From jessica.callegaro at mcin.ca  Mon Nov  1 09:41:13 2021
From: jessica.callegaro at mcin.ca (Jessica Callegaro)
Date: Mon, 1 Nov 2021 09:41:13 -0400
Subject: [Loris-dev] failed uploading through imaging Uploader module
In-Reply-To: <CALw_=Q0DHfqZWLUkDJ6tAjKta7EWepraGigifUOytk=Wk5awEA@mail.gmail.com>
References: <CALw_=Q0DHfqZWLUkDJ6tAjKta7EWepraGigifUOytk=Wk5awEA@mail.gmail.com>
Message-ID: <CAE30ZxaKNiSj98fUDhd=wF3JtLEQ=f64E+QHSxYJ8Eb_0D7LMA@mail.gmail.com>

Hi Mandana,

I might be wrong but it looks like there is a space in your file name
between V1 and the .zip extension.

Also you should increase the file size limit on your VM so that you can
upload large imaging files. Here's some documentation on how to do that:
https://loris-hq.readthedocs.io/en/latest/docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/02_Website_Configuration/Handling_Large_File_Uploads.html

Hope this helped!

Best,
Jessica Callegaro
CCNA-LORIS Software Developer
Montreal Neurological Institute
McGill University
jessica.callegaro at mcin.ca


On Fri, Oct 29, 2021 at 7:12 PM mandana mazaheri <mndmazaheri at gmail.com>
wrote:

> Hi LorisDev Team,
>
> I am trying to upload a compressed file (zip) through Imaging Uploader in
> the LORIS frontend, but I get the following error message, could you assist
> me with how I should proceed?
> [image: image.png]
>
>
> _______________________________________________
> 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/20211101/8aa57713/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 81566 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211101/8aa57713/attachment-0001.png>

From mndmazaheri at gmail.com  Mon Nov  1 13:56:43 2021
From: mndmazaheri at gmail.com (mandana mazaheri)
Date: Mon, 1 Nov 2021 10:56:43 -0700
Subject: [Loris-dev] failed uploading through imaging Uploader module
In-Reply-To: <CAE30ZxaKNiSj98fUDhd=wF3JtLEQ=f64E+QHSxYJ8Eb_0D7LMA@mail.gmail.com>
References: <CALw_=Q0DHfqZWLUkDJ6tAjKta7EWepraGigifUOytk=Wk5awEA@mail.gmail.com>
 <CAE30ZxaKNiSj98fUDhd=wF3JtLEQ=f64E+QHSxYJ8Eb_0D7LMA@mail.gmail.com>
Message-ID: <CALw_=Q1uWT8RYYPzSMLkf0qNSS+d1n=B4QrLxgOudvqKDeE1cA@mail.gmail.com>

Dear Jessica,

Thank you for your response, the file name does not have space there, I
checked it again.
And about the VM, I have sent a ticket and requested for setting up an
Ubuntu VM but no one responded yet.

Thank you
Mandana

On Mon, Nov 1, 2021 at 6:41 AM Jessica Callegaro <jessica.callegaro at mcin.ca>
wrote:

> Hi Mandana,
>
> I might be wrong but it looks like there is a space in your file name
> between V1 and the .zip extension.
>
> Also you should increase the file size limit on your VM so that you can
> upload large imaging files. Here's some documentation on how to do that:
> https://loris-hq.readthedocs.io/en/latest/docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/02_Website_Configuration/Handling_Large_File_Uploads.html
>
> Hope this helped!
>
> Best,
> Jessica Callegaro
> CCNA-LORIS Software Developer
> Montreal Neurological Institute
> McGill University
> jessica.callegaro at mcin.ca
>
>
> On Fri, Oct 29, 2021 at 7:12 PM mandana mazaheri <mndmazaheri at gmail.com>
> wrote:
>
>> Hi LorisDev Team,
>>
>> I am trying to upload a compressed file (zip) through Imaging Uploader in
>> the LORIS frontend, but I get the following error message, could you assist
>> me with how I should proceed?
>> [image: image.png]
>>
>>
>> _______________________________________________
>> 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/20211101/f8179bcc/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 81566 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211101/f8179bcc/attachment-0001.png>

From AMORALESPINZON at BWH.HARVARD.EDU  Mon Nov  1 14:06:02 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Mon, 1 Nov 2021 18:06:02 +0000
Subject: [Loris-dev] Re-upload rejected scans
Message-ID: <8259DCE6-A6ED-479C-846A-9F9E67D33DE0@bwh.harvard.edu>

Dear LorisDev team,

I uploaded some MRI visits to a dataset using the wrong combination of PSCID and CandId. LORIS detected this, and put the scans in the "MRI Violated Scans" with this comment "PSCID and CandID of the image mismatch?. 

I would like to remove this MRI visit but I cannot remove them so that I can reupload them. On one side I don't see an uploadId that I can get to remove the scans. On the other hand, I resolved the problem using the "rejected option" but I cannot re-upload the visits. When re-uploading I am getting the following error:

===
The user 'lorisadmin' has already inserted this study. 
The unique study ID is '1.2.826.0.2.202387.200189250087163090034121192183204101173055193'.
This is the information retained from the first time the study was inserted:

* Taken from dir                   :    /tmp/ImagingUpload-17-33-ica8OF
* Archive target location          :    /xxx/loris_data/xxx/data/tarchive/DCM__ImagingUpload-17-33-ica8OF.tar
* Name of creating host            :    1xx.xxx.xxx.49
* Name of host OS                  :    Linux
* Created by user                  :    lorisadmin
* Archived on                      :    2021-10-21 17:36:20
* dicomSummary version             :    1 
* dicomTar version                 :    1  
* md5sum for DICOM tarball         :    aeb2fb07433d5ee6bd1fdf43f653c236  ImagingUpload-17-33-ica8OF.tar 
* md5sum for DICOM tarball gzipped :    670ce2246efc599566344d0a4101eb50  ImagingUpload-17-33-ica8OF.tar.gz 
* md5sum for complete archive      :    47953dd83530d53b670e12ec98494dbb  DCM__ImagingUpload-17-33-ica8OF.tar
===

How can I remove those scans so that I can reupload them.

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 


From nicolasbrossard.mni at gmail.com  Mon Nov  1 15:29:07 2021
From: nicolasbrossard.mni at gmail.com (Nicolas Brossard)
Date: Mon, 1 Nov 2021 15:29:07 -0400
Subject: [Loris-dev] failed uploading through imaging Uploader module
In-Reply-To: <CALw_=Q0DHfqZWLUkDJ6tAjKta7EWepraGigifUOytk=Wk5awEA@mail.gmail.com>
References: <CALw_=Q0DHfqZWLUkDJ6tAjKta7EWepraGigifUOytk=Wk5awEA@mail.gmail.com>
Message-ID: <CAHaEUvry4DUQj78UYbdPvMs78_CGCr9421bv_snoUQO2y6rWVQ@mail.gmail.com>

Hi Mandana,

What do you get when you run the Unix/Linux program file
<https://www.geeksforgeeks.org/file-command-in-linux-with-examples/> on the
file that you are trying to upload?


Nicolas


On Fri, Oct 29, 2021 at 7:12 PM mandana mazaheri <mndmazaheri at gmail.com>
wrote:

> Hi LorisDev Team,
>
> I am trying to upload a compressed file (zip) through Imaging Uploader in
> the LORIS frontend, but I get the following error message, could you assist
> me with how I should proceed?
> [image: image.png]
>
>
> _______________________________________________
> 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/20211101/c7fa7a8b/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 81566 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211101/c7fa7a8b/attachment-0001.png>

From mndmazaheri at gmail.com  Mon Nov  1 15:37:56 2021
From: mndmazaheri at gmail.com (mandana mazaheri)
Date: Mon, 1 Nov 2021 12:37:56 -0700
Subject: [Loris-dev] failed uploading through imaging Uploader module
In-Reply-To: <CAHaEUvry4DUQj78UYbdPvMs78_CGCr9421bv_snoUQO2y6rWVQ@mail.gmail.com>
References: <CALw_=Q0DHfqZWLUkDJ6tAjKta7EWepraGigifUOytk=Wk5awEA@mail.gmail.com>
 <CAHaEUvry4DUQj78UYbdPvMs78_CGCr9421bv_snoUQO2y6rWVQ@mail.gmail.com>
Message-ID: <CALw_=Q38_79NkuxyC+k7NvRDHdsusSPyJpUF4eKjTfaNuU4NbA@mail.gmail.com>

Hi Nicolas,

Thank you for your response, I get:
DCC211_696846_V1.zip: Zip archive data, at least v2.0 to extract

Regards

On Mon, Nov 1, 2021 at 12:34 PM Nicolas Brossard <
nicolasbrossard.mni at gmail.com> wrote:

> Hi Mandana,
>
> What do you get when you run the Unix/Linux program file
> <https://www.geeksforgeeks.org/file-command-in-linux-with-examples/> on
> the file that you are trying to upload?
>
>
> Nicolas
>
>
> On Fri, Oct 29, 2021 at 7:12 PM mandana mazaheri <mndmazaheri at gmail.com>
> wrote:
>
>> Hi LorisDev Team,
>>
>> I am trying to upload a compressed file (zip) through Imaging Uploader in
>> the LORIS frontend, but I get the following error message, could you assist
>> me with how I should proceed?
>> [image: image.png]
>>
>>
>> _______________________________________________
>> 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/20211101/bed0e54b/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 81566 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211101/bed0e54b/attachment-0001.png>

From cecile.madjar at mcin.ca  Tue Nov  2 15:02:56 2021
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Tue, 2 Nov 2021 15:02:56 -0400
Subject: [Loris-dev] Re-upload rejected scans
In-Reply-To: <8259DCE6-A6ED-479C-846A-9F9E67D33DE0@bwh.harvard.edu>
References: <8259DCE6-A6ED-479C-846A-9F9E67D33DE0@bwh.harvard.edu>
Message-ID: <CAMkiY3eQcMEuvtm2RmLcDE5n86QKoJ_oc_7V9z02z7K+SO=RQg@mail.gmail.com>

Hi Alfredo,

How come there is no upload associated with this scan? I don't see how it
is possible for a DICOM study unless you did some manual deletion instead
of running the delete script?

You could always manually delete the entry for the mislabelled scan in the
tarchive table. Usually, deleting from tarchive will also delete the
attached entries present in tarchive_series and tarchive_files.

Hope this helps,

C?cile

On Mon, Nov 1, 2021 at 2:10 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Dear LorisDev team,
>
> I uploaded some MRI visits to a dataset using the wrong combination of
> PSCID and CandId. LORIS detected this, and put the scans in the "MRI
> Violated Scans" with this comment "PSCID and CandID of the image mismatch?.
>
> I would like to remove this MRI visit but I cannot remove them so that I
> can reupload them. On one side I don't see an uploadId that I can get to
> remove the scans. On the other hand, I resolved the problem using the
> "rejected option" but I cannot re-upload the visits. When re-uploading I am
> getting the following error:
>
> ===
> The user 'lorisadmin' has already inserted this study.
> The unique study ID is
> '1.2.826.0.2.202387.200189250087163090034121192183204101173055193'.
> This is the information retained from the first time the study was
> inserted:
>
> * Taken from dir                   :    /tmp/ImagingUpload-17-33-ica8OF
> * Archive target location          :
> /xxx/loris_data/xxx/data/tarchive/DCM__ImagingUpload-17-33-ica8OF.tar
> * Name of creating host            :    1xx.xxx.xxx.49
> * Name of host OS                  :    Linux
> * Created by user                  :    lorisadmin
> * Archived on                      :    2021-10-21 17:36:20
> * dicomSummary version             :    1
> * dicomTar version                 :    1
> * md5sum for DICOM tarball         :    aeb2fb07433d5ee6bd1fdf43f653c236
> ImagingUpload-17-33-ica8OF.tar
> * md5sum for DICOM tarball gzipped :    670ce2246efc599566344d0a4101eb50
> ImagingUpload-17-33-ica8OF.tar.gz
> * md5sum for complete archive      :    47953dd83530d53b670e12ec98494dbb
> DCM__ImagingUpload-17-33-ica8OF.tar
> ===
>
> How can I remove those scans so that I can reupload them.
>
> 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 Mass General
> Brigham Compliance HelpLine at
> http://www.massgeneralbrigham.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.
> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
> _______________________________________________
> 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/20211102/75062b02/attachment.html>

From AMORALESPINZON at BWH.HARVARD.EDU  Wed Nov  3 13:35:31 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Wed, 3 Nov 2021 17:35:31 +0000
Subject: [Loris-dev] Re-upload rejected scans
In-Reply-To: <CAMkiY3eQcMEuvtm2RmLcDE5n86QKoJ_oc_7V9z02z7K+SO=RQg@mail.gmail.com>
References: <8259DCE6-A6ED-479C-846A-9F9E67D33DE0@bwh.harvard.edu>
 <CAMkiY3eQcMEuvtm2RmLcDE5n86QKoJ_oc_7V9z02z7K+SO=RQg@mail.gmail.com>
Message-ID: <06E9EFB7-B034-4866-ADA9-AD341C6C750B@bwh.harvard.edu>

Hi C?cile,

I did used the script for deleting images given an uploadId. I haven?t done any manual deletion. Happy to show you the state of the database if this is helpful.

