:
>>
>>> Hi loris support.
>>>
>>> I hope you are well. I would like to report a problem with respect to
>>> signing in to the loris front-end. Despite signing in normally a month ago,
>>> we are now getting a "blank" white page after logging in.
>>>
>>> Below are the logs from /var/log/httpd/loris-error.log:
>>>
>>> [Thu Feb 06 14:36:20.838065 2020] [php7:notice] [pid 7015] [client
>>> 10.0.2.4:55302] PHP Notice:  Undefined variable: isStudySite in
>>> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php on line 130,
>>> referer: http://loris/
>>> [Thu Feb 06 14:36:20.838108 2020] [php7:warn] [pid 7015] [client
>>> 10.0.2.4:55302] PHP Warning:  in_array() expects parameter 2 to be
>>> array, null given in
>>> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php on line 130,
>>> referer: http://loris/
>>> [Thu Feb 06 14:36:20.838469 2020] [php7:error] [pid 7015] [client
>>> 10.0.2.4:55302] PHP Fatal error:  Uncaught TypeError: explode() expects
>>> parameter 2 to be string, null given in
>>> /srv/www/loris/php/libraries/User.class.inc:272\nStack trace:\n#0
>>> /srv/www/loris/php/libraries/User.class.inc(272): explode(';', NULL)\n#1
>>> /srv/www/loris/modules/dashboard/php/dashboard.class.inc(40):
>>> User->getSiteNames()\n#2
>>> /srv/www/loris/php/libraries/NDB_Form.class.inc(188):
>>> LORIS\\dashboard\\Dashboard->setup()\n#3
>>> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php(171):
>>> NDB_Form->handle(Object(Zend\\Diactoros\\ServerRequest))\n#4
>>> /srv/www/loris/src/Middleware/PageDecorationMiddleware.php(49):
>>> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest),
>>> Object(LORIS\\dashboard\\Dashboard))\n#5
>>> /srv/www/loris/php/libraries/NDB_Page.class.inc(659):
>>> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest),
>>> Object(LORIS\\dashboard\\Dashboard))\n#6
>>> /srv/www/loris/php/libraries/Module.class.inc(341):
>>> NDB_Page->process(Object(Zend\\Diactoros\\ServerRequest),
>>> Object(LORIS\\dashboar in /srv/www/loris/php/libraries/User.class.inc on
>>> line 272, referer: http://loris/
>>>
>>> We would appreciate any help with this.
>>>
>>> Best wishes,
>>> Ioannis
>>> _______________________________________________
>>> 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 rida.abou-haidar at mcin.ca  Thu Feb  6 20:10:58 2020
From: rida.abou-haidar at mcin.ca (Rida Abou-Haidar)
Date: Thu, 6 Feb 2020 20:10:58 -0500
Subject: [Loris-dev] blank page after login
In-Reply-To: <CAH3c6xLvwNRBQc5SzEPBc2YF29X+KNZuXgjb8wVwozwWiQsfug@mail.gmail.com>
References: <CAH3c6xJ36EPmYY69hyUOw8rjmi7_=-ztfd4Jizw-ixhvst3KCw@mail.gmail.com>
 <CABbkjAir2n8qY6UpNdVBucPwixagPtu5cT5rUwHuKq6-qUstng@mail.gmail.com>
 <CAMpvQ9jNA7B2v=6FC8zTpG3K16gbBfs8ROyQEJXGd8QUMvPDGA@mail.gmail.com>
 <CAH3c6xLvwNRBQc5SzEPBc2YF29X+KNZuXgjb8wVwozwWiQsfug@mail.gmail.com>
Message-ID: <CABbkjAhw4pGAg5myDWMO5iQ-jStX3d85wwhHHOsApNxWqQOPQQ@mail.gmail.com>

Check your users table.

It looks like only user with Id 2 is associated with a site. is that the
user you are logging in from ?

Rida Abou-Haidar
Software Developer
Montreal Neurological Institute
McGill University
rida.abou-haidar at mcin.ca


On Thu, Feb 6, 2020 at 8:08 PM Ioannis Pappas <ioannis at berkeley.edu> wrote:

> Hi Ling and Rida.
> Apologies for the late reply.
>
> [ioannis at loris ~]$ rpm -q httpd
> httpd-2.4.6-90.el7.centos.x86_64
>
> Also
>
> [ioannis at loris ~]$ mysql -V
> mysql  Ver 15.1 Distrib 10.3.20-MariaDB, for Linux (x86_64) using readline
> 5.1
>
> I think I have loris version 21. What's the best way for me to look at
> the version?
> These are my two tables:
>
> MariaDB [loris_database]> SELECT * FROM psc;
>
> +----------+----------+---------+---------+------+---------+------+--------+--------+----------+----------+-------+-----------+---------+------------+
> | CenterID | Name     | PSCArea | Address | City | StateID | ZIP  | Phone1
> | Phone2 | Contact1 | Contact2 | Alias | MRI_alias | Account | Study_site |
>
> +----------+----------+---------+---------+------+---------+------+--------+--------+----------+----------+-------+-----------+---------+------------+
> |        1 | MT | NULL    | NULL    | NULL |    NULL | NULL | NULL   |
> NULL   | NULL     | NULL     | MT    | MT        | NULL    | Y          |
> |        2 | BC | NULL    | NULL    | NULL |    NULL | NULL | NULL   |
> NULL   | NULL     | NULL     | BR    | BR        | NULL    | Y          |
>
> +----------+----------+---------+---------+------+---------+------+--------+--------+----------+----------+-------+-----------+---------+------------+
> 2 rows in set (0.028 sec)
>
> MariaDB [loris_database]> SELECT * FROM user_psc_rel;
> +--------+----------+
> | UserID | CenterID |
> +--------+----------+
> |      2 |        1 |
> +--------+----------+
> 1 row in set (0.000 sec)
>
> I might have done something wrong here. The user is not associated with
> the center id?
> Best wishes,
> Ioannis
>
> On Thu, Feb 6, 2020 at 4:49 PM Ling Ma <lingyun.ma at mcin.ca> wrote:
>
>> Hi Ioannis,
>>
>> I just guess that you are using version 21. also guess that the reason
>> could be that you have no psc associated with the user, you need to check
>> tables* psc, user_psc_rel* to see if the user has a psc record.
>>
>> Best regards,
>> Ling Ma
>> Consultant
>>
>> On Thu, Feb 6, 2020 at 7:26 PM Rida Abou-Haidar <rida.abou-haidar at mcin.ca>
>> wrote:
>>
>>> Hi Ioannis,
>>>
>>> Could you tell us which version of LORIS you are currently using and
>>> your PHP and MySQL versions as well please?
>>>
>>> Did you recently upgrade any of those? what might have caused a
>>> difference from last month to this month ?
>>>
>>> Best,
>>> Rida Abou-Haidar
>>> Software Developer
>>> Montreal Neurological Institute
>>> McGill University
>>> rida.abou-haidar at mcin.ca
>>>
>>>
>>> On Thu, Feb 6, 2020 at 7:08 PM Ioannis Pappas <ioannis at berkeley.edu>
>>> wrote:
>>>
>>>> Hi loris support.
>>>>
>>>> I hope you are well. I would like to report a problem with respect to
>>>> signing in to the loris front-end. Despite signing in normally a month ago,
>>>> we are now getting a "blank" white page after logging in.
>>>>
>>>> Below are the logs from /var/log/httpd/loris-error.log:
>>>>
>>>> [Thu Feb 06 14:36:20.838065 2020] [php7:notice] [pid 7015] [client
>>>> 10.0.2.4:55302] PHP Notice:  Undefined variable: isStudySite in
>>>> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php on line 130,
>>>> referer: http://loris/
>>>> [Thu Feb 06 14:36:20.838108 2020] [php7:warn] [pid 7015] [client
>>>> 10.0.2.4:55302] PHP Warning:  in_array() expects parameter 2 to be
>>>> array, null given in
>>>> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php on line 130,
>>>> referer: http://loris/
>>>> [Thu Feb 06 14:36:20.838469 2020] [php7:error] [pid 7015] [client
>>>> 10.0.2.4:55302] PHP Fatal error:  Uncaught TypeError: explode()
>>>> expects parameter 2 to be string, null given in
>>>> /srv/www/loris/php/libraries/User.class.inc:272\nStack trace:\n#0
>>>> /srv/www/loris/php/libraries/User.class.inc(272): explode(';', NULL)\n#1
>>>> /srv/www/loris/modules/dashboard/php/dashboard.class.inc(40):
>>>> User->getSiteNames()\n#2
>>>> /srv/www/loris/php/libraries/NDB_Form.class.inc(188):
>>>> LORIS\\dashboard\\Dashboard->setup()\n#3
>>>> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php(171):
>>>> NDB_Form->handle(Object(Zend\\Diactoros\\ServerRequest))\n#4
>>>> /srv/www/loris/src/Middleware/PageDecorationMiddleware.php(49):
>>>> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest),
>>>> Object(LORIS\\dashboard\\Dashboard))\n#5
>>>> /srv/www/loris/php/libraries/NDB_Page.class.inc(659):
>>>> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest),
>>>> Object(LORIS\\dashboard\\Dashboard))\n#6
>>>> /srv/www/loris/php/libraries/Module.class.inc(341):
>>>> NDB_Page->process(Object(Zend\\Diactoros\\ServerRequest),
>>>> Object(LORIS\\dashboar in /srv/www/loris/php/libraries/User.class.inc on
>>>> line 272, referer: http://loris/
>>>>
>>>> We would appreciate any help with this.
>>>>
>>>> Best wishes,
>>>> Ioannis
>>>> _______________________________________________
>>>> 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 ioannis at berkeley.edu  Thu Feb  6 21:44:08 2020
From: ioannis at berkeley.edu (Ioannis Pappas)
Date: Thu, 6 Feb 2020 18:44:08 -0800
Subject: [Loris-dev] blank page after login
In-Reply-To: <CABbkjAhw4pGAg5myDWMO5iQ-jStX3d85wwhHHOsApNxWqQOPQQ@mail.gmail.com>
References: <CAH3c6xJ36EPmYY69hyUOw8rjmi7_=-ztfd4Jizw-ixhvst3KCw@mail.gmail.com>
 <CABbkjAir2n8qY6UpNdVBucPwixagPtu5cT5rUwHuKq6-qUstng@mail.gmail.com>
 <CAMpvQ9jNA7B2v=6FC8zTpG3K16gbBfs8ROyQEJXGd8QUMvPDGA@mail.gmail.com>
 <CAH3c6xLvwNRBQc5SzEPBc2YF29X+KNZuXgjb8wVwozwWiQsfug@mail.gmail.com>
 <CABbkjAhw4pGAg5myDWMO5iQ-jStX3d85wwhHHOsApNxWqQOPQQ@mail.gmail.com>
Message-ID: <CAH3c6xL=jC+b=kgfYvia_vcmcwbOKTHC+g8Xckith4ePJqG2OQ@mail.gmail.com>

Hi Rida.

For some reason the user_psc_rel table wasn't what I wanted it to be.
All is well now. Thank you for pointing me to this fix so quickly!

Best wishes,
Ioannis

On Thu, Feb 6, 2020 at 5:11 PM Rida Abou-Haidar <rida.abou-haidar at mcin.ca>
wrote:

> Check your users table.
>
> It looks like only user with Id 2 is associated with a site. is that the
> user you are logging in from ?
>
> Rida Abou-Haidar
> Software Developer
> Montreal Neurological Institute
> McGill University
> rida.abou-haidar at mcin.ca
>
>
> On Thu, Feb 6, 2020 at 8:08 PM Ioannis Pappas <ioannis at berkeley.edu>
> wrote:
>
>> Hi Ling and Rida.
>> Apologies for the late reply.
>>
>> [ioannis at loris ~]$ rpm -q httpd
>> httpd-2.4.6-90.el7.centos.x86_64
>>
>> Also
>>
>> [ioannis at loris ~]$ mysql -V
>> mysql  Ver 15.1 Distrib 10.3.20-MariaDB, for Linux (x86_64) using
>> readline 5.1
>>
>> I think I have loris version 21. What's the best way for me to look at
>> the version?
>> These are my two tables:
>>
>> MariaDB [loris_database]> SELECT * FROM psc;
>>
>> +----------+----------+---------+---------+------+---------+------+--------+--------+----------+----------+-------+-----------+---------+------------+
>> | CenterID | Name     | PSCArea | Address | City | StateID | ZIP  |
>> Phone1 | Phone2 | Contact1 | Contact2 | Alias | MRI_alias | Account |
>> Study_site |
>>
>> +----------+----------+---------+---------+------+---------+------+--------+--------+----------+----------+-------+-----------+---------+------------+
>> |        1 | MT | NULL    | NULL    | NULL |    NULL | NULL | NULL   |
>> NULL   | NULL     | NULL     | MT    | MT        | NULL    | Y          |
>> |        2 | BC | NULL    | NULL    | NULL |    NULL | NULL | NULL   |
>> NULL   | NULL     | NULL     | BR    | BR        | NULL    | Y          |
>>
>> +----------+----------+---------+---------+------+---------+------+--------+--------+----------+----------+-------+-----------+---------+------------+
>> 2 rows in set (0.028 sec)
>>
>> MariaDB [loris_database]> SELECT * FROM user_psc_rel;
>> +--------+----------+
>> | UserID | CenterID |
>> +--------+----------+
>> |      2 |        1 |
>> +--------+----------+
>> 1 row in set (0.000 sec)
>>
>> I might have done something wrong here. The user is not associated with
>> the center id?
>> Best wishes,
>> Ioannis
>>
>> On Thu, Feb 6, 2020 at 4:49 PM Ling Ma <lingyun.ma at mcin.ca> wrote:
>>
>>> Hi Ioannis,
>>>
>>> I just guess that you are using version 21. also guess that the reason
>>> could be that you have no psc associated with the user, you need to check
>>> tables* psc, user_psc_rel* to see if the user has a psc record.
>>>
>>> Best regards,
>>> Ling Ma
>>> Consultant
>>>
>>> On Thu, Feb 6, 2020 at 7:26 PM Rida Abou-Haidar <
>>> rida.abou-haidar at mcin.ca> wrote:
>>>
>>>> Hi Ioannis,
>>>>
>>>> Could you tell us which version of LORIS you are currently using and
>>>> your PHP and MySQL versions as well please?
>>>>
>>>> Did you recently upgrade any of those? what might have caused a
>>>> difference from last month to this month ?
>>>>
>>>> Best,
>>>> Rida Abou-Haidar
>>>> Software Developer
>>>> Montreal Neurological Institute
>>>> McGill University
>>>> rida.abou-haidar at mcin.ca
>>>>
>>>>
>>>> On Thu, Feb 6, 2020 at 7:08 PM Ioannis Pappas <ioannis at berkeley.edu>
>>>> wrote:
>>>>
>>>>> Hi loris support.
>>>>>
>>>>> I hope you are well. I would like to report a problem with respect to
>>>>> signing in to the loris front-end. Despite signing in normally a month ago,
>>>>> we are now getting a "blank" white page after logging in.
>>>>>
>>>>> Below are the logs from /var/log/httpd/loris-error.log:
>>>>>
>>>>> [Thu Feb 06 14:36:20.838065 2020] [php7:notice] [pid 7015] [client
>>>>> 10.0.2.4:55302] PHP Notice:  Undefined variable: isStudySite in
>>>>> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php on line 130,
>>>>> referer: http://loris/
>>>>> [Thu Feb 06 14:36:20.838108 2020] [php7:warn] [pid 7015] [client
>>>>> 10.0.2.4:55302] PHP Warning:  in_array() expects parameter 2 to be
>>>>> array, null given in
>>>>> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php on line 130,
>>>>> referer: http://loris/
>>>>> [Thu Feb 06 14:36:20.838469 2020] [php7:error] [pid 7015] [client
>>>>> 10.0.2.4:55302] PHP Fatal error:  Uncaught TypeError: explode()
>>>>> expects parameter 2 to be string, null given in
>>>>> /srv/www/loris/php/libraries/User.class.inc:272\nStack trace:\n#0
>>>>> /srv/www/loris/php/libraries/User.class.inc(272): explode(';', NULL)\n#1
>>>>> /srv/www/loris/modules/dashboard/php/dashboard.class.inc(40):
>>>>> User->getSiteNames()\n#2
>>>>> /srv/www/loris/php/libraries/NDB_Form.class.inc(188):
>>>>> LORIS\\dashboard\\Dashboard->setup()\n#3
>>>>> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php(171):
>>>>> NDB_Form->handle(Object(Zend\\Diactoros\\ServerRequest))\n#4
>>>>> /srv/www/loris/src/Middleware/PageDecorationMiddleware.php(49):
>>>>> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest),
>>>>> Object(LORIS\\dashboard\\Dashboard))\n#5
>>>>> /srv/www/loris/php/libraries/NDB_Page.class.inc(659):
>>>>> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest),
>>>>> Object(LORIS\\dashboard\\Dashboard))\n#6
>>>>> /srv/www/loris/php/libraries/Module.class.inc(341):
>>>>> NDB_Page->process(Object(Zend\\Diactoros\\ServerRequest),
>>>>> Object(LORIS\\dashboar in /srv/www/loris/php/libraries/User.class.inc on
>>>>> line 272, referer: http://loris/
>>>>>
>>>>> We would appreciate any help with this.
>>>>>
>>>>> Best wishes,
>>>>> Ioannis
>>>>> _______________________________________________
>>>>> 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 rida.abou-haidar at mcin.ca  Thu Feb  6 22:02:06 2020
From: rida.abou-haidar at mcin.ca (Rida Abou-Haidar)
Date: Thu, 6 Feb 2020 22:02:06 -0500
Subject: [Loris-dev] blank page after login
In-Reply-To: <CAH3c6xL=jC+b=kgfYvia_vcmcwbOKTHC+g8Xckith4ePJqG2OQ@mail.gmail.com>
References: <CAH3c6xJ36EPmYY69hyUOw8rjmi7_=-ztfd4Jizw-ixhvst3KCw@mail.gmail.com>
 <CABbkjAir2n8qY6UpNdVBucPwixagPtu5cT5rUwHuKq6-qUstng@mail.gmail.com>
 <CAMpvQ9jNA7B2v=6FC8zTpG3K16gbBfs8ROyQEJXGd8QUMvPDGA@mail.gmail.com>
 <CAH3c6xLvwNRBQc5SzEPBc2YF29X+KNZuXgjb8wVwozwWiQsfug@mail.gmail.com>
 <CABbkjAhw4pGAg5myDWMO5iQ-jStX3d85wwhHHOsApNxWqQOPQQ@mail.gmail.com>
 <CAH3c6xL=jC+b=kgfYvia_vcmcwbOKTHC+g8Xckith4ePJqG2OQ@mail.gmail.com>
Message-ID: <CABbkjAjAs4cL4aQDQqyqYxg4wA889qy2+fnstQdkHTZiprQKsQ@mail.gmail.com>

Glad to hear it!

Thanks Ling for answering so quickly.

Best to both of you,
Rida Abou-Haidar
CCNA Software Developer
Montreal Neurological Institute
McGill University
rida.abou-haidar at mcin.ca

On Thu., Feb. 6, 2020, 9:44 p.m. Ioannis Pappas <ioannis at berkeley.edu>
wrote:

> Hi Rida.
>
> For some reason the user_psc_rel table wasn't what I wanted it to be.
> All is well now. Thank you for pointing me to this fix so quickly!
>
> Best wishes,
> Ioannis
>
> On Thu, Feb 6, 2020 at 5:11 PM Rida Abou-Haidar <rida.abou-haidar at mcin.ca>
> wrote:
>
>> Check your users table.
>>
>> It looks like only user with Id 2 is associated with a site. is that the
>> user you are logging in from ?
>>
>> Rida Abou-Haidar
>> Software Developer
>> Montreal Neurological Institute
>> McGill University
>> rida.abou-haidar at mcin.ca
>>
>>
>> On Thu, Feb 6, 2020 at 8:08 PM Ioannis Pappas <ioannis at berkeley.edu>
>> wrote:
>>
>>> Hi Ling and Rida.
>>> Apologies for the late reply.
>>>
>>> [ioannis at loris ~]$ rpm -q httpd
>>> httpd-2.4.6-90.el7.centos.x86_64
>>>
>>> Also
>>>
>>> [ioannis at loris ~]$ mysql -V
>>> mysql  Ver 15.1 Distrib 10.3.20-MariaDB, for Linux (x86_64) using
>>> readline 5.1
>>>
>>> I think I have loris version 21. What's the best way for me to look at
>>> the version?
>>> These are my two tables:
>>>
>>> MariaDB [loris_database]> SELECT * FROM psc;
>>>
>>> +----------+----------+---------+---------+------+---------+------+--------+--------+----------+----------+-------+-----------+---------+------------+
>>> | CenterID | Name     | PSCArea | Address | City | StateID | ZIP  |
>>> Phone1 | Phone2 | Contact1 | Contact2 | Alias | MRI_alias | Account |
>>> Study_site |
>>>
>>> +----------+----------+---------+---------+------+---------+------+--------+--------+----------+----------+-------+-----------+---------+------------+
>>> |        1 | MT | NULL    | NULL    | NULL |    NULL | NULL | NULL   |
>>> NULL   | NULL     | NULL     | MT    | MT        | NULL    | Y          |
>>> |        2 | BC | NULL    | NULL    | NULL |    NULL | NULL | NULL   |
>>> NULL   | NULL     | NULL     | BR    | BR        | NULL    | Y          |
>>>
>>> +----------+----------+---------+---------+------+---------+------+--------+--------+----------+----------+-------+-----------+---------+------------+
>>> 2 rows in set (0.028 sec)
>>>
>>> MariaDB [loris_database]> SELECT * FROM user_psc_rel;
>>> +--------+----------+
>>> | UserID | CenterID |
>>> +--------+----------+
>>> |      2 |        1 |
>>> +--------+----------+
>>> 1 row in set (0.000 sec)
>>>
>>> I might have done something wrong here. The user is not associated with
>>> the center id?
>>> Best wishes,
>>> Ioannis
>>>
>>> On Thu, Feb 6, 2020 at 4:49 PM Ling Ma <lingyun.ma at mcin.ca> wrote:
>>>
>>>> Hi Ioannis,
>>>>
>>>> I just guess that you are using version 21. also guess that the reason
>>>> could be that you have no psc associated with the user, you need to check
>>>> tables* psc, user_psc_rel* to see if the user has a psc record.
>>>>
>>>> Best regards,
>>>> Ling Ma
>>>> Consultant
>>>>
>>>> On Thu, Feb 6, 2020 at 7:26 PM Rida Abou-Haidar <
>>>> rida.abou-haidar at mcin.ca> wrote:
>>>>
>>>>> Hi Ioannis,
>>>>>
>>>>> Could you tell us which version of LORIS you are currently using and
>>>>> your PHP and MySQL versions as well please?
>>>>>
>>>>> Did you recently upgrade any of those? what might have caused a
>>>>> difference from last month to this month ?
>>>>>
>>>>> Best,
>>>>> Rida Abou-Haidar
>>>>> Software Developer
>>>>> Montreal Neurological Institute
>>>>> McGill University
>>>>> rida.abou-haidar at mcin.ca
>>>>>
>>>>>
>>>>> On Thu, Feb 6, 2020 at 7:08 PM Ioannis Pappas <ioannis at berkeley.edu>
>>>>> wrote:
>>>>>
>>>>>> Hi loris support.
>>>>>>
>>>>>> I hope you are well. I would like to report a problem with respect to
>>>>>> signing in to the loris front-end. Despite signing in normally a month ago,
>>>>>> we are now getting a "blank" white page after logging in.
>>>>>>
>>>>>> Below are the logs from /var/log/httpd/loris-error.log:
>>>>>>
>>>>>> [Thu Feb 06 14:36:20.838065 2020] [php7:notice] [pid 7015] [client
>>>>>> 10.0.2.4:55302] PHP Notice:  Undefined variable: isStudySite in
>>>>>> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php on line 130,
>>>>>> referer: http://loris/
>>>>>> [Thu Feb 06 14:36:20.838108 2020] [php7:warn] [pid 7015] [client
>>>>>> 10.0.2.4:55302] PHP Warning:  in_array() expects parameter 2 to be
>>>>>> array, null given in
>>>>>> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php on line 130,
>>>>>> referer: http://loris/
>>>>>> [Thu Feb 06 14:36:20.838469 2020] [php7:error] [pid 7015] [client
>>>>>> 10.0.2.4:55302] PHP Fatal error:  Uncaught TypeError: explode()
>>>>>> expects parameter 2 to be string, null given in
>>>>>> /srv/www/loris/php/libraries/User.class.inc:272\nStack trace:\n#0
>>>>>> /srv/www/loris/php/libraries/User.class.inc(272): explode(';', NULL)\n#1
>>>>>> /srv/www/loris/modules/dashboard/php/dashboard.class.inc(40):
>>>>>> User->getSiteNames()\n#2
>>>>>> /srv/www/loris/php/libraries/NDB_Form.class.inc(188):
>>>>>> LORIS\\dashboard\\Dashboard->setup()\n#3
>>>>>> /srv/www/loris/src/Middleware/UserPageDecorationMiddleware.php(171):
>>>>>> NDB_Form->handle(Object(Zend\\Diactoros\\ServerRequest))\n#4
>>>>>> /srv/www/loris/src/Middleware/PageDecorationMiddleware.php(49):
>>>>>> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest),
>>>>>> Object(LORIS\\dashboard\\Dashboard))\n#5
>>>>>> /srv/www/loris/php/libraries/NDB_Page.class.inc(659):
>>>>>> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest),
>>>>>> Object(LORIS\\dashboard\\Dashboard))\n#6
>>>>>> /srv/www/loris/php/libraries/Module.class.inc(341):
>>>>>> NDB_Page->process(Object(Zend\\Diactoros\\ServerRequest),
>>>>>> Object(LORIS\\dashboar in /srv/www/loris/php/libraries/User.class.inc on
>>>>>> line 272, referer: http://loris/
>>>>>>
>>>>>> We would appreciate any help with this.
>>>>>>
>>>>>> Best wishes,
>>>>>> Ioannis
>>>>>> _______________________________________________
>>>>>> 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 Feb  7 10:44:23 2020
From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos)
Date: Fri, 7 Feb 2020 17:44:23 +0200
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAMpvQ9ifuSdu9_v2mpCmvK3o7zMibq=cE7k32O7Kp_S8V_=5Cw@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>
 <CAMpvQ9ifuSdu9_v2mpCmvK3o7zMibq=cE7k32O7Kp_S8V_=5Cw@mail.gmail.com>
Message-ID: <CAKHj7uQ1DrVNQSBBvuzEG2vNUSCrH45MJ6ChQZ23j9HEUaaVSQ@mail.gmail.com>

Hi Ling,

are those the entries you meant? If only I execute it from browser it adds
the port 8088, still I can't see it using the curl query.

[image: image.png]

This time i copied the curl query directly from firefox, I only omitted the
Cookie parameter below.

curl 'http://localhost/installdb.php' -H 'User-Agent: Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:72.0) Gecko/20100101 Firefox/72.0' -H 'Accept:
text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8'
-H 'Accept-Language: en-US,en;q=0.5' --compressed -H 'Content-Type:
application/x-www-form-urlencoded' -H 'Origin: http://localhost:8088' -H
'Connection: keep-alive' -H 'Referer: http://localhost:8088/installdb.php'
--H 'Upgrade-Insecure-Requests: 1' --data
'dbhost=172.28.1.2&dbadminuser=root&dbadminpassword=neopass&dbname=LORIS&formname=validaterootaccount'

curl 'http://localhost/installdb.php' -H 'User-Agent: Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:72.0) Gecko/20100101 Firefox/72.0' -H 'Accept:
text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8'
-H 'Accept-Language: en-US,en;q=0.5' --compressed -H 'Content-Type:
application/x-www-form-urlencoded' -H 'Origin: http://localhost:8088' -H
'Connection: keep-alive' -H 'Referer: http://localhost:8088/installdb.php'-H
'Upgrade-Insecure-Requests: 1' --data
'lorismysqluser=lorisuser&lorismysqlpassword=neopass&frontenduser=lorisuser&frontendpassword=1234&formname=createmysqlaccount&dbname=LORIS&dbhost=172.28.1.2&dbadminuser=root&dbadminpassword=neopass'

Thanks

???? ???, 31 ??? 2020 ???? 5:35 ?.?., ?/? Ling Ma <lingyun.ma at mcin.ca>
??????:

> 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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From lingyun.ma at mcin.ca  Fri Feb  7 10:53:16 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Fri, 7 Feb 2020 10:53:16 -0500
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAKHj7uQ1DrVNQSBBvuzEG2vNUSCrH45MJ6ChQZ23j9HEUaaVSQ@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>
 <CAMpvQ9ifuSdu9_v2mpCmvK3o7zMibq=cE7k32O7Kp_S8V_=5Cw@mail.gmail.com>
 <CAKHj7uQ1DrVNQSBBvuzEG2vNUSCrH45MJ6ChQZ23j9HEUaaVSQ@mail.gmail.com>
Message-ID: <CAMpvQ9iv1R43MKyUEzXvLVuLYTVNtBE+kDhWiPNYR9NZrOA_0g@mail.gmail.com>

Hi Sotirios,

You can check hostname and url using a SQL like "select * from Config where
configid in (select id from ConfigSettings where name = 'url' or name =
'host');"

As a result, you can update the Config value with a script once you have
installed the Loris,

like "UPDATE Config set Value = 'http://localhost:8080' WHERE ConfigID =
(SELECT ID from ConfigSettings WHERE name = 'url');
like "UPDATE Config set Value = 'localhost:8080' WHERE ConfigID = (SELECT
ID from ConfigSettings WHERE name = 'host');

I suppose an easy script in whatever language could do the job, like sh,
python, php, whatever.

Best regards,
Ling Ma


On Fri, Feb 7, 2020 at 10:44 AM Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:

> Hi Ling,
>
> are those the entries you meant? If only I execute it from browser it adds
> the port 8088, still I can't see it using the curl query.
>
> [image: image.png]
>
> This time i copied the curl query directly from firefox, I only omitted
> the Cookie parameter below.
>
> curl 'http://localhost/installdb.php' -H 'User-Agent: Mozilla/5.0 (X11;
> Ubuntu; Linux x86_64; rv:72.0) Gecko/20100101 Firefox/72.0' -H 'Accept:
> text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8'
> -H 'Accept-Language: en-US,en;q=0.5' --compressed -H 'Content-Type:
> application/x-www-form-urlencoded' -H 'Origin: http://localhost:8088' -H
> 'Connection: keep-alive' -H 'Referer: http://localhost:8088/installdb.php'
> --H 'Upgrade-Insecure-Requests: 1' --data
> 'dbhost=172.28.1.2&dbadminuser=root&dbadminpassword=neopass&dbname=LORIS&formname=validaterootaccount'
>
> curl 'http://localhost/installdb.php' -H 'User-Agent: Mozilla/5.0 (X11;
> Ubuntu; Linux x86_64; rv:72.0) Gecko/20100101 Firefox/72.0' -H 'Accept:
> text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8'
> -H 'Accept-Language: en-US,en;q=0.5' --compressed -H 'Content-Type:
> application/x-www-form-urlencoded' -H 'Origin: http://localhost:8088' -H
> 'Connection: keep-alive' -H 'Referer:
> http://localhost:8088/installdb.php'-H 'Upgrade-Insecure-Requests: 1'
> --data
> 'lorismysqluser=lorisuser&lorismysqlpassword=neopass&frontenduser=lorisuser&frontendpassword=1234&formname=createmysqlaccount&dbname=LORIS&dbhost=172.28.1.2&dbadminuser=root&dbadminpassword=neopass'
>
> Thanks
>
> ???? ???, 31 ??? 2020 ???? 5:35 ?.?., ?/? Ling Ma <lingyun.ma at mcin.ca>
> ??????:
>
>> 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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From AMORALESPINZON at bwh.harvard.edu  Tue Feb 18 16:31:38 2020
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Tue, 18 Feb 2020 21:31:38 +0000
Subject: [Loris-dev] Update LORIS to v21.0.0
Message-ID: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>

Hi C?cile,

I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and then to v22.0.0). I had no issues to get to v20.3.0 but now, moving to v21.0.0, I have two issues:

1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS website. I get a 500 error. Any ideas on what should I check?

2. In the instructions to upgrade to v21.0.0, the second point says:

"Run make from the Loris root directory to update all dependencies.?"

However when I run ?make? In the Loris root direction it does nothing. Here is the result:

===
lorisadmin at ipmsa-loris:/var/www/loris$ make
make: *** No targets specified and no makefile found.  Stop.
===

It that the right directory? Maybe I am missing some files?

Thank you for your help.

Best,
Alfredo.
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From lingyun.ma at mcin.ca  Tue Feb 18 16:44:09 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Tue, 18 Feb 2020 16:44:09 -0500
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
Message-ID: <CAMpvQ9hQnybvKfqhBPHtDvo5pZv71z-dNqy79rc3+S=oF_pUhQ@mail.gmail.com>

Hi Alfredo,

I happen to see this message, I try to answer this.
1. You can go to your web server's error log, for example, if you are
running Apache2, then open /var/log/apache2/error.log to see what goes
wrong.
2. You need to run tools/install.sh to create a Makefile. Please read the
corresponding installation guide for further details.

Hope I could help.

Best regards,
Ling Ma
Dev Consultant


On Tue, Feb 18, 2020 at 4:32 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi C?cile,
>
> I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and then
> to v22.0.0). I had no issues to get to v20.3.0 but now, moving to v21.0.0,
> I have two issues:
>
> 1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS
> website. I get a 500 error. Any ideas on what should I check?
>
> 2. In the instructions to upgrade to v21.0.0, the second point says:
>
> "Run make from the Loris root directory to update all dependencies.?"
>
> However when I run ?make? In the Loris root direction it does nothing.
> Here is the result:
>
> ===
> *lorisadmin at ipmsa-loris*:*/var/www/loris*$ make
> make: *** No targets specified and no makefile found.  Stop.
> ===
>
> It that the right directory? Maybe I am missing some files?
>
> Thank you for your help.
>
> Best,
> Alfredo.
> _______________________________________________
> 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  Wed Feb 19 11:41:34 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Wed, 19 Feb 2020 11:41:34 -0500
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <CAMpvQ9hQnybvKfqhBPHtDvo5pZv71z-dNqy79rc3+S=oF_pUhQ@mail.gmail.com>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
 <CAMpvQ9hQnybvKfqhBPHtDvo5pZv71z-dNqy79rc3+S=oF_pUhQ@mail.gmail.com>
Message-ID: <CAMpvQ9jkwdq5ev6QDsQBXHFgAoOVGJtL+pcA1EdxHSfDAsaPPA@mail.gmail.com>

My excuses, Alfredo, the "Makefile" is present in 21.0 version release
file, it is not be created by install.sh as I assumed. You need to get the
latest files for the Version 21.0 and 22.0 depending on the stages of your
process.

Best regards,
Ling Ma

On Tue, Feb 18, 2020 at 4:44 PM Ling Ma <lingyun.ma at mcin.ca> wrote:

> Hi Alfredo,
>
> I happen to see this message, I try to answer this.
> 1. You can go to your web server's error log, for example, if you are
> running Apache2, then open /var/log/apache2/error.log to see what goes
> wrong.
> 2. You need to run tools/install.sh to create a Makefile. Please read the
> corresponding installation guide for further details.
>
> Hope I could help.
>
> Best regards,
> Ling Ma
> Dev Consultant
>
>
> On Tue, Feb 18, 2020 at 4:32 PM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Hi C?cile,
>>
>> I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and then
>> to v22.0.0). I had no issues to get to v20.3.0 but now, moving to v21.0.0,
>> I have two issues:
>>
>> 1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS
>> website. I get a 500 error. Any ideas on what should I check?
>>
>> 2. In the instructions to upgrade to v21.0.0, the second point says:
>>
>> "Run make from the Loris root directory to update all dependencies.?"
>>
>> However when I run ?make? In the Loris root direction it does nothing.
>> Here is the result:
>>
>> ===
>> *lorisadmin at ipmsa-loris*:*/var/www/loris*$ make
>> make: *** No targets specified and no makefile found.  Stop.
>> ===
>>
>> It that the right directory? Maybe I am missing some files?
>>
>> Thank you for your help.
>>
>> Best,
>> Alfredo.
>> _______________________________________________
>> 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 Feb 19 12:15:23 2020
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Wed, 19 Feb 2020 12:15:23 -0500
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
Message-ID: <CAMkiY3e1JkHqWt3oMFDGyHsr26F4LPUOS6gO8hzm-nCbCFm7DQ@mail.gmail.com>

Hi Alfredo,

Sorry to hear you are experiencing issues with the upgrade to 21.0.0. See
below.

On Tue, Feb 18, 2020 at 4:31 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi C?cile,
>
> I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and then
> to v22.0.0). I had no issues to get to v20.3.0 but now, moving to v21.0.0,
> I have two issues:
>
> 1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS
> website. I get a 500 error. Any ideas on what should I check?
>

Could you send us what you see in the Apache error file for that 500 error?
Although, might be worth focusing on fixing your second issue before we
dive too much into that one.


> 2. In the instructions to upgrade to v21.0.0, the second point says:
>
> "Run make from the Loris root directory to update all dependencies.?"
>
> However when I run ?make? In the Loris root direction it does nothing.
> Here is the result:
>
> ===
> *lorisadmin at ipmsa-loris*:*/var/www/loris*$ make
> make: *** No targets specified and no makefile found.  Stop.
> ===
>
It that the right directory? Maybe I am missing some files?
>

Are you sure you are on the 21.0.0 release of LORIS before you run make? Do
you see a Makefile in your /var/www/loris directory? In theory it is
supposed to be there on branch 21.0.0 (
https://github.com/aces/Loris/tree/v21.0.0)

Hope this helps.

C?cile


> Thank you for your help.
>
> Best,
> Alfredo.
>
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From AMORALESPINZON at bwh.harvard.edu  Wed Feb 19 17:07:36 2020
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Wed, 19 Feb 2020 22:07:36 +0000
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <CAMkiY3e1JkHqWt3oMFDGyHsr26F4LPUOS6gO8hzm-nCbCFm7DQ@mail.gmail.com>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
 <CAMkiY3e1JkHqWt3oMFDGyHsr26F4LPUOS6gO8hzm-nCbCFm7DQ@mail.gmail.com>
Message-ID: <62049B06-1DB0-4E4C-8610-3BB2D629CE4F@bwh.harvard.edu>

Dear Ling and C?cile,

Thank for your responses.

I had an issue with "git checkout?, somehow I had to remove some files before being able to checkout the v21.0.0. That was the reason I didn?t have the make file. Now that I have it, I have some errors:

After running ?make? I have the following error:

===
    WARNING in configuration
    The 'mode' option has not been set, webpack will fallback to 'production' for this value. Set 'mode' option to 'development' or 'production' to enable defaults for each environment.
    You can also set it to 'none' to disable any default behavior. Learn more: https://webpack.js.org/concepts/mode/
composer install --no-dev
> mkdir -p project/libraries
Loading composer repositories with package information
Installing dependencies from lock file
Your requirements could not be resolved to an installable set of packages.

  Problem 1
    - Installation request for php-http/guzzle6-adapter v2.0.1 -> satisfiable by php-http/guzzle6-adapter[v2.0.1].
    - php-http/guzzle6-adapter v2.0.1 requires php ^7.1 -> your PHP version (7.0.33) does not satisfy that requirement.
===

Do I have to upgrade PHP to 7.1?

Thank you again for your help.

Regards,
Alfredo.


On Feb 19, 2020, at 12:15 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Sorry to hear you are experiencing issues with the upgrade to 21.0.0. See below.

On Tue, Feb 18, 2020 at 4:31 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and then to v22.0.0). I had no issues to get to v20.3.0 but now, moving to v21.0.0, I have two issues:

1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS website. I get a 500 error. Any ideas on what should I check?

Could you send us what you see in the Apache error file for that 500 error? Although, might be worth focusing on fixing your second issue before we dive too much into that one.

2. In the instructions to upgrade to v21.0.0, the second point says:

"Run make from the Loris root directory to update all dependencies.?"

However when I run ?make? In the Loris root direction it does nothing. Here is the result:

===
lorisadmin at ipmsa-loris:/var/www/loris$ make
make: *** No targets specified and no makefile found.  Stop.
===
It that the right directory? Maybe I am missing some files?

Are you sure you are on the 21.0.0 release of LORIS before you run make? Do you see a Makefile in your /var/www/loris directory? In theory it is supposed to be there on branch 21.0.0 (https://github.com/aces/Loris/tree/v21.0.0)

Hope this helps.

C?cile


Thank you for your help.

Best,
Alfredo.



The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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From lingyun.ma at mcin.ca  Wed Feb 19 17:18:01 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Wed, 19 Feb 2020 17:18:01 -0500
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <62049B06-1DB0-4E4C-8610-3BB2D629CE4F@bwh.harvard.edu>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
 <CAMkiY3e1JkHqWt3oMFDGyHsr26F4LPUOS6gO8hzm-nCbCFm7DQ@mail.gmail.com>
 <62049B06-1DB0-4E4C-8610-3BB2D629CE4F@bwh.harvard.edu>
Message-ID: <CAMpvQ9hN-vTERXCkXtgBVdg+_GEgk4J6cDizJ6vQDpaOy_YAxQ@mail.gmail.com>

Hi Alfredo,

The warning is OK to ignore. As to php, please check v21 version
requirements, I believe a php minimum 7.1 even 7.2 is required.

In fact, PHP 5.6 is no longer supported.

Best regards,
Ling Ma

On Wed., Feb. 19, 2020, 5:07 p.m. Morales Pinzon, Alfredo, <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Dear Ling and C?cile,
>
> Thank for your responses.
>
> I had an issue with "git checkout?, somehow I had to remove some files
> before being able to checkout the v21.0.0. That was the reason I didn?t
> have the make file. Now that I have it, I have some errors:
>
> After running ?make? I have the following error:
>
> ===
>     *WARNING in configuration*
> *    The 'mode' option has not been set, webpack will fallback to
> 'production' for this value. Set 'mode' option to 'development' or
> 'production' to enable defaults for each environment.*
> *    You can also set it to 'none' to disable any default behavior. Learn
> more: https://webpack.js.org/concepts/mode/
> <https://webpack.js.org/concepts/mode/>*
> composer install --no-dev
> > mkdir -p project/libraries
> Loading composer repositories with package information
> Installing dependencies from lock file
> Your requirements could not be resolved to an installable set of packages.
>
>   Problem 1
>     - Installation request for php-http/guzzle6-adapter v2.0.1 ->
> satisfiable by php-http/guzzle6-adapter[v2.0.1].
>     - php-http/guzzle6-adapter v2.0.1 requires php ^7.1 -> your PHP
> version (7.0.33) does not satisfy that requirement.
> ===
>
> Do I have to upgrade PHP to 7.1?
>
> Thank you again for your help.
>
> Regards,
> Alfredo.
>
>
> On Feb 19, 2020, at 12:15 PM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> Sorry to hear you are experiencing issues with the upgrade to 21.0.0. See
> below.
>
> On Tue, Feb 18, 2020 at 4:31 PM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Hi C?cile,
>>
>> I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and then
>> to v22.0.0). I had no issues to get to v20.3.0 but now, moving to v21.0.0,
>> I have two issues:
>>
>> 1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS
>> website. I get a 500 error. Any ideas on what should I check?
>>
>
> Could you send us what you see in the Apache error file for that 500
> error? Although, might be worth focusing on fixing your second issue before
> we dive too much into that one.
>
>
>> 2. In the instructions to upgrade to v21.0.0, the second point says:
>>
>> "Run make from the Loris root directory to update all dependencies.?"
>>
>> However when I run ?make? In the Loris root direction it does nothing.
>> Here is the result:
>>
>> ===
>> *lorisadmin at ipmsa-loris*:*/var/www/loris*$ make
>> make: *** No targets specified and no makefile found.  Stop.
>> ===
>>
> It that the right directory? Maybe I am missing some files?
>>
>
> Are you sure you are on the 21.0.0 release of LORIS before you run make?
> Do you see a Makefile in your /var/www/loris directory? In theory it is
> supposed to be there on branch 21.0.0 (
> https://github.com/aces/Loris/tree/v21.0.0)
>
> Hope this helps.
>
> C?cile
>
>
>> Thank you for your help.
>>
>> Best,
>> Alfredo.
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
-------------- next part --------------
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From AMORALESPINZON at bwh.harvard.edu  Wed Feb 19 17:28:59 2020
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Wed, 19 Feb 2020 22:28:59 +0000
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <CAMpvQ9hN-vTERXCkXtgBVdg+_GEgk4J6cDizJ6vQDpaOy_YAxQ@mail.gmail.com>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
 <CAMkiY3e1JkHqWt3oMFDGyHsr26F4LPUOS6gO8hzm-nCbCFm7DQ@mail.gmail.com>
 <62049B06-1DB0-4E4C-8610-3BB2D629CE4F@bwh.harvard.edu>
 <CAMpvQ9hN-vTERXCkXtgBVdg+_GEgk4J6cDizJ6vQDpaOy_YAxQ@mail.gmail.com>
Message-ID: <E2FB11C8-D40E-4754-8D0B-D35FDBFF47DF@bwh.harvard.edu>

Hi Ling Ma,

Thank you. I will upgrade to PHP 7.2.

BTW, I cannot find the requirements for PHP for v21, I am looking at this link:

https://github.com/aces/Loris/releases/tag/v21.0.0

Regards,
Alfredo.


On Feb 19, 2020, at 5:18 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

The warning is OK to ignore. As to php, please check v21 version requirements, I believe a php minimum 7.1 even 7.2 is required.

In fact, PHP 5.6 is no longer supported.

Best regards,
Ling Ma

On Wed., Feb. 19, 2020, 5:07 p.m. Morales Pinzon, Alfredo, <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear Ling and C?cile,

Thank for your responses.

I had an issue with "git checkout?, somehow I had to remove some files before being able to checkout the v21.0.0. That was the reason I didn?t have the make file. Now that I have it, I have some errors:

After running ?make? I have the following error:

===
    WARNING in configuration
    The 'mode' option has not been set, webpack will fallback to 'production' for this value. Set 'mode' option to 'development' or 'production' to enable defaults for each environment.
    You can also set it to 'none' to disable any default behavior. Learn more: https://webpack.js.org/concepts/mode/
composer install --no-dev
> mkdir -p project/libraries
Loading composer repositories with package information
Installing dependencies from lock file
Your requirements could not be resolved to an installable set of packages.

  Problem 1
    - Installation request for php-http/guzzle6-adapter v2.0.1 -> satisfiable by php-http/guzzle6-adapter[v2.0.1].
    - php-http/guzzle6-adapter v2.0.1 requires php ^7.1 -> your PHP version (7.0.33) does not satisfy that requirement.
===

Do I have to upgrade PHP to 7.1?

Thank you again for your help.

Regards,
Alfredo.


On Feb 19, 2020, at 12:15 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Sorry to hear you are experiencing issues with the upgrade to 21.0.0. See below.

On Tue, Feb 18, 2020 at 4:31 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and then to v22.0.0). I had no issues to get to v20.3.0 but now, moving to v21.0.0, I have two issues:

1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS website. I get a 500 error. Any ideas on what should I check?

Could you send us what you see in the Apache error file for that 500 error? Although, might be worth focusing on fixing your second issue before we dive too much into that one.

2. In the instructions to upgrade to v21.0.0, the second point says:

"Run make from the Loris root directory to update all dependencies.?"

However when I run ?make? In the Loris root direction it does nothing. Here is the result:

===
lorisadmin at ipmsa-loris:/var/www/loris$ make
make: *** No targets specified and no makefile found.  Stop.
===
It that the right directory? Maybe I am missing some files?

Are you sure you are on the 21.0.0 release of LORIS before you run make? Do you see a Makefile in your /var/www/loris directory? In theory it is supposed to be there on branch 21.0.0 (https://github.com/aces/Loris/tree/v21.0.0)

Hope this helps.

C?cile


Thank you for your help.

Best,
Alfredo.



The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

-------------- next part --------------
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From lingyun.ma at mcin.ca  Wed Feb 19 17:47:02 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Wed, 19 Feb 2020 17:47:02 -0500
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <E2FB11C8-D40E-4754-8D0B-D35FDBFF47DF@bwh.harvard.edu>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
 <CAMkiY3e1JkHqWt3oMFDGyHsr26F4LPUOS6gO8hzm-nCbCFm7DQ@mail.gmail.com>
 <62049B06-1DB0-4E4C-8610-3BB2D629CE4F@bwh.harvard.edu>
 <CAMpvQ9hN-vTERXCkXtgBVdg+_GEgk4J6cDizJ6vQDpaOy_YAxQ@mail.gmail.com>
 <E2FB11C8-D40E-4754-8D0B-D35FDBFF47DF@bwh.harvard.edu>
Message-ID: <CAMpvQ9gBuqQCrNJakqH2MLsh8r2zScatfQqG8mvwXAvCcseK1g@mail.gmail.com>

Hi Alfredo,

If you check this link:

https://github.com/aces/Loris/blob/21.0-release/README.md

and

https://github.com/aces/Loris/blob/22.0-release/README.md

You will see that the system requires:

*System Requirements*

   - Apache *2.4* or higher
   - MySQL >= 5.7 (or MariaDB >= 10.3)
   - PHP *7.2* or higher
   - Composer <https://getcomposer.org/>
   - NodeJS *8.0* or higher
   - NPM
   - make

Please make sure that you have all the latest or recent versions for each
of them, otherwise you will run into trouble later.

Ling Ma

On Wed, Feb 19, 2020 at 5:29 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi Ling Ma,
>
> Thank you. I will upgrade to PHP 7.2.
>
> BTW, I cannot find the requirements for PHP for v21, I am looking at this
> link:
>
> https://github.com/aces/Loris/releases/tag/v21.0.0
>
> Regards,
> Alfredo.
>
>
> On Feb 19, 2020, at 5:18 PM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> The warning is OK to ignore. As to php, please check v21 version
> requirements, I believe a php minimum 7.1 even 7.2 is required.
>
> In fact, PHP 5.6 is no longer supported.
>
> Best regards,
> Ling Ma
>
> On Wed., Feb. 19, 2020, 5:07 p.m. Morales Pinzon, Alfredo, <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Dear Ling and C?cile,
>>
>> Thank for your responses.
>>
>> I had an issue with "git checkout?, somehow I had to remove some files
>> before being able to checkout the v21.0.0. That was the reason I didn?t
>> have the make file. Now that I have it, I have some errors:
>>
>> After running ?make? I have the following error:
>>
>> ===
>>     *WARNING in configuration*
>> *    The 'mode' option has not been set, webpack will fallback to
>> 'production' for this value. Set 'mode' option to 'development' or
>> 'production' to enable defaults for each environment.*
>> *    You can also set it to 'none' to disable any default behavior. Learn
>> more: https://webpack.js.org/concepts/mode/
>> <https://webpack.js.org/concepts/mode/>*
>> composer install --no-dev
>> > mkdir -p project/libraries
>> Loading composer repositories with package information
>> Installing dependencies from lock file
>> Your requirements could not be resolved to an installable set of packages.
>>
>>   Problem 1
>>     - Installation request for php-http/guzzle6-adapter v2.0.1 ->
>> satisfiable by php-http/guzzle6-adapter[v2.0.1].
>>     - php-http/guzzle6-adapter v2.0.1 requires php ^7.1 -> your PHP
>> version (7.0.33) does not satisfy that requirement.
>> ===
>>
>> Do I have to upgrade PHP to 7.1?
>>
>> Thank you again for your help.
>>
>> Regards,
>> Alfredo.
>>
>>
>> On Feb 19, 2020, at 12:15 PM, Cecile Madjar <cecile.madjar at mcin.ca>
>> wrote:
>>
>>         External Email - Use Caution
>>
>> Hi Alfredo,
>>
>> Sorry to hear you are experiencing issues with the upgrade to 21.0.0. See
>> below.
>>
>> On Tue, Feb 18, 2020 at 4:31 PM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>>> Hi C?cile,
>>>
>>> I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and then
>>> to v22.0.0). I had no issues to get to v20.3.0 but now, moving to v21.0.0,
>>> I have two issues:
>>>
>>> 1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS
>>> website. I get a 500 error. Any ideas on what should I check?
>>>
>>
>> Could you send us what you see in the Apache error file for that 500
>> error? Although, might be worth focusing on fixing your second issue before
>> we dive too much into that one.
>>
>>
>>> 2. In the instructions to upgrade to v21.0.0, the second point says:
>>>
>>> "Run make from the Loris root directory to update all dependencies.?"
>>>
>>> However when I run ?make? In the Loris root direction it does nothing.
>>> Here is the result:
>>>
>>> ===
>>> *lorisadmin at ipmsa-loris*:*/var/www/loris*$ make
>>> make: *** No targets specified and no makefile found.  Stop.
>>> ===
>>>
>> It that the right directory? Maybe I am missing some files?
>>>
>>
>> Are you sure you are on the 21.0.0 release of LORIS before you run make?
>> Do you see a Makefile in your /var/www/loris directory? In theory it is
>> supposed to be there on branch 21.0.0 (
>> https://github.com/aces/Loris/tree/v21.0.0)
>>
>> Hope this helps.
>>
>> C?cile
>>
>>
>>> Thank you for your help.
>>>
>>> Best,
>>> Alfredo.
>>>
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>
>
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From AMORALESPINZON at bwh.harvard.edu  Wed Feb 19 18:18:12 2020
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Wed, 19 Feb 2020 23:18:12 +0000
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <CAMpvQ9gBuqQCrNJakqH2MLsh8r2zScatfQqG8mvwXAvCcseK1g@mail.gmail.com>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
 <CAMkiY3e1JkHqWt3oMFDGyHsr26F4LPUOS6gO8hzm-nCbCFm7DQ@mail.gmail.com>
 <62049B06-1DB0-4E4C-8610-3BB2D629CE4F@bwh.harvard.edu>
 <CAMpvQ9hN-vTERXCkXtgBVdg+_GEgk4J6cDizJ6vQDpaOy_YAxQ@mail.gmail.com>
 <E2FB11C8-D40E-4754-8D0B-D35FDBFF47DF@bwh.harvard.edu>
 <CAMpvQ9gBuqQCrNJakqH2MLsh8r2zScatfQqG8mvwXAvCcseK1g@mail.gmail.com>
Message-ID: <35780192-BAF2-4F5F-AABB-53142C683BA2@bwh.harvard.edu>

Hi Ling Ma,

Thank you for the information. I would suggest to add this link to each release, where the upgrading instructions are listed, and also mention upgrading system requirements if needed.

Continuing with the upgrade to v21.0.0. I checked that all the system requirements are met. Now, in having this error when executing data_dictionary_cleaner.php:

===
lorisadmin at ipmsa-loris:/var/www/loris/tools/single_use$ php data_dictionary_cleaner.php
PHP Fatal error:  Uncaught Error: Call to undefined function simplexml_load_file() in /var/www/loris/php/libraries/NDB_Config.class.inc:96
Stack trace:
#0 /var/www/loris/php/libraries/NDB_Config.class.inc(70): NDB_Config->load('/var/www/loris/...')
#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton('/var/www/loris/...')
#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config('/var/www/loris/...')
#3 /var/www/loris/tools/generic_includes.php(25): NDB_Client->initialize('/var/www/loris/...')
#4 /var/www/loris/tools/single_use/data_dictionary_cleaner.php(24): require_once('/var/www/loris/...')
#5 {main}
  thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 96
===

Any ideas on how to solve this?