I will try deleting from the tarchive table and let you know.

Best,
Alfredo.

On Nov 2, 2021, at 2:02 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

How come there is no upload associated with this scan? I don't see how it is possible for a DICOM study unless you did some manual deletion instead of running the delete script?

You could always manually delete the entry for the mislabelled scan in the tarchive table. Usually, deleting from tarchive will also delete the attached entries present in tarchive_series and tarchive_files.

Hope this helps,

C?cile

On Mon, Nov 1, 2021 at 2:10 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LorisDev team,

I uploaded some MRI visits to a dataset using the wrong combination of PSCID and CandId. LORIS detected this, and put the scans in the "MRI Violated Scans" with this comment "PSCID and CandID of the image mismatch?.

I would like to remove this MRI visit but I cannot remove them so that I can reupload them. On one side I don't see an uploadId that I can get to remove the scans. On the other hand, I resolved the problem using the "rejected option" but I cannot re-upload the visits. When re-uploading I am getting the following error:

===
The user 'lorisadmin' has already inserted this study.
The unique study ID is '1.2.826.0.2.202387.200189250087163090034121192183204101173055193'.
This is the information retained from the first time the study was inserted:

* Taken from dir                   :    /tmp/ImagingUpload-17-33-ica8OF
* Archive target location          :    /xxx/loris_data/xxx/data/tarchive/DCM__ImagingUpload-17-33-ica8OF.tar
* Name of creating host            :    1xx.xxx.xxx.49
* Name of host OS                  :    Linux
* Created by user                  :    lorisadmin
* Archived on                      :    2021-10-21 17:36:20
* dicomSummary version             :    1
* dicomTar version                 :    1
* md5sum for DICOM tarball         :    aeb2fb07433d5ee6bd1fdf43f653c236  ImagingUpload-17-33-ica8OF.tar
* md5sum for DICOM tarball gzipped :    670ce2246efc599566344d0a4101eb50  ImagingUpload-17-33-ica8OF.tar.gz
* md5sum for complete archive      :    47953dd83530d53b670e12ec98494dbb  DCM__ImagingUpload-17-33-ica8OF.tar
===

How can I remove those scans so that I can reupload them.

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1dC3022UrfJ1Tg4EQfcDedkjYirxCoHF6HZar8-G92PVZPaA0r43-PnuZauOvSLmGxVnuN5coWnJ7ax3PrArgWYLkH-sZwar_zx8ONPDJFqykzweHRMor5eXjWL4zV_-CkYmzTSv0ebTNoV1jGd4UfAEL6RodxIPuF1csrsrBG0M9TJuewXyi7mArjQ45PRjgN21P--ZbUycg57B9Hr1rAYqloMdQRASjGwlc_I7HhDRWwqZMUsrMr8EViNSu5adlKzbb2G9aE--MVh4uZKojyA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

_______________________________________________
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://secure-web.cisco.com/1UBngX2kYVGkdtEtcFhhJw-t0DrdD5T0rRSFU3jMMntPxUciuera8xIAbOWnhiE4Jqvb3vJOT4KRVEE72dzjNmDqxVgIOALEuoxH8l9Eo0cooEakq8xqzmOg4qINyyQZyoy1w040f0Krd6QV2UB3l6Oz7zIsIcoi268BTr9mbI-NlhIQMgvVHam41L7La6x7ijTZeQZeJfrvt4NddWX6uOUzL9MF9WyXApCqlzLC7EH8fANEyq9aRIK-StN-GMPOO3r5_f02EEItUWuLpcjY3Vw/https%3A%2F%2Fmailman.bic.mni.mcgill.ca%2Fmailman%2Flistinfo%2Floris-dev>

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211103/94bd6036/attachment-0001.html>

From joh17964 at umn.edu  Wed Nov 10 14:28:53 2021
From: joh17964 at umn.edu (Eli Johnson)
Date: Wed, 10 Nov 2021 13:28:53 -0600
Subject: [Loris-dev] Error on data dictionary
Message-ID: <CAKcpJh5PTSCVZjY3Kx+ESBEm-gEePyq+Q+rgF0iF-gShwADDhw@mail.gmail.com>

Hi,

I am updating from LORIS v23.0.2 to v23.0.8 (running on RHEL7). Everything
is working except the data dictionary. I'm getting an error when trying to
load the data dictionary module. The data dictionary page contains the text
"An error occurred while loading the page", there is nothing logged in the
apache error-log, the browser console reports "SyntaxError: Unexpected end
of JSON input" on dataDictIndex.js:49.  I'm not super familiar with react
so I'm not sure how to find the source of the error although it looks like
it's occurring on *fetchData*. Any idea why this would happen or
suggestions on how to debug?

Thanks,
Eli

Eli Johnson
Developer/Data Manager
Institute of Child Development
University of Minnesota
joh17964 at umn.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211110/da21c5d8/attachment.html>

From dave.macfarlane at mcin.ca  Thu Nov 11 09:24:02 2021
From: dave.macfarlane at mcin.ca (Dave MacFarlane)
Date: Thu, 11 Nov 2021 09:24:02 -0500
Subject: [Loris-dev] Error on data dictionary
In-Reply-To: <CAKcpJh5PTSCVZjY3Kx+ESBEm-gEePyq+Q+rgF0iF-gShwADDhw@mail.gmail.com>
References: <CAKcpJh5PTSCVZjY3Kx+ESBEm-gEePyq+Q+rgF0iF-gShwADDhw@mail.gmail.com>
Message-ID: <CAN9cDwG3=Cnqp_1NNSJ+5t9822sx=eqjgUchB4p=PYV6O=e7YQ@mail.gmail.com>

Hi Eli,

I'm not sure why that would have broken between 2 bug fix releases, but the
error "SyntaxError: Unexpected end of JSON input" implies that the attempt
to fetch the fields returned invalid input. This can happen if, for
instance, an exception is thrown by the ajax request. If you open the
network tab* in your developer tools before loading the page there should
be a request for "(your url)/datadict/fields". Click on that, and then the
"Response" tab* in the network tools and you should get a better idea of
what's being returned to debug.

* That's how they're labeled in Firefox. I'm not sure off the top of my
head what the labels are in Chrome but it should be similar.

On Wed, Nov 10, 2021 at 2:29 PM Eli Johnson <joh17964 at umn.edu> wrote:

> Hi,
>
> I am updating from LORIS v23.0.2 to v23.0.8 (running on RHEL7). Everything
> is working except the data dictionary. I'm getting an error when trying to
> load the data dictionary module. The data dictionary page contains the text
> "An error occurred while loading the page", there is nothing logged in the
> apache error-log, the browser console reports "SyntaxError: Unexpected end
> of JSON input" on dataDictIndex.js:49.  I'm not super familiar with react
> so I'm not sure how to find the source of the error although it looks like
> it's occurring on *fetchData*. Any idea why this would happen or
> suggestions on how to debug?
>
> Thanks,
> Eli
>
> Eli Johnson
> Developer/Data Manager
> Institute of Child Development
> University of Minnesota
> joh17964 at umn.edu
> _______________________________________________
> 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/20211111/0546cadc/attachment.html>

From joh17964 at umn.edu  Thu Nov 11 19:17:09 2021
From: joh17964 at umn.edu (Eli Johnson)
Date: Thu, 11 Nov 2021 18:17:09 -0600
Subject: [Loris-dev] Error on data dictionary
In-Reply-To: <CAN9cDwG3=Cnqp_1NNSJ+5t9822sx=eqjgUchB4p=PYV6O=e7YQ@mail.gmail.com>
References: <CAKcpJh5PTSCVZjY3Kx+ESBEm-gEePyq+Q+rgF0iF-gShwADDhw@mail.gmail.com>
 <CAN9cDwG3=Cnqp_1NNSJ+5t9822sx=eqjgUchB4p=PYV6O=e7YQ@mail.gmail.com>
Message-ID: <CAKcpJh4AH=kTK6Bu4LpEcmLrvoUMidE5CVP9L1fbt=Pn35OQ9w@mail.gmail.com>

Hi Dave,

I reverted to the v23.0.0 version of the datadict module and it's working
properly again.

I did inspect the returned values -- the json data package returned by
"<lorisurl>/datadict/?format=json" appears to be cut off. For some reason
it looks like ~40 newlines have been added before the json begins and then
an equivalent number of characters have been cut off from the end. I didn't
find any obvious issues when briefly inspecting the v23.0.8 changes to
php/datadict.class.inc but something there appears to be the source of the
issue.

Best,
Eli


Eli Johnson
Developer/Data Manager
Institute of Child Development
University of Minnesota
joh17964 at umn.edu


On Thu, Nov 11, 2021 at 8:24 AM Dave MacFarlane <dave.macfarlane at mcin.ca>
wrote:

> Hi Eli,
>
> I'm not sure why that would have broken between 2 bug fix releases, but
> the error "SyntaxError: Unexpected end of JSON input" implies that the
> attempt to fetch the fields returned invalid input. This can happen if, for
> instance, an exception is thrown by the ajax request. If you open the
> network tab* in your developer tools before loading the page there should
> be a request for "(your url)/datadict/fields". Click on that, and then the
> "Response" tab* in the network tools and you should get a better idea of
> what's being returned to debug.
>
> * That's how they're labeled in Firefox. I'm not sure off the top of my
> head what the labels are in Chrome but it should be similar.
>
> On Wed, Nov 10, 2021 at 2:29 PM Eli Johnson <joh17964 at umn.edu> wrote:
>
>> Hi,
>>
>> I am updating from LORIS v23.0.2 to v23.0.8 (running on RHEL7).
>> Everything is working except the data dictionary. I'm getting an error when
>> trying to load the data dictionary module. The data dictionary page
>> contains the text "An error occurred while loading the page", there is
>> nothing logged in the apache error-log, the browser console reports
>> "SyntaxError: Unexpected end of JSON input" on dataDictIndex.js:49.  I'm
>> not super familiar with react so I'm not sure how to find the source of the
>> error although it looks like it's occurring on *fetchData*. Any idea why
>> this would happen or suggestions on how to debug?
>>
>> Thanks,
>> Eli
>>
>> Eli Johnson
>> Developer/Data Manager
>> Institute of Child Development
>> University of Minnesota
>> joh17964 at umn.edu
>> _______________________________________________
>> 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/20211111/2f266b44/attachment.html>

From dave.macfarlane at mcin.ca  Tue Nov 16 12:29:45 2021
From: dave.macfarlane at mcin.ca (Dave MacFarlane)
Date: Tue, 16 Nov 2021 12:29:45 -0500
Subject: [Loris-dev] Error on data dictionary
In-Reply-To: <CAKcpJh4AH=kTK6Bu4LpEcmLrvoUMidE5CVP9L1fbt=Pn35OQ9w@mail.gmail.com>
References: <CAKcpJh5PTSCVZjY3Kx+ESBEm-gEePyq+Q+rgF0iF-gShwADDhw@mail.gmail.com>
 <CAN9cDwG3=Cnqp_1NNSJ+5t9822sx=eqjgUchB4p=PYV6O=e7YQ@mail.gmail.com>
 <CAKcpJh4AH=kTK6Bu4LpEcmLrvoUMidE5CVP9L1fbt=Pn35OQ9w@mail.gmail.com>
Message-ID: <CAN9cDwEZOnr7EEaENsppKsxf+nfpwcG2hA+Sb=t4uCakv5joFw@mail.gmail.com>

Hi Eli,

I'm not able to reproduce this on the raisinbread dataset. It sounds like
LORIS is generating the "Content-Length" header based on the json data, but
something is printing newlines before the output is sent, resulting in the
browser reading those, and then stopping reading once Content-length bytes
are read.

The main change in the diff between the v23.0.0 and v23.0.8 versions in the
module seems to be that it instantiates instruments to get the table name
now, suggesting it might be a problem originating from one of your
instruments. I tried adding a print newline into the setup function of an
arbitrary instrument and got warnings such as:

*Warning*: Cannot modify header information - headers already sent by
(output started at
/home/driusan/Code/Loris/project/instruments/NDB_BVL_Instrument_mri_parameter_form.class.inc:53)
in */home/driusan/Code/Loris/htdocs/index.php* on line *60*

but it's possible that the display of the warning is php.ini sensitive. I
also tried adding newlines after the PHP closing tag in some files and got
the same warning.

Those warnings some from the PHP side, but on the loris side there should
also be an error logged to your apache logs if there's a problem
instantiating the instrument:

error_log(
"There was a problem instantiating the instrument ".
"'$instrument'. Make sure the instrument is valid and ".
"functional in order for it to be displayed in the data ".
"dictionary."
);

It shouldn't cause newlines to be printed, but it's possible that something
in the attempt to instantiate the instrument does. Do you get that error in
your logs?

- Dave

On Thu, Nov 11, 2021 at 7:17 PM Eli Johnson <joh17964 at umn.edu> wrote:

> Hi Dave,
>
> I reverted to the v23.0.0 version of the datadict module and it's working
> properly again.
>
> I did inspect the returned values -- the json data package returned by
> "<lorisurl>/datadict/?format=json" appears to be cut off. For some reason
> it looks like ~40 newlines have been added before the json begins and then
> an equivalent number of characters have been cut off from the end. I didn't
> find any obvious issues when briefly inspecting the v23.0.8 changes to
> php/datadict.class.inc but something there appears to be the source of the
> issue.
>
> Best,
> Eli
>
>
> Eli Johnson
> Developer/Data Manager
> Institute of Child Development
> University of Minnesota
> joh17964 at umn.edu
>
>
> On Thu, Nov 11, 2021 at 8:24 AM Dave MacFarlane <dave.macfarlane at mcin.ca>
> wrote:
>
>> Hi Eli,
>>
>> I'm not sure why that would have broken between 2 bug fix releases, but
>> the error "SyntaxError: Unexpected end of JSON input" implies that the
>> attempt to fetch the fields returned invalid input. This can happen if, for
>> instance, an exception is thrown by the ajax request. If you open the
>> network tab* in your developer tools before loading the page there should
>> be a request for "(your url)/datadict/fields". Click on that, and then the
>> "Response" tab* in the network tools and you should get a better idea of
>> what's being returned to debug.
>>
>> * That's how they're labeled in Firefox. I'm not sure off the top of my
>> head what the labels are in Chrome but it should be similar.
>>
>> On Wed, Nov 10, 2021 at 2:29 PM Eli Johnson <joh17964 at umn.edu> wrote:
>>
>>> Hi,
>>>
>>> I am updating from LORIS v23.0.2 to v23.0.8 (running on RHEL7).
>>> Everything is working except the data dictionary. I'm getting an error when
>>> trying to load the data dictionary module. The data dictionary page
>>> contains the text "An error occurred while loading the page", there is
>>> nothing logged in the apache error-log, the browser console reports
>>> "SyntaxError: Unexpected end of JSON input" on dataDictIndex.js:49.  I'm
>>> not super familiar with react so I'm not sure how to find the source of the
>>> error although it looks like it's occurring on *fetchData*. Any idea
>>> why this would happen or suggestions on how to debug?
>>>
>>> Thanks,
>>> Eli
>>>
>>> Eli Johnson
>>> Developer/Data Manager
>>> Institute of Child Development
>>> University of Minnesota
>>> joh17964 at umn.edu
>>> _______________________________________________
>>> 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/20211116/2894e433/attachment.html>

From joh17964 at umn.edu  Wed Nov 17 18:21:00 2021
From: joh17964 at umn.edu (Eli Johnson)
Date: Wed, 17 Nov 2021 17:21:00 -0600
Subject: [Loris-dev] Error on data dictionary
In-Reply-To: <CAN9cDwEZOnr7EEaENsppKsxf+nfpwcG2hA+Sb=t4uCakv5joFw@mail.gmail.com>
References: <CAKcpJh5PTSCVZjY3Kx+ESBEm-gEePyq+Q+rgF0iF-gShwADDhw@mail.gmail.com>
 <CAN9cDwG3=Cnqp_1NNSJ+5t9822sx=eqjgUchB4p=PYV6O=e7YQ@mail.gmail.com>
 <CAKcpJh4AH=kTK6Bu4LpEcmLrvoUMidE5CVP9L1fbt=Pn35OQ9w@mail.gmail.com>
 <CAN9cDwEZOnr7EEaENsppKsxf+nfpwcG2hA+Sb=t4uCakv5joFw@mail.gmail.com>
Message-ID: <CAKcpJh6EkCr2d_AvbNre5G9a_er2B5g12hjTLU1FZ=sBha7wmg@mail.gmail.com>

Hi Dave,

There was nothing logged in the apache error log. I don't think I have
newlines in any of the instruments. If this is just an issue with our
instance of LORIS and you can't recreate the issue, I can troubleshoot it
more in the future. For now it's not urgent. I'll follow up if I have
further questions.

-Eli

Eli Johnson
Developer/Data Manager
Institute of Child Development
University of Minnesota
joh17964 at umn.edu


On Tue, Nov 16, 2021 at 11:29 AM Dave MacFarlane <dave.macfarlane at mcin.ca>
wrote:

> Hi Eli,
>
> I'm not able to reproduce this on the raisinbread dataset. It sounds like
> LORIS is generating the "Content-Length" header based on the json data, but
> something is printing newlines before the output is sent, resulting in the
> browser reading those, and then stopping reading once Content-length bytes
> are read.
>
> The main change in the diff between the v23.0.0 and v23.0.8 versions in
> the module seems to be that it instantiates instruments to get the table
> name now, suggesting it might be a problem originating from one of your
> instruments. I tried adding a print newline into the setup function of an
> arbitrary instrument and got warnings such as:
>
> *Warning*: Cannot modify header information - headers already sent by
> (output started at
> /home/driusan/Code/Loris/project/instruments/NDB_BVL_Instrument_mri_parameter_form.class.inc:53)
> in */home/driusan/Code/Loris/htdocs/index.php* on line *60*
>
> but it's possible that the display of the warning is php.ini sensitive. I
> also tried adding newlines after the PHP closing tag in some files and got
> the same warning.
>
> Those warnings some from the PHP side, but on the loris side there should
> also be an error logged to your apache logs if there's a problem
> instantiating the instrument:
>
> error_log(
> "There was a problem instantiating the instrument ".
> "'$instrument'. Make sure the instrument is valid and ".
> "functional in order for it to be displayed in the data ".
> "dictionary."
> );
>
> It shouldn't cause newlines to be printed, but it's possible that
> something in the attempt to instantiate the instrument does. Do you get
> that error in your logs?
>
> - Dave
>
> On Thu, Nov 11, 2021 at 7:17 PM Eli Johnson <joh17964 at umn.edu> wrote:
>
>> Hi Dave,
>>
>> I reverted to the v23.0.0 version of the datadict module and it's working
>> properly again.
>>
>> I did inspect the returned values -- the json data package returned by
>> "<lorisurl>/datadict/?format=json" appears to be cut off. For some reason
>> it looks like ~40 newlines have been added before the json begins and then
>> an equivalent number of characters have been cut off from the end. I didn't
>> find any obvious issues when briefly inspecting the v23.0.8 changes to
>> php/datadict.class.inc but something there appears to be the source of the
>> issue.
>>
>> Best,
>> Eli
>>
>>
>> Eli Johnson
>> Developer/Data Manager
>> Institute of Child Development
>> University of Minnesota
>> joh17964 at umn.edu
>>
>>
>> On Thu, Nov 11, 2021 at 8:24 AM Dave MacFarlane <dave.macfarlane at mcin.ca>
>> wrote:
>>
>>> Hi Eli,
>>>
>>> I'm not sure why that would have broken between 2 bug fix releases, but
>>> the error "SyntaxError: Unexpected end of JSON input" implies that the
>>> attempt to fetch the fields returned invalid input. This can happen if, for
>>> instance, an exception is thrown by the ajax request. If you open the
>>> network tab* in your developer tools before loading the page there should
>>> be a request for "(your url)/datadict/fields". Click on that, and then the
>>> "Response" tab* in the network tools and you should get a better idea of
>>> what's being returned to debug.
>>>
>>> * That's how they're labeled in Firefox. I'm not sure off the top of my
>>> head what the labels are in Chrome but it should be similar.
>>>
>>> On Wed, Nov 10, 2021 at 2:29 PM Eli Johnson <joh17964 at umn.edu> wrote:
>>>
>>>> Hi,
>>>>
>>>> I am updating from LORIS v23.0.2 to v23.0.8 (running on RHEL7).
>>>> Everything is working except the data dictionary. I'm getting an error when
>>>> trying to load the data dictionary module. The data dictionary page
>>>> contains the text "An error occurred while loading the page", there is
>>>> nothing logged in the apache error-log, the browser console reports
>>>> "SyntaxError: Unexpected end of JSON input" on dataDictIndex.js:49.  I'm
>>>> not super familiar with react so I'm not sure how to find the source of the
>>>> error although it looks like it's occurring on *fetchData*. Any idea
>>>> why this would happen or suggestions on how to debug?
>>>>
>>>> Thanks,
>>>> Eli
>>>>
>>>> Eli Johnson
>>>> Developer/Data Manager
>>>> Institute of Child Development
>>>> University of Minnesota
>>>> joh17964 at umn.edu
>>>> _______________________________________________
>>>> 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/20211117/977fe18a/attachment.html>

From AMORALESPINZON at BWH.HARVARD.EDU  Thu Nov 25 20:09:25 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Fri, 26 Nov 2021 01:09:25 +0000
Subject: [Loris-dev]  MINC insertion
In-Reply-To: <CAMkiY3eHjFAd1-bKdCx_5_k1nf2Mx_GCKDs2htAaTxxFoPqKhQ@mail.gmail.com>
References: <DBD132E4-4075-42F5-82EA-62C4EA86A33A@mcgill.ca>
 <CAMkiY3fKNoN1U=t3mjM2VnOgWU56=0-YadQwLkc6xZOGUc-mvA@mail.gmail.com>
 <ED989A0A-3A12-4161-AF6A-8F7586F7DDFE@bwh.harvard.edu>
 <CAMkiY3eHjFAd1-bKdCx_5_k1nf2Mx_GCKDs2htAaTxxFoPqKhQ@mail.gmail.com>
Message-ID: <63278E0B-C75D-467E-9A2C-579BC947EBC3@bwh.harvard.edu>

Hi C?cile,

I?m getting the following error when inserting a minc file using the minc_insertion.pl script:

===
$ perl minc_insertion.pl -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc  -verbose -acquisition_protocol t1c -create_minc_pics

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1018.

ERROR: Failed to insert record in table mri_scanner:

The following database commands failed:
PREPARE s FROM 'INSERT INTO mri_scanner (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

Could you help me figuring out what is happening? Is there something I should add to the minc headers?