Regards,
Alfredo.

On Feb 19, 2020, at 5:47 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

If you check this link:

https://github.com/aces/Loris/blob/21.0-release/README.md

and

https://github.com/aces/Loris/blob/22.0-release/README.md

You will see that the system requires:

System Requirements

  *   Apache 2.4 or higher
  *   MySQL >= 5.7 (or MariaDB >= 10.3)
  *   PHP 7.2 or higher
  *   Composer<https://getcomposer.org/>
  *   NodeJS 8.0 or higher
  *   NPM
  *   make

Please make sure that you have all the latest or recent versions for each of them, otherwise you will run into trouble later.

Ling Ma

On Wed, Feb 19, 2020 at 5:29 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Ling Ma,

Thank you. I will upgrade to PHP 7.2.

BTW, I cannot find the requirements for PHP for v21, I am looking at this link:

https://github.com/aces/Loris/releases/tag/v21.0.0

Regards,
Alfredo.


On Feb 19, 2020, at 5:18 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

The warning is OK to ignore. As to php, please check v21 version requirements, I believe a php minimum 7.1 even 7.2 is required.

In fact, PHP 5.6 is no longer supported.

Best regards,
Ling Ma

On Wed., Feb. 19, 2020, 5:07 p.m. Morales Pinzon, Alfredo, <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear Ling and C?cile,

Thank for your responses.

I had an issue with "git checkout?, somehow I had to remove some files before being able to checkout the v21.0.0. That was the reason I didn?t have the make file. Now that I have it, I have some errors:

After running ?make? I have the following error:

===
    WARNING in configuration
    The 'mode' option has not been set, webpack will fallback to 'production' for this value. Set 'mode' option to 'development' or 'production' to enable defaults for each environment.
    You can also set it to 'none' to disable any default behavior. Learn more: https://webpack.js.org/concepts/mode/
composer install --no-dev
> mkdir -p project/libraries
Loading composer repositories with package information
Installing dependencies from lock file
Your requirements could not be resolved to an installable set of packages.

  Problem 1
    - Installation request for php-http/guzzle6-adapter v2.0.1 -> satisfiable by php-http/guzzle6-adapter[v2.0.1].
    - php-http/guzzle6-adapter v2.0.1 requires php ^7.1 -> your PHP version (7.0.33) does not satisfy that requirement.
===

Do I have to upgrade PHP to 7.1?

Thank you again for your help.

Regards,
Alfredo.


On Feb 19, 2020, at 12:15 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Sorry to hear you are experiencing issues with the upgrade to 21.0.0. See below.

On Tue, Feb 18, 2020 at 4:31 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and then to v22.0.0). I had no issues to get to v20.3.0 but now, moving to v21.0.0, I have two issues:

1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS website. I get a 500 error. Any ideas on what should I check?

Could you send us what you see in the Apache error file for that 500 error? Although, might be worth focusing on fixing your second issue before we dive too much into that one.

2. In the instructions to upgrade to v21.0.0, the second point says:

"Run make from the Loris root directory to update all dependencies.?"

However when I run ?make? In the Loris root direction it does nothing. Here is the result:

===
lorisadmin at ipmsa-loris:/var/www/loris$ make
make: *** No targets specified and no makefile found.  Stop.
===
It that the right directory? Maybe I am missing some files?

Are you sure you are on the 21.0.0 release of LORIS before you run make? Do you see a Makefile in your /var/www/loris directory? In theory it is supposed to be there on branch 21.0.0 (https://github.com/aces/Loris/tree/v21.0.0)

Hope this helps.

C?cile


Thank you for your help.

Best,
Alfredo.



The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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From lingyun.ma at mcin.ca  Wed Feb 19 19:23:34 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Wed, 19 Feb 2020 19:23:34 -0500
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <35780192-BAF2-4F5F-AABB-53142C683BA2@bwh.harvard.edu>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
 <CAMkiY3e1JkHqWt3oMFDGyHsr26F4LPUOS6gO8hzm-nCbCFm7DQ@mail.gmail.com>
 <62049B06-1DB0-4E4C-8610-3BB2D629CE4F@bwh.harvard.edu>
 <CAMpvQ9hN-vTERXCkXtgBVdg+_GEgk4J6cDizJ6vQDpaOy_YAxQ@mail.gmail.com>
 <E2FB11C8-D40E-4754-8D0B-D35FDBFF47DF@bwh.harvard.edu>
 <CAMpvQ9gBuqQCrNJakqH2MLsh8r2zScatfQqG8mvwXAvCcseK1g@mail.gmail.com>
 <35780192-BAF2-4F5F-AABB-53142C683BA2@bwh.harvard.edu>
Message-ID: <CAMpvQ9jhtrQrqgAqvjWFMN_vHkHNM0C4vPd5HkDGTLAC1T9sxg@mail.gmail.com>

Hi Alfredo,

Since simplexml_load_file is part of php-xml package, I feel that you need
to install php7.2-xml if you are using PHP7.2. In Ubuntu you install this
package with apt-get install php7.2-xml, and make sure that this module is
enabled in Apache2 if you are using Apache2. You can check which module is
enabled via phpinfo() call from a PHP enabled web page, or just check your
Apache2 PHP modules, the later is easier.

Good luck.

Ling Ma

On Wed, Feb 19, 2020 at 6:18 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi Ling Ma,
>
> Thank you for the information. I would suggest to add this link to each
> release, where the upgrading instructions are listed, and also mention
> upgrading system requirements if needed.
>
> Continuing with the upgrade to v21.0.0. I checked that all the system
> requirements are met. Now, in having this error when executing
> data_dictionary_cleaner.php:
>
> ===
> *lorisadmin at ipmsa-loris*:*/var/www/loris/tools/single_use*$ php
> data_dictionary_cleaner.php
> PHP Fatal error:  Uncaught Error: Call to undefined function
> simplexml_load_file() in
> /var/www/loris/php/libraries/NDB_Config.class.inc:96
> Stack trace:
> #0 /var/www/loris/php/libraries/NDB_Config.class.inc(70):
> NDB_Config->load('/var/www/loris/...')
> #1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118):
> NDB_Config::singleton('/var/www/loris/...')
> #2 /var/www/loris/php/libraries/NDB_Client.class.inc(54):
> NDB_Factory->config('/var/www/loris/...')
> #3 /var/www/loris/tools/generic_includes.php(25):
> NDB_Client->initialize('/var/www/loris/...')
> #4 /var/www/loris/tools/single_use/data_dictionary_cleaner.php(24):
> require_once('/var/www/loris/...')
> #5 {main}
>   thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 96
> ===
>
> Any ideas on how to solve this?
>
> Regards,
> Alfredo.
>
> On Feb 19, 2020, at 5:47 PM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> If you check this link:
>
> https://github.com/aces/Loris/blob/21.0-release/README.md
>
> and
>
> https://github.com/aces/Loris/blob/22.0-release/README.md
>
> You will see that the system requires:
>
> *System Requirements*
>
>    - Apache *2.4* or higher
>    - MySQL >= 5.7 (or MariaDB >= 10.3)
>    - PHP *7.2* or higher
>    - Composer <https://getcomposer.org/>
>    - NodeJS *8.0* or higher
>    - NPM
>    - make
>
> Please make sure that you have all the latest or recent versions for each
> of them, otherwise you will run into trouble later.
>
> Ling Ma
>
> On Wed, Feb 19, 2020 at 5:29 PM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Hi Ling Ma,
>>
>> Thank you. I will upgrade to PHP 7.2.
>>
>> BTW, I cannot find the requirements for PHP for v21, I am looking at this
>> link:
>>
>> https://github.com/aces/Loris/releases/tag/v21.0.0
>>
>> Regards,
>> Alfredo.
>>
>>
>> On Feb 19, 2020, at 5:18 PM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>>
>>         External Email - Use Caution
>>
>> Hi Alfredo,
>>
>> The warning is OK to ignore. As to php, please check v21 version
>> requirements, I believe a php minimum 7.1 even 7.2 is required.
>>
>> In fact, PHP 5.6 is no longer supported.
>>
>> Best regards,
>> Ling Ma
>>
>> On Wed., Feb. 19, 2020, 5:07 p.m. Morales Pinzon, Alfredo, <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>>> Dear Ling and C?cile,
>>>
>>> Thank for your responses.
>>>
>>> I had an issue with "git checkout?, somehow I had to remove some files
>>> before being able to checkout the v21.0.0. That was the reason I didn?t
>>> have the make file. Now that I have it, I have some errors:
>>>
>>> After running ?make? I have the following error:
>>>
>>> ===
>>>     *WARNING in configuration*
>>> *    The 'mode' option has not been set, webpack will fallback to
>>> 'production' for this value. Set 'mode' option to 'development' or
>>> 'production' to enable defaults for each environment.*
>>> *    You can also set it to 'none' to disable any default behavior.
>>> Learn more: https://webpack.js.org/concepts/mode/
>>> <https://webpack.js.org/concepts/mode/>*
>>> composer install --no-dev
>>> > mkdir -p project/libraries
>>> Loading composer repositories with package information
>>> Installing dependencies from lock file
>>> Your requirements could not be resolved to an installable set of
>>> packages.
>>>
>>>   Problem 1
>>>     - Installation request for php-http/guzzle6-adapter v2.0.1 ->
>>> satisfiable by php-http/guzzle6-adapter[v2.0.1].
>>>     - php-http/guzzle6-adapter v2.0.1 requires php ^7.1 -> your PHP
>>> version (7.0.33) does not satisfy that requirement.
>>> ===
>>>
>>> Do I have to upgrade PHP to 7.1?
>>>
>>> Thank you again for your help.
>>>
>>> Regards,
>>> Alfredo.
>>>
>>>
>>> On Feb 19, 2020, at 12:15 PM, Cecile Madjar <cecile.madjar at mcin.ca>
>>> wrote:
>>>
>>>         External Email - Use Caution
>>>
>>> Hi Alfredo,
>>>
>>> Sorry to hear you are experiencing issues with the upgrade to 21.0.0.
>>> See below.
>>>
>>> On Tue, Feb 18, 2020 at 4:31 PM Morales Pinzon, Alfredo <
>>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>>
>>>> Hi C?cile,
>>>>
>>>> I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and
>>>> then to v22.0.0). I had no issues to get to v20.3.0 but now, moving to
>>>> v21.0.0, I have two issues:
>>>>
>>>> 1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS
>>>> website. I get a 500 error. Any ideas on what should I check?
>>>>
>>>
>>> Could you send us what you see in the Apache error file for that 500
>>> error? Although, might be worth focusing on fixing your second issue before
>>> we dive too much into that one.
>>>
>>>
>>>> 2. In the instructions to upgrade to v21.0.0, the second point says:
>>>>
>>>> "Run make from the Loris root directory to update all dependencies.?"
>>>>
>>>> However when I run ?make? In the Loris root direction it does nothing.
>>>> Here is the result:
>>>>
>>>> ===
>>>> *lorisadmin at ipmsa-loris*:*/var/www/loris*$ make
>>>> make: *** No targets specified and no makefile found.  Stop.
>>>> ===
>>>>
>>> It that the right directory? Maybe I am missing some files?
>>>>
>>>
>>> Are you sure you are on the 21.0.0 release of LORIS before you run make?
>>> Do you see a Makefile in your /var/www/loris directory? In theory it is
>>> supposed to be there on branch 21.0.0 (
>>> https://github.com/aces/Loris/tree/v21.0.0)
>>>
>>> Hope this helps.
>>>
>>> C?cile
>>>
>>>
>>>> Thank you for your help.
>>>>
>>>> Best,
>>>> Alfredo.
>>>>
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>
>>
>
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From ioannis at berkeley.edu  Wed Feb 19 22:40:55 2020
From: ioannis at berkeley.edu (Ioannis Pappas)
Date: Wed, 19 Feb 2020 19:40:55 -0800
Subject: [Loris-dev] question regarding visit labels
Message-ID: <CAH3c6x+b2+Z3N8-W1fstTOi+Q-v9XWi9eqmRkyZpyJeAZezo=A@mail.gmail.com>

Hi Loris support.
I hope you are well. I m using Loris version 21.0.1. I have two questions
if you allow me. 1) First I am trying to manually define my visit labels
like this in project/config.xml

<visitLabel subprojectID="1">
            <generation>sequence</generation>
            <regex>/^[A-Z0-9]{2}$/i</regex>
            <length>2</length>
            <suggest>V%value%</suggest>
            <labelSet>
                <item value="V1">V01</item>
                <item value="V2">V02</item>
                <item value="V3">V03</item>
            </labelSet>
</visitLabel>

which is very similar to the one you provide in the documentation

  <visitLabel subprojectID="1">
      <generation>sequence</generation>
      <regex>/^[A-Z0-9]{2}$/i</regex>
      <length>2</length>
      <suggest>V%value%</suggest>       <!--  %value% will be substituted
for the next unique number  -->
      <labelSet>
          <item value="V1">V1 label description</item>
          <item value="V2">V2 label description</tem>
      </labelSet>
   </visitLabel>

However when I am trying to experiment and upload a scan (e.g. via the
Imaging Uploader gui) the values don't show up in the dropdown box for the
visit labels. Am I doing something foolish and wrong?

2) From my understanding the uploaded scans will be automatically
identified (in terms of whether this is t1,t2,or flair for example) via the
min and max specifications in the mri_protocol table (that is further
connected to the mri_scan_type table). Is this correct? Subsequently any
violations will be defined based on these bounds.

Best wishes,
Ioannis
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From lingyun.ma at mcin.ca  Thu Feb 20 11:11:56 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Thu, 20 Feb 2020 11:11:56 -0500
Subject: [Loris-dev] question regarding visit labels
In-Reply-To: <CAH3c6x+b2+Z3N8-W1fstTOi+Q-v9XWi9eqmRkyZpyJeAZezo=A@mail.gmail.com>
References: <CAH3c6x+b2+Z3N8-W1fstTOi+Q-v9XWi9eqmRkyZpyJeAZezo=A@mail.gmail.com>
Message-ID: <CAMpvQ9hH+aH9Hu2PxZ2HdM190hPMvXW8rUAZk0QOxkTg3hTMuQ@mail.gmail.com>

Hi Ioannis,

1) The Image Uploader's Visit labels are those already existed, populated
from session table. While <visitLabel> session is used to create a
visitLabel which you could use to generate a timepoints, then the
visitLabel might be visible in image uploader.
2). The mri_protocol min, max specifications are not used to identify the
violations, the violations could be flag only if the protocol is unknown.

Best regards,
Ling Ma
Dev consultant

On Wed, Feb 19, 2020 at 10:41 PM Ioannis Pappas <ioannis at berkeley.edu>
wrote:

> Hi Loris support.
> I hope you are well. I m using Loris version 21.0.1. I have two questions
> if you allow me. 1) First I am trying to manually define my visit labels
> like this in project/config.xml
>
> <visitLabel subprojectID="1">
>             <generation>sequence</generation>
>             <regex>/^[A-Z0-9]{2}$/i</regex>
>             <length>2</length>
>             <suggest>V%value%</suggest>
>             <labelSet>
>                 <item value="V1">V01</item>
>                 <item value="V2">V02</item>
>                 <item value="V3">V03</item>
>             </labelSet>
> </visitLabel>
>
> which is very similar to the one you provide in the documentation
>
>   <visitLabel subprojectID="1">
>       <generation>sequence</generation>
>       <regex>/^[A-Z0-9]{2}$/i</regex>
>       <length>2</length>
>       <suggest>V%value%</suggest>       <!--  %value% will be substituted
> for the next unique number  -->
>       <labelSet>
>           <item value="V1">V1 label description</item>
>           <item value="V2">V2 label description</tem>
>       </labelSet>
>    </visitLabel>
>
> However when I am trying to experiment and upload a scan (e.g. via the
> Imaging Uploader gui) the values don't show up in the dropdown box for the
> visit labels. Am I doing something foolish and wrong?
>
> 2) From my understanding the uploaded scans will be automatically
> identified (in terms of whether this is t1,t2,or flair for example) via the
> min and max specifications in the mri_protocol table (that is further
> connected to the mri_scan_type table). Is this correct? Subsequently any
> violations will be defined based on these bounds.
>
> Best wishes,
> Ioannis
> _______________________________________________
> 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 Feb 20 11:13:35 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Thu, 20 Feb 2020 11:13:35 -0500
Subject: [Loris-dev] question regarding visit labels
In-Reply-To: <CAMpvQ9hH+aH9Hu2PxZ2HdM190hPMvXW8rUAZk0QOxkTg3hTMuQ@mail.gmail.com>
References: <CAH3c6x+b2+Z3N8-W1fstTOi+Q-v9XWi9eqmRkyZpyJeAZezo=A@mail.gmail.com>
 <CAMpvQ9hH+aH9Hu2PxZ2HdM190hPMvXW8rUAZk0QOxkTg3hTMuQ@mail.gmail.com>
Message-ID: <CAMpvQ9hgeqnNnixWcA2DU3sxfeT=qaxPTN04Rb9XW3ks+KkTYw@mail.gmail.com>

2) or "does not match the requirement specified in the mri_protocol_checks"

On Thu, Feb 20, 2020 at 11:11 AM Ling Ma <lingyun.ma at mcin.ca> wrote:

> Hi Ioannis,
>
> 1) The Image Uploader's Visit labels are those already existed, populated
> from session table. While <visitLabel> session is used to create a
> visitLabel which you could use to generate a timepoints, then the
> visitLabel might be visible in image uploader.
> 2). The mri_protocol min, max specifications are not used to identify the
> violations, the violations could be flag only if the protocol is unknown.
>
> Best regards,
> Ling Ma
> Dev consultant
>
> On Wed, Feb 19, 2020 at 10:41 PM Ioannis Pappas <ioannis at berkeley.edu>
> wrote:
>
>> Hi Loris support.
>> I hope you are well. I m using Loris version 21.0.1. I have two questions
>> if you allow me. 1) First I am trying to manually define my visit labels
>> like this in project/config.xml
>>
>> <visitLabel subprojectID="1">
>>             <generation>sequence</generation>
>>             <regex>/^[A-Z0-9]{2}$/i</regex>
>>             <length>2</length>
>>             <suggest>V%value%</suggest>
>>             <labelSet>
>>                 <item value="V1">V01</item>
>>                 <item value="V2">V02</item>
>>                 <item value="V3">V03</item>
>>             </labelSet>
>> </visitLabel>
>>
>> which is very similar to the one you provide in the documentation
>>
>>   <visitLabel subprojectID="1">
>>       <generation>sequence</generation>
>>       <regex>/^[A-Z0-9]{2}$/i</regex>
>>       <length>2</length>
>>       <suggest>V%value%</suggest>       <!--  %value% will be substituted
>> for the next unique number  -->
>>       <labelSet>
>>           <item value="V1">V1 label description</item>
>>           <item value="V2">V2 label description</tem>
>>       </labelSet>
>>    </visitLabel>
>>
>> However when I am trying to experiment and upload a scan (e.g. via the
>> Imaging Uploader gui) the values don't show up in the dropdown box for the
>> visit labels. Am I doing something foolish and wrong?
>>
>> 2) From my understanding the uploaded scans will be automatically
>> identified (in terms of whether this is t1,t2,or flair for example) via the
>> min and max specifications in the mri_protocol table (that is further
>> connected to the mri_scan_type table). Is this correct? Subsequently any
>> violations will be defined based on these bounds.
>>
>> Best wishes,
>> Ioannis
>> _______________________________________________
>> 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 ioannis at berkeley.edu  Thu Feb 20 11:14:57 2020
From: ioannis at berkeley.edu (Ioannis Pappas)
Date: Thu, 20 Feb 2020 08:14:57 -0800
Subject: [Loris-dev] question regarding visit labels
In-Reply-To: <CAMpvQ9hgeqnNnixWcA2DU3sxfeT=qaxPTN04Rb9XW3ks+KkTYw@mail.gmail.com>
References: <CAH3c6x+b2+Z3N8-W1fstTOi+Q-v9XWi9eqmRkyZpyJeAZezo=A@mail.gmail.com>
 <CAMpvQ9hH+aH9Hu2PxZ2HdM190hPMvXW8rUAZk0QOxkTg3hTMuQ@mail.gmail.com>
 <CAMpvQ9hgeqnNnixWcA2DU3sxfeT=qaxPTN04Rb9XW3ks+KkTYw@mail.gmail.com>
Message-ID: <53D30A2D-47C3-4FC3-8B30-E9A7AB071DC5@berkeley.edu>

Thank you Ling. That make sense!

Best wishes,
Ioannis

> On Feb 20, 2020, at 8:13 AM, Ling Ma <lingyun.ma at mcin.ca> wrote:
> 
> 2) or "does not match the requirement specified in the mri_protocol_checks"
> 
> On Thu, Feb 20, 2020 at 11:11 AM Ling Ma <lingyun.ma at mcin.ca <mailto:lingyun.ma at mcin.ca>> wrote:
> Hi Ioannis,
> 
> 1) The Image Uploader's Visit labels are those already existed, populated from session table. While <visitLabel> session is used to create a visitLabel which you could use to generate a timepoints, then the visitLabel might be visible in image uploader.
> 2). The mri_protocol min, max specifications are not used to identify the violations, the violations could be flag only if the protocol is unknown.
> 
> Best regards,
> Ling Ma
> Dev consultant
> 
> On Wed, Feb 19, 2020 at 10:41 PM Ioannis Pappas <ioannis at berkeley.edu <mailto:ioannis at berkeley.edu>> wrote:
> Hi Loris support.
> I hope you are well. I m using Loris version 21.0.1. I have two questions if you allow me. 1) First I am trying to manually define my visit labels like this in project/config.xml
> 
> <visitLabel subprojectID="1">
>             <generation>sequence</generation>
>             <regex>/^[A-Z0-9]{2}$/i</regex>
>             <length>2</length>
>             <suggest>V%value%</suggest>
>             <labelSet>
>                 <item value="V1">V01</item>
>                 <item value="V2">V02</item>
>                 <item value="V3">V03</item>
>             </labelSet>
> </visitLabel>
> 
> which is very similar to the one you provide in the documentation
> 
>   <visitLabel subprojectID="1">
>       <generation>sequence</generation> 
>       <regex>/^[A-Z0-9]{2}$/i</regex>
>       <length>2</length>
>       <suggest>V%value%</suggest>       <!--  %value% will be substituted for the next unique number  -->
>       <labelSet>
>           <item value="V1">V1 label description</item>   
>           <item value="V2">V2 label description</tem>   
>       </labelSet>
>    </visitLabel>
> 
> However when I am trying to experiment and upload a scan (e.g. via the Imaging Uploader gui) the values don't show up in the dropdown box for the visit labels. Am I doing something foolish and wrong?
> 
> 2) From my understanding the uploaded scans will be automatically identified (in terms of whether this is t1,t2,or flair for example) via the min and max specifications in the mri_protocol table (that is further connected to the mri_scan_type table). Is this correct? Subsequently any violations will be defined based on these bounds. 
> 
> Best wishes,
> Ioannis
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca <mailto:Loris-dev at bic.mni.mcgill.ca>
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev <https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev>

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From AMORALESPINZON at bwh.harvard.edu  Fri Feb 21 09:59:39 2020
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Fri, 21 Feb 2020 14:59:39 +0000
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <CAMpvQ9jhtrQrqgAqvjWFMN_vHkHNM0C4vPd5HkDGTLAC1T9sxg@mail.gmail.com>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
 <CAMkiY3e1JkHqWt3oMFDGyHsr26F4LPUOS6gO8hzm-nCbCFm7DQ@mail.gmail.com>
 <62049B06-1DB0-4E4C-8610-3BB2D629CE4F@bwh.harvard.edu>
 <CAMpvQ9hN-vTERXCkXtgBVdg+_GEgk4J6cDizJ6vQDpaOy_YAxQ@mail.gmail.com>
 <E2FB11C8-D40E-4754-8D0B-D35FDBFF47DF@bwh.harvard.edu>
 <CAMpvQ9gBuqQCrNJakqH2MLsh8r2zScatfQqG8mvwXAvCcseK1g@mail.gmail.com>
 <35780192-BAF2-4F5F-AABB-53142C683BA2@bwh.harvard.edu>
 <CAMpvQ9jhtrQrqgAqvjWFMN_vHkHNM0C4vPd5HkDGTLAC1T9sxg@mail.gmail.com>
Message-ID: <812F97F8-245D-4EC3-A637-C7166F5C2CA1@bwh.harvard.edu>

Dear Ling Ma and C?cile,

Thank you for the help and tips. After installing php7.2-xml and php7.2-mysql I was able to finish all the steps listed in the upgrade process. I followed this post to upgrade to PHP 7.2: https://medium.com/andrewmmc-io/upgrade-php-version-to-7-2-from-7-0-c005a0926642

Now we come back to the first error. Actually, the server is not running right now. I have the following error:

===
[Fri Feb 21 09:25:33.848915 2020] [:error] [pid 27936] [client 216.15.126.108:52419] PHP Parse error:  syntax error, unexpected '?', expecting variable (T_VARIABLE) in /var/www/loris/php/libraries/NDB_Client.class.inc on line 49
===

After modifying the line 49 in NDB_Client.class.inc from

===
function initialize(?string $configFile = null)
===

to (removing the ?)

===
function initialize(string $configFile = null)
===

but I got the following error:

===
[Fri Feb 21 09:37:18.042287 2020] [:error] [pid 715] [client 216.15.126.108:52603] PHP Parse error:  syntax error, unexpected '?', expecting variable (T_VARIABLE) in /var/www/loris/php/libraries/NDB_Factory.class.inc on line 109
===

Is this an error in the code or I am missing something?

Thank you for help.

Best,
Alfredo.

On Feb 19, 2020, at 7:23 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Since simplexml_load_file is part of php-xml package, I feel that you need to install php7.2-xml if you are using PHP7.2. In Ubuntu you install this package with apt-get install php7.2-xml, and make sure that this module is enabled in Apache2 if you are using Apache2. You can check which module is enabled via phpinfo() call from a PHP enabled web page, or just check your Apache2 PHP modules, the later is easier.

Good luck.

Ling Ma

On Wed, Feb 19, 2020 at 6:18 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Ling Ma,

Thank you for the information. I would suggest to add this link to each release, where the upgrading instructions are listed, and also mention upgrading system requirements if needed.

Continuing with the upgrade to v21.0.0. I checked that all the system requirements are met. Now, in having this error when executing data_dictionary_cleaner.php:

===
lorisadmin at ipmsa-loris:/var/www/loris/tools/single_use$ php data_dictionary_cleaner.php
PHP Fatal error:  Uncaught Error: Call to undefined function simplexml_load_file() in /var/www/loris/php/libraries/NDB_Config.class.inc:96
Stack trace:
#0 /var/www/loris/php/libraries/NDB_Config.class.inc(70): NDB_Config->load('/var/www/loris/...')
#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton('/var/www/loris/...')
#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config('/var/www/loris/...')
#3 /var/www/loris/tools/generic_includes.php(25): NDB_Client->initialize('/var/www/loris/...')
#4 /var/www/loris/tools/single_use/data_dictionary_cleaner.php(24): require_once('/var/www/loris/...')
#5 {main}
  thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 96
===

Any ideas on how to solve this?

Regards,
Alfredo.

On Feb 19, 2020, at 5:47 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

If you check this link:

https://github.com/aces/Loris/blob/21.0-release/README.md

and

https://github.com/aces/Loris/blob/22.0-release/README.md

You will see that the system requires:

System Requirements

  *   Apache 2.4 or higher
  *   MySQL >= 5.7 (or MariaDB >= 10.3)
  *   PHP 7.2 or higher
  *   Composer<https://getcomposer.org/>
  *   NodeJS 8.0 or higher
  *   NPM
  *   make

Please make sure that you have all the latest or recent versions for each of them, otherwise you will run into trouble later.

Ling Ma

On Wed, Feb 19, 2020 at 5:29 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Ling Ma,

Thank you. I will upgrade to PHP 7.2.