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211126/c7a79cae/attachment.html>

From cecile.madjar at mcin.ca  Fri Nov 26 09:55:06 2021
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Fri, 26 Nov 2021 09:55:06 -0500
Subject: [Loris-dev] MINC insertion
In-Reply-To: <63278E0B-C75D-467E-9A2C-579BC947EBC3@bwh.harvard.edu>
References: <DBD132E4-4075-42F5-82EA-62C4EA86A33A@mcgill.ca>
 <CAMkiY3fKNoN1U=t3mjM2VnOgWU56=0-YadQwLkc6xZOGUc-mvA@mail.gmail.com>
 <ED989A0A-3A12-4161-AF6A-8F7586F7DDFE@bwh.harvard.edu>
 <CAMkiY3eHjFAd1-bKdCx_5_k1nf2Mx_GCKDs2htAaTxxFoPqKhQ@mail.gmail.com>
 <63278E0B-C75D-467E-9A2C-579BC947EBC3@bwh.harvard.edu>
Message-ID: <CAMkiY3fJcP0O=j++Rjjmymh9QqMofBY0NaTw0YH8GYTco7ZxSg@mail.gmail.com>

Hi Alfredo,

Could you point me to the version of the code you are using on GitHub so I
can take a look at the correct MRI.pm file.

Thank you!

C?cile

On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi C?cile,
>
> I?m getting the following error when inserting a minc file using the
> minc_insertion.pl script:
>
> ===
> $ perl minc_insertion.pl -profile prod -force -mincPath
> /data/BGI102001_207019_screening.mnc  -verbose -acquisition_protocol t1c
> -create_minc_pics
>
> DBD::mysql::db do failed: Cannot add or update a child row: a foreign key
> constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1`
> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at
> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
> 1018.
>
> ERROR: Failed to insert record in table mri_scanner:
>
> The following database commands failed:
> PREPARE s FROM 'INSERT INTO mri_scanner
> (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
> SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
> 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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN
> KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
> ===
>
> Could you help me figuring out what is happening? Is there something I
> should add to the minc headers?
>
> 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 Mass General
> Brigham Compliance HelpLine at
> http://www.massgeneralbrigham.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.
>
> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211126/1f5f6daf/attachment-0001.html>

From AMORALESPINZON at BWH.HARVARD.EDU  Fri Nov 26 10:55:21 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Fri, 26 Nov 2021 15:55:21 +0000
Subject: [Loris-dev] MINC insertion
In-Reply-To: <CAMkiY3fJcP0O=j++Rjjmymh9QqMofBY0NaTw0YH8GYTco7ZxSg@mail.gmail.com>
References: <DBD132E4-4075-42F5-82EA-62C4EA86A33A@mcgill.ca>
 <CAMkiY3fKNoN1U=t3mjM2VnOgWU56=0-YadQwLkc6xZOGUc-mvA@mail.gmail.com>
 <ED989A0A-3A12-4161-AF6A-8F7586F7DDFE@bwh.harvard.edu>
 <CAMkiY3eHjFAd1-bKdCx_5_k1nf2Mx_GCKDs2htAaTxxFoPqKhQ@mail.gmail.com>
 <63278E0B-C75D-467E-9A2C-579BC947EBC3@bwh.harvard.edu>
 <CAMkiY3fJcP0O=j++Rjjmymh9QqMofBY0NaTw0YH8GYTco7ZxSg@mail.gmail.com>
Message-ID: <53B91CC9-99CE-4E76-A080-9E902115673A@bwh.harvard.edu>

Hi C?cile,

This is the branch that we are using in the IPMSA project:

https://github.com/SPINEProject/Loris-MRI/tree/v23.0.3_IPMSA

Best,
Alfredo.

On Nov 26, 2021, at 9:55 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Could you point me to the version of the code you are using on GitHub so I can take a look at the correct MRI.pm file.

Thank you!

C?cile

On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I?m getting the following error when inserting a minc file using the minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> script:

===
$ perl minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc  -verbose -acquisition_protocol t1c -create_minc_pics

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1018.

ERROR: Failed to insert record in table mri_scanner:

The following database commands failed:
PREPARE s FROM 'INSERT INTO mri_scanner (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

Could you help me figuring out what is happening? Is there something I should add to the minc headers?

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/10DEfcj-Ova6W7NFLUPao--zc_ba_3Yk63CTqhSG5Ca4FJWekd8J8afbwCr_p31UYqWdlWd2rAqSBE3jLmNtkj6jzu0Deh3bP7WsUj3yX1B4Iv_RzcWr2nfZ7f8_OUQvlNL5D_jqwZyNdyv_JUiP0dLvm0NprWoJtFmmA4jwKQ4X8BKNoa6LBbiWMVYizEQDtUP5c9bc0XDPr-wYz3SlyBzIrLOxha8XYY4l8tLxS_skKp_uX_4jMesLtI_DCQza3WckhpQ7-43tcveIJ9vz-wKKRp31RbQkfDcbgexXsRG1oCpy-6zP8ggtvzNLZ0VSxSBDRZD7ti7dI0bPJXah5pg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.

Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211126/0367cf3b/attachment-0001.html>

From cecile.madjar at mcin.ca  Fri Nov 26 11:13:43 2021
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Fri, 26 Nov 2021 11:13:43 -0500
Subject: [Loris-dev] MINC insertion
In-Reply-To: <53B91CC9-99CE-4E76-A080-9E902115673A@bwh.harvard.edu>
References: <DBD132E4-4075-42F5-82EA-62C4EA86A33A@mcgill.ca>
 <CAMkiY3fKNoN1U=t3mjM2VnOgWU56=0-YadQwLkc6xZOGUc-mvA@mail.gmail.com>
 <ED989A0A-3A12-4161-AF6A-8F7586F7DDFE@bwh.harvard.edu>
 <CAMkiY3eHjFAd1-bKdCx_5_k1nf2Mx_GCKDs2htAaTxxFoPqKhQ@mail.gmail.com>
 <63278E0B-C75D-467E-9A2C-579BC947EBC3@bwh.harvard.edu>
 <CAMkiY3fJcP0O=j++Rjjmymh9QqMofBY0NaTw0YH8GYTco7ZxSg@mail.gmail.com>
 <53B91CC9-99CE-4E76-A080-9E902115673A@bwh.harvard.edu>
Message-ID: <CAMkiY3fUqgyP-BoFb71aOjBLfnPNRqt1UyQSEq6Q2TtObsNFoA@mail.gmail.com>

Thank you Alfredo.

I wonder whether the variable $centerID is null when provided to the query
here
<https://github.com/SPINEProject/Loris-MRI/blob/19f469cce904ebe93ba5f641533e4c0ef39fadab/uploadNeuroDB/NeuroDB/MRI.pm#L1012>
in your case.

Could you add in MRI.pm line 1018 the following print statements and let me
know what you get? (Right before the $dbh->do($query);
print($centerID);
print($query);

Thank you!

C?cile

On Fri, Nov 26, 2021 at 10:55 AM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi C?cile,
>
> This is the branch that we are using in the IPMSA project:
>
> https://github.com/SPINEProject/Loris-MRI/tree/v23.0.3_IPMSA
>
> Best,
> Alfredo.
>
> On Nov 26, 2021, at 9:55 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> Could you point me to the version of the code you are using on GitHub so I
> can take a look at the correct MRI.pm file.
>
> Thank you!
>
> C?cile
>
> On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Hi C?cile,
>>
>> I?m getting the following error when inserting a minc file using the
>> minc_insertion.pl
>> <http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl>
>> script:
>>
>> ===
>> $ perl minc_insertion.pl
>> <http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl>
>> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc
>> -verbose -acquisition_protocol t1c -create_minc_pics
>>
>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign key
>> constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1`
>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at
>> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
>> 1018.
>>
>> ERROR: Failed to insert record in table mri_scanner:
>>
>> The following database commands failed:
>> PREPARE s FROM 'INSERT INTO mri_scanner
>> (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
>> SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
>> 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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN
>> KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
>> ===
>>
>> Could you help me figuring out what is happening? Is there something I
>> should add to the minc headers?
>>
>> 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 Mass General
>> Brigham Compliance HelpLine at
>> http://www.massgeneralbrigham.org/complianceline
>> <http://secure-web.cisco.com/10DEfcj-Ova6W7NFLUPao--zc_ba_3Yk63CTqhSG5Ca4FJWekd8J8afbwCr_p31UYqWdlWd2rAqSBE3jLmNtkj6jzu0Deh3bP7WsUj3yX1B4Iv_RzcWr2nfZ7f8_OUQvlNL5D_jqwZyNdyv_JUiP0dLvm0NprWoJtFmmA4jwKQ4X8BKNoa6LBbiWMVYizEQDtUP5c9bc0XDPr-wYz3SlyBzIrLOxha8XYY4l8tLxS_skKp_uX_4jMesLtI_DCQza3WckhpQ7-43tcveIJ9vz-wKKRp31RbQkfDcbgexXsRG1oCpy-6zP8ggtvzNLZ0VSxSBDRZD7ti7dI0bPJXah5pg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>> . 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.
>>
>> Please note that this e-mail is not secure (encrypted).  If you do not
>> wish to continue communication over unencrypted e-mail, please notify the
>> sender of this message immediately.  Continuing to send or respond to
>> e-mail after receiving this message means you understand and accept this
>> risk and wish to continue to communicate over unencrypted e-mail.
>>
>
> 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 Mass General
> Brigham Compliance HelpLine at
> http://www.massgeneralbrigham.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.
>
> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211126/ca8c99fa/attachment.html>

From AMORALESPINZON at BWH.HARVARD.EDU  Fri Nov 26 14:34:08 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Fri, 26 Nov 2021 19:34:08 +0000
Subject: [Loris-dev] MINC insertion
In-Reply-To: <CAMkiY3fUqgyP-BoFb71aOjBLfnPNRqt1UyQSEq6Q2TtObsNFoA@mail.gmail.com>
References: <DBD132E4-4075-42F5-82EA-62C4EA86A33A@mcgill.ca>
 <CAMkiY3fKNoN1U=t3mjM2VnOgWU56=0-YadQwLkc6xZOGUc-mvA@mail.gmail.com>
 <ED989A0A-3A12-4161-AF6A-8F7586F7DDFE@bwh.harvard.edu>
 <CAMkiY3eHjFAd1-bKdCx_5_k1nf2Mx_GCKDs2htAaTxxFoPqKhQ@mail.gmail.com>
 <63278E0B-C75D-467E-9A2C-579BC947EBC3@bwh.harvard.edu>
 <CAMkiY3fJcP0O=j++Rjjmymh9QqMofBY0NaTw0YH8GYTco7ZxSg@mail.gmail.com>
 <53B91CC9-99CE-4E76-A080-9E902115673A@bwh.harvard.edu>
 <CAMkiY3fUqgyP-BoFb71aOjBLfnPNRqt1UyQSEq6Q2TtObsNFoA@mail.gmail.com>
Message-ID: <79E009D1-6AA8-4090-812A-F7405AE257C9@bwh.harvard.edu>

Hi C?cile,

Thank you for answer.

I included the following lines:

===
                  . " NOW(),   'NeuroDB::MRI', 'Scanner'          ) ";
+        print "\nCenter ID: " . $centerID . "\n\n";
+        print "\nQuery:" . $query . "\n\n";
         $dbh->do($query);
     }
===

And I got the following output:

===
perl minc_insertion.pl -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc -verbose -acquisition_protocol t1c -create_minc_pics

log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-14-31-d7FH_S.log
    SELECT       ArchiveLocation     FROM       tarchive     WHERE       TarchiveID = (                      SELECT TarchiveID                      FROM tarchive_series                      WHERE SeriesUID=? AND EchoTime=?                    )
Center ID: 0


Query:INSERT INTO candidate (CandID,          PSCID,  RegistrationCenterID, Date_active,   Date_registered, UserID, Entity_type                       ) VALUES (442627, 'scanner',      0,  NOW(),    NOW(),   'NeuroDB::MRI', 'Scanner'          )

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1020.
ERROR: Failed to insert record in table mri_scanner:
The following database commands failed:
        PREPARE s FROM 'INSERT INTO mri_scanner (CandID,Model,Manufacturer,Serial_number,Software) VALUES (?,?,?,?,?)';
        SET @x1='442627', at x2='Sonata', at x3='Siemens', at x4='syngo_MR_2004A_4VA25A';
        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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

I think it?s important to mention that this candidate was created by the bids importing script. Maybe there is center associated with the candidates when using the bids script?