BTW, I cannot find the requirements for PHP for v21, I am looking at this link:

https://github.com/aces/Loris/releases/tag/v21.0.0

Regards,
Alfredo.


On Feb 19, 2020, at 5:18 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

The warning is OK to ignore. As to php, please check v21 version requirements, I believe a php minimum 7.1 even 7.2 is required.

In fact, PHP 5.6 is no longer supported.

Best regards,
Ling Ma

On Wed., Feb. 19, 2020, 5:07 p.m. Morales Pinzon, Alfredo, <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear Ling and C?cile,

Thank for your responses.

I had an issue with "git checkout?, somehow I had to remove some files before being able to checkout the v21.0.0. That was the reason I didn?t have the make file. Now that I have it, I have some errors:

After running ?make? I have the following error:

===
    WARNING in configuration
    The 'mode' option has not been set, webpack will fallback to 'production' for this value. Set 'mode' option to 'development' or 'production' to enable defaults for each environment.
    You can also set it to 'none' to disable any default behavior. Learn more: https://webpack.js.org/concepts/mode/
composer install --no-dev
> mkdir -p project/libraries
Loading composer repositories with package information
Installing dependencies from lock file
Your requirements could not be resolved to an installable set of packages.

  Problem 1
    - Installation request for php-http/guzzle6-adapter v2.0.1 -> satisfiable by php-http/guzzle6-adapter[v2.0.1].
    - php-http/guzzle6-adapter v2.0.1 requires php ^7.1 -> your PHP version (7.0.33) does not satisfy that requirement.
===

Do I have to upgrade PHP to 7.1?

Thank you again for your help.

Regards,
Alfredo.


On Feb 19, 2020, at 12:15 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Sorry to hear you are experiencing issues with the upgrade to 21.0.0. See below.

On Tue, Feb 18, 2020 at 4:31 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and then to v22.0.0). I had no issues to get to v20.3.0 but now, moving to v21.0.0, I have two issues:

1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS website. I get a 500 error. Any ideas on what should I check?

Could you send us what you see in the Apache error file for that 500 error? Although, might be worth focusing on fixing your second issue before we dive too much into that one.

2. In the instructions to upgrade to v21.0.0, the second point says:

"Run make from the Loris root directory to update all dependencies.?"

However when I run ?make? In the Loris root direction it does nothing. Here is the result:

===
lorisadmin at ipmsa-loris:/var/www/loris$ make
make: *** No targets specified and no makefile found.  Stop.
===
It that the right directory? Maybe I am missing some files?

Are you sure you are on the 21.0.0 release of LORIS before you run make? Do you see a Makefile in your /var/www/loris directory? In theory it is supposed to be there on branch 21.0.0 (https://github.com/aces/Loris/tree/v21.0.0)

Hope this helps.

C?cile


Thank you for your help.

Best,
Alfredo.



The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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From lingyun.ma at mcin.ca  Fri Feb 21 10:02:33 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Fri, 21 Feb 2020 10:02:33 -0500
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <812F97F8-245D-4EC3-A637-C7166F5C2CA1@bwh.harvard.edu>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
 <CAMkiY3e1JkHqWt3oMFDGyHsr26F4LPUOS6gO8hzm-nCbCFm7DQ@mail.gmail.com>
 <62049B06-1DB0-4E4C-8610-3BB2D629CE4F@bwh.harvard.edu>
 <CAMpvQ9hN-vTERXCkXtgBVdg+_GEgk4J6cDizJ6vQDpaOy_YAxQ@mail.gmail.com>
 <E2FB11C8-D40E-4754-8D0B-D35FDBFF47DF@bwh.harvard.edu>
 <CAMpvQ9gBuqQCrNJakqH2MLsh8r2zScatfQqG8mvwXAvCcseK1g@mail.gmail.com>
 <35780192-BAF2-4F5F-AABB-53142C683BA2@bwh.harvard.edu>
 <CAMpvQ9jhtrQrqgAqvjWFMN_vHkHNM0C4vPd5HkDGTLAC1T9sxg@mail.gmail.com>
 <812F97F8-245D-4EC3-A637-C7166F5C2CA1@bwh.harvard.edu>
Message-ID: <CAMpvQ9gxALXS2aNdFxQ_5Jn1FAQgMhx3G8XsuSU2Ee8Xf6Gt8Q@mail.gmail.com>

Hi Alfredo,

You installed PHP7.2, but you might not use the new version, you might need
to restart the Apache2, or enable Apache2 to use PHP7.2. Because currently
your server is still running PHP7.0 or PHP5.6. Because "?" is part of PHP7.1

Please check.

Good luck.

Ling Ma

On Fri, Feb 21, 2020 at 9:59 AM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Dear Ling Ma and C?cile,
>
> Thank you for the help and tips. After installing php7.2-xml and
> php7.2-mysql I was able to finish all the steps listed in the upgrade
> process. I followed this post to upgrade to PHP 7.2:
> https://medium.com/andrewmmc-io/upgrade-php-version-to-7-2-from-7-0-c005a0926642
>
> Now we come back to the first error. Actually, the server is not running
> right now. I have the following error:
>
> ===
> [Fri Feb 21 09:25:33.848915 2020] [:error] [pid 27936] [client
> 216.15.126.108:52419] PHP Parse error:  syntax error, unexpected '?',
> expecting variable (T_VARIABLE) in
> /var/www/loris/php/libraries/NDB_Client.class.inc on line 49
> ===
>
> After modifying the line 49 in NDB_Client.class.inc from
>
> ===
> function initialize(?string $configFile = null)
> ===
>
> to (removing the ?)
>
> ===
> function initialize(string $configFile = null)
> ===
>
> but I got the following error:
>
> ===
> [Fri Feb 21 09:37:18.042287 2020] [:error] [pid 715] [client
> 216.15.126.108:52603] PHP Parse error:  syntax error, unexpected '?',
> expecting variable (T_VARIABLE) in
> /var/www/loris/php/libraries/NDB_Factory.class.inc on line 109
> ===
>
> Is this an error in the code or I am missing something?
>
> Thank you for help.
>
> Best,
> Alfredo.
>
> On Feb 19, 2020, at 7:23 PM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> Since simplexml_load_file is part of php-xml package, I feel that you
> need to install php7.2-xml if you are using PHP7.2. In Ubuntu you install
> this package with apt-get install php7.2-xml, and make sure that this
> module is enabled in Apache2 if you are using Apache2. You can check which
> module is enabled via phpinfo() call from a PHP enabled web page, or just
> check your Apache2 PHP modules, the later is easier.
>
> Good luck.
>
> Ling Ma
>
> On Wed, Feb 19, 2020 at 6:18 PM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Hi Ling Ma,
>>
>> Thank you for the information. I would suggest to add this link to each
>> release, where the upgrading instructions are listed, and also mention
>> upgrading system requirements if needed.
>>
>> Continuing with the upgrade to v21.0.0. I checked that all the system
>> requirements are met. Now, in having this error when executing
>> data_dictionary_cleaner.php:
>>
>> ===
>> *lorisadmin at ipmsa-loris*:*/var/www/loris/tools/single_use*$ php
>> data_dictionary_cleaner.php
>> PHP Fatal error:  Uncaught Error: Call to undefined function
>> simplexml_load_file() in
>> /var/www/loris/php/libraries/NDB_Config.class.inc:96
>> Stack trace:
>> #0 /var/www/loris/php/libraries/NDB_Config.class.inc(70):
>> NDB_Config->load('/var/www/loris/...')
>> #1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118):
>> NDB_Config::singleton('/var/www/loris/...')
>> #2 /var/www/loris/php/libraries/NDB_Client.class.inc(54):
>> NDB_Factory->config('/var/www/loris/...')
>> #3 /var/www/loris/tools/generic_includes.php(25):
>> NDB_Client->initialize('/var/www/loris/...')
>> #4 /var/www/loris/tools/single_use/data_dictionary_cleaner.php(24):
>> require_once('/var/www/loris/...')
>> #5 {main}
>>   thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 96
>> ===
>>
>> Any ideas on how to solve this?
>>
>> Regards,
>> Alfredo.
>>
>> On Feb 19, 2020, at 5:47 PM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>>
>>         External Email - Use Caution
>>
>> Hi Alfredo,
>>
>> If you check this link:
>>
>> https://github.com/aces/Loris/blob/21.0-release/README.md
>>
>> and
>>
>> https://github.com/aces/Loris/blob/22.0-release/README.md
>>
>> You will see that the system requires:
>>
>> *System Requirements*
>>
>>    - Apache *2.4* or higher
>>    - MySQL >= 5.7 (or MariaDB >= 10.3)
>>    - PHP *7.2* or higher
>>    - Composer <https://getcomposer.org/>
>>    - NodeJS *8.0* or higher
>>    - NPM
>>    - make
>>
>> Please make sure that you have all the latest or recent versions for each
>> of them, otherwise you will run into trouble later.
>>
>> Ling Ma
>>
>> On Wed, Feb 19, 2020 at 5:29 PM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>>> Hi Ling Ma,
>>>
>>> Thank you. I will upgrade to PHP 7.2.
>>>
>>> BTW, I cannot find the requirements for PHP for v21, I am looking at
>>> this link:
>>>
>>> https://github.com/aces/Loris/releases/tag/v21.0.0
>>>
>>> Regards,
>>> Alfredo.
>>>
>>>
>>> On Feb 19, 2020, at 5:18 PM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>>>
>>>         External Email - Use Caution
>>>
>>> Hi Alfredo,
>>>
>>> The warning is OK to ignore. As to php, please check v21 version
>>> requirements, I believe a php minimum 7.1 even 7.2 is required.
>>>
>>> In fact, PHP 5.6 is no longer supported.
>>>
>>> Best regards,
>>> Ling Ma
>>>
>>> On Wed., Feb. 19, 2020, 5:07 p.m. Morales Pinzon, Alfredo, <
>>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>>
>>>> Dear Ling and C?cile,
>>>>
>>>> Thank for your responses.
>>>>
>>>> I had an issue with "git checkout?, somehow I had to remove some files
>>>> before being able to checkout the v21.0.0. That was the reason I didn?t
>>>> have the make file. Now that I have it, I have some errors:
>>>>
>>>> After running ?make? I have the following error:
>>>>
>>>> ===
>>>>     *WARNING in configuration*
>>>> *    The 'mode' option has not been set, webpack will fallback to
>>>> 'production' for this value. Set 'mode' option to 'development' or
>>>> 'production' to enable defaults for each environment.*
>>>> *    You can also set it to 'none' to disable any default behavior.
>>>> Learn more: https://webpack.js.org/concepts/mode/
>>>> <https://webpack.js.org/concepts/mode/>*
>>>> composer install --no-dev
>>>> > mkdir -p project/libraries
>>>> Loading composer repositories with package information
>>>> Installing dependencies from lock file
>>>> Your requirements could not be resolved to an installable set of
>>>> packages.
>>>>
>>>>   Problem 1
>>>>     - Installation request for php-http/guzzle6-adapter v2.0.1 ->
>>>> satisfiable by php-http/guzzle6-adapter[v2.0.1].
>>>>     - php-http/guzzle6-adapter v2.0.1 requires php ^7.1 -> your PHP
>>>> version (7.0.33) does not satisfy that requirement.
>>>> ===
>>>>
>>>> Do I have to upgrade PHP to 7.1?
>>>>
>>>> Thank you again for your help.
>>>>
>>>> Regards,
>>>> Alfredo.
>>>>
>>>>
>>>> On Feb 19, 2020, at 12:15 PM, Cecile Madjar <cecile.madjar at mcin.ca>
>>>> wrote:
>>>>
>>>>         External Email - Use Caution
>>>>
>>>> Hi Alfredo,
>>>>
>>>> Sorry to hear you are experiencing issues with the upgrade to 21.0.0.
>>>> See below.
>>>>
>>>> On Tue, Feb 18, 2020 at 4:31 PM Morales Pinzon, Alfredo <
>>>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>>>
>>>>> Hi C?cile,
>>>>>
>>>>> I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and
>>>>> then to v22.0.0). I had no issues to get to v20.3.0 but now, moving to
>>>>> v21.0.0, I have two issues:
>>>>>
>>>>> 1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS
>>>>> website. I get a 500 error. Any ideas on what should I check?
>>>>>
>>>>
>>>> Could you send us what you see in the Apache error file for that 500
>>>> error? Although, might be worth focusing on fixing your second issue before
>>>> we dive too much into that one.
>>>>
>>>>
>>>>> 2. In the instructions to upgrade to v21.0.0, the second point says:
>>>>>
>>>>> "Run make from the Loris root directory to update all dependencies.?"
>>>>>
>>>>> However when I run ?make? In the Loris root direction it does nothing.
>>>>> Here is the result:
>>>>>
>>>>> ===
>>>>> *lorisadmin at ipmsa-loris*:*/var/www/loris*$ make
>>>>> make: *** No targets specified and no makefile found.  Stop.
>>>>> ===
>>>>>
>>>> It that the right directory? Maybe I am missing some files?
>>>>>
>>>>
>>>> Are you sure you are on the 21.0.0 release of LORIS before you run
>>>> make? Do you see a Makefile in your /var/www/loris directory? In theory it
>>>> is supposed to be there on branch 21.0.0 (
>>>> https://github.com/aces/Loris/tree/v21.0.0)
>>>>
>>>> Hope this helps.
>>>>
>>>> C?cile
>>>>
>>>>
>>>>> Thank you for your help.
>>>>>
>>>>> Best,
>>>>> Alfredo.
>>>>>
>>>>
>>>>
>>>> The information in this e-mail is intended only for the person to whom
>>>> it is
>>>> addressed. If you believe this e-mail was sent to you in error and the
>>>> e-mail
>>>> contains patient information, please contact the Partners Compliance
>>>> HelpLine at
>>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>>> in error
>>>> but does not contain patient information, please contact the sender and
>>>> properly
>>>> dispose of the e-mail.
>>>>
>>>
>>>
>>
>
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From lingyun.ma at mcin.ca  Fri Feb 21 10:09:28 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Fri, 21 Feb 2020 10:09:28 -0500
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <CAMpvQ9gxALXS2aNdFxQ_5Jn1FAQgMhx3G8XsuSU2Ee8Xf6Gt8Q@mail.gmail.com>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
 <CAMkiY3e1JkHqWt3oMFDGyHsr26F4LPUOS6gO8hzm-nCbCFm7DQ@mail.gmail.com>
 <62049B06-1DB0-4E4C-8610-3BB2D629CE4F@bwh.harvard.edu>
 <CAMpvQ9hN-vTERXCkXtgBVdg+_GEgk4J6cDizJ6vQDpaOy_YAxQ@mail.gmail.com>
 <E2FB11C8-D40E-4754-8D0B-D35FDBFF47DF@bwh.harvard.edu>
 <CAMpvQ9gBuqQCrNJakqH2MLsh8r2zScatfQqG8mvwXAvCcseK1g@mail.gmail.com>
 <35780192-BAF2-4F5F-AABB-53142C683BA2@bwh.harvard.edu>
 <CAMpvQ9jhtrQrqgAqvjWFMN_vHkHNM0C4vPd5HkDGTLAC1T9sxg@mail.gmail.com>
 <812F97F8-245D-4EC3-A637-C7166F5C2CA1@bwh.harvard.edu>
 <CAMpvQ9gxALXS2aNdFxQ_5Jn1FAQgMhx3G8XsuSU2Ee8Xf6Gt8Q@mail.gmail.com>
Message-ID: <CAMpvQ9grbH4+m7Ru7HbfXbA=JkxvBQH4+NezR3ERiedZHDb9JA@mail.gmail.com>

If you go to "/etc/apache2/mods-enabled", you can easily find which PHP
version is enabled if after restart Apache2 you still have problem. Please
don't modify source code to remove "?", there should be a lot of them, not
possible to remove all.

On Fri, Feb 21, 2020 at 10:02 AM Ling Ma <lingyun.ma at mcin.ca> wrote:

> Hi Alfredo,
>
> You installed PHP7.2, but you might not use the new version, you might
> need to restart the Apache2, or enable Apache2 to use PHP7.2. Because
> currently your server is still running PHP7.0 or PHP5.6. Because "?" is
> part of PHP7.1
>
> Please check.
>
> Good luck.
>
> Ling Ma
>
> On Fri, Feb 21, 2020 at 9:59 AM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Dear Ling Ma and C?cile,
>>
>> Thank you for the help and tips. After installing php7.2-xml and
>> php7.2-mysql I was able to finish all the steps listed in the upgrade
>> process. I followed this post to upgrade to PHP 7.2:
>> https://medium.com/andrewmmc-io/upgrade-php-version-to-7-2-from-7-0-c005a0926642
>>
>> Now we come back to the first error. Actually, the server is not running
>> right now. I have the following error:
>>
>> ===
>> [Fri Feb 21 09:25:33.848915 2020] [:error] [pid 27936] [client
>> 216.15.126.108:52419] PHP Parse error:  syntax error, unexpected '?',
>> expecting variable (T_VARIABLE) in
>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 49
>> ===
>>
>> After modifying the line 49 in NDB_Client.class.inc from
>>
>> ===
>> function initialize(?string $configFile = null)
>> ===
>>
>> to (removing the ?)
>>
>> ===
>> function initialize(string $configFile = null)
>> ===
>>
>> but I got the following error:
>>
>> ===
>> [Fri Feb 21 09:37:18.042287 2020] [:error] [pid 715] [client
>> 216.15.126.108:52603] PHP Parse error:  syntax error, unexpected '?',
>> expecting variable (T_VARIABLE) in
>> /var/www/loris/php/libraries/NDB_Factory.class.inc on line 109
>> ===
>>
>> Is this an error in the code or I am missing something?
>>
>> Thank you for help.
>>
>> Best,
>> Alfredo.
>>
>> On Feb 19, 2020, at 7:23 PM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>>
>>         External Email - Use Caution
>>
>> Hi Alfredo,
>>
>> Since simplexml_load_file is part of php-xml package, I feel that you
>> need to install php7.2-xml if you are using PHP7.2. In Ubuntu you install
>> this package with apt-get install php7.2-xml, and make sure that this
>> module is enabled in Apache2 if you are using Apache2. You can check which
>> module is enabled via phpinfo() call from a PHP enabled web page, or just
>> check your Apache2 PHP modules, the later is easier.
>>
>> Good luck.
>>
>> Ling Ma
>>
>> On Wed, Feb 19, 2020 at 6:18 PM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>>> Hi Ling Ma,
>>>
>>> Thank you for the information. I would suggest to add this link to each
>>> release, where the upgrading instructions are listed, and also mention
>>> upgrading system requirements if needed.
>>>
>>> Continuing with the upgrade to v21.0.0. I checked that all the system
>>> requirements are met. Now, in having this error when executing
>>> data_dictionary_cleaner.php:
>>>
>>> ===
>>> *lorisadmin at ipmsa-loris*:*/var/www/loris/tools/single_use*$ php
>>> data_dictionary_cleaner.php
>>> PHP Fatal error:  Uncaught Error: Call to undefined function
>>> simplexml_load_file() in
>>> /var/www/loris/php/libraries/NDB_Config.class.inc:96
>>> Stack trace:
>>> #0 /var/www/loris/php/libraries/NDB_Config.class.inc(70):
>>> NDB_Config->load('/var/www/loris/...')
>>> #1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118):
>>> NDB_Config::singleton('/var/www/loris/...')
>>> #2 /var/www/loris/php/libraries/NDB_Client.class.inc(54):
>>> NDB_Factory->config('/var/www/loris/...')
>>> #3 /var/www/loris/tools/generic_includes.php(25):
>>> NDB_Client->initialize('/var/www/loris/...')
>>> #4 /var/www/loris/tools/single_use/data_dictionary_cleaner.php(24):
>>> require_once('/var/www/loris/...')
>>> #5 {main}
>>>   thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 96
>>> ===
>>>
>>> Any ideas on how to solve this?
>>>
>>> Regards,
>>> Alfredo.
>>>
>>> On Feb 19, 2020, at 5:47 PM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>>>
>>>         External Email - Use Caution
>>>
>>> Hi Alfredo,
>>>
>>> If you check this link:
>>>
>>> https://github.com/aces/Loris/blob/21.0-release/README.md
>>>
>>> and
>>>
>>> https://github.com/aces/Loris/blob/22.0-release/README.md
>>>
>>> You will see that the system requires:
>>>
>>> *System Requirements*
>>>
>>>    - Apache *2.4* or higher
>>>    - MySQL >= 5.7 (or MariaDB >= 10.3)
>>>    - PHP *7.2* or higher
>>>    - Composer <https://getcomposer.org/>
>>>    - NodeJS *8.0* or higher
>>>    - NPM
>>>    - make
>>>
>>> Please make sure that you have all the latest or recent versions for
>>> each of them, otherwise you will run into trouble later.
>>>
>>> Ling Ma
>>>
>>> On Wed, Feb 19, 2020 at 5:29 PM Morales Pinzon, Alfredo <
>>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>>
>>>> Hi Ling Ma,
>>>>
>>>> Thank you. I will upgrade to PHP 7.2.
>>>>
>>>> BTW, I cannot find the requirements for PHP for v21, I am looking at
>>>> this link:
>>>>
>>>> https://github.com/aces/Loris/releases/tag/v21.0.0
>>>>
>>>> Regards,
>>>> Alfredo.
>>>>
>>>>
>>>> On Feb 19, 2020, at 5:18 PM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>>>>
>>>>         External Email - Use Caution
>>>>
>>>> Hi Alfredo,
>>>>
>>>> The warning is OK to ignore. As to php, please check v21 version
>>>> requirements, I believe a php minimum 7.1 even 7.2 is required.
>>>>
>>>> In fact, PHP 5.6 is no longer supported.
>>>>
>>>> Best regards,
>>>> Ling Ma
>>>>
>>>> On Wed., Feb. 19, 2020, 5:07 p.m. Morales Pinzon, Alfredo, <
>>>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>>>
>>>>> Dear Ling and C?cile,
>>>>>
>>>>> Thank for your responses.
>>>>>
>>>>> I had an issue with "git checkout?, somehow I had to remove some files
>>>>> before being able to checkout the v21.0.0. That was the reason I didn?t
>>>>> have the make file. Now that I have it, I have some errors:
>>>>>
>>>>> After running ?make? I have the following error:
>>>>>
>>>>> ===
>>>>>     *WARNING in configuration*
>>>>> *    The 'mode' option has not been set, webpack will fallback to
>>>>> 'production' for this value. Set 'mode' option to 'development' or
>>>>> 'production' to enable defaults for each environment.*
>>>>> *    You can also set it to 'none' to disable any default behavior.
>>>>> Learn more: https://webpack.js.org/concepts/mode/
>>>>> <https://webpack.js.org/concepts/mode/>*
>>>>> composer install --no-dev
>>>>> > mkdir -p project/libraries
>>>>> Loading composer repositories with package information
>>>>> Installing dependencies from lock file
>>>>> Your requirements could not be resolved to an installable set of
>>>>> packages.
>>>>>
>>>>>   Problem 1
>>>>>     - Installation request for php-http/guzzle6-adapter v2.0.1 ->
>>>>> satisfiable by php-http/guzzle6-adapter[v2.0.1].
>>>>>     - php-http/guzzle6-adapter v2.0.1 requires php ^7.1 -> your PHP
>>>>> version (7.0.33) does not satisfy that requirement.
>>>>> ===
>>>>>
>>>>> Do I have to upgrade PHP to 7.1?
>>>>>
>>>>> Thank you again for your help.
>>>>>
>>>>> Regards,
>>>>> Alfredo.
>>>>>
>>>>>
>>>>> On Feb 19, 2020, at 12:15 PM, Cecile Madjar <cecile.madjar at mcin.ca>
>>>>> wrote:
>>>>>
>>>>>         External Email - Use Caution
>>>>>
>>>>> Hi Alfredo,
>>>>>
>>>>> Sorry to hear you are experiencing issues with the upgrade to 21.0.0.
>>>>> See below.
>>>>>
>>>>> On Tue, Feb 18, 2020 at 4:31 PM Morales Pinzon, Alfredo <
>>>>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>>>>
>>>>>> Hi C?cile,
>>>>>>
>>>>>> I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and
>>>>>> then to v22.0.0). I had no issues to get to v20.3.0 but now, moving to
>>>>>> v21.0.0, I have two issues:
>>>>>>
>>>>>> 1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS
>>>>>> website. I get a 500 error. Any ideas on what should I check?
>>>>>>
>>>>>
>>>>> Could you send us what you see in the Apache error file for that 500
>>>>> error? Although, might be worth focusing on fixing your second issue before
>>>>> we dive too much into that one.
>>>>>
>>>>>
>>>>>> 2. In the instructions to upgrade to v21.0.0, the second point says:
>>>>>>
>>>>>> "Run make from the Loris root directory to update all dependencies.?"
>>>>>>
>>>>>> However when I run ?make? In the Loris root direction it does
>>>>>> nothing. Here is the result:
>>>>>>
>>>>>> ===
>>>>>> *lorisadmin at ipmsa-loris*:*/var/www/loris*$ make
>>>>>> make: *** No targets specified and no makefile found.  Stop.
>>>>>> ===
>>>>>>
>>>>> It that the right directory? Maybe I am missing some files?
>>>>>>
>>>>>
>>>>> Are you sure you are on the 21.0.0 release of LORIS before you run
>>>>> make? Do you see a Makefile in your /var/www/loris directory? In theory it
>>>>> is supposed to be there on branch 21.0.0 (
>>>>> https://github.com/aces/Loris/tree/v21.0.0)
>>>>>
>>>>> Hope this helps.
>>>>>
>>>>> C?cile
>>>>>
>>>>>
>>>>>> Thank you for your help.
>>>>>>
>>>>>> Best,
>>>>>> Alfredo.
>>>>>>
>>>>>
>>>>>
>>>>> The information in this e-mail is intended only for the person to whom
>>>>> it is
>>>>> addressed. If you believe this e-mail was sent to you in error and the
>>>>> e-mail
>>>>> contains patient information, please contact the Partners Compliance
>>>>> HelpLine at
>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>> you in error
>>>>> but does not contain patient information, please contact the sender
>>>>> and properly
>>>>> dispose of the e-mail.
>>>>>
>>>>
>>>>
>>>
>>
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From AMORALESPINZON at bwh.harvard.edu  Fri Feb 21 17:06:37 2020
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Fri, 21 Feb 2020 22:06:37 +0000
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <CAMpvQ9grbH4+m7Ru7HbfXbA=JkxvBQH4+NezR3ERiedZHDb9JA@mail.gmail.com>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
 <CAMkiY3e1JkHqWt3oMFDGyHsr26F4LPUOS6gO8hzm-nCbCFm7DQ@mail.gmail.com>
 <62049B06-1DB0-4E4C-8610-3BB2D629CE4F@bwh.harvard.edu>
 <CAMpvQ9hN-vTERXCkXtgBVdg+_GEgk4J6cDizJ6vQDpaOy_YAxQ@mail.gmail.com>
 <E2FB11C8-D40E-4754-8D0B-D35FDBFF47DF@bwh.harvard.edu>
 <CAMpvQ9gBuqQCrNJakqH2MLsh8r2zScatfQqG8mvwXAvCcseK1g@mail.gmail.com>
 <35780192-BAF2-4F5F-AABB-53142C683BA2@bwh.harvard.edu>
 <CAMpvQ9jhtrQrqgAqvjWFMN_vHkHNM0C4vPd5HkDGTLAC1T9sxg@mail.gmail.com>
 <812F97F8-245D-4EC3-A637-C7166F5C2CA1@bwh.harvard.edu>
 <CAMpvQ9gxALXS2aNdFxQ_5Jn1FAQgMhx3G8XsuSU2Ee8Xf6Gt8Q@mail.gmail.com>
 <CAMpvQ9grbH4+m7Ru7HbfXbA=JkxvBQH4+NezR3ERiedZHDb9JA@mail.gmail.com>
Message-ID: <39754C63-3409-4E5A-8256-18A045EC5B5E@bwh.harvard.edu>

Hi Ling Ma,

All set regarding php 7.2, is now enable and working. Going back to the error in the website: when I select Imaging -> Imaging Browser I got a 500 error in the front-end and the following error in the server:

===
[Fri Feb 21 12:27:21.231227 2020] [php7:error] [pid 17787] [client 170.223.207.1:46078] PHP Fatal error:  Allowed memory size of 134217728 bytes exhausted (tried to allocate 20480 bytes) in /var/www/loris/php/libraries/Database.class.inc on line 714, referer: https://ipmsa-loris.bic.mni.mcgill.ca/
===

Any ideas?

Thank you in advance.

Best,
Alfredo.

On Feb 21, 2020, at 10:09 AM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:


        External Email - Use Caution

If you go to "/etc/apache2/mods-enabled", you can easily find which PHP version is enabled if after restart Apache2 you still have problem. Please don't modify source code to remove "?", there should be a lot of them, not possible to remove all.

On Fri, Feb 21, 2020 at 10:02 AM Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:
Hi Alfredo,

You installed PHP7.2, but you might not use the new version, you might need to restart the Apache2, or enable Apache2 to use PHP7.2. Because currently your server is still running PHP7.0 or PHP5.6. Because "?" is part of PHP7.1

Please check.

Good luck.

Ling Ma

On Fri, Feb 21, 2020 at 9:59 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear Ling Ma and C?cile,

Thank you for the help and tips. After installing php7.2-xml and php7.2-mysql I was able to finish all the steps listed in the upgrade process. I followed this post to upgrade to PHP 7.2: https://medium.com/andrewmmc-io/upgrade-php-version-to-7-2-from-7-0-c005a0926642

Now we come back to the first error. Actually, the server is not running right now. I have the following error:

===
[Fri Feb 21 09:25:33.848915 2020] [:error] [pid 27936] [client 216.15.126.108:52419<http://216.15.126.108:52419/>] PHP Parse error:  syntax error, unexpected '?', expecting variable (T_VARIABLE) in /var/www/loris/php/libraries/NDB_Client.class.inc on line 49
===

After modifying the line 49 in NDB_Client.class.inc from

===
function initialize(?string $configFile = null)
===

to (removing the ?)

===
function initialize(string $configFile = null)
===

but I got the following error:

===
[Fri Feb 21 09:37:18.042287 2020] [:error] [pid 715] [client 216.15.126.108:52603<http://216.15.126.108:52603/>] PHP Parse error:  syntax error, unexpected '?', expecting variable (T_VARIABLE) in /var/www/loris/php/libraries/NDB_Factory.class.inc on line 109
===

Is this an error in the code or I am missing something?

Thank you for help.

Best,
Alfredo.

On Feb 19, 2020, at 7:23 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Since simplexml_load_file is part of php-xml package, I feel that you need to install php7.2-xml if you are using PHP7.2. In Ubuntu you install this package with apt-get install php7.2-xml, and make sure that this module is enabled in Apache2 if you are using Apache2. You can check which module is enabled via phpinfo() call from a PHP enabled web page, or just check your Apache2 PHP modules, the later is easier.

Good luck.

Ling Ma

On Wed, Feb 19, 2020 at 6:18 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Ling Ma,

Thank you for the information. I would suggest to add this link to each release, where the upgrading instructions are listed, and also mention upgrading system requirements if needed.

Continuing with the upgrade to v21.0.0. I checked that all the system requirements are met. Now, in having this error when executing data_dictionary_cleaner.php:

===
lorisadmin at ipmsa-loris:/var/www/loris/tools/single_use$ php data_dictionary_cleaner.php
PHP Fatal error:  Uncaught Error: Call to undefined function simplexml_load_file() in /var/www/loris/php/libraries/NDB_Config.class.inc:96
Stack trace:
#0 /var/www/loris/php/libraries/NDB_Config.class.inc(70): NDB_Config->load('/var/www/loris/...')
#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton('/var/www/loris/...')
#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config('/var/www/loris/...')
#3 /var/www/loris/tools/generic_includes.php(25): NDB_Client->initialize('/var/www/loris/...')
#4 /var/www/loris/tools/single_use/data_dictionary_cleaner.php(24): require_once('/var/www/loris/...')
#5 {main}
  thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 96
===

Any ideas on how to solve this?

Regards,
Alfredo.

On Feb 19, 2020, at 5:47 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

If you check this link:

https://github.com/aces/Loris/blob/21.0-release/README.md

and

https://github.com/aces/Loris/blob/22.0-release/README.md

You will see that the system requires:

System Requirements

  *   Apache 2.4 or higher
  *   MySQL >= 5.7 (or MariaDB >= 10.3)
  *   PHP 7.2 or higher
  *   Composer<https://getcomposer.org/>
  *   NodeJS 8.0 or higher
  *   NPM
  *   make

Please make sure that you have all the latest or recent versions for each of them, otherwise you will run into trouble later.

Ling Ma

On Wed, Feb 19, 2020 at 5:29 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Ling Ma,

Thank you. I will upgrade to PHP 7.2.

BTW, I cannot find the requirements for PHP for v21, I am looking at this link:

https://github.com/aces/Loris/releases/tag/v21.0.0

Regards,
Alfredo.


On Feb 19, 2020, at 5:18 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

The warning is OK to ignore. As to php, please check v21 version requirements, I believe a php minimum 7.1 even 7.2 is required.

In fact, PHP 5.6 is no longer supported.

Best regards,
Ling Ma

On Wed., Feb. 19, 2020, 5:07 p.m. Morales Pinzon, Alfredo, <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear Ling and C?cile,

Thank for your responses.

I had an issue with "git checkout?, somehow I had to remove some files before being able to checkout the v21.0.0. That was the reason I didn?t have the make file. Now that I have it, I have some errors:

After running ?make? I have the following error:

===
    WARNING in configuration
    The 'mode' option has not been set, webpack will fallback to 'production' for this value. Set 'mode' option to 'development' or 'production' to enable defaults for each environment.
    You can also set it to 'none' to disable any default behavior. Learn more: https://webpack.js.org/concepts/mode/
composer install --no-dev
> mkdir -p project/libraries
Loading composer repositories with package information
Installing dependencies from lock file
Your requirements could not be resolved to an installable set of packages.

  Problem 1
    - Installation request for php-http/guzzle6-adapter v2.0.1 -> satisfiable by php-http/guzzle6-adapter[v2.0.1].
    - php-http/guzzle6-adapter v2.0.1 requires php ^7.1 -> your PHP version (7.0.33) does not satisfy that requirement.
===

Do I have to upgrade PHP to 7.1?

Thank you again for your help.

Regards,
Alfredo.


On Feb 19, 2020, at 12:15 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Sorry to hear you are experiencing issues with the upgrade to 21.0.0. See below.

On Tue, Feb 18, 2020 at 4:31 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and then to v22.0.0). I had no issues to get to v20.3.0 but now, moving to v21.0.0, I have two issues:

1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS website. I get a 500 error. Any ideas on what should I check?

Could you send us what you see in the Apache error file for that 500 error? Although, might be worth focusing on fixing your second issue before we dive too much into that one.

2. In the instructions to upgrade to v21.0.0, the second point says:

"Run make from the Loris root directory to update all dependencies.?"

However when I run ?make? In the Loris root direction it does nothing. Here is the result:

===
lorisadmin at ipmsa-loris:/var/www/loris$ make
make: *** No targets specified and no makefile found.  Stop.
===
It that the right directory? Maybe I am missing some files?

Are you sure you are on the 21.0.0 release of LORIS before you run make? Do you see a Makefile in your /var/www/loris directory? In theory it is supposed to be there on branch 21.0.0 (https://github.com/aces/Loris/tree/v21.0.0)

Hope this helps.

C?cile


Thank you for your help.

Best,
Alfredo.



The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.




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From lingyun.ma at mcin.ca  Fri Feb 21 17:12:51 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Fri, 21 Feb 2020 17:12:51 -0500
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <39754C63-3409-4E5A-8256-18A045EC5B5E@bwh.harvard.edu>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
 <CAMkiY3e1JkHqWt3oMFDGyHsr26F4LPUOS6gO8hzm-nCbCFm7DQ@mail.gmail.com>
 <62049B06-1DB0-4E4C-8610-3BB2D629CE4F@bwh.harvard.edu>
 <CAMpvQ9hN-vTERXCkXtgBVdg+_GEgk4J6cDizJ6vQDpaOy_YAxQ@mail.gmail.com>
 <E2FB11C8-D40E-4754-8D0B-D35FDBFF47DF@bwh.harvard.edu>
 <CAMpvQ9gBuqQCrNJakqH2MLsh8r2zScatfQqG8mvwXAvCcseK1g@mail.gmail.com>
 <35780192-BAF2-4F5F-AABB-53142C683BA2@bwh.harvard.edu>
 <CAMpvQ9jhtrQrqgAqvjWFMN_vHkHNM0C4vPd5HkDGTLAC1T9sxg@mail.gmail.com>
 <812F97F8-245D-4EC3-A637-C7166F5C2CA1@bwh.harvard.edu>
 <CAMpvQ9gxALXS2aNdFxQ_5Jn1FAQgMhx3G8XsuSU2Ee8Xf6Gt8Q@mail.gmail.com>
 <CAMpvQ9grbH4+m7Ru7HbfXbA=JkxvBQH4+NezR3ERiedZHDb9JA@mail.gmail.com>
 <39754C63-3409-4E5A-8256-18A045EC5B5E@bwh.harvard.edu>
Message-ID: <CAMpvQ9iBBdv32M=KpST+BOqz0hKbe2X5BZ6eSaVaG64+5KQfVg@mail.gmail.com>

Evidently the RAM is not enough, I am outside, I don't have the recommended
value for you. You can check document for how much. I would recommend to
increase the PHP memory allowance. Try to check PHP document for that,
otherwise I can check later. Or maybe any other people knows better on this
subject could help you.

Good weekend.

Ling

On Fri., Feb. 21, 2020, 5:06 p.m. Morales Pinzon, Alfredo, <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi Ling Ma,
>
> All set regarding php 7.2, is now enable and working. Going back to the
> error in the website: when I select Imaging -> Imaging Browser I got a 500
> error in the front-end and the following error in the server:
>
> ===
> [Fri Feb 21 12:27:21.231227 2020] [php7:error] [pid 17787] [client
> 170.223.207.1:46078] PHP Fatal error:  Allowed memory size of 134217728
> bytes exhausted (tried to allocate 20480 bytes) in
> /var/www/loris/php/libraries/Database.class.inc on line 714, referer:
> https://ipmsa-loris.bic.mni.mcgill.ca/
> ===
>
> Any ideas?
>
> Thank you in advance.
>
> Best,
> Alfredo.
>
> On Feb 21, 2020, at 10:09 AM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> If you go to "/etc/apache2/mods-enabled", you can easily find which PHP
> version is enabled if after restart Apache2 you still have problem. Please
> don't modify source code to remove "?", there should be a lot of them, not
> possible to remove all.
>
> On Fri, Feb 21, 2020 at 10:02 AM Ling Ma <lingyun.ma at mcin.ca> wrote:
>
>> Hi Alfredo,
>>
>> You installed PHP7.2, but you might not use the new version, you might
>> need to restart the Apache2, or enable Apache2 to use PHP7.2. Because
>> currently your server is still running PHP7.0 or PHP5.6. Because "?" is
>> part of PHP7.1
>>
>> Please check.
>>
>> Good luck.
>>
>> Ling Ma
>>
>> On Fri, Feb 21, 2020 at 9:59 AM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>>> Dear Ling Ma and C?cile,
>>>
>>> Thank you for the help and tips. After installing php7.2-xml and
>>> php7.2-mysql I was able to finish all the steps listed in the upgrade
>>> process. I followed this post to upgrade to PHP 7.2:
>>> https://medium.com/andrewmmc-io/upgrade-php-version-to-7-2-from-7-0-c005a0926642
>>>
>>> Now we come back to the first error. Actually, the server is not running
>>> right now. I have the following error:
>>>
>>> ===
>>> [Fri Feb 21 09:25:33.848915 2020] [:error] [pid 27936] [client
>>> 216.15.126.108:52419] PHP Parse error:  syntax error, unexpected '?',
>>> expecting variable (T_VARIABLE) in
>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 49
>>> ===
>>>
>>> After modifying the line 49 in NDB_Client.class.inc from
>>>
>>> ===
>>> function initialize(?string $configFile = null)
>>> ===
>>>
>>> to (removing the ?)
>>>
>>> ===
>>> function initialize(string $configFile = null)
>>> ===
>>>
>>> but I got the following error:
>>>
>>> ===
>>> [Fri Feb 21 09:37:18.042287 2020] [:error] [pid 715] [client
>>> 216.15.126.108:52603] PHP Parse error:  syntax error, unexpected '?',
>>> expecting variable (T_VARIABLE) in
>>> /var/www/loris/php/libraries/NDB_Factory.class.inc on line 109
>>> ===
>>>
>>> Is this an error in the code or I am missing something?
>>>
>>> Thank you for help.
>>>
>>> Best,
>>> Alfredo.
>>>
>>> On Feb 19, 2020, at 7:23 PM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>>>
>>>         External Email - Use Caution
>>>
>>> Hi Alfredo,
>>>
>>> Since simplexml_load_file is part of php-xml package, I feel that you
>>> need to install php7.2-xml if you are using PHP7.2. In Ubuntu you install
>>> this package with apt-get install php7.2-xml, and make sure that this
>>> module is enabled in Apache2 if you are using Apache2. You can check which
>>> module is enabled via phpinfo() call from a PHP enabled web page, or just
>>> check your Apache2 PHP modules, the later is easier.
>>>
>>> Good luck.
>>>
>>> Ling Ma
>>>
>>> On Wed, Feb 19, 2020 at 6:18 PM Morales Pinzon, Alfredo <
>>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>>
>>>> Hi Ling Ma,
>>>>
>>>> Thank you for the information. I would suggest to add this link to each
>>>> release, where the upgrading instructions are listed, and also mention
>>>> upgrading system requirements if needed.
>>>>
>>>> Continuing with the upgrade to v21.0.0. I checked that all the system
>>>> requirements are met. Now, in having this error when executing
>>>> data_dictionary_cleaner.php:
>>>>
>>>> ===
>>>> *lorisadmin at ipmsa-loris*:*/var/www/loris/tools/single_use*$ php
>>>> data_dictionary_cleaner.php
>>>> PHP Fatal error:  Uncaught Error: Call to undefined function
>>>> simplexml_load_file() in
>>>> /var/www/loris/php/libraries/NDB_Config.class.inc:96
>>>> Stack trace:
>>>> #0 /var/www/loris/php/libraries/NDB_Config.class.inc(70):
>>>> NDB_Config->load('/var/www/loris/...')
>>>> #1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118):
>>>> NDB_Config::singleton('/var/www/loris/...')
>>>> #2 /var/www/loris/php/libraries/NDB_Client.class.inc(54):
>>>> NDB_Factory->config('/var/www/loris/...')
>>>> #3 /var/www/loris/tools/generic_includes.php(25):
>>>> NDB_Client->initialize('/var/www/loris/...')
>>>> #4 /var/www/loris/tools/single_use/data_dictionary_cleaner.php(24):
>>>> require_once('/var/www/loris/...')
>>>> #5 {main}
>>>>   thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 96
>>>> ===
>>>>
>>>> Any ideas on how to solve this?
>>>>
>>>> Regards,
>>>> Alfredo.
>>>>
>>>> On Feb 19, 2020, at 5:47 PM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>>>>
>>>>         External Email - Use Caution
>>>>
>>>> Hi Alfredo,
>>>>
>>>> If you check this link:
>>>>
>>>> https://github.com/aces/Loris/blob/21.0-release/README.md
>>>>
>>>> and
>>>>
>>>> https://github.com/aces/Loris/blob/22.0-release/README.md
>>>>
>>>> You will see that the system requires:
>>>>
>>>> *System Requirements*
>>>>
>>>>    - Apache *2.4* or higher
>>>>    - MySQL >= 5.7 (or MariaDB >= 10.3)
>>>>    - PHP *7.2* or higher
>>>>    - Composer <https://getcomposer.org/>
>>>>    - NodeJS *8.0* or higher
>>>>    - NPM
>>>>    - make
>>>>
>>>> Please make sure that you have all the latest or recent versions for
>>>> each of them, otherwise you will run into trouble later.
>>>>
>>>> Ling Ma
>>>>
>>>> On Wed, Feb 19, 2020 at 5:29 PM Morales Pinzon, Alfredo <
>>>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>>>
>>>>> Hi Ling Ma,
>>>>>
>>>>> Thank you. I will upgrade to PHP 7.2.
>>>>>
>>>>> BTW, I cannot find the requirements for PHP for v21, I am looking at
>>>>> this link:
>>>>>
>>>>> https://github.com/aces/Loris/releases/tag/v21.0.0
>>>>>
>>>>> Regards,
>>>>> Alfredo.
>>>>>
>>>>>
>>>>> On Feb 19, 2020, at 5:18 PM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>>>>>
>>>>>         External Email - Use Caution
>>>>>
>>>>> Hi Alfredo,
>>>>>
>>>>> The warning is OK to ignore. As to php, please check v21 version
>>>>> requirements, I believe a php minimum 7.1 even 7.2 is required.
>>>>>
>>>>> In fact, PHP 5.6 is no longer supported.
>>>>>
>>>>> Best regards,
>>>>> Ling Ma
>>>>>
>>>>> On Wed., Feb. 19, 2020, 5:07 p.m. Morales Pinzon, Alfredo, <
>>>>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>>>>
>>>>>> Dear Ling and C?cile,
>>>>>>
>>>>>> Thank for your responses.
>>>>>>
>>>>>> I had an issue with "git checkout?, somehow I had to remove some
>>>>>> files before being able to checkout the v21.0.0. That was the reason I
>>>>>> didn?t have the make file. Now that I have it, I have some errors:
>>>>>>
>>>>>> After running ?make? I have the following error:
>>>>>>
>>>>>> ===
>>>>>>     *WARNING in configuration*
>>>>>> *    The 'mode' option has not been set, webpack will fallback to
>>>>>> 'production' for this value. Set 'mode' option to 'development' or
>>>>>> 'production' to enable defaults for each environment.*
>>>>>> *    You can also set it to 'none' to disable any default behavior.
>>>>>> Learn more: https://webpack.js.org/concepts/mode/
>>>>>> <https://webpack.js.org/concepts/mode/>*
>>>>>> composer install --no-dev
>>>>>> > mkdir -p project/libraries
>>>>>> Loading composer repositories with package information
>>>>>> Installing dependencies from lock file
>>>>>> Your requirements could not be resolved to an installable set of
>>>>>> packages.
>>>>>>
>>>>>>   Problem 1
>>>>>>     - Installation request for php-http/guzzle6-adapter v2.0.1 ->
>>>>>> satisfiable by php-http/guzzle6-adapter[v2.0.1].
>>>>>>     - php-http/guzzle6-adapter v2.0.1 requires php ^7.1 -> your PHP
>>>>>> version (7.0.33) does not satisfy that requirement.
>>>>>> ===
>>>>>>
>>>>>> Do I have to upgrade PHP to 7.1?
>>>>>>
>>>>>> Thank you again for your help.
>>>>>>
>>>>>> Regards,
>>>>>> Alfredo.
>>>>>>
>>>>>>
>>>>>> On Feb 19, 2020, at 12:15 PM, Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>> wrote:
>>>>>>
>>>>>>         External Email - Use Caution
>>>>>>
>>>>>> Hi Alfredo,
>>>>>>
>>>>>> Sorry to hear you are experiencing issues with the upgrade to 21.0.0.
>>>>>> See below.
>>>>>>
>>>>>> On Tue, Feb 18, 2020 at 4:31 PM Morales Pinzon, Alfredo <
>>>>>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>>>>>
>>>>>>> Hi C?cile,
>>>>>>>
>>>>>>> I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and
>>>>>>> then to v22.0.0). I had no issues to get to v20.3.0 but now, moving to
>>>>>>> v21.0.0, I have two issues:
>>>>>>>
>>>>>>> 1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS
>>>>>>> website. I get a 500 error. Any ideas on what should I check?
>>>>>>>
>>>>>>
>>>>>> Could you send us what you see in the Apache error file for that 500
>>>>>> error? Although, might be worth focusing on fixing your second issue before
>>>>>> we dive too much into that one.
>>>>>>
>>>>>>
>>>>>>> 2. In the instructions to upgrade to v21.0.0, the second point says:
>>>>>>>
>>>>>>> "Run make from the Loris root directory to update all dependencies.
>>>>>>> ?"
>>>>>>>
>>>>>>> However when I run ?make? In the Loris root direction it does
>>>>>>> nothing. Here is the result:
>>>>>>>
>>>>>>> ===
>>>>>>> *lorisadmin at ipmsa-loris*:*/var/www/loris*$ make
>>>>>>> make: *** No targets specified and no makefile found.  Stop.
>>>>>>> ===
>>>>>>>
>>>>>> It that the right directory? Maybe I am missing some files?
>>>>>>>
>>>>>>
>>>>>> Are you sure you are on the 21.0.0 release of LORIS before you run
>>>>>> make? Do you see a Makefile in your /var/www/loris directory? In theory it
>>>>>> is supposed to be there on branch 21.0.0 (
>>>>>> https://github.com/aces/Loris/tree/v21.0.0)
>>>>>>
>>>>>> Hope this helps.
>>>>>>
>>>>>> C?cile
>>>>>>
>>>>>>
>>>>>>> Thank you for your help.
>>>>>>>
>>>>>>> Best,
>>>>>>> Alfredo.
>>>>>>>
>>>>>>
>>>>>>
>>>>>> The information in this e-mail is intended only for the person to
>>>>>> whom it is
>>>>>> addressed. If you believe this e-mail was sent to you in error and
>>>>>> the e-mail
>>>>>> contains patient information, please contact the Partners Compliance
>>>>>> HelpLine at
>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>> you in error
>>>>>> but does not contain patient information, please contact the sender
>>>>>> and properly
>>>>>> dispose of the e-mail.
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>
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From melanie.legault2 at mcgill.ca  Mon Feb 24 07:32:12 2020
From: melanie.legault2 at mcgill.ca (Melanie Legault, Mrs)
Date: Mon, 24 Feb 2020 12:32:12 +0000
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <CAMpvQ9iBBdv32M=KpST+BOqz0hKbe2X5BZ6eSaVaG64+5KQfVg@mail.gmail.com>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
 <CAMkiY3e1JkHqWt3oMFDGyHsr26F4LPUOS6gO8hzm-nCbCFm7DQ@mail.gmail.com>
 <62049B06-1DB0-4E4C-8610-3BB2D629CE4F@bwh.harvard.edu>
 <CAMpvQ9hN-vTERXCkXtgBVdg+_GEgk4J6cDizJ6vQDpaOy_YAxQ@mail.gmail.com>
 <E2FB11C8-D40E-4754-8D0B-D35FDBFF47DF@bwh.harvard.edu>
 <CAMpvQ9gBuqQCrNJakqH2MLsh8r2zScatfQqG8mvwXAvCcseK1g@mail.gmail.com>
 <35780192-BAF2-4F5F-AABB-53142C683BA2@bwh.harvard.edu>
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 <812F97F8-245D-4EC3-A637-C7166F5C2CA1@bwh.harvard.edu>
 <CAMpvQ9gxALXS2aNdFxQ_5Jn1FAQgMhx3G8XsuSU2Ee8Xf6Gt8Q@mail.gmail.com>
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 <39754C63-3409-4E5A-8256-18A045EC5B5E@bwh.harvard.edu>,
 <CAMpvQ9iBBdv32M=KpST+BOqz0hKbe2X5BZ6eSaVaG64+5KQfVg@mail.gmail.com>
Message-ID: <YTXPR0101MB1616132205D82F8EA74E1BA8CFEC0@YTXPR0101MB1616.CANPRD01.PROD.OUTLOOK.COM>

Hello Alfredo,

You may find which parameters you need to change in php.ini file to handle large file in https://github.com/aces/Loris/blob/master/docs/wiki/00%20-%20SERVER%20INSTALL%20AND%20CONFIGURATION/02%20-%20Website%20Configuration/Handling%20Large%20File%20Uploads.md

A restart of the Apache server will be needed after updating the file.

Regards,


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 Ling Ma <lingyun.ma at mcin.ca>
Sent: February 21, 2020 17:12
To: Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu>
Cc: Sridar Narayanan, Dr. <sridar.narayanan at mcgill.ca>; loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>; Rozie Arnaoutelis, Ms. <rozie.arnaoutelis at mcgill.ca>; Zografos Caramanos, Mr <zografos.caramanos at mcgill.ca>; Douglas Arnold, Dr. <douglas.arnold at mcgill.ca>; Guttmann, Charles, M.D. <guttmann at bwh.harvard.edu>
Subject: Re: [Loris-dev] Update LORIS to v21.0.0

Evidently the RAM is not enough, I am outside, I don't have the recommended value for you. You can check document for how much. I would recommend to increase the PHP memory allowance. Try to check PHP document for that, otherwise I can check later. Or maybe any other people knows better on this subject could help you.

Good weekend.

Ling

On Fri., Feb. 21, 2020, 5:06 p.m. Morales Pinzon, Alfredo, <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Ling Ma,

All set regarding php 7.2, is now enable and working. Going back to the error in the website: when I select Imaging -> Imaging Browser I got a 500 error in the front-end and the following error in the server:

===
[Fri Feb 21 12:27:21.231227 2020] [php7:error] [pid 17787] [client 170.223.207.1:46078<http://170.223.207.1:46078>] PHP Fatal error:  Allowed memory size of 134217728 bytes exhausted (tried to allocate 20480 bytes) in /var/www/loris/php/libraries/Database.class.inc on line 714, referer: https://ipmsa-loris.bic.mni.mcgill.ca/
===

Any ideas?

Thank you in advance.

Best,
Alfredo.

On Feb 21, 2020, at 10:09 AM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:


        External Email - Use Caution

If you go to "/etc/apache2/mods-enabled", you can easily find which PHP version is enabled if after restart Apache2 you still have problem. Please don't modify source code to remove "?", there should be a lot of them, not possible to remove all.

On Fri, Feb 21, 2020 at 10:02 AM Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:
Hi Alfredo,

You installed PHP7.2, but you might not use the new version, you might need to restart the Apache2, or enable Apache2 to use PHP7.2. Because currently your server is still running PHP7.0 or PHP5.6. Because "?" is part of PHP7.1

Please check.

Good luck.

Ling Ma

On Fri, Feb 21, 2020 at 9:59 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear Ling Ma and C?cile,

Thank you for the help and tips. After installing php7.2-xml and php7.2-mysql I was able to finish all the steps listed in the upgrade process. I followed this post to upgrade to PHP 7.2: https://medium.com/andrewmmc-io/upgrade-php-version-to-7-2-from-7-0-c005a0926642

Now we come back to the first error. Actually, the server is not running right now. I have the following error:

===
[Fri Feb 21 09:25:33.848915 2020] [:error] [pid 27936] [client 216.15.126.108:52419<http://216.15.126.108:52419/>] PHP Parse error:  syntax error, unexpected '?', expecting variable (T_VARIABLE) in /var/www/loris/php/libraries/NDB_Client.class.inc on line 49
===

After modifying the line 49 in NDB_Client.class.inc from

===
function initialize(?string $configFile = null)
===

to (removing the ?)

===
function initialize(string $configFile = null)
===

but I got the following error:

===
[Fri Feb 21 09:37:18.042287 2020] [:error] [pid 715] [client 216.15.126.108:52603<http://216.15.126.108:52603/>] PHP Parse error:  syntax error, unexpected '?', expecting variable (T_VARIABLE) in /var/www/loris/php/libraries/NDB_Factory.class.inc on line 109
===

Is this an error in the code or I am missing something?

Thank you for help.