Let me know your thoughts.

Best,
Alfredo.

On Nov 26, 2021, at 11:13 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Thank you Alfredo.

I wonder whether the variable $centerID is null when provided to the query here<https://secure-web.cisco.com/1BZxp6fiw85BciAlo2QCPeT44gOAdEJUbAAAM3VJsTVYkl_27h-GCDhXtVO-8fh2ghdX3L0808bpAkrN-4-dTSIuf12yvdTBrdZ5Wl5YcKE3s4BTaFeJPBISOXE6-2TppWqpX8R4fldLsB6dpee4WAltjKy3u6ZJa01r-_Up1j5vB6cy_vbAyEgWl_Ft7ACUJ4VwQkwh01nnF8cpg5ePrLbF5bQw28VLFdg3Uo7dO81Ow5-zFCp5KKdHX0KX7vdIPmPuijtNDX9V5jT_YKMml5cX_tM2IVASxDa-wmo0JijRQ7k6oCTwK52FO0yRmVVeFj4108ZlyK2avqXijVKYreQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm%23L1012> in your case.

Could you add in MRI.pm line 1018 the following print statements and let me know what you get? (Right before the $dbh->do($query);
print($centerID);
print($query);

Thank you!

C?cile

On Fri, Nov 26, 2021 at 10:55 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

This is the branch that we are using in the IPMSA project:

https://github.com/SPINEProject/Loris-MRI/tree/v23.0.3_IPMSA<https://secure-web.cisco.com/1_p5UjMqREHagXmmz7NxbZe91yrcn34HNneKcFN4qKhR9mT7798DmL7TgbLwjpDr1U0bQaX2Rdqcdu3-l5R95gEJ5AzIbYu4-psDEz9Gw3fmrcgxEel3V6rugNzEisR_jZbIG2f2KPrVumnb1MY-TJCYuPQqzVuM_3KHLYTzVKha7RbWAHq6GLefQmer8auU6BALsWue7RBcrrbG9kbGC-S-e1DZ-WP4gVNTDegrcGaghwyxclA9m6SZqs-OljIR6E7IViTaySgZuDnOp5meeyJlKdlksyj5cGVErq4YprL6I9uHWuLjB-06KBUFTBK6C1E38yyToTkJVVH-8LKRPKg/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Ftree%2Fv23.0.3_IPMSA>

Best,
Alfredo.

On Nov 26, 2021, at 9:55 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Could you point me to the version of the code you are using on GitHub so I can take a look at the correct MRI.pm file.

Thank you!

C?cile

On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I?m getting the following error when inserting a minc file using the minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> script:

===
$ perl minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc  -verbose -acquisition_protocol t1c -create_minc_pics

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1018.

ERROR: Failed to insert record in table mri_scanner:

The following database commands failed:
PREPARE s FROM 'INSERT INTO mri_scanner (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

Could you help me figuring out what is happening? Is there something I should add to the minc headers?

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/10DEfcj-Ova6W7NFLUPao--zc_ba_3Yk63CTqhSG5Ca4FJWekd8J8afbwCr_p31UYqWdlWd2rAqSBE3jLmNtkj6jzu0Deh3bP7WsUj3yX1B4Iv_RzcWr2nfZ7f8_OUQvlNL5D_jqwZyNdyv_JUiP0dLvm0NprWoJtFmmA4jwKQ4X8BKNoa6LBbiWMVYizEQDtUP5c9bc0XDPr-wYz3SlyBzIrLOxha8XYY4l8tLxS_skKp_uX_4jMesLtI_DCQza3WckhpQ7-43tcveIJ9vz-wKKRp31RbQkfDcbgexXsRG1oCpy-6zP8ggtvzNLZ0VSxSBDRZD7ti7dI0bPJXah5pg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.

Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1_sf0B_pY6Veyn85uEgw5ObBiM-QA382bc3nDvcSdrZOKA6no0I3vr4IK-5T3aDVnNH0xdP0QPSlWZoWkQ_GwFwWpmsSr4ck4dMGnU4VytPp-LDqG94cvmqnN5tL76lwADrn6xIQWpzuk5L8BVaZWrrrGjDSpYdGwV3AIPq2zzJhN9hBT5o5FBx0LlHEf-E7onD9zSqkkZiu9_atJraKUgpCCauEab0PbqWsTxYk0edTnIC6LbDq3t55qVy6FVWQybcR-n1rq2GND31ubWD7fk0h2dvddl4PnBk7PwnBZ6n6Q3S6lZvD9wWk_5ShEkjxI4GLdc2m60Frytk5an8XeeQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.

Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211126/3f3467c5/attachment-0001.html>

From cecile.madjar at mcin.ca  Fri Nov 26 15:31:20 2021
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Fri, 26 Nov 2021 15:31:20 -0500
Subject: [Loris-dev] MINC insertion
In-Reply-To: <79E009D1-6AA8-4090-812A-F7405AE257C9@bwh.harvard.edu>
References: <DBD132E4-4075-42F5-82EA-62C4EA86A33A@mcgill.ca>
 <CAMkiY3fKNoN1U=t3mjM2VnOgWU56=0-YadQwLkc6xZOGUc-mvA@mail.gmail.com>
 <ED989A0A-3A12-4161-AF6A-8F7586F7DDFE@bwh.harvard.edu>
 <CAMkiY3eHjFAd1-bKdCx_5_k1nf2Mx_GCKDs2htAaTxxFoPqKhQ@mail.gmail.com>
 <63278E0B-C75D-467E-9A2C-579BC947EBC3@bwh.harvard.edu>
 <CAMkiY3fJcP0O=j++Rjjmymh9QqMofBY0NaTw0YH8GYTco7ZxSg@mail.gmail.com>
 <53B91CC9-99CE-4E76-A080-9E902115673A@bwh.harvard.edu>
 <CAMkiY3fUqgyP-BoFb71aOjBLfnPNRqt1UyQSEq6Q2TtObsNFoA@mail.gmail.com>
 <79E009D1-6AA8-4090-812A-F7405AE257C9@bwh.harvard.edu>
Message-ID: <CAMkiY3eFwZbaCZXdBc-eS6Skp9-bSz5mHH6A2WwwS83_2WNmhg@mail.gmail.com>

Hi Alfredo,

I notice that the CenterID for the site is 0. Do you have an entry in the
psc table for a CenterID=0?

The problem here is that the data comes from a new scanner and the pipeline
tries to first register a new candidate for the scanner (scanner candidate)
before adding an entry in the mri_scanner table. To determine the site of
the scanner, the pipeline uses the determinePSC
<https://github.com/SPINEProject/Loris-MRI/blob/19f469cce904ebe93ba5f641533e4c0ef39fadab/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm#L503>
function of MRIProcessingUtility.pm (called by minc_insertion.pl in line 454
<https://github.com/SPINEProject/Loris-MRI/blob/19f469cce904ebe93ba5f641533e4c0ef39fadab/uploadNeuroDB/minc_insertion.pl#L454>).
I would be curious to see what the $center_name and $centerID values
returned are.

Could you also copy the code you have in your prod file for the function
getSubjectIDs?

Finally, could you check that the candidate BGI102001_207019 does have a
RegistrationCenterID set and if there is already a screening session
created in the session table, that the CenterID of that session has
properly been set?

Thank you!

C?cile

On Fri, Nov 26, 2021 at 2:34 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi C?cile,
>
> Thank you for answer.
>
> I included the following lines:
>
> ===
>                   . " NOW(),   'NeuroDB::MRI', 'Scanner'          ) ";
> +        print "\nCenter ID: " . $centerID . "\n\n";
> +        print "\nQuery:" . $query . "\n\n";
>          $dbh->do($query);
>      }
> ===
>
> And I got the following output:
>
> ===
> perl minc_insertion.pl -profile prod -force -mincPath
> /data/BGI102001_207019_screening.mnc -verbose -acquisition_protocol t1c
> -create_minc_pics
>
> log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is
> /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-14-31-d7FH_S.log
>     SELECT       ArchiveLocation     FROM       tarchive     WHERE
> TarchiveID = (                      SELECT TarchiveID
> FROM tarchive_series                      WHERE SeriesUID=? AND EchoTime=?
>                   )
> Center ID: 0
>
>
> Query:INSERT INTO candidate (CandID,          PSCID,
> RegistrationCenterID, Date_active,   Date_registered, UserID, Entity_type
>                     ) VALUES (442627, 'scanner',      0,  NOW(),    NOW(),
>   'NeuroDB::MRI', 'Scanner'          )
>
> DBD::mysql::db do failed: Cannot add or update a child row: a foreign key
> constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1`
> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at
> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
> 1020.
> ERROR: Failed to insert record in table mri_scanner:
> The following database commands failed:
>         PREPARE s FROM 'INSERT INTO mri_scanner
> (CandID,Model,Manufacturer,Serial_number,Software) VALUES (?,?,?,?,?)';
>         SET
> @x1='442627', at x2='Sonata', at x3='Siemens', at x4='syngo_MR_2004A_4VA25A';
>         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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN
> KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
> ===
>
> I think it?s important to mention that this candidate was created by the
> bids importing script. Maybe there is center associated with the candidates
> when using the bids script?
>
> Let me know your thoughts.
>
> Best,
> Alfredo.
>
> On Nov 26, 2021, at 11:13 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Thank you Alfredo.
>
> I wonder whether the variable $centerID is null when provided to the query
> here
> <https://secure-web.cisco.com/1BZxp6fiw85BciAlo2QCPeT44gOAdEJUbAAAM3VJsTVYkl_27h-GCDhXtVO-8fh2ghdX3L0808bpAkrN-4-dTSIuf12yvdTBrdZ5Wl5YcKE3s4BTaFeJPBISOXE6-2TppWqpX8R4fldLsB6dpee4WAltjKy3u6ZJa01r-_Up1j5vB6cy_vbAyEgWl_Ft7ACUJ4VwQkwh01nnF8cpg5ePrLbF5bQw28VLFdg3Uo7dO81Ow5-zFCp5KKdHX0KX7vdIPmPuijtNDX9V5jT_YKMml5cX_tM2IVASxDa-wmo0JijRQ7k6oCTwK52FO0yRmVVeFj4108ZlyK2avqXijVKYreQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm%23L1012>
> in your case.
>
> Could you add in MRI.pm line 1018 the following print statements and let
> me know what you get? (Right before the $dbh->do($query);
> print($centerID);
> print($query);
>
> Thank you!
>
> C?cile
>
> On Fri, Nov 26, 2021 at 10:55 AM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Hi C?cile,
>>
>> This is the branch that we are using in the IPMSA project:
>>
>> https://github.com/SPINEProject/Loris-MRI/tree/v23.0.3_IPMSA
>> <https://secure-web.cisco.com/1_p5UjMqREHagXmmz7NxbZe91yrcn34HNneKcFN4qKhR9mT7798DmL7TgbLwjpDr1U0bQaX2Rdqcdu3-l5R95gEJ5AzIbYu4-psDEz9Gw3fmrcgxEel3V6rugNzEisR_jZbIG2f2KPrVumnb1MY-TJCYuPQqzVuM_3KHLYTzVKha7RbWAHq6GLefQmer8auU6BALsWue7RBcrrbG9kbGC-S-e1DZ-WP4gVNTDegrcGaghwyxclA9m6SZqs-OljIR6E7IViTaySgZuDnOp5meeyJlKdlksyj5cGVErq4YprL6I9uHWuLjB-06KBUFTBK6C1E38yyToTkJVVH-8LKRPKg/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Ftree%2Fv23.0.3_IPMSA>
>>
>> Best,
>> Alfredo.
>>
>> On Nov 26, 2021, at 9:55 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>>
>>         External Email - Use Caution
>>
>> Hi Alfredo,
>>
>> Could you point me to the version of the code you are using on GitHub so
>> I can take a look at the correct MRI.pm file.
>>
>> Thank you!
>>
>> C?cile
>>
>> On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>>> Hi C?cile,
>>>
>>> I?m getting the following error when inserting a minc file using the
>>> minc_insertion.pl
>>> <http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl>
>>> script:
>>>
>>> ===
>>> $ perl minc_insertion.pl
>>> <http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl>
>>> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc
>>> -verbose -acquisition_protocol t1c -create_minc_pics
>>>
>>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign
>>> key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT
>>> `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc`
>>> (`CenterID`)) at
>>> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
>>> 1018.
>>>
>>> ERROR: Failed to insert record in table mri_scanner:
>>>
>>> The following database commands failed:
>>> PREPARE s FROM 'INSERT INTO mri_scanner
>>> (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
>>> SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
>>> 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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT
>>> `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate`
>>> (`CandID`)) (error code 1452)
>>> ===
>>>
>>> Could you help me figuring out what is happening? Is there something I
>>> should add to the minc headers?
>>>
>>> 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 Mass General
>>> Brigham Compliance HelpLine at
>>> http://www.massgeneralbrigham.org/complianceline
>>> <http://secure-web.cisco.com/10DEfcj-Ova6W7NFLUPao--zc_ba_3Yk63CTqhSG5Ca4FJWekd8J8afbwCr_p31UYqWdlWd2rAqSBE3jLmNtkj6jzu0Deh3bP7WsUj3yX1B4Iv_RzcWr2nfZ7f8_OUQvlNL5D_jqwZyNdyv_JUiP0dLvm0NprWoJtFmmA4jwKQ4X8BKNoa6LBbiWMVYizEQDtUP5c9bc0XDPr-wYz3SlyBzIrLOxha8XYY4l8tLxS_skKp_uX_4jMesLtI_DCQza3WckhpQ7-43tcveIJ9vz-wKKRp31RbQkfDcbgexXsRG1oCpy-6zP8ggtvzNLZ0VSxSBDRZD7ti7dI0bPJXah5pg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>>> . 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.
>>>
>>> Please note that this e-mail is not secure (encrypted).  If you do not
>>> wish to continue communication over unencrypted e-mail, please notify the
>>> sender of this message immediately.  Continuing to send or respond to
>>> e-mail after receiving this message means you understand and accept this
>>> risk and wish to continue to communicate over unencrypted e-mail.
>>>
>>
>> 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 Mass General
>> Brigham Compliance HelpLine at
>> http://www.massgeneralbrigham.org/complianceline
>> <http://secure-web.cisco.com/1_sf0B_pY6Veyn85uEgw5ObBiM-QA382bc3nDvcSdrZOKA6no0I3vr4IK-5T3aDVnNH0xdP0QPSlWZoWkQ_GwFwWpmsSr4ck4dMGnU4VytPp-LDqG94cvmqnN5tL76lwADrn6xIQWpzuk5L8BVaZWrrrGjDSpYdGwV3AIPq2zzJhN9hBT5o5FBx0LlHEf-E7onD9zSqkkZiu9_atJraKUgpCCauEab0PbqWsTxYk0edTnIC6LbDq3t55qVy6FVWQybcR-n1rq2GND31ubWD7fk0h2dvddl4PnBk7PwnBZ6n6Q3S6lZvD9wWk_5ShEkjxI4GLdc2m60Frytk5an8XeeQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>> . 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.
>>
>> Please note that this e-mail is not secure (encrypted).  If you do not
>> wish to continue communication over unencrypted e-mail, please notify the
>> sender of this message immediately.  Continuing to send or respond to
>> e-mail after receiving this message means you understand and accept this
>> risk and wish to continue to communicate over unencrypted e-mail.
>>
>
> 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 Mass General
> Brigham Compliance HelpLine at
> http://www.massgeneralbrigham.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.
>
> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211126/befc36d1/attachment-0001.html>