Best,
Alfredo.

On Feb 19, 2020, at 7:23 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Since simplexml_load_file is part of php-xml package, I feel that you need to install php7.2-xml if you are using PHP7.2. In Ubuntu you install this package with apt-get install php7.2-xml, and make sure that this module is enabled in Apache2 if you are using Apache2. You can check which module is enabled via phpinfo() call from a PHP enabled web page, or just check your Apache2 PHP modules, the later is easier.

Good luck.

Ling Ma

On Wed, Feb 19, 2020 at 6:18 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Ling Ma,

Thank you for the information. I would suggest to add this link to each release, where the upgrading instructions are listed, and also mention upgrading system requirements if needed.

Continuing with the upgrade to v21.0.0. I checked that all the system requirements are met. Now, in having this error when executing data_dictionary_cleaner.php:

===
lorisadmin at ipmsa-loris:/var/www/loris/tools/single_use$ php data_dictionary_cleaner.php
PHP Fatal error:  Uncaught Error: Call to undefined function simplexml_load_file() in /var/www/loris/php/libraries/NDB_Config.class.inc:96
Stack trace:
#0 /var/www/loris/php/libraries/NDB_Config.class.inc(70): NDB_Config->load('/var/www/loris/...')
#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton('/var/www/loris/...')
#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config('/var/www/loris/...')
#3 /var/www/loris/tools/generic_includes.php(25): NDB_Client->initialize('/var/www/loris/...')
#4 /var/www/loris/tools/single_use/data_dictionary_cleaner.php(24): require_once('/var/www/loris/...')
#5 {main}
  thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 96
===

Any ideas on how to solve this?

Regards,
Alfredo.

On Feb 19, 2020, at 5:47 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

If you check this link:

https://github.com/aces/Loris/blob/21.0-release/README.md

and

https://github.com/aces/Loris/blob/22.0-release/README.md

You will see that the system requires:

System Requirements

  *   Apache 2.4 or higher
  *   MySQL >= 5.7 (or MariaDB >= 10.3)
  *   PHP 7.2 or higher
  *   Composer<https://getcomposer.org/>
  *   NodeJS 8.0 or higher
  *   NPM
  *   make

Please make sure that you have all the latest or recent versions for each of them, otherwise you will run into trouble later.

Ling Ma

On Wed, Feb 19, 2020 at 5:29 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Ling Ma,

Thank you. I will upgrade to PHP 7.2.

BTW, I cannot find the requirements for PHP for v21, I am looking at this link:

https://github.com/aces/Loris/releases/tag/v21.0.0

Regards,
Alfredo.


On Feb 19, 2020, at 5:18 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

The warning is OK to ignore. As to php, please check v21 version requirements, I believe a php minimum 7.1 even 7.2 is required.

In fact, PHP 5.6 is no longer supported.

Best regards,
Ling Ma

On Wed., Feb. 19, 2020, 5:07 p.m. Morales Pinzon, Alfredo, <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear Ling and C?cile,

Thank for your responses.

I had an issue with "git checkout?, somehow I had to remove some files before being able to checkout the v21.0.0. That was the reason I didn?t have the make file. Now that I have it, I have some errors:

After running ?make? I have the following error:

===
    WARNING in configuration
    The 'mode' option has not been set, webpack will fallback to 'production' for this value. Set 'mode' option to 'development' or 'production' to enable defaults for each environment.
    You can also set it to 'none' to disable any default behavior. Learn more: https://webpack.js.org/concepts/mode/
composer install --no-dev
> mkdir -p project/libraries
Loading composer repositories with package information
Installing dependencies from lock file
Your requirements could not be resolved to an installable set of packages.

  Problem 1
    - Installation request for php-http/guzzle6-adapter v2.0.1 -> satisfiable by php-http/guzzle6-adapter[v2.0.1].
    - php-http/guzzle6-adapter v2.0.1 requires php ^7.1 -> your PHP version (7.0.33) does not satisfy that requirement.
===

Do I have to upgrade PHP to 7.1?

Thank you again for your help.

Regards,
Alfredo.


On Feb 19, 2020, at 12:15 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Sorry to hear you are experiencing issues with the upgrade to 21.0.0. See below.

On Tue, Feb 18, 2020 at 4:31 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and then to v22.0.0). I had no issues to get to v20.3.0 but now, moving to v21.0.0, I have two issues:

1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS website. I get a 500 error. Any ideas on what should I check?

Could you send us what you see in the Apache error file for that 500 error? Although, might be worth focusing on fixing your second issue before we dive too much into that one.

2. In the instructions to upgrade to v21.0.0, the second point says:

"Run make from the Loris root directory to update all dependencies.?"

However when I run ?make? In the Loris root direction it does nothing. Here is the result:

===
lorisadmin at ipmsa-loris:/var/www/loris$ make
make: *** No targets specified and no makefile found.  Stop.
===
It that the right directory? Maybe I am missing some files?

Are you sure you are on the 21.0.0 release of LORIS before you run make? Do you see a Makefile in your /var/www/loris directory? In theory it is supposed to be there on branch 21.0.0 (https://github.com/aces/Loris/tree/v21.0.0)

Hope this helps.

C?cile


Thank you for your help.

Best,
Alfredo.



The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.




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From christine.rogers at mcgill.ca  Mon Feb 24 13:22:47 2020
From: christine.rogers at mcgill.ca (Christine Rogers, Ms.)
Date: Mon, 24 Feb 2020 18:22:47 +0000
Subject: [Loris-dev] Troubleshooting Imaging Browser not loading for 22.0.0
	release
Message-ID: <CALbt7NDvsQ5uu2rB4Nex-qx6vQF9UJAyq99C=j2DCVMvfSObLw@mail.gmail.com>

Hi Loris team and community,
i'm forwarding a question from Blake (below) from Max Planck in Tuebingen --he's encountering a (known) bug in the 22.0.0 Imaging Browser where the module doesn't load (issue #6088)

His apache error log output is below.
Blake is running Ubuntu and has installed 22.0.0, and uploaded some test DICOMs.  He's applied the proposed bugfix #6089, without success (see below).

Could someone help resolve / share a solution for this ?
Thanks,
Christine

---------- Forwarded message ---------
From: Blake Fitch <blake.fitch at tuebingen.mpg.de<mailto:blake.fitch at tuebingen.mpg.de>>
Date: Fri, Feb 21, 2020 at 11:11 AM
Subject: Re: Fix for Imaging Browser not loading
To: Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>>



Hi Christine,

I did the new patch. Looks the same. here's there error log entry that pops out.

[Fri Feb 21 16:09:51.361760 2020] [php7:warn] [pid 25261] [client 10.38.124.254:55712<http://10.38.124.254:55712>] PHP Warning:  PDOStatement::execute(): SQLSTATE[42000]: Syntax error or access violation: 1064 You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '//              \n            CASE \n                WHEN s.MRIQCPending='Y' THEN ' at line 30 in /var/www/loris/src/Data/Provisioners/DBRowProvisioner.php on line 81, referer: http://10.38.133.3/imaging_browser/
[Fri Feb 21 16:09:51.361873 2020] [php7:error] [pid 25261] [client 10.38.124.254:55712<http://10.38.124.254:55712>] PHP Fatal error:  Uncaught Exception: Invalid SQL statement: SELECT \n              p.Name as Site,\n              c.PSCID as PSCID,\n              c.CandID as DCCID,\n              Project.Name as project,\n              s.Visit_label as visitLabel,\n              \n            CASE s.MRIQCStatus\n                WHEN 'Fail' THEN\n                    IF(s.MRIQCPending='Y', 'Pending Fail', 'Fail')\n                WHEN 'Pass' THEN\n                    IF(s.MRIQCPending='Y', 'Pending Pass', 'Pass') \n                ELSE s.MRIQCStatus\n            END \n             as Visit_QC_Status,\n              DATE_FORMAT(MIN(pf.Value), "%Y-%m-%d") as First_Acquisition,\n              FROM_UNIXTIME(MIN(f.InsertTime)) as First_Insertion,\n              FROM_UNIXTIME(MAX(fqc.QCLastChangeTime)) as Last_QC,\n              \n            CASE \n                COALESCE(Max(fqc.QCLastChangeTime), 'new')\n                WHEN 'new' THEN 'new'\n                WHEN ''    THEN 'new'\n                WHEN NULL  THEN 'new'\n                ELSE ''\n            END as New_Da in /var/www/loris/src/Data/Provisioners/DBRowProvisioner.php on line 84, referer: http://10.38.133.3/imaging_browser/

Best,
Blake

On 21.02.20 17:05, Christine Rogers, Ms. wrote:
... bugfix --  updated here:
 https://github.com/aces/Loris/commit/f62edcb1c1af07328f4b34e8051fba1a6fb12ff5



--

christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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From christine.rogers at mcgill.ca  Mon Feb 24 13:33:35 2020
From: christine.rogers at mcgill.ca (Christine Rogers, Ms.)
Date: Mon, 24 Feb 2020 18:33:35 +0000
Subject: [Loris-dev] Troubleshooting Imaging Browser not loading for
 22.0.0 release
In-Reply-To: <CALbt7NDvsQ5uu2rB4Nex-qx6vQF9UJAyq99C=j2DCVMvfSObLw@mail.gmail.com>
References: <CALbt7NDvsQ5uu2rB4Nex-qx6vQF9UJAyq99C=j2DCVMvfSObLw@mail.gmail.com>
Message-ID: <CALbt7NCe3wMOTVFoWu_7S7nRdBMm7yAwU_Do+t6+WLAj59mJPw@mail.gmail.com>

Hi Blake,
First/next troubleshooting question --

Could you verify you're using the latest update from this bugfix:
https://github.com/aces/Loris/pull/6089/commits/c78af4ebc97d354b6820c51c8bb746e0e0e554f5

This may resolve it, let us know --
Thanks,
Christine

On Mon, Feb 24, 2020 at 1:23 PM Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>> wrote:
Hi Loris team and community,
i'm forwarding a question from Blake (below) from Max Planck in Tuebingen --he's encountering a (known) bug in the 22.0.0 Imaging Browser where the module doesn't load (issue #6088)

His apache error log output is below.
Blake is running Ubuntu and has installed 22.0.0, and uploaded some test DICOMs.  He's applied the proposed bugfix #6089, without success (see below).

Could someone help resolve / share a solution for this ?
Thanks,
Christine

---------- Forwarded message ---------
From: Blake Fitch <blake.fitch at tuebingen.mpg.de<mailto:blake.fitch at tuebingen.mpg.de>>
Date: Fri, Feb 21, 2020 at 11:11 AM
Subject: Re: Fix for Imaging Browser not loading
To: Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>>



Hi Christine,

I did the new patch. Looks the same. here's there error log entry that pops out.

[Fri Feb 21 16:09:51.361760 2020] [php7:warn] [pid 25261] [client 10.38.124.254:55712<http://10.38.124.254:55712>] PHP Warning:  PDOStatement::execute(): SQLSTATE[42000]: Syntax error or access violation: 1064 You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '//              \n            CASE \n                WHEN s.MRIQCPending='Y' THEN ' at line 30 in /var/www/loris/src/Data/Provisioners/DBRowProvisioner.php on line 81, referer: http://10.38.133.3/imaging_browser/
[Fri Feb 21 16:09:51.361873 2020] [php7:error] [pid 25261] [client 10.38.124.254:55712<http://10.38.124.254:55712>] PHP Fatal error:  Uncaught Exception: Invalid SQL statement: SELECT \n              p.Name as Site,\n              c.PSCID as PSCID,\n              c.CandID as DCCID,\n              Project.Name as project,\n              s.Visit_label as visitLabel,\n              \n            CASE s.MRIQCStatus\n                WHEN 'Fail' THEN\n                    IF(s.MRIQCPending='Y', 'Pending Fail', 'Fail')\n                WHEN 'Pass' THEN\n                    IF(s.MRIQCPending='Y', 'Pending Pass', 'Pass') \n                ELSE s.MRIQCStatus\n            END \n             as Visit_QC_Status,\n              DATE_FORMAT(MIN(pf.Value), "%Y-%m-%d") as First_Acquisition,\n              FROM_UNIXTIME(MIN(f.InsertTime)) as First_Insertion,\n              FROM_UNIXTIME(MAX(fqc.QCLastChangeTime)) as Last_QC,\n              \n            CASE \n                COALESCE(Max(fqc.QCLastChangeTime), 'new')\n                WHEN 'new' THEN 'new'\n                WHEN ''    THEN 'new'\n                WHEN NULL  THEN 'new'\n                ELSE ''\n            END as New_Da in /var/www/loris/src/Data/Provisioners/DBRowProvisioner.php on line 84, referer: http://10.38.133.3/imaging_browser/

Best,
Blake


--

christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
_______________________________________________
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https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev


--

christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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From AMORALESPINZON at bwh.harvard.edu  Mon Feb 24 17:53:56 2020
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Mon, 24 Feb 2020 22:53:56 +0000
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <YTXPR0101MB1616132205D82F8EA74E1BA8CFEC0@YTXPR0101MB1616.CANPRD01.PROD.OUTLOOK.COM>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
 <CAMkiY3e1JkHqWt3oMFDGyHsr26F4LPUOS6gO8hzm-nCbCFm7DQ@mail.gmail.com>
 <62049B06-1DB0-4E4C-8610-3BB2D629CE4F@bwh.harvard.edu>
 <CAMpvQ9hN-vTERXCkXtgBVdg+_GEgk4J6cDizJ6vQDpaOy_YAxQ@mail.gmail.com>
 <E2FB11C8-D40E-4754-8D0B-D35FDBFF47DF@bwh.harvard.edu>
 <CAMpvQ9gBuqQCrNJakqH2MLsh8r2zScatfQqG8mvwXAvCcseK1g@mail.gmail.com>
 <35780192-BAF2-4F5F-AABB-53142C683BA2@bwh.harvard.edu>
 <CAMpvQ9jhtrQrqgAqvjWFMN_vHkHNM0C4vPd5HkDGTLAC1T9sxg@mail.gmail.com>
 <812F97F8-245D-4EC3-A637-C7166F5C2CA1@bwh.harvard.edu>
 <CAMpvQ9gxALXS2aNdFxQ_5Jn1FAQgMhx3G8XsuSU2Ee8Xf6Gt8Q@mail.gmail.com>
 <CAMpvQ9grbH4+m7Ru7HbfXbA=JkxvBQH4+NezR3ERiedZHDb9JA@mail.gmail.com>
 <39754C63-3409-4E5A-8256-18A045EC5B5E@bwh.harvard.edu>
 <CAMpvQ9iBBdv32M=KpST+BOqz0hKbe2X5BZ6eSaVaG64+5KQfVg@mail.gmail.com>
 <YTXPR0101MB1616132205D82F8EA74E1BA8CFEC0@YTXPR0101MB1616.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <D7CCD4F8-3CE4-4DE8-B0DF-07622FC08D79@bwh.harvard.edu>

Dear Melanie and Ling Ma,

I made the suggested changes in the link that Melanie sent but the error was still appearing. It turned out that the proper parameter to set was ?memory_limit?. I set it like this:

memory_limit = 150M

Now the imaging link is working.

Thank you for your help.

Regards,
Alfredo.

On Feb 24, 2020, at 7:32 AM, Melanie Legault, Mrs <melanie.legault2 at mcgill.ca<mailto:melanie.legault2 at mcgill.ca>> wrote:

        External Email - Use Caution

Hello Alfredo,

You may find which parameters you need to change in php.ini file to handle large file inhttps://github.com/aces/Loris/blob/master/docs/wiki/00%20-%20SERVER%20INSTALL%20AND%20CONFIGURATION/02%20-%20Website%20Configuration/Handling%20Large%20File%20Uploads.md

A restart of the Apache server will be needed after updating the file.

Regards,

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<mailto:loris-dev-bounces at bic.mni.mcgill.ca> <loris-dev-bounces at bic.mni.mcgill.ca<mailto:loris-dev-bounces at bic.mni.mcgill.ca>> on behalf of Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>>
Sent: February 21, 2020 17:12
To: Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>>
Cc: Sridar Narayanan, Dr. <sridar.narayanan at mcgill.ca<mailto:sridar.narayanan at mcgill.ca>>; loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca> <loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>>; Rozie Arnaoutelis, Ms. <rozie.arnaoutelis at mcgill.ca<mailto:rozie.arnaoutelis at mcgill.ca>>; Zografos Caramanos, Mr <zografos.caramanos at mcgill.ca<mailto:zografos.caramanos at mcgill.ca>>; Douglas Arnold, Dr. <douglas.arnold at mcgill.ca<mailto:douglas.arnold at mcgill.ca>>; Guttmann, Charles, M.D. <guttmann at bwh.harvard.edu<mailto:guttmann at bwh.harvard.edu>>
Subject: Re: [Loris-dev] Update LORIS to v21.0.0

Evidently the RAM is not enough, I am outside, I don't have the recommended value for you. You can check document for how much. I would recommend to increase the PHP memory allowance. Try to check PHP document for that, otherwise I can check later. Or maybe any other people knows better on this subject could help you.

Good weekend.

Ling

On Fri., Feb. 21, 2020, 5:06 p.m. Morales Pinzon, Alfredo, <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Ling Ma,

All set regarding php 7.2, is now enable and working. Going back to the error in the website: when I select Imaging -> Imaging Browser I got a 500 error in the front-end and the following error in the server:

===
[Fri Feb 21 12:27:21.231227 2020] [php7:error] [pid 17787] [client 170.223.207.1:46078<http://170.223.207.1:46078/>] PHP Fatal error:  Allowed memory size of 134217728 bytes exhausted (tried to allocate 20480 bytes) in /var/www/loris/php/libraries/Database.class.inc on line 714, referer: https://ipmsa-loris.bic.mni.mcgill.ca/
===

Any ideas?

Thank you in advance.

Best,
Alfredo.

On Feb 21, 2020, at 10:09 AM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:

        External Email - Use Caution

If you go to "/etc/apache2/mods-enabled", you can easily find which PHP version is enabled if after restart Apache2 you still have problem. Please don't modify source code to remove "?", there should be a lot of them, not possible to remove all.

On Fri, Feb 21, 2020 at 10:02 AM Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:
Hi Alfredo,

You installed PHP7.2, but you might not use the new version, you might need to restart the Apache2, or enable Apache2 to use PHP7.2. Because currently your server is still running PHP7.0 or PHP5.6. Because "?" is part of PHP7.1

Please check.

Good luck.

Ling Ma

On Fri, Feb 21, 2020 at 9:59 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear Ling Ma and C?cile,

Thank you for the help and tips. After installing php7.2-xml and php7.2-mysql I was able to finish all the steps listed in the upgrade process. I followed this post to upgrade to PHP 7.2: https://medium.com/andrewmmc-io/upgrade-php-version-to-7-2-from-7-0-c005a0926642

Now we come back to the first error. Actually, the server is not running right now. I have the following error:

===
[Fri Feb 21 09:25:33.848915 2020] [:error] [pid 27936] [client 216.15.126.108:52419<http://216.15.126.108:52419/>] PHP Parse error:  syntax error, unexpected '?', expecting variable (T_VARIABLE) in /var/www/loris/php/libraries/NDB_Client.class.inc on line 49
===

After modifying the line 49 in NDB_Client.class.inc from

===
function initialize(?string $configFile = null)
===

to (removing the ?)

===
function initialize(string $configFile = null)
===

but I got the following error:

===
[Fri Feb 21 09:37:18.042287 2020] [:error] [pid 715] [client 216.15.126.108:52603<http://216.15.126.108:52603/>] PHP Parse error:  syntax error, unexpected '?', expecting variable (T_VARIABLE) in /var/www/loris/php/libraries/NDB_Factory.class.inc on line 109
===

Is this an error in the code or I am missing something?

Thank you for help.

Best,
Alfredo.

On Feb 19, 2020, at 7:23 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:

        External Email - Use Caution

Hi Alfredo,

Since simplexml_load_file is part of php-xml package, I feel that you need to install php7.2-xml if you are using PHP7.2. In Ubuntu you install this package with apt-get install php7.2-xml, and make sure that this module is enabled in Apache2 if you are using Apache2. You can check which module is enabled via phpinfo() call from a PHP enabled web page, or just check your Apache2 PHP modules, the later is easier.

Good luck.

Ling Ma

On Wed, Feb 19, 2020 at 6:18 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Ling Ma,

Thank you for the information. I would suggest to add this link to each release, where the upgrading instructions are listed, and also mention upgrading system requirements if needed.

Continuing with the upgrade to v21.0.0. I checked that all the system requirements are met. Now, in having this error when executing data_dictionary_cleaner.php:

===
lorisadmin at ipmsa-loris:/var/www/loris/tools/single_use$ php data_dictionary_cleaner.php
PHP Fatal error:  Uncaught Error: Call to undefined function simplexml_load_file() in /var/www/loris/php/libraries/NDB_Config.class.inc:96
Stack trace:
#0 /var/www/loris/php/libraries/NDB_Config.class.inc(70): NDB_Config->load('/var/www/loris/...')
#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton('/var/www/loris/...')
#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config('/var/www/loris/...')
#3 /var/www/loris/tools/generic_includes.php(25): NDB_Client->initialize('/var/www/loris/...')
#4 /var/www/loris/tools/single_use/data_dictionary_cleaner.php(24): require_once('/var/www/loris/...')
#5 {main}
  thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 96
===

Any ideas on how to solve this?

Regards,
Alfredo.

On Feb 19, 2020, at 5:47 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:

        External Email - Use Caution

Hi Alfredo,

If you check this link:

https://github.com/aces/Loris/blob/21.0-release/README.md

and

https://github.com/aces/Loris/blob/22.0-release/README.md

You will see that the system requires:

System Requirements

  *   Apache 2.4 or higher
  *   MySQL >= 5.7 (or MariaDB >= 10.3)
  *   PHP 7.2 or higher
  *   Composer<https://getcomposer.org/>
  *   NodeJS 8.0 or higher
  *   NPM
  *   make

Please make sure that you have all the latest or recent versions for each of them, otherwise you will run into trouble later.

Ling Ma

On Wed, Feb 19, 2020 at 5:29 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Ling Ma,

Thank you. I will upgrade to PHP 7.2.

BTW, I cannot find the requirements for PHP for v21, I am looking at this link:

https://github.com/aces/Loris/releases/tag/v21.0.0

Regards,
Alfredo.


On Feb 19, 2020, at 5:18 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:

        External Email - Use Caution

Hi Alfredo,

The warning is OK to ignore. As to php, please check v21 version requirements, I believe a php minimum 7.1 even 7.2 is required.

In fact, PHP 5.6 is no longer supported.

Best regards,
Ling Ma

On Wed., Feb. 19, 2020, 5:07 p.m. Morales Pinzon, Alfredo, <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear Ling and C?cile,

Thank for your responses.

I had an issue with "git checkout?, somehow I had to remove some files before being able to checkout the v21.0.0. That was the reason I didn?t have the make file. Now that I have it, I have some errors:

After running ?make? I have the following error:

===
    WARNING in configuration
    The 'mode' option has not been set, webpack will fallback to 'production' for this value. Set 'mode' option to 'development' or 'production' to enable defaults for each environment.
    You can also set it to 'none' to disable any default behavior. Learn more: https://webpack.js.org/concepts/mode/
composer install --no-dev
> mkdir -p project/libraries
Loading composer repositories with package information
Installing dependencies from lock file
Your requirements could not be resolved to an installable set of packages.

  Problem 1
    - Installation request for php-http/guzzle6-adapter v2.0.1 -> satisfiable by php-http/guzzle6-adapter[v2.0.1].
    - php-http/guzzle6-adapter v2.0.1 requires php ^7.1 -> your PHP version (7.0.33) does not satisfy that requirement.
===

Do I have to upgrade PHP to 7.1?

Thank you again for your help.

Regards,
Alfredo.


On Feb 19, 2020, at 12:15 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:

        External Email - Use Caution

Hi Alfredo,

Sorry to hear you are experiencing issues with the upgrade to 21.0.0. See below.

On Tue, Feb 18, 2020 at 4:31 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and then to v22.0.0). I had no issues to get to v20.3.0 but now, moving to v21.0.0, I have two issues:

1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS website. I get a 500 error. Any ideas on what should I check?

Could you send us what you see in the Apache error file for that 500 error? Although, might be worth focusing on fixing your second issue before we dive too much into that one.

2. In the instructions to upgrade to v21.0.0, the second point says:

"Run make from the Loris root directory to update all dependencies.?"

However when I run ?make? In the Loris root direction it does nothing. Here is the result:

===
lorisadmin at ipmsa-loris:/var/www/loris$ make
make: *** No targets specified and no makefile found.  Stop.
===
It that the right directory? Maybe I am missing some files?

Are you sure you are on the 21.0.0 release of LORIS before you run make? Do you see a Makefile in your /var/www/loris directory? In theory it is supposed to be there on branch 21.0.0 (https://github.com/aces/Loris/tree/v21.0.0)

Hope this helps.

C?cile


Thank you for your help.

Best,
Alfredo.


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From blake.fitch at tuebingen.mpg.de  Tue Feb 25 04:31:26 2020
From: blake.fitch at tuebingen.mpg.de (Blake Fitch)
Date: Tue, 25 Feb 2020 10:31:26 +0100
Subject: [Loris-dev] Troubleshooting Imaging Browser not loading for
 22.0.0 release
In-Reply-To: <CALbt7NCe3wMOTVFoWu_7S7nRdBMm7yAwU_Do+t6+WLAj59mJPw@mail.gmail.com>
References: <CALbt7NDvsQ5uu2rB4Nex-qx6vQF9UJAyq99C=j2DCVMvfSObLw@mail.gmail.com>
 <CALbt7NCe3wMOTVFoWu_7S7nRdBMm7yAwU_Do+t6+WLAj59mJPw@mail.gmail.com>
Message-ID: <ac88f33a-4e3f-d685-2930-bce3643f5b19@tuebingen.mpg.de>

Hi Christine,

I have ensured that he code matches the link you sent. I did the edit, 
ran make in /var/www/loris, and restarted apache. I still get:
"An error occured while loading the page."

Here is a snapshot of the code in that area of the file:

Best,
Blake

On 24.02.20 19:33, Christine Rogers, Ms. wrote:
> Hi Blake,
> First/next troubleshooting question --
>
> Could you verify you're using the latest?update from this bugfix:
> https://github.com/aces/Loris/pull/6089/commits/c78af4ebc97d354b6820c51c8bb746e0e0e554f5
>
> This may resolve it, let us know --
> Thanks,
> Christine
>
> On Mon, Feb 24, 2020 at 1:23 PM Christine Rogers, Ms. 
> <christine.rogers at mcgill.ca <mailto:christine.rogers at mcgill.ca>> wrote:
>
>     Hi Loris team and community,
>     i'm forwarding a question from Blake (below) from Max Planck in
>     Tuebingen --he's encountering a (known) bug in the 22.0.0 Imaging
>     Browser where the module doesn't load (issue #6088)
>
>     His apache error log output is below.
>     Blake is running Ubuntu and has installed 22.0.0, and uploaded
>     some test DICOMs.? He's applied the proposed bugfix #6089, without
>     success (see below).
>
>     Could someone help resolve / share a solution for this ?
>     Thanks,
>     Christine
>
>     ---------- Forwarded message ---------
>     From: *Blake Fitch* <blake.fitch at tuebingen.mpg.de
>     <mailto:blake.fitch at tuebingen.mpg.de>>
>     Date: Fri, Feb 21, 2020 at 11:11 AM
>     Subject: Re: Fix for Imaging Browser not loading
>     To: Christine Rogers, Ms. <christine.rogers at mcgill.ca
>     <mailto:christine.rogers at mcgill.ca>>
>
>
>     Hi Christine,
>
>     I did the new patch. Looks the same. here's there error log entry
>     that pops out.
>
>     [Fri Feb 21 16:09:51.361760 2020] [php7:warn] [pid 25261] [client
>     10.38.124.254:55712 <http://10.38.124.254:55712>] PHP Warning:
>     PDOStatement::execute(): SQLSTATE[42000]: Syntax error or access
>     violation: 1064 You have an error in your SQL syntax; check the
>     manual that corresponds to your MySQL server version for the right
>     syntax to use near '//????????????? \n??????????? CASE
>     \n??????????????? WHEN s.MRIQCPending='Y' THEN ' at line 30 in
>     /var/www/loris/src/Data/Provisioners/DBRowProvisioner.php on line
>     81, referer: http://10.38.133.3/imaging_browser/
>     [Fri Feb 21 16:09:51.361873 2020] [php7:error] [pid 25261] [client
>     10.38.124.254:55712 <http://10.38.124.254:55712>] PHP Fatal error:
>     Uncaught Exception: Invalid SQL statement: SELECT \n?????????????
>     p.Name as Site,\n????????????? c.PSCID as PSCID,\n?????????????
>     c.CandID as DCCID,\n????????????? Project.Name as
>     project,\n????????????? s.Visit_label as
>     visitLabel,\n????????????? \n CASE s.MRIQCStatus\n???????????????
>     WHEN 'Fail' THEN\n IF(s.MRIQCPending='Y', 'Pending Fail',
>     'Fail')\n??????????????? WHEN 'Pass' THEN\n IF(s.MRIQCPending='Y',
>     'Pending Pass', 'Pass') \n??????????????? ELSE
>     s.MRIQCStatus\n??????????? END \n???????????? as
>     Visit_QC_Status,\n DATE_FORMAT(MIN(pf.Value), "%Y-%m-%d") as
>     First_Acquisition,\n FROM_UNIXTIME(MIN(f.InsertTime)) as
>     First_Insertion,\n FROM_UNIXTIME(MAX(fqc.QCLastChangeTime)) as
>     Last_QC,\n????????????? \n??????????? CASE \n
>     COALESCE(Max(fqc.QCLastChangeTime), 'new')\n??????????????? WHEN
>     'new' THEN 'new'\n??????????????? WHEN ''??? THEN
>     'new'\n??????????????? WHEN NULL? THEN 'new'\n??????????????? ELSE
>     ''\n END as New_Da in
>     /var/www/loris/src/Data/Provisioners/DBRowProvisioner.php on line
>     84, referer: http://10.38.133.3/imaging_browser/
>
>     Best,
>     Blake
>
>
>
>     -- 
>
>     christine.rogers at mcgill.ca <mailto: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 <mailto:Loris-dev at bic.mni.mcgill.ca>
>     https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
>
>
> -- 
>
> christine.rogers at mcgill.ca <mailto:christine.rogers at mcgill.ca>
> McGill Centre for Integrative Neuroscience | MCIN.ca
> Montreal Neurological Institute
> McGill University | Montreal | Canada
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From melanie.legault2 at mcgill.ca  Tue Feb 25 07:01:03 2020
From: melanie.legault2 at mcgill.ca (Melanie Legault, Mrs)
Date: Tue, 25 Feb 2020 12:01:03 +0000
Subject: [Loris-dev] Update LORIS to v21.0.0
In-Reply-To: <D7CCD4F8-3CE4-4DE8-B0DF-07622FC08D79@bwh.harvard.edu>
References: <9EE776FE-7387-4819-AD12-7E0E7200322E@bwh.harvard.edu>
 <CAMkiY3e1JkHqWt3oMFDGyHsr26F4LPUOS6gO8hzm-nCbCFm7DQ@mail.gmail.com>
 <62049B06-1DB0-4E4C-8610-3BB2D629CE4F@bwh.harvard.edu>
 <CAMpvQ9hN-vTERXCkXtgBVdg+_GEgk4J6cDizJ6vQDpaOy_YAxQ@mail.gmail.com>
 <E2FB11C8-D40E-4754-8D0B-D35FDBFF47DF@bwh.harvard.edu>
 <CAMpvQ9gBuqQCrNJakqH2MLsh8r2zScatfQqG8mvwXAvCcseK1g@mail.gmail.com>
 <35780192-BAF2-4F5F-AABB-53142C683BA2@bwh.harvard.edu>
 <CAMpvQ9jhtrQrqgAqvjWFMN_vHkHNM0C4vPd5HkDGTLAC1T9sxg@mail.gmail.com>
 <812F97F8-245D-4EC3-A637-C7166F5C2CA1@bwh.harvard.edu>
 <CAMpvQ9gxALXS2aNdFxQ_5Jn1FAQgMhx3G8XsuSU2Ee8Xf6Gt8Q@mail.gmail.com>
 <CAMpvQ9grbH4+m7Ru7HbfXbA=JkxvBQH4+NezR3ERiedZHDb9JA@mail.gmail.com>
 <39754C63-3409-4E5A-8256-18A045EC5B5E@bwh.harvard.edu>
 <CAMpvQ9iBBdv32M=KpST+BOqz0hKbe2X5BZ6eSaVaG64+5KQfVg@mail.gmail.com>
 <YTXPR0101MB1616132205D82F8EA74E1BA8CFEC0@YTXPR0101MB1616.CANPRD01.PROD.OUTLOOK.COM>,
 <D7CCD4F8-3CE4-4DE8-B0DF-07622FC08D79@bwh.harvard.edu>
Message-ID: <YTXPR0101MB1616C28F8DFC374C17EFD8D2CFED0@YTXPR0101MB1616.CANPRD01.PROD.OUTLOOK.COM>

Hello Alfredo,

Thanks for sharing with us the parameter that needed to be adjusted. I will create a pull request to add it to the document.

Regards,


M?lanie


________________________________
From: Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU>
Sent: February 24, 2020 17:53
To: Melanie Legault, Mrs <melanie.legault2 at mcgill.ca>; Ling Ma <lingyun.ma at mcin.ca>
Cc: Sridar Narayanan, Dr. <sridar.narayanan at mcgill.ca>; loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>; Rozie Arnaoutelis, Ms. <rozie.arnaoutelis at mcgill.ca>; Zografos Caramanos, Mr <zografos.caramanos at mcgill.ca>; Douglas Arnold, Dr. <douglas.arnold at mcgill.ca>; Guttmann, Charles,M.D. <guttmann at bwh.harvard.edu>
Subject: Re: [Loris-dev] Update LORIS to v21.0.0

Dear Melanie and Ling Ma,

I made the suggested changes in the link that Melanie sent but the error was still appearing. It turned out that the proper parameter to set was ?memory_limit?. I set it like this:

memory_limit = 150M

Now the imaging link is working.

Thank you for your help.

Regards,
Alfredo.

On Feb 24, 2020, at 7:32 AM, Melanie Legault, Mrs <melanie.legault2 at mcgill.ca<mailto:melanie.legault2 at mcgill.ca>> wrote:

        External Email - Use Caution

Hello Alfredo,

You may find which parameters you need to change in php.ini file to handle large file inhttps://github.com/aces/Loris/blob/master/docs/wiki/00%20-%20SERVER%20INSTALL%20AND%20CONFIGURATION/02%20-%20Website%20Configuration/Handling%20Large%20File%20Uploads.md

A restart of the Apache server will be needed after updating the file.

Regards,

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<mailto:loris-dev-bounces at bic.mni.mcgill.ca> <loris-dev-bounces at bic.mni.mcgill.ca<mailto:loris-dev-bounces at bic.mni.mcgill.ca>> on behalf of Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>>
Sent: February 21, 2020 17:12
To: Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>>
Cc: Sridar Narayanan, Dr. <sridar.narayanan at mcgill.ca<mailto:sridar.narayanan at mcgill.ca>>; loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca> <loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>>; Rozie Arnaoutelis, Ms. <rozie.arnaoutelis at mcgill.ca<mailto:rozie.arnaoutelis at mcgill.ca>>; Zografos Caramanos, Mr <zografos.caramanos at mcgill.ca<mailto:zografos.caramanos at mcgill.ca>>; Douglas Arnold, Dr. <douglas.arnold at mcgill.ca<mailto:douglas.arnold at mcgill.ca>>; Guttmann, Charles, M.D. <guttmann at bwh.harvard.edu<mailto:guttmann at bwh.harvard.edu>>
Subject: Re: [Loris-dev] Update LORIS to v21.0.0

Evidently the RAM is not enough, I am outside, I don't have the recommended value for you. You can check document for how much. I would recommend to increase the PHP memory allowance. Try to check PHP document for that, otherwise I can check later. Or maybe any other people knows better on this subject could help you.

Good weekend.

Ling

On Fri., Feb. 21, 2020, 5:06 p.m. Morales Pinzon, Alfredo, <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Ling Ma,

All set regarding php 7.2, is now enable and working. Going back to the error in the website: when I select Imaging -> Imaging Browser I got a 500 error in the front-end and the following error in the server:

===
[Fri Feb 21 12:27:21.231227 2020] [php7:error] [pid 17787] [client 170.223.207.1:46078<http://170.223.207.1:46078/>] PHP Fatal error:  Allowed memory size of 134217728 bytes exhausted (tried to allocate 20480 bytes) in /var/www/loris/php/libraries/Database.class.inc on line 714, referer: https://ipmsa-loris.bic.mni.mcgill.ca/
===

Any ideas?

Thank you in advance.

Best,
Alfredo.

On Feb 21, 2020, at 10:09 AM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:

        External Email - Use Caution

If you go to "/etc/apache2/mods-enabled", you can easily find which PHP version is enabled if after restart Apache2 you still have problem. Please don't modify source code to remove "?", there should be a lot of them, not possible to remove all.

On Fri, Feb 21, 2020 at 10:02 AM Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:
Hi Alfredo,

You installed PHP7.2, but you might not use the new version, you might need to restart the Apache2, or enable Apache2 to use PHP7.2. Because currently your server is still running PHP7.0 or PHP5.6. Because "?" is part of PHP7.1

Please check.

Good luck.

Ling Ma

On Fri, Feb 21, 2020 at 9:59 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear Ling Ma and C?cile,

Thank you for the help and tips. After installing php7.2-xml and php7.2-mysql I was able to finish all the steps listed in the upgrade process. I followed this post to upgrade to PHP 7.2: https://medium.com/andrewmmc-io/upgrade-php-version-to-7-2-from-7-0-c005a0926642

Now we come back to the first error. Actually, the server is not running right now. I have the following error:

===
[Fri Feb 21 09:25:33.848915 2020] [:error] [pid 27936] [client 216.15.126.108:52419<http://216.15.126.108:52419/>] PHP Parse error:  syntax error, unexpected '?', expecting variable (T_VARIABLE) in /var/www/loris/php/libraries/NDB_Client.class.inc on line 49
===

After modifying the line 49 in NDB_Client.class.inc from

===
function initialize(?string $configFile = null)
===

to (removing the ?)

===
function initialize(string $configFile = null)
===

but I got the following error:

===
[Fri Feb 21 09:37:18.042287 2020] [:error] [pid 715] [client 216.15.126.108:52603<http://216.15.126.108:52603/>] PHP Parse error:  syntax error, unexpected '?', expecting variable (T_VARIABLE) in /var/www/loris/php/libraries/NDB_Factory.class.inc on line 109
===

Is this an error in the code or I am missing something?

Thank you for help.

Best,
Alfredo.

On Feb 19, 2020, at 7:23 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:

        External Email - Use Caution

Hi Alfredo,

Since simplexml_load_file is part of php-xml package, I feel that you need to install php7.2-xml if you are using PHP7.2. In Ubuntu you install this package with apt-get install php7.2-xml, and make sure that this module is enabled in Apache2 if you are using Apache2. You can check which module is enabled via phpinfo() call from a PHP enabled web page, or just check your Apache2 PHP modules, the later is easier.

Good luck.

Ling Ma

On Wed, Feb 19, 2020 at 6:18 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Ling Ma,

Thank you for the information. I would suggest to add this link to each release, where the upgrading instructions are listed, and also mention upgrading system requirements if needed.

Continuing with the upgrade to v21.0.0. I checked that all the system requirements are met. Now, in having this error when executing data_dictionary_cleaner.php:

===
lorisadmin at ipmsa-loris:/var/www/loris/tools/single_use$ php data_dictionary_cleaner.php
PHP Fatal error:  Uncaught Error: Call to undefined function simplexml_load_file() in /var/www/loris/php/libraries/NDB_Config.class.inc:96
Stack trace:
#0 /var/www/loris/php/libraries/NDB_Config.class.inc(70): NDB_Config->load('/var/www/loris/...')
#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton('/var/www/loris/...')
#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config('/var/www/loris/...')
#3 /var/www/loris/tools/generic_includes.php(25): NDB_Client->initialize('/var/www/loris/...')
#4 /var/www/loris/tools/single_use/data_dictionary_cleaner.php(24): require_once('/var/www/loris/...')
#5 {main}
  thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 96
===

Any ideas on how to solve this?

Regards,
Alfredo.

On Feb 19, 2020, at 5:47 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:

        External Email - Use Caution

Hi Alfredo,

If you check this link:

https://github.com/aces/Loris/blob/21.0-release/README.md

and

https://github.com/aces/Loris/blob/22.0-release/README.md

You will see that the system requires:

System Requirements

  *   Apache 2.4 or higher
  *   MySQL >= 5.7 (or MariaDB >= 10.3)
  *   PHP 7.2 or higher
  *   Composer<https://getcomposer.org/>
  *   NodeJS 8.0 or higher
  *   NPM
  *   make

Please make sure that you have all the latest or recent versions for each of them, otherwise you will run into trouble later.

Ling Ma

On Wed, Feb 19, 2020 at 5:29 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Ling Ma,

Thank you. I will upgrade to PHP 7.2.

BTW, I cannot find the requirements for PHP for v21, I am looking at this link:

https://github.com/aces/Loris/releases/tag/v21.0.0

Regards,
Alfredo.


On Feb 19, 2020, at 5:18 PM, Ling Ma <lingyun.ma at mcin.ca<mailto:lingyun.ma at mcin.ca>> wrote:

        External Email - Use Caution

Hi Alfredo,

The warning is OK to ignore. As to php, please check v21 version requirements, I believe a php minimum 7.1 even 7.2 is required.

In fact, PHP 5.6 is no longer supported.

Best regards,
Ling Ma

On Wed., Feb. 19, 2020, 5:07 p.m. Morales Pinzon, Alfredo, <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear Ling and C?cile,

Thank for your responses.

I had an issue with "git checkout?, somehow I had to remove some files before being able to checkout the v21.0.0. That was the reason I didn?t have the make file. Now that I have it, I have some errors:

After running ?make? I have the following error:

===
    WARNING in configuration
    The 'mode' option has not been set, webpack will fallback to 'production' for this value. Set 'mode' option to 'development' or 'production' to enable defaults for each environment.
    You can also set it to 'none' to disable any default behavior. Learn more: https://webpack.js.org/concepts/mode/
composer install --no-dev
> mkdir -p project/libraries
Loading composer repositories with package information
Installing dependencies from lock file
Your requirements could not be resolved to an installable set of packages.

  Problem 1
    - Installation request for php-http/guzzle6-adapter v2.0.1 -> satisfiable by php-http/guzzle6-adapter[v2.0.1].
    - php-http/guzzle6-adapter v2.0.1 requires php ^7.1 -> your PHP version (7.0.33) does not satisfy that requirement.
===

Do I have to upgrade PHP to 7.1?

Thank you again for your help.

Regards,
Alfredo.


On Feb 19, 2020, at 12:15 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:

        External Email - Use Caution

Hi Alfredo,

Sorry to hear you are experiencing issues with the upgrade to 21.0.0. See below.

On Tue, Feb 18, 2020 at 4:31 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I am in the process of upgrading LORIS from v20.1.1 to v21.0.0 (and then to v22.0.0). I had no issues to get to v20.3.0 but now, moving to v21.0.0, I have two issues:

1. I cannot access the link ?Imaging->Imaging Browser? in the LORIS website. I get a 500 error. Any ideas on what should I check?

Could you send us what you see in the Apache error file for that 500 error? Although, might be worth focusing on fixing your second issue before we dive too much into that one.

2. In the instructions to upgrade to v21.0.0, the second point says:

"Run make from the Loris root directory to update all dependencies.?"

However when I run ?make? In the Loris root direction it does nothing. Here is the result:

===
lorisadmin at ipmsa-loris:/var/www/loris$ make
make: *** No targets specified and no makefile found.  Stop.
===
It that the right directory? Maybe I am missing some files?

Are you sure you are on the 21.0.0 release of LORIS before you run make? Do you see a Makefile in your /var/www/loris directory? In theory it is supposed to be there on branch 21.0.0 (https://github.com/aces/Loris/tree/v21.0.0)

Hope this helps.

C?cile


Thank you for your help.

Best,
Alfredo.


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From lingyun.ma at mcin.ca  Tue Feb 25 07:19:59 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Tue, 25 Feb 2020 07:19:59 -0500
Subject: [Loris-dev] Troubleshooting Imaging Browser not loading for
 22.0.0 release
In-Reply-To: <ac88f33a-4e3f-d685-2930-bce3643f5b19@tuebingen.mpg.de>
References: <CALbt7NDvsQ5uu2rB4Nex-qx6vQF9UJAyq99C=j2DCVMvfSObLw@mail.gmail.com>
 <CALbt7NCe3wMOTVFoWu_7S7nRdBMm7yAwU_Do+t6+WLAj59mJPw@mail.gmail.com>
 <ac88f33a-4e3f-d685-2930-bce3643f5b19@tuebingen.mpg.de>
Message-ID: <CAMpvQ9h8uWjC8Tf+x_=NZLLfP9zqy8sG6Xrj2AHq-dXf513ATw@mail.gmail.com>

Hi Blake,

The $modalities_subquery seems to be the only place where it is possible to
create a wrong SQL when this variable is empty and when the Loris-MRI is
not installed, which will create a favorite environment for image_browser.
I am wondering what your MySQL server version is, version 5.7 or above? If
yes, what is the step you have taken to install Loris? If you have followed
the exact installation instructions, then I am wondering whether you could
share your zipped database dump, which should not be big since this is a
new installation, so that we could investigate what has happened. Thanks a
lot and sorry for the trouble.

Another possibility is to check the MySQL parameters used in sql_mode?
Which could be checked via "SELECT @@sql_mode;", could you also check that
value? What is the value you see? Since image_browser uses a relatively
complicated query, it is possible that a parameter might make the syntax
not valid.

Best regards,
Ling Ma
Dev consultant.

On Tue, Feb 25, 2020 at 4:32 AM Blake Fitch <blake.fitch at tuebingen.mpg.de>
wrote:

> Hi Christine,
>
> I have ensured that he code matches the link you sent. I did the edit, ran
> make in /var/www/loris, and restarted apache. I still get:
> "An error occured while loading the page."
>
> Here is a snapshot of the code in that area of the file:
>
> Best,
> Blake
> On 24.02.20 19:33, Christine Rogers, Ms. wrote:
>
> Hi Blake,
> First/next troubleshooting question --
>
> Could you verify you're using the latest update from this bugfix:
>
> https://github.com/aces/Loris/pull/6089/commits/c78af4ebc97d354b6820c51c8bb746e0e0e554f5
>
> This may resolve it, let us know --
> Thanks,
> Christine
>
> On Mon, Feb 24, 2020 at 1:23 PM Christine Rogers, Ms. <
> christine.rogers at mcgill.ca> wrote:
>
>> Hi Loris team and community,
>> i'm forwarding a question from Blake (below) from Max Planck in Tuebingen
>> --he's encountering a (known) bug in the 22.0.0 Imaging Browser where the
>> module doesn't load (issue #6088)
>>
>> His apache error log output is below.
>> Blake is running Ubuntu and has installed 22.0.0, and uploaded some test
>> DICOMs.  He's applied the proposed bugfix #6089, without success (see
>> below).
>>
>> Could someone help resolve / share a solution for this ?
>> Thanks,
>> Christine
>>
>> ---------- Forwarded message ---------
>> From: Blake Fitch <blake.fitch at tuebingen.mpg.de>
>> Date: Fri, Feb 21, 2020 at 11:11 AM
>> Subject: Re: Fix for Imaging Browser not loading
>> To: Christine Rogers, Ms. <christine.rogers at mcgill.ca>
>>
>>
>> Hi Christine,
>>
>> I did the new patch. Looks the same. here's there error log entry that
>> pops out.
>>
>> [Fri Feb 21 16:09:51.361760 2020] [php7:warn] [pid 25261] [client
>> 10.38.124.254:55712] PHP Warning:  PDOStatement::execute():
>> SQLSTATE[42000]: Syntax error or access violation: 1064 You have an error
>> in your SQL syntax; check the manual that corresponds to your MySQL server
>> version for the right syntax to use near '//              \n
>> CASE \n                WHEN s.MRIQCPending='Y' THEN ' at line 30 in
>> /var/www/loris/src/Data/Provisioners/DBRowProvisioner.php on line 81,
>> referer: http://10.38.133.3/imaging_browser/
>> [Fri Feb 21 16:09:51.361873 2020] [php7:error] [pid 25261] [client
>> 10.38.124.254:55712] PHP Fatal error:  Uncaught Exception: Invalid SQL
>> statement: SELECT \n              p.Name as Site,\n              c.PSCID as
>> PSCID,\n              c.CandID as DCCID,\n              Project.Name as
>> project,\n              s.Visit_label as visitLabel,\n
>> \n            CASE s.MRIQCStatus\n                WHEN 'Fail'
>> THEN\n                    IF(s.MRIQCPending='Y', 'Pending Fail',
>> 'Fail')\n                WHEN 'Pass' THEN\n
>> IF(s.MRIQCPending='Y', 'Pending Pass', 'Pass') \n                ELSE
>> s.MRIQCStatus\n            END \n             as
>> Visit_QC_Status,\n              DATE_FORMAT(MIN(pf.Value), "%Y-%m-%d") as
>> First_Acquisition,\n              FROM_UNIXTIME(MIN(f.InsertTime)) as
>> First_Insertion,\n              FROM_UNIXTIME(MAX(fqc.QCLastChangeTime)) as
>> Last_QC,\n              \n            CASE \n
>> COALESCE(Max(fqc.QCLastChangeTime), 'new')\n                WHEN 'new' THEN
>> 'new'\n                WHEN ''    THEN 'new'\n                WHEN NULL
>> THEN 'new'\n                ELSE ''\n            END as New_Da in
>> /var/www/loris/src/Data/Provisioners/DBRowProvisioner.php on line 84,
>> referer: http://10.38.133.3/imaging_browser/
>>
>> Best,
>> Blake
>>
>>
>> --
>>
>> 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
>
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From lingyun.ma at mcin.ca  Tue Feb 25 07:22:34 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Tue, 25 Feb 2020 07:22:34 -0500
Subject: [Loris-dev] Troubleshooting Imaging Browser not loading for
 22.0.0 release
In-Reply-To: <CAMpvQ9h8uWjC8Tf+x_=NZLLfP9zqy8sG6Xrj2AHq-dXf513ATw@mail.gmail.com>
References: <CALbt7NDvsQ5uu2rB4Nex-qx6vQF9UJAyq99C=j2DCVMvfSObLw@mail.gmail.com>
 <CALbt7NCe3wMOTVFoWu_7S7nRdBMm7yAwU_Do+t6+WLAj59mJPw@mail.gmail.com>
 <ac88f33a-4e3f-d685-2930-bce3643f5b19@tuebingen.mpg.de>
 <CAMpvQ9h8uWjC8Tf+x_=NZLLfP9zqy8sG6Xrj2AHq-dXf513ATw@mail.gmail.com>
Message-ID: <CAMpvQ9i5m5Gf2u7ndS+90mOghCEFBscm00hOWbCniiBf6aj8qw@mail.gmail.com>

Hi Blake,

I just rechecked the image your shared, I saw the problem: you should not
add "//" in front of the several lines in your code, I saw three of them,
which will make the syntax totally invalid, because it is not a command
line, they are a whole command wrapped in several lines.