From samir.das at mcgill.ca  Sat Nov 27 21:25:30 2021
From: samir.das at mcgill.ca (Samir Das)
Date: Sun, 28 Nov 2021 02:25:30 +0000
Subject: [Loris-dev] RAM/ Memory requirements
In-Reply-To: <99B67BC1EEE7BC4E8F6D4B2EEC1F75A329D07F@DONAR.cnio.es>
References: <b8fb30bfb46b4c9aa7aa2c05fa9284c3@YQBPR0101MB4211.CANPRD01.PROD.OUTLOOK.COM>
 <CALbt7NCJedQ1Uiy4z9Ue14x79NwObHVseB6Fh1PFaqJbzhyj5g@mail.gmail.com>
 <99B67BC1EEE7BC4E8F6D4B2EEC1F75A327FA94@DONAR.cnio.es>
 <YT2PR01MB5266AFC42B6F65846A7EA1B0EA9D9@YT2PR01MB5266.CANPRD01.PROD.OUTLOOK.COM>
 <99B67BC1EEE7BC4E8F6D4B2EEC1F75A329D07F@DONAR.cnio.es>
Message-ID: <YT2PR01MB5266F77B2B191BBC2A301C51EA659@YT2PR01MB5266.CANPRD01.PROD.OUTLOOK.COM>

Hi Olga,

We are happy to help. Perhaps, your group could register on the loris-dev mailing list, and you could pose your question(s) there. You'll have access to the full array of developers. Then, if that isn't fruitful, we can book a time to go through this on a Zoom call? We deal with a great deal of support requests and this is the most effective way to triage them. Sometimes, the issue is quite simple to solve.

Best,

Samir Das



________________________________
From: Rico_D?ez.Olga <oricod at ext.cnio.es>
Sent: Monday, November 22, 2021 5:02 AM
To: Samir Das <samir.das at mcgill.ca>; Christine Rogers <rogers at bic.mni.mcgill.ca>
Cc: loris.info at mcin.ca <loris.info at mcin.ca>
Subject: RE: RAM/ Memory requirements


Hi Samir and thanks for your clarifying response,



These are really good news for my team.



I was wondering if you or a member of your team will have some time to help us with the installation, since we have been dealing with it some weeks and don?t know what is wrong.

Maybe we could connect via zoom or something and resolve this matter in a moment with your help, better than trying it by our own and spending more weeks dealing with it.





Could we make this?



Thanks in advance,

Olga





De: Samir Das <samir.das at mcgill.ca>
Enviado el: s?bado, 20 de noviembre de 2021 17:48
Para: Rico_D?ez.Olga <oricod at ext.cnio.es>; Christine Rogers <rogers at bic.mni.mcgill.ca>
CC: loris.info at mcin.ca
Asunto: Re: RAM/ Memory requirements



CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe



Hi Olga,



Apologies for the delayed response. This email got missed somehow. Importing data formats other than DICOMS is routinely done. We typically import them using our Derived Data script (even though this is raw data). Any visualization of the files might not work with our native viewer (BrainBrowser), but other viewers can be plugged into the LORIS environment (since LORIS is open source). Let me know if you have any further questions.



Best,

Samir Das

________________________________

From: Rico_D?ez.Olga <oricod at ext.cnio.es>
Sent: Wednesday, October 27, 2021 11:19 AM
To: Christine Rogers <rogers at bic.mni.mcgill.ca>
Cc: loris.info at mcin.ca <loris.info at mcin.ca>
Subject: RE: RAM/ Memory requirements



Hello Christine,



The Project would be managing data from clinical data, and forms, to medical (TC, MRI) and pathological imaging and also genomic data.

So we will try to use it as a connection between all these heterogenious data.



So I have got another question, for pathological data, the images are very heavy and also are in different format from DICOM ( .czi format), is there any posibility to custmize the data base in Loris to be able to import these format images?





Thanks for all the info, its been very useful.

Olga Rico.



De: Christine Rogers <rogers at bic.mni.mcgill.ca>
Enviado el: martes, 26 de octubre de 2021 0:38
Para: Rico_D?ez.Olga <oricod at ext.cnio.es>
CC: loris.info at mcin.ca
Asunto: Re: RAM/ Memory requirements



CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe



Hello,

Thank you for your inquiry --

For the RAM requirements, this often depends on the size of files in your dataset.  For storage space on server/disk, this is estimated around 3x your dataset size, depending on the types of data you have.

LORIS is installed on a Unix system, and additional context for requirements is available in our LORIS Governance document, attached.



Could you let us know a few details about your project, so that I can give you better information for your research context?  It would be good to know what types of data you are collecting (mri scans, biosamples, etc) and the kind of research project.



Thank you, and please don't hesitate with further questions.

Christine



On Wed, Oct 13, 2021 at 10:29 AM Rico_D?ez.Olga <oricod at ext.cnio.es<mailto:oricod at ext.cnio.es>> wrote:

Good mooring team,



I would like to ask you a short doubth about LORIS, ?what are the memory or RAM requirements for the use and installation of LORIS?

Thanks in advance,



Olga Rico.



[Imagen quitada por el remitente. Hazte Amigo del CNIO. M?s investigaci?n, menos c?ncer]<https://www.cnio.es/es/colaborar/comocolaborar.asp>

Fb Amigos del CNIO<https://www.facebook.com/AmigosdelCNIO/> |  Tw @CNIOStopCancer<https://twitter.com/CNIOStopCancer> |  Youtube canalcnio<https://www.youtube.com/canalcnio>


**ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protecci?n de los datos personales de las personas f?sicas, la informaci?n personal que nos pueda facilitar a trav?s de este correo electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de tramitar el objeto del presente correo electr?nico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no ser?n comunicados a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga exigido por una ley. Ud. podr? ejercer los derechos de acceso, rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos en: delegado_lopd at cnio.es<mailto:delegado_lopd at cnio.es>. Para el caso de que Ud. precise conocer informaci?n adicional sobre el tratamiento de sus datos personales, puede consultar dicha informaci?n adicional en el siguiente enlace dentro de nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp

**LEGAL NOTICE**: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message.
Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es<mailto:delegado_lopd at cnio.es>. If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp




--

Research Project Officer
christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
McGill Centre for Integrative Neuroscience | MCIN.ca

Montreal Neurological Institute-Hospital

McGill University | Montreal | Canada


**ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protecci?n de los datos personales de las personas f?sicas, la informaci?n personal que nos pueda facilitar a trav?s de este correo electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de tramitar el objeto del presente correo electr?nico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no ser?n comunicados a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga exigido por una ley. Ud. podr? ejercer los derechos de acceso, rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer informaci?n adicional sobre el tratamiento de sus datos personales, puede consultar dicha informaci?n adicional en el siguiente enlace dentro de nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp

**LEGAL NOTICE**: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message.
Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp


**ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protecci?n de los datos personales de las personas f?sicas, la informaci?n personal que nos pueda facilitar a trav?s de este correo electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de tramitar el objeto del presente correo electr?nico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no ser?n comunicados a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga exigido por una ley. Ud. podr? ejercer los derechos de acceso, rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer informaci?n adicional sobre el tratamiento de sus datos personales, puede consultar dicha informaci?n adicional en el siguiente enlace dentro de nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp

**LEGAL NOTICE**: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message.
Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211128/14bda366/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ~WRD000.jpg
Type: image/jpeg
Size: 823 bytes
Desc: ~WRD000.jpg
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211128/14bda366/attachment-0001.jpg>

From AMORALESPINZON at BWH.HARVARD.EDU  Sun Nov 28 12:42:44 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Sun, 28 Nov 2021 17:42:44 +0000
Subject: [Loris-dev] MINC insertion
In-Reply-To: <CAMkiY3eFwZbaCZXdBc-eS6Skp9-bSz5mHH6A2WwwS83_2WNmhg@mail.gmail.com>
References: <DBD132E4-4075-42F5-82EA-62C4EA86A33A@mcgill.ca>
 <CAMkiY3fKNoN1U=t3mjM2VnOgWU56=0-YadQwLkc6xZOGUc-mvA@mail.gmail.com>
 <ED989A0A-3A12-4161-AF6A-8F7586F7DDFE@bwh.harvard.edu>
 <CAMkiY3eHjFAd1-bKdCx_5_k1nf2Mx_GCKDs2htAaTxxFoPqKhQ@mail.gmail.com>
 <63278E0B-C75D-467E-9A2C-579BC947EBC3@bwh.harvard.edu>
 <CAMkiY3fJcP0O=j++Rjjmymh9QqMofBY0NaTw0YH8GYTco7ZxSg@mail.gmail.com>
 <53B91CC9-99CE-4E76-A080-9E902115673A@bwh.harvard.edu>
 <CAMkiY3fUqgyP-BoFb71aOjBLfnPNRqt1UyQSEq6Q2TtObsNFoA@mail.gmail.com>
 <79E009D1-6AA8-4090-812A-F7405AE257C9@bwh.harvard.edu>
 <CAMkiY3eFwZbaCZXdBc-eS6Skp9-bSz5mHH6A2WwwS83_2WNmhg@mail.gmail.com>
Message-ID: <94B44F39-0E17-4C7B-AE35-490F8BF95ABD@bwh.harvard.edu>

Hi C?cile,

Thank you, it looks like we?re getting closer to find a solution. Find the answers to your questions inline below.