Best regards,
Ling Ma

On Tue, Feb 25, 2020 at 7:19 AM Ling Ma <lingyun.ma at mcin.ca> wrote:

> Hi Blake,
>
> The $modalities_subquery seems to be the only place where it is possible
> to create a wrong SQL when this variable is empty and when the Loris-MRI is
> not installed, which will create a favorite environment for image_browser.
> I am wondering what your MySQL server version is, version 5.7 or above? If
> yes, what is the step you have taken to install Loris? If you have followed
> the exact installation instructions, then I am wondering whether you could
> share your zipped database dump, which should not be big since this is a
> new installation, so that we could investigate what has happened. Thanks a
> lot and sorry for the trouble.
>
> Another possibility is to check the MySQL parameters used in sql_mode?
> Which could be checked via "SELECT @@sql_mode;", could you also check
> that value? What is the value you see? Since image_browser uses a
> relatively complicated query, it is possible that a parameter might make
> the syntax not valid.
>
> Best regards,
> Ling Ma
> Dev consultant.
>
> On Tue, Feb 25, 2020 at 4:32 AM Blake Fitch <blake.fitch at tuebingen.mpg.de>
> wrote:
>
>> Hi Christine,
>>
>> I have ensured that he code matches the link you sent. I did the edit,
>> ran make in /var/www/loris, and restarted apache. I still get:
>> "An error occured while loading the page."
>>
>> Here is a snapshot of the code in that area of the file:
>>
>> Best,
>> Blake
>> On 24.02.20 19:33, Christine Rogers, Ms. wrote:
>>
>> Hi Blake,
>> First/next troubleshooting question --
>>
>> Could you verify you're using the latest update from this bugfix:
>>
>> https://github.com/aces/Loris/pull/6089/commits/c78af4ebc97d354b6820c51c8bb746e0e0e554f5
>>
>> This may resolve it, let us know --
>> Thanks,
>> Christine
>>
>> On Mon, Feb 24, 2020 at 1:23 PM Christine Rogers, Ms. <
>> christine.rogers at mcgill.ca> wrote:
>>
>>> Hi Loris team and community,
>>> i'm forwarding a question from Blake (below) from Max Planck in
>>> Tuebingen --he's encountering a (known) bug in the 22.0.0 Imaging Browser
>>> where the module doesn't load (issue #6088)
>>>
>>> His apache error log output is below.
>>> Blake is running Ubuntu and has installed 22.0.0, and uploaded some test
>>> DICOMs.  He's applied the proposed bugfix #6089, without success (see
>>> below).
>>>
>>> Could someone help resolve / share a solution for this ?
>>> Thanks,
>>> Christine
>>>
>>> ---------- Forwarded message ---------
>>> From: Blake Fitch <blake.fitch at tuebingen.mpg.de>
>>> Date: Fri, Feb 21, 2020 at 11:11 AM
>>> Subject: Re: Fix for Imaging Browser not loading
>>> To: Christine Rogers, Ms. <christine.rogers at mcgill.ca>
>>>
>>>
>>> Hi Christine,
>>>
>>> I did the new patch. Looks the same. here's there error log entry that
>>> pops out.
>>>
>>> [Fri Feb 21 16:09:51.361760 2020] [php7:warn] [pid 25261] [client
>>> 10.38.124.254:55712] PHP Warning:  PDOStatement::execute():
>>> SQLSTATE[42000]: Syntax error or access violation: 1064 You have an error
>>> in your SQL syntax; check the manual that corresponds to your MySQL server
>>> version for the right syntax to use near '//              \n
>>> CASE \n                WHEN s.MRIQCPending='Y' THEN ' at line 30 in
>>> /var/www/loris/src/Data/Provisioners/DBRowProvisioner.php on line 81,
>>> referer: http://10.38.133.3/imaging_browser/
>>> [Fri Feb 21 16:09:51.361873 2020] [php7:error] [pid 25261] [client
>>> 10.38.124.254:55712] PHP Fatal error:  Uncaught Exception: Invalid SQL
>>> statement: SELECT \n              p.Name as Site,\n              c.PSCID as
>>> PSCID,\n              c.CandID as DCCID,\n              Project.Name as
>>> project,\n              s.Visit_label as visitLabel,\n
>>> \n            CASE s.MRIQCStatus\n                WHEN 'Fail'
>>> THEN\n                    IF(s.MRIQCPending='Y', 'Pending Fail',
>>> 'Fail')\n                WHEN 'Pass' THEN\n
>>> IF(s.MRIQCPending='Y', 'Pending Pass', 'Pass') \n                ELSE
>>> s.MRIQCStatus\n            END \n             as
>>> Visit_QC_Status,\n              DATE_FORMAT(MIN(pf.Value), "%Y-%m-%d") as
>>> First_Acquisition,\n              FROM_UNIXTIME(MIN(f.InsertTime)) as
>>> First_Insertion,\n              FROM_UNIXTIME(MAX(fqc.QCLastChangeTime)) as
>>> Last_QC,\n              \n            CASE \n
>>> COALESCE(Max(fqc.QCLastChangeTime), 'new')\n                WHEN 'new' THEN
>>> 'new'\n                WHEN ''    THEN 'new'\n                WHEN NULL
>>> THEN 'new'\n                ELSE ''\n            END as New_Da in
>>> /var/www/loris/src/Data/Provisioners/DBRowProvisioner.php on line 84,
>>> referer: http://10.38.133.3/imaging_browser/
>>>
>>> Best,
>>> Blake
>>>
>>>
>>> --
>>>
>>> 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
>>
>
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From lingyun.ma at mcin.ca  Tue Feb 25 07:27:33 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Tue, 25 Feb 2020 07:27:33 -0500
Subject: [Loris-dev] Troubleshooting Imaging Browser not loading for
 22.0.0 release
In-Reply-To: <CAMpvQ9i5m5Gf2u7ndS+90mOghCEFBscm00hOWbCniiBf6aj8qw@mail.gmail.com>
References: <CALbt7NDvsQ5uu2rB4Nex-qx6vQF9UJAyq99C=j2DCVMvfSObLw@mail.gmail.com>
 <CALbt7NCe3wMOTVFoWu_7S7nRdBMm7yAwU_Do+t6+WLAj59mJPw@mail.gmail.com>
 <ac88f33a-4e3f-d685-2930-bce3643f5b19@tuebingen.mpg.de>
 <CAMpvQ9h8uWjC8Tf+x_=NZLLfP9zqy8sG6Xrj2AHq-dXf513ATw@mail.gmail.com>
 <CAMpvQ9i5m5Gf2u7ndS+90mOghCEFBscm00hOWbCniiBf6aj8qw@mail.gmail.com>
Message-ID: <CAMpvQ9iTTAzaLTcxeWsMeQf==3kq2brVxfVBSFhxUEvvQwdJKg@mail.gmail.com>

Correction: That part of code is not a PHP command line, it is a whole SQL
query command separated in several lines. The SQL doesn't accept "//" as a
comment

On Tue, Feb 25, 2020 at 7:22 AM Ling Ma <lingyun.ma at mcin.ca> wrote:

> Hi Blake,
>
> I just rechecked the image your shared, I saw the problem: you should not
> add "//" in front of the several lines in your code, I saw three of them,
> which will make the syntax totally invalid, because it is not a command
> line, they are a whole command wrapped in several lines.
>
>
> Best regards,
> Ling Ma
>
> On Tue, Feb 25, 2020 at 7:19 AM Ling Ma <lingyun.ma at mcin.ca> wrote:
>
>> Hi Blake,
>>
>> The $modalities_subquery seems to be the only place where it is possible
>> to create a wrong SQL when this variable is empty and when the Loris-MRI is
>> not installed, which will create a favorite environment for image_browser.
>> I am wondering what your MySQL server version is, version 5.7 or above? If
>> yes, what is the step you have taken to install Loris? If you have followed
>> the exact installation instructions, then I am wondering whether you could
>> share your zipped database dump, which should not be big since this is a
>> new installation, so that we could investigate what has happened. Thanks a
>> lot and sorry for the trouble.
>>
>> Another possibility is to check the MySQL parameters used in sql_mode?
>> Which could be checked via "SELECT @@sql_mode;", could you also check
>> that value? What is the value you see? Since image_browser uses a
>> relatively complicated query, it is possible that a parameter might make
>> the syntax not valid.
>>
>> Best regards,
>> Ling Ma
>> Dev consultant.
>>
>> On Tue, Feb 25, 2020 at 4:32 AM Blake Fitch <blake.fitch at tuebingen.mpg.de>
>> wrote:
>>
>>> Hi Christine,
>>>
>>> I have ensured that he code matches the link you sent. I did the edit,
>>> ran make in /var/www/loris, and restarted apache. I still get:
>>> "An error occured while loading the page."
>>>
>>> Here is a snapshot of the code in that area of the file:
>>>
>>> Best,
>>> Blake
>>> On 24.02.20 19:33, Christine Rogers, Ms. wrote:
>>>
>>> Hi Blake,
>>> First/next troubleshooting question --
>>>
>>> Could you verify you're using the latest update from this bugfix:
>>>
>>> https://github.com/aces/Loris/pull/6089/commits/c78af4ebc97d354b6820c51c8bb746e0e0e554f5
>>>
>>> This may resolve it, let us know --
>>> Thanks,
>>> Christine
>>>
>>> On Mon, Feb 24, 2020 at 1:23 PM Christine Rogers, Ms. <
>>> christine.rogers at mcgill.ca> wrote:
>>>
>>>> Hi Loris team and community,
>>>> i'm forwarding a question from Blake (below) from Max Planck in
>>>> Tuebingen --he's encountering a (known) bug in the 22.0.0 Imaging Browser
>>>> where the module doesn't load (issue #6088)
>>>>
>>>> His apache error log output is below.
>>>> Blake is running Ubuntu and has installed 22.0.0, and uploaded some
>>>> test DICOMs.  He's applied the proposed bugfix #6089, without success (see
>>>> below).
>>>>
>>>> Could someone help resolve / share a solution for this ?
>>>> Thanks,
>>>> Christine
>>>>
>>>> ---------- Forwarded message ---------
>>>> From: Blake Fitch <blake.fitch at tuebingen.mpg.de>
>>>> Date: Fri, Feb 21, 2020 at 11:11 AM
>>>> Subject: Re: Fix for Imaging Browser not loading
>>>> To: Christine Rogers, Ms. <christine.rogers at mcgill.ca>
>>>>
>>>>
>>>> Hi Christine,
>>>>
>>>> I did the new patch. Looks the same. here's there error log entry that
>>>> pops out.
>>>>
>>>> [Fri Feb 21 16:09:51.361760 2020] [php7:warn] [pid 25261] [client
>>>> 10.38.124.254:55712] PHP Warning:  PDOStatement::execute():
>>>> SQLSTATE[42000]: Syntax error or access violation: 1064 You have an error
>>>> in your SQL syntax; check the manual that corresponds to your MySQL server
>>>> version for the right syntax to use near '//              \n
>>>> CASE \n                WHEN s.MRIQCPending='Y' THEN ' at line 30 in
>>>> /var/www/loris/src/Data/Provisioners/DBRowProvisioner.php on line 81,
>>>> referer: http://10.38.133.3/imaging_browser/
>>>> [Fri Feb 21 16:09:51.361873 2020] [php7:error] [pid 25261] [client
>>>> 10.38.124.254:55712] PHP Fatal error:  Uncaught Exception: Invalid SQL
>>>> statement: SELECT \n              p.Name as Site,\n              c.PSCID as
>>>> PSCID,\n              c.CandID as DCCID,\n              Project.Name as
>>>> project,\n              s.Visit_label as visitLabel,\n
>>>> \n            CASE s.MRIQCStatus\n                WHEN 'Fail'
>>>> THEN\n                    IF(s.MRIQCPending='Y', 'Pending Fail',
>>>> 'Fail')\n                WHEN 'Pass' THEN\n
>>>> IF(s.MRIQCPending='Y', 'Pending Pass', 'Pass') \n                ELSE
>>>> s.MRIQCStatus\n            END \n             as
>>>> Visit_QC_Status,\n              DATE_FORMAT(MIN(pf.Value), "%Y-%m-%d") as
>>>> First_Acquisition,\n              FROM_UNIXTIME(MIN(f.InsertTime)) as
>>>> First_Insertion,\n              FROM_UNIXTIME(MAX(fqc.QCLastChangeTime)) as
>>>> Last_QC,\n              \n            CASE \n
>>>> COALESCE(Max(fqc.QCLastChangeTime), 'new')\n                WHEN 'new' THEN
>>>> 'new'\n                WHEN ''    THEN 'new'\n                WHEN NULL
>>>> THEN 'new'\n                ELSE ''\n            END as New_Da in
>>>> /var/www/loris/src/Data/Provisioners/DBRowProvisioner.php on line 84,
>>>> referer: http://10.38.133.3/imaging_browser/
>>>>
>>>> Best,
>>>> Blake
>>>>
>>>>
>>>> --
>>>>
>>>> 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
>>>
>>
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From blake.fitch at tuebingen.mpg.de  Tue Feb 25 07:33:36 2020
From: blake.fitch at tuebingen.mpg.de (Blake Fitch)
Date: Tue, 25 Feb 2020 13:33:36 +0100
Subject: [Loris-dev] Troubleshooting Imaging Browser not loading for
 22.0.0 release
In-Reply-To: <CAMpvQ9iTTAzaLTcxeWsMeQf==3kq2brVxfVBSFhxUEvvQwdJKg@mail.gmail.com>
References: <CALbt7NDvsQ5uu2rB4Nex-qx6vQF9UJAyq99C=j2DCVMvfSObLw@mail.gmail.com>
 <CALbt7NCe3wMOTVFoWu_7S7nRdBMm7yAwU_Do+t6+WLAj59mJPw@mail.gmail.com>
 <ac88f33a-4e3f-d685-2930-bce3643f5b19@tuebingen.mpg.de>
 <CAMpvQ9h8uWjC8Tf+x_=NZLLfP9zqy8sG6Xrj2AHq-dXf513ATw@mail.gmail.com>
 <CAMpvQ9i5m5Gf2u7ndS+90mOghCEFBscm00hOWbCniiBf6aj8qw@mail.gmail.com>
 <CAMpvQ9iTTAzaLTcxeWsMeQf==3kq2brVxfVBSFhxUEvvQwdJKg@mail.gmail.com>
Message-ID: <6144e392-b373-e983-6d4e-fbe51392f232@tuebingen.mpg.de>

Hi Ling Ma,

That made that page work. Thank you.

Best,
Blake

On 25.02.20 13:27, Ling Ma wrote:
> Correction: That part of code is not a PHP command line, it is a whole 
> SQL query command separated in several lines. The SQL doesn't accept 
> "//" as a comment
>
> On Tue, Feb 25, 2020 at 7:22 AM Ling Ma <lingyun.ma at mcin.ca 
> <mailto:lingyun.ma at mcin.ca>> wrote:
>
>     Hi Blake,
>
>     I just rechecked the image your shared, I saw the problem: you
>     should not add "//" in front of the several lines in your code,?I
>     saw three of them, which will make the syntax totally invalid,
>     because it is not a command line, they are a whole command wrapped
>     in several lines.
>
>
>     Best regards,
>     Ling Ma
>
>     On Tue, Feb 25, 2020 at 7:19 AM Ling Ma <lingyun.ma at mcin.ca
>     <mailto:lingyun.ma at mcin.ca>> wrote:
>
>         Hi Blake,
>
>         The $modalities_subquery seems to be the only place where it
>         is possible to create?a wrong SQL when this variable is empty
>         and when the Loris-MRI is not installed,?which will create a
>         favorite environment for image_browser. I am wondering what
>         your MySQL server version is, version 5.7 or above? If yes,
>         what is the step you have taken to install Loris? If you have
>         followed the exact installation instructions, then I am
>         wondering whether you could share your zipped database dump,
>         which should not be big since this is a new installation, so
>         that we could investigate?what has happened. Thanks a lot and
>         sorry for the trouble.
>
>         Another possibility is to check the MySQL parameters used in
>         sql_mode? Which could be checked via "SELECT@@sql_mode;",
>         could you also check that value? What is the value you see?
>         Since image_browser uses a relatively complicated query, it is
>         possible that a parameter might make the syntax not valid.
>
>         Best regards,
>         Ling Ma
>         Dev consultant.
>
>         On Tue, Feb 25, 2020 at 4:32 AM Blake Fitch
>         <blake.fitch at tuebingen.mpg.de
>         <mailto:blake.fitch at tuebingen.mpg.de>> wrote:
>
>             Hi Christine,
>
>             I have ensured that he code matches the link you sent. I
>             did the edit, ran make in /var/www/loris, and restarted
>             apache. I still get:
>             "An error occured while loading the page."
>
>             Here is a snapshot of the code in that area of the file:
>
>             Best,
>             Blake
>
>             On 24.02.20 19:33, Christine Rogers, Ms. wrote:
>>             Hi Blake,
>>             First/next troubleshooting question --
>>
>>             Could you verify you're using the latest?update from this
>>             bugfix:
>>             https://github.com/aces/Loris/pull/6089/commits/c78af4ebc97d354b6820c51c8bb746e0e0e554f5
>>
>>             This may resolve it, let us know --
>>             Thanks,
>>             Christine
>>
>>             On Mon, Feb 24, 2020 at 1:23 PM Christine Rogers, Ms.
>>             <christine.rogers at mcgill.ca
>>             <mailto:christine.rogers at mcgill.ca>> wrote:
>>
>>                 Hi Loris team and community,
>>                 i'm forwarding a question from Blake (below) from Max
>>                 Planck in Tuebingen --he's encountering a (known) bug
>>                 in the 22.0.0 Imaging Browser where the module
>>                 doesn't load (issue #6088)
>>
>>                 His apache error log output is below.
>>                 Blake is running Ubuntu and has installed 22.0.0, and
>>                 uploaded some test DICOMs.? He's applied the proposed
>>                 bugfix #6089, without success (see below).
>>
>>                 Could someone help resolve / share a solution for this ?
>>                 Thanks,
>>                 Christine
>>
>>                 ---------- Forwarded message ---------
>>                 From: *Blake Fitch* <blake.fitch at tuebingen.mpg.de
>>                 <mailto:blake.fitch at tuebingen.mpg.de>>
>>                 Date: Fri, Feb 21, 2020 at 11:11 AM
>>                 Subject: Re: Fix for Imaging Browser not loading
>>                 To: Christine Rogers, Ms. <christine.rogers at mcgill.ca
>>                 <mailto:christine.rogers at mcgill.ca>>
>>
>>
>>                 Hi Christine,
>>
>>                 I did the new patch. Looks the same. here's there
>>                 error log entry that pops out.
>>
>>                 [Fri Feb 21 16:09:51.361760 2020] [php7:warn] [pid
>>                 25261] [client 10.38.124.254:55712
>>                 <http://10.38.124.254:55712>] PHP Warning:
>>                 PDOStatement::execute(): SQLSTATE[42000]: Syntax
>>                 error or access violation: 1064 You have an error in
>>                 your SQL syntax; check the manual that corresponds to
>>                 your MySQL server version for the right syntax to use
>>                 near '// \n??????????? CASE \n??????????????? WHEN
>>                 s.MRIQCPending='Y' THEN ' at line 30 in
>>                 /var/www/loris/src/Data/Provisioners/DBRowProvisioner.php
>>                 on line 81, referer: http://10.38.133.3/imaging_browser/
>>                 [Fri Feb 21 16:09:51.361873 2020] [php7:error] [pid
>>                 25261] [client 10.38.124.254:55712
>>                 <http://10.38.124.254:55712>] PHP Fatal error:?
>>                 Uncaught Exception: Invalid SQL statement: SELECT
>>                 \n????????????? p.Name as Site,\n?????????????
>>                 c.PSCID as PSCID,\n c.CandID as DCCID,\n Project.Name
>>                 as project,\n s.Visit_label as visitLabel,\n
>>                 \n??????????? CASE s.MRIQCStatus\n WHEN 'Fail' THEN\n
>>                 IF(s.MRIQCPending='Y', 'Pending Fail', 'Fail')\n WHEN
>>                 'Pass' THEN\n IF(s.MRIQCPending='Y', 'Pending Pass',
>>                 'Pass') \n??????????????? ELSE s.MRIQCStatus\n END
>>                 \n???????????? as Visit_QC_Status,\n
>>                 DATE_FORMAT(MIN(pf.Value), "%Y-%m-%d") as
>>                 First_Acquisition,\n FROM_UNIXTIME(MIN(f.InsertTime))
>>                 as First_Insertion,\n
>>                 FROM_UNIXTIME(MAX(fqc.QCLastChangeTime)) as
>>                 Last_QC,\n \n??????????? CASE \n
>>                 COALESCE(Max(fqc.QCLastChangeTime),
>>                 'new')\n??????????????? WHEN 'new' THEN
>>                 'new'\n??????????????? WHEN ''??? THEN
>>                 'new'\n??????????????? WHEN NULL? THEN
>>                 'new'\n??????????????? ELSE ''\n??????????? END as
>>                 New_Da in
>>                 /var/www/loris/src/Data/Provisioners/DBRowProvisioner.php
>>                 on line 84, referer: http://10.38.133.3/imaging_browser/
>>
>>                 Best,
>>                 Blake
>>
>>
>>
>>                 -- 
>>
>>                 christine.rogers at mcgill.ca
>>                 <mailto: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
>>                 <mailto:Loris-dev at bic.mni.mcgill.ca>
>>                 https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>
>>
>>
>>             -- 
>>
>>             christine.rogers at mcgill.ca
>>             <mailto: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
>             <mailto:Loris-dev at bic.mni.mcgill.ca>
>             https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
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From blake.fitch at tuebingen.mpg.de  Tue Feb 25 07:43:46 2020
From: blake.fitch at tuebingen.mpg.de (Blake Fitch)
Date: Tue, 25 Feb 2020 13:43:46 +0100
Subject: [Loris-dev] Imaging Uploader stuck at Progres Not Started
In-Reply-To: <CAMpvQ9iTTAzaLTcxeWsMeQf==3kq2brVxfVBSFhxUEvvQwdJKg@mail.gmail.com>
References: <CALbt7NDvsQ5uu2rB4Nex-qx6vQF9UJAyq99C=j2DCVMvfSObLw@mail.gmail.com>
 <CALbt7NCe3wMOTVFoWu_7S7nRdBMm7yAwU_Do+t6+WLAj59mJPw@mail.gmail.com>
 <ac88f33a-4e3f-d685-2930-bce3643f5b19@tuebingen.mpg.de>
 <CAMpvQ9h8uWjC8Tf+x_=NZLLfP9zqy8sG6Xrj2AHq-dXf513ATw@mail.gmail.com>
 <CAMpvQ9i5m5Gf2u7ndS+90mOghCEFBscm00hOWbCniiBf6aj8qw@mail.gmail.com>
 <CAMpvQ9iTTAzaLTcxeWsMeQf==3kq2brVxfVBSFhxUEvvQwdJKg@mail.gmail.com>
Message-ID: <7d7bae86-76c3-afa9-1d7c-dd38cd801722@tuebingen.mpg.de>

Hi Ling Ma,

Thank you for the fix on the imaging uploader page.

My next issue is that my uploads don't seem to be processing. On the 
table on the snapshot below, you'll see under the Progress tab "Not 
Started". What do I have to do to get my uploads processed?

Best,
Blake

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From blake.fitch at tuebingen.mpg.de  Tue Feb 25 08:01:58 2020
From: blake.fitch at tuebingen.mpg.de (Blake Fitch)
Date: Tue, 25 Feb 2020 14:01:58 +0100
Subject: [Loris-dev] Imaging Uploader stuck at Progres Not Started
In-Reply-To: <7d7bae86-76c3-afa9-1d7c-dd38cd801722@tuebingen.mpg.de>
References: <CALbt7NDvsQ5uu2rB4Nex-qx6vQF9UJAyq99C=j2DCVMvfSObLw@mail.gmail.com>
 <CALbt7NCe3wMOTVFoWu_7S7nRdBMm7yAwU_Do+t6+WLAj59mJPw@mail.gmail.com>
 <ac88f33a-4e3f-d685-2930-bce3643f5b19@tuebingen.mpg.de>
 <CAMpvQ9h8uWjC8Tf+x_=NZLLfP9zqy8sG6Xrj2AHq-dXf513ATw@mail.gmail.com>
 <CAMpvQ9i5m5Gf2u7ndS+90mOghCEFBscm00hOWbCniiBf6aj8qw@mail.gmail.com>
 <CAMpvQ9iTTAzaLTcxeWsMeQf==3kq2brVxfVBSFhxUEvvQwdJKg@mail.gmail.com>
 <7d7bae86-76c3-afa9-1d7c-dd38cd801722@tuebingen.mpg.de>
Message-ID: <bfc6c471-b8e7-a901-fff7-223d962dd731@tuebingen.mpg.de>

Further to this ...

On 25.02.20 13:43, Blake Fitch wrote:
>
> Hi Ling Ma,
>
> Thank you for the fix on the imaging uploader page.
>
> My next issue is that my uploads don't seem to be processing. On the 
> table on the snapshot below, you'll see under the Progress tab "Not 
> Started". What do I have to do to get my uploads processed?
>
> Best,
> Blake
>
>
> _______________________________________________
> 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  Tue Feb 25 08:03:05 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Tue, 25 Feb 2020 08:03:05 -0500
Subject: [Loris-dev] Imaging Uploader stuck at Progres Not Started
In-Reply-To: <7d7bae86-76c3-afa9-1d7c-dd38cd801722@tuebingen.mpg.de>
References: <CALbt7NDvsQ5uu2rB4Nex-qx6vQF9UJAyq99C=j2DCVMvfSObLw@mail.gmail.com>
 <CALbt7NCe3wMOTVFoWu_7S7nRdBMm7yAwU_Do+t6+WLAj59mJPw@mail.gmail.com>
 <ac88f33a-4e3f-d685-2930-bce3643f5b19@tuebingen.mpg.de>
 <CAMpvQ9h8uWjC8Tf+x_=NZLLfP9zqy8sG6Xrj2AHq-dXf513ATw@mail.gmail.com>
 <CAMpvQ9i5m5Gf2u7ndS+90mOghCEFBscm00hOWbCniiBf6aj8qw@mail.gmail.com>
 <CAMpvQ9iTTAzaLTcxeWsMeQf==3kq2brVxfVBSFhxUEvvQwdJKg@mail.gmail.com>
 <7d7bae86-76c3-afa9-1d7c-dd38cd801722@tuebingen.mpg.de>
Message-ID: <CAMpvQ9hYU2f1KcnRK6GyZYBNb+FSSG+jfNFyThMrbpdnVZ-_Dg@mail.gmail.com>

Hi Blake,

You need to install Loris-MRI, which could be found at
https://github.com/aces/Loris-MRI, follow the instructions and process the
images with the command like imaging_upload_file with parameters, then you
can see the images if all goes well.

Thanks.

Regards,
Ling Ma

On Tue, Feb 25, 2020 at 7:43 AM Blake Fitch <blake.fitch at tuebingen.mpg.de>
wrote:

> Hi Ling Ma,
>
> Thank you for the fix on the imaging uploader page.
>
> My next issue is that my uploads don't seem to be processing. On the table
> on the snapshot below, you'll see under the Progress tab "Not Started".
> What do I have to do to get my uploads processed?
>
> Best,
> Blake
>
>
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From lingyun.ma at mcin.ca  Tue Feb 25 08:05:23 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Tue, 25 Feb 2020 08:05:23 -0500
Subject: [Loris-dev] Imaging Uploader stuck at Progres Not Started
In-Reply-To: <bfc6c471-b8e7-a901-fff7-223d962dd731@tuebingen.mpg.de>
References: <CALbt7NDvsQ5uu2rB4Nex-qx6vQF9UJAyq99C=j2DCVMvfSObLw@mail.gmail.com>
 <CALbt7NCe3wMOTVFoWu_7S7nRdBMm7yAwU_Do+t6+WLAj59mJPw@mail.gmail.com>
 <ac88f33a-4e3f-d685-2930-bce3643f5b19@tuebingen.mpg.de>
 <CAMpvQ9h8uWjC8Tf+x_=NZLLfP9zqy8sG6Xrj2AHq-dXf513ATw@mail.gmail.com>
 <CAMpvQ9i5m5Gf2u7ndS+90mOghCEFBscm00hOWbCniiBf6aj8qw@mail.gmail.com>
 <CAMpvQ9iTTAzaLTcxeWsMeQf==3kq2brVxfVBSFhxUEvvQwdJKg@mail.gmail.com>
 <7d7bae86-76c3-afa9-1d7c-dd38cd801722@tuebingen.mpg.de>
 <bfc6c471-b8e7-a901-fff7-223d962dd731@tuebingen.mpg.de>
Message-ID: <CAMpvQ9heCEQuH2PcCxnmQFEQ0XMxVXp7ofzYJHAh7DgOofJJXg@mail.gmail.com>

You need to install Loris-MRI and configure some upload location,
permissions etc, otherwise the image might not have been even uploaded, and
which is of course not processed. If not processed, nothing will be
displayed.

On Tue, Feb 25, 2020 at 8:02 AM Blake Fitch <blake.fitch at tuebingen.mpg.de>
wrote:

> Further to this ...
>
> On 25.02.20 13:43, Blake Fitch wrote:
>
> Hi Ling Ma,
>
> Thank you for the fix on the imaging uploader page.
>
> My next issue is that my uploads don't seem to be processing. On the table
> on the snapshot below, you'll see under the Progress tab "Not Started".
> What do I have to do to get my uploads processed?
>
> Best,
> Blake
>
>
> _______________________________________________
> Loris-dev mailing listLoris-dev at bic.mni.mcgill.cahttps://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  Thu Feb 27 11:08:54 2020
From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos)
Date: Thu, 27 Feb 2020 18:08:54 +0200
Subject: [Loris-dev] Customize page
Message-ID: <CAKHj7uQFOERakGvXKpBXAiw_4-Ho=6pFvHM6pGN1zcNnvBhm2w@mail.gmail.com>

Hi,

We would like to customize the Selection Filter given in
https://demo.loris.ca/dicom_archive/ page. Also we would like to add a new
column on the existing table shown ( that batch column will be contained in
the files table ). Could you give some info on how to proceed?

The desired result is as shown in that image

[image: image.png]

Thank you

Sotirios
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From lingyun.ma at mcin.ca  Thu Feb 27 11:27:07 2020
From: lingyun.ma at mcin.ca (Ling Ma)
Date: Thu, 27 Feb 2020 11:27:07 -0500
Subject: [Loris-dev] Customize page
In-Reply-To: <CAKHj7uQFOERakGvXKpBXAiw_4-Ho=6pFvHM6pGN1zcNnvBhm2w@mail.gmail.com>
References: <CAKHj7uQFOERakGvXKpBXAiw_4-Ho=6pFvHM6pGN1zcNnvBhm2w@mail.gmail.com>
Message-ID: <CAMpvQ9iKY48+VKsfVezRUD9PUri+CqGm-vbN41Of5BGyCVUOpg@mail.gmail.com>

Hi Sotirios,

You will need to customize the dicom_archive modules which resides under
<web root>/modules/dicom_archive, we recommend against modifying directly
the module, instead you copy that module into project/modules to do any
customization there, then run "composer install" to let the Loris know that
you want to use your customized version. Then you need to run "make" under
the <web root> to compile jsx to js.

The table and the filter are written in ReactJS, as long as you have some
knowledge of ReactJS and PHP, you could go ahead to do it.

Best regards,
Ling Ma

On Thu, Feb 27, 2020 at 11:09 AM Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:

> Hi,
>
> We would like to customize the Selection Filter given in
> https://demo.loris.ca/dicom_archive/ page. Also we would like to add a
> new column on the existing table shown ( that batch column will be
> contained in the files table ). Could you give some info on how to proceed?
>
> The desired result is as shown in that image
>
> [image: image.png]
>
> Thank you
>
> Sotirios
>
> _______________________________________________
> 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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