Happy to debug over Zoom if it?s easier for you.

Best,
Alfredo.


On Nov 26, 2021, at 3:31 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

I notice that the CenterID for the site is 0. Do you have an entry in the psc table for a CenterID=0?
No, we don?t have it. The CenterID starts at 1.
===
select * from psc where CenterID=0;
Empty set (0.00 sec)
===

The problem here is that the data comes from a new scanner and the pipeline tries to first register a new candidate for the scanner (scanner candidate) before adding an entry in the mri_scanner table. To determine the site of the scanner, the pipeline uses the determinePSC<https://secure-web.cisco.com/1Dc-fajrB7Ud53q9lvqwcvWI66c8Sjd_VWPzsGJnI1xtsFo2tce71aRhvXOFAeXFyiXWHCRtrsuOUxz9FTymBxjmkO9QVm92NieBTkPQt3sHgPQQUT2j2bpLa-AQKrAp6CJLMFA3SshUHX9tSHCkDZl4-687CTtyUYa8o_QDxRn0UEiy6yqufe-DTaVIJxY2bFtGERf0kTxBUy4JaS_ZiEHYQ3uGUjy9x3F25dMV0RZ_8hv74gXSGJW3t7AJ2zm-stvAEvizinmIQrzN-OP0L0FTHPAmoHzn0NFzDCrYvCDnMCfBNCexzjhZ9JcsQSpQS_LK_oW8UEy8ObHNoEsbzKA/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRIProcessingUtility.pm%23L503> function of MRIProcessingUtility.pm (called by minc_insertion.pl<http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl> in line 454<https://secure-web.cisco.com/1UWbEiJQk9qeievujOxfe9vFYw_u8x2SaJKAYzS6WrKuX-cWcA62bpRkJ-fOL-6hCS2oSzF8ye-G99zRPL7lv-ggMi48rbGxbcOhqRu-S7FGWEZpc-vb_j_YA73XsG7Od4qBB98i5AMLyLXi5SZAwP5E_nbdjI626BeW24SmnD6Hd_MocuW8oOqNs4mTZSGh8EkMpO-BOuH4bMikoRDLakpW-VmFznZ130h0pg4vTAAfwsjwTvbjqHgFlzExIBUHDqgaeYpD5aWuC1jjiXxEy182es4Wv0VMpe5btqKR8f0VjaB-rl2G6tC0A8q5fHAfkY5fNxpYViSFAv6jJO-8F8w/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2Fminc_insertion.pl%23L454>). I would be curious to see what the $center_name and $centerID values returned are.
These are the returned values. Maybe we need to look deeper into this.
===
determinePSC->Center name: UNKN
determinePSC->Center ID: 0
===


Could you also copy the code you have in your prod file for the function getSubjectIDs?

You mean this file ?mri/dicom-archive/.loris_mri/prod?, right? Find the function enclosed.


Finally, could you check that the candidate BGI102001_207019 does have a RegistrationCenterID set and if there is already a screening session created in the session table, that the CenterID of that session has properly been set?


The candidate has a RegistrationCenterID (843):
===
select * from candidate where CandID=207019 \G;
*************************** 1. row ***************************
                  ID: 8974
              CandID: 207019
               PSCID: BGI102001
          ExternalID: NULL
                 DoB: 1969-05-15
                 EDC: NULL
                 Sex: Female
RegistrationCenterID: 843
RegistrationProjectID: 12
           Ethnicity: NULL
              Active: Y
         Date_active: 2021-05-27
        RegisteredBy: dataman
              UserID: dataman
     Date_registered: 2021-05-27
flagged_caveatemptor: false
      flagged_reason: NULL
       flagged_other: NULL
flagged_other_status: NULL
            Testdate: 2021-06-09 10:55:35
         Entity_type: Human
          ProbandSex: NULL
          ProbandDoB: NULL
                 DoD: NULL
1 row in set (0.00 sec)
===

The session with the proper values already exists:
===
mysql> select * from session where CandID=207019 and Visit_label="screening" \G;
*************************** 1. row ***************************
                 ID: 127260
             CandID: 207019
           CenterID: 843
            VisitNo: 1
        Visit_label: screening
       SubprojectID: 2
          Submitted: N
      Current_stage: Not Started
  Date_stage_change: NULL
          Screening: NULL
     Date_screening: NULL
              Visit: NULL
         Date_visit: NULL
           Approval: NULL
      Date_approval: NULL
             Active: Y
        Date_active: 2021-05-27
       RegisteredBy: dataman
             UserID: dataman
    Date_registered: 2021-05-27
           Testdate: 2021-06-10 18:35:41
   Hardcopy_request: -
        BVLQCStatus: NULL
          BVLQCType: NULL
     BVLQCExclusion: NULL
                QCd: NULL
          Scan_done: Y
        MRIQCStatus:
       MRIQCPending: N
MRIQCFirstChangeTime: NULL
MRIQCLastChangeTime: NULL
          MRICaveat: false
          ProjectID: 12
         languageID: 1
1 row in set (0.00 sec)
===

Thank you!

C?cile

On Fri, Nov 26, 2021 at 2:34 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Thank you for answer.

I included the following lines:

===
                  . " NOW(),   'NeuroDB::MRI', 'Scanner'          ) ";
+        print "\nCenter ID: " . $centerID . "\n\n";
+        print "\nQuery:" . $query . "\n\n";
         $dbh->do($query);
     }
===

And I got the following output:

===
perl minc_insertion.pl<http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc -verbose -acquisition_protocol t1c -create_minc_pics

log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-14-31-d7FH_S.log
    SELECT       ArchiveLocation     FROM       tarchive     WHERE       TarchiveID = (                      SELECT TarchiveID                      FROM tarchive_series                      WHERE SeriesUID=? AND EchoTime=?                    )
Center ID: 0


Query:INSERT INTO candidate (CandID,          PSCID,  RegistrationCenterID, Date_active,   Date_registered, UserID, Entity_type                       ) VALUES (442627, 'scanner',      0,  NOW(),    NOW(),   'NeuroDB::MRI', 'Scanner'          )

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1020.
ERROR: Failed to insert record in table mri_scanner:
The following database commands failed:
        PREPARE s FROM 'INSERT INTO mri_scanner (CandID,Model,Manufacturer,Serial_number,Software) VALUES (?,?,?,?,?)';
        SET @x1='442627', at x2='Sonata', at x3='Siemens', at x4='syngo_MR_2004A_4VA25A';
        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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

I think it?s important to mention that this candidate was created by the bids importing script. Maybe there is center associated with the candidates when using the bids script?

Let me know your thoughts.

Best,
Alfredo.

On Nov 26, 2021, at 11:13 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Thank you Alfredo.

I wonder whether the variable $centerID is null when provided to the query here<https://secure-web.cisco.com/1BZxp6fiw85BciAlo2QCPeT44gOAdEJUbAAAM3VJsTVYkl_27h-GCDhXtVO-8fh2ghdX3L0808bpAkrN-4-dTSIuf12yvdTBrdZ5Wl5YcKE3s4BTaFeJPBISOXE6-2TppWqpX8R4fldLsB6dpee4WAltjKy3u6ZJa01r-_Up1j5vB6cy_vbAyEgWl_Ft7ACUJ4VwQkwh01nnF8cpg5ePrLbF5bQw28VLFdg3Uo7dO81Ow5-zFCp5KKdHX0KX7vdIPmPuijtNDX9V5jT_YKMml5cX_tM2IVASxDa-wmo0JijRQ7k6oCTwK52FO0yRmVVeFj4108ZlyK2avqXijVKYreQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm%23L1012> in your case.

Could you add in MRI.pm line 1018 the following print statements and let me know what you get? (Right before the $dbh->do($query);
print($centerID);
print($query);

Thank you!

C?cile

On Fri, Nov 26, 2021 at 10:55 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

This is the branch that we are using in the IPMSA project:

https://github.com/SPINEProject/Loris-MRI/tree/v23.0.3_IPMSA<https://secure-web.cisco.com/1_p5UjMqREHagXmmz7NxbZe91yrcn34HNneKcFN4qKhR9mT7798DmL7TgbLwjpDr1U0bQaX2Rdqcdu3-l5R95gEJ5AzIbYu4-psDEz9Gw3fmrcgxEel3V6rugNzEisR_jZbIG2f2KPrVumnb1MY-TJCYuPQqzVuM_3KHLYTzVKha7RbWAHq6GLefQmer8auU6BALsWue7RBcrrbG9kbGC-S-e1DZ-WP4gVNTDegrcGaghwyxclA9m6SZqs-OljIR6E7IViTaySgZuDnOp5meeyJlKdlksyj5cGVErq4YprL6I9uHWuLjB-06KBUFTBK6C1E38yyToTkJVVH-8LKRPKg/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Ftree%2Fv23.0.3_IPMSA>

Best,
Alfredo.

On Nov 26, 2021, at 9:55 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Could you point me to the version of the code you are using on GitHub so I can take a look at the correct MRI.pm file.

Thank you!

C?cile

On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I?m getting the following error when inserting a minc file using the minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> script:

===
$ perl minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc  -verbose -acquisition_protocol t1c -create_minc_pics

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1018.

ERROR: Failed to insert record in table mri_scanner:

The following database commands failed:
PREPARE s FROM 'INSERT INTO mri_scanner (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

Could you help me figuring out what is happening? Is there something I should add to the minc headers?

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/10DEfcj-Ova6W7NFLUPao--zc_ba_3Yk63CTqhSG5Ca4FJWekd8J8afbwCr_p31UYqWdlWd2rAqSBE3jLmNtkj6jzu0Deh3bP7WsUj3yX1B4Iv_RzcWr2nfZ7f8_OUQvlNL5D_jqwZyNdyv_JUiP0dLvm0NprWoJtFmmA4jwKQ4X8BKNoa6LBbiWMVYizEQDtUP5c9bc0XDPr-wYz3SlyBzIrLOxha8XYY4l8tLxS_skKp_uX_4jMesLtI_DCQza3WckhpQ7-43tcveIJ9vz-wKKRp31RbQkfDcbgexXsRG1oCpy-6zP8ggtvzNLZ0VSxSBDRZD7ti7dI0bPJXah5pg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.


Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1_sf0B_pY6Veyn85uEgw5ObBiM-QA382bc3nDvcSdrZOKA6no0I3vr4IK-5T3aDVnNH0xdP0QPSlWZoWkQ_GwFwWpmsSr4ck4dMGnU4VytPp-LDqG94cvmqnN5tL76lwADrn6xIQWpzuk5L8BVaZWrrrGjDSpYdGwV3AIPq2zzJhN9hBT5o5FBx0LlHEf-E7onD9zSqkkZiu9_atJraKUgpCCauEab0PbqWsTxYk0edTnIC6LbDq3t55qVy6FVWQybcR-n1rq2GND31ubWD7fk0h2dvddl4PnBk7PwnBZ6n6Q3S6lZvD9wWk_5ShEkjxI4GLdc2m60Frytk5an8XeeQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.


Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/14m8jq3YFX-kL4WHSOD3NyklDH3_1jO6LrSN9gvfM5CyvUtE7cihaLOo51ulZdVQKgs5rOFUrgJxphRC2W3gjEcYsYyqJP3GlMV3sJHwLGLwsGvslUlp9df_5QkEDbk0OiO4v-SgA4uMhT6od0larJxEIegxbPKpy9GmlloLw6cDlPw0voUhi7Y0kxA_zjwDvxaVMhZ7RIpojsrcwl2crdOHamo_wQI9pz9cAU_qxwUGkhiSfwtcCe8i-UtBjbSEY9dM0SpejAYJqhqEpOK_aCqQ4_wOl8FxQWWNK2nOsD7QawkuH5liIxDIL5XojDqICa2oljEN17RtZIEy425vItA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.


Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211128/0c18b7f8/attachment-0001.html>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: getSubjectIDs.txt
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211128/0c18b7f8/attachment-0001.txt>

From cecile.madjar at mcin.ca  Mon Nov 29 08:40:32 2021
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Mon, 29 Nov 2021 08:40:32 -0500
Subject: [Loris-dev] MINC insertion
In-Reply-To: <94B44F39-0E17-4C7B-AE35-490F8BF95ABD@bwh.harvard.edu>
References: <DBD132E4-4075-42F5-82EA-62C4EA86A33A@mcgill.ca>
 <CAMkiY3fKNoN1U=t3mjM2VnOgWU56=0-YadQwLkc6xZOGUc-mvA@mail.gmail.com>
 <ED989A0A-3A12-4161-AF6A-8F7586F7DDFE@bwh.harvard.edu>
 <CAMkiY3eHjFAd1-bKdCx_5_k1nf2Mx_GCKDs2htAaTxxFoPqKhQ@mail.gmail.com>
 <63278E0B-C75D-467E-9A2C-579BC947EBC3@bwh.harvard.edu>
 <CAMkiY3fJcP0O=j++Rjjmymh9QqMofBY0NaTw0YH8GYTco7ZxSg@mail.gmail.com>
 <53B91CC9-99CE-4E76-A080-9E902115673A@bwh.harvard.edu>
 <CAMkiY3fUqgyP-BoFb71aOjBLfnPNRqt1UyQSEq6Q2TtObsNFoA@mail.gmail.com>
 <79E009D1-6AA8-4090-812A-F7405AE257C9@bwh.harvard.edu>
 <CAMkiY3eFwZbaCZXdBc-eS6Skp9-bSz5mHH6A2WwwS83_2WNmhg@mail.gmail.com>
 <94B44F39-0E17-4C7B-AE35-490F8BF95ABD@bwh.harvard.edu>
Message-ID: <CAMkiY3erKTvEXScZofQeP-u2jFh4GK4gPEJnD7TgFuqsPYqSiQ@mail.gmail.com>

Hi Alfredo,

I think we are indeed narrowing where the error happens. It looks like for
some reason this getPSC
<https://github.com/SPINEProject/Loris-MRI/blob/v23.0.3_IPMSA/uploadNeuroDB/NeuroDB/MRI.pm>
function is returning "UNKN", 0. It might be related to the Alias or
MRI_alias content of the psc table for CenterID 843.

What do you get when you run the following query?
SELECT * FROM psc WHERE CenterID=843;

In the Alias or MRI_alias column, you should be able to see BGI so that the
scanner candidate can be identified with the proper site.

Let me know,

C?cile

On Sun, Nov 28, 2021 at 12:42 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi C?cile,
>
> Thank you, it looks like we?re getting closer to find a solution. Find the
> answers to your questions inline below.
>
> Happy to debug over Zoom if it?s easier for you.
>
> Best,
> Alfredo.
>
>
> On Nov 26, 2021, at 3:31 PM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> I notice that the CenterID for the site is 0. Do you have an entry in the
> psc table for a CenterID=0?
>
> No, we don?t have it. The CenterID starts at 1.
> ===
> select * from psc where CenterID=0;
> Empty set (0.00 sec)
> ===
>
>
> The problem here is that the data comes from a new scanner and the
> pipeline tries to first register a new candidate for the scanner (scanner
> candidate) before adding an entry in the mri_scanner table. To determine
> the site of the scanner, the pipeline uses the determinePSC
> <https://secure-web.cisco.com/1Dc-fajrB7Ud53q9lvqwcvWI66c8Sjd_VWPzsGJnI1xtsFo2tce71aRhvXOFAeXFyiXWHCRtrsuOUxz9FTymBxjmkO9QVm92NieBTkPQt3sHgPQQUT2j2bpLa-AQKrAp6CJLMFA3SshUHX9tSHCkDZl4-687CTtyUYa8o_QDxRn0UEiy6yqufe-DTaVIJxY2bFtGERf0kTxBUy4JaS_ZiEHYQ3uGUjy9x3F25dMV0RZ_8hv74gXSGJW3t7AJ2zm-stvAEvizinmIQrzN-OP0L0FTHPAmoHzn0NFzDCrYvCDnMCfBNCexzjhZ9JcsQSpQS_LK_oW8UEy8ObHNoEsbzKA/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRIProcessingUtility.pm%23L503>
> function of MRIProcessingUtility.pm (called by minc_insertion.pl
> <http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl>
> in line 454
> <https://secure-web.cisco.com/1UWbEiJQk9qeievujOxfe9vFYw_u8x2SaJKAYzS6WrKuX-cWcA62bpRkJ-fOL-6hCS2oSzF8ye-G99zRPL7lv-ggMi48rbGxbcOhqRu-S7FGWEZpc-vb_j_YA73XsG7Od4qBB98i5AMLyLXi5SZAwP5E_nbdjI626BeW24SmnD6Hd_MocuW8oOqNs4mTZSGh8EkMpO-BOuH4bMikoRDLakpW-VmFznZ130h0pg4vTAAfwsjwTvbjqHgFlzExIBUHDqgaeYpD5aWuC1jjiXxEy182es4Wv0VMpe5btqKR8f0VjaB-rl2G6tC0A8q5fHAfkY5fNxpYViSFAv6jJO-8F8w/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2Fminc_insertion.pl%23L454>).
> I would be curious to see what the $center_name and $centerID values
> returned are.
>
> These are the returned values. Maybe we need to look deeper into this.
> ===
> determinePSC->Center name: UNKN
> determinePSC->Center ID: 0
> ===
>
>
> Could you also copy the code you have in your prod file for the function
> getSubjectIDs?
>
>
> You mean this file ?mri/dicom-archive/.loris_mri/prod?, right? Find the
> function enclosed.
>
>
> Finally, could you check that the candidate BGI102001_207019 does have a
> RegistrationCenterID set and if there is already a screening session
> created in the session table, that the CenterID of that session has
> properly been set?
>
>
> The candidate has a RegistrationCenterID (843):
> ===
> select * from candidate where CandID=207019 \G;
> *************************** 1. row ***************************
>                   ID: 8974
>               CandID: 207019
>                PSCID: BGI102001
>           ExternalID: NULL
>                  DoB: 1969-05-15
>                  EDC: NULL
>                  Sex: Female
> RegistrationCenterID: 843
> RegistrationProjectID: 12
>            Ethnicity: NULL
>               Active: Y
>          Date_active: 2021-05-27
>         RegisteredBy: dataman
>               UserID: dataman
>      Date_registered: 2021-05-27
> flagged_caveatemptor: false
>       flagged_reason: NULL
>        flagged_other: NULL
> flagged_other_status: NULL
>             Testdate: 2021-06-09 10:55:35
>          Entity_type: Human
>           ProbandSex: NULL
>           ProbandDoB: NULL
>                  DoD: NULL
> 1 row in set (0.00 sec)
> ===
>
> The session with the proper values already exists:
> ===
> mysql> select * from session where CandID=207019 and
> Visit_label="screening" \G;
> *************************** 1. row ***************************
>                  ID: 127260
>              CandID: 207019
>            CenterID: 843
>             VisitNo: 1
>         Visit_label: screening
>        SubprojectID: 2
>           Submitted: N
>       Current_stage: Not Started
>   Date_stage_change: NULL
>           Screening: NULL
>      Date_screening: NULL
>               Visit: NULL
>          Date_visit: NULL
>            Approval: NULL
>       Date_approval: NULL
>              Active: Y
>         Date_active: 2021-05-27
>        RegisteredBy: dataman
>              UserID: dataman
>     Date_registered: 2021-05-27
>            Testdate: 2021-06-10 18:35:41
>    Hardcopy_request: -
>         BVLQCStatus: NULL
>           BVLQCType: NULL
>      BVLQCExclusion: NULL
>                 QCd: NULL
>           Scan_done: Y
>         MRIQCStatus:
>        MRIQCPending: N
> MRIQCFirstChangeTime: NULL
> MRIQCLastChangeTime: NULL
>           MRICaveat: false
>           ProjectID: 12
>          languageID: 1
> 1 row in set (0.00 sec)
> ===
>
> Thank you!
>
> C?cile
>
> On Fri, Nov 26, 2021 at 2:34 PM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
> Hi C?cile,
>
> Thank you for answer.
>
> I included the following lines:
>
> ===
>                   . " NOW(),   'NeuroDB::MRI', 'Scanner'          ) ";
> +        print "\nCenter ID: " . $centerID . "\n\n";
> +        print "\nQuery:" . $query . "\n\n";
>          $dbh->do($query);
>      }
> ===
>
> And I got the following output:
>
> ===
> perl minc_insertion.pl
> <http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl>
> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc
> -verbose -acquisition_protocol t1c -create_minc_pics
>
> log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is
> /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-14-31-d7FH_S.log
>     SELECT       ArchiveLocation     FROM       tarchive     WHERE
> TarchiveID = (                      SELECT TarchiveID
> FROM tarchive_series                      WHERE SeriesUID=? AND EchoTime=?
>                   )
> Center ID: 0
>
>
> Query:INSERT INTO candidate (CandID,          PSCID,
> RegistrationCenterID, Date_active,   Date_registered, UserID, Entity_type
>                     ) VALUES (442627, 'scanner',      0,  NOW(),    NOW(),
>   'NeuroDB::MRI', 'Scanner'          )
>
> DBD::mysql::db do failed: Cannot add or update a child row: a foreign key
> constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1`
> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at
> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
> 1020.
> ERROR: Failed to insert record in table mri_scanner:
> The following database commands failed:
>         PREPARE s FROM 'INSERT INTO mri_scanner
> (CandID,Model,Manufacturer,Serial_number,Software) VALUES (?,?,?,?,?)';
>         SET
> @x1='442627', at x2='Sonata', at x3='Siemens', at x4='syngo_MR_2004A_4VA25A';
>         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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN
> KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
> ===
>
> I think it?s important to mention that this candidate was created by the
> bids importing script. Maybe there is center associated with the candidates
> when using the bids script?
>
> Let me know your thoughts.
>
> Best,
> Alfredo.
>
> On Nov 26, 2021, at 11:13 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Thank you Alfredo.
>
> I wonder whether the variable $centerID is null when provided to the query
> here
> <https://secure-web.cisco.com/1BZxp6fiw85BciAlo2QCPeT44gOAdEJUbAAAM3VJsTVYkl_27h-GCDhXtVO-8fh2ghdX3L0808bpAkrN-4-dTSIuf12yvdTBrdZ5Wl5YcKE3s4BTaFeJPBISOXE6-2TppWqpX8R4fldLsB6dpee4WAltjKy3u6ZJa01r-_Up1j5vB6cy_vbAyEgWl_Ft7ACUJ4VwQkwh01nnF8cpg5ePrLbF5bQw28VLFdg3Uo7dO81Ow5-zFCp5KKdHX0KX7vdIPmPuijtNDX9V5jT_YKMml5cX_tM2IVASxDa-wmo0JijRQ7k6oCTwK52FO0yRmVVeFj4108ZlyK2avqXijVKYreQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm%23L1012>
> in your case.
>
> Could you add in MRI.pm line 1018 the following print statements and let
> me know what you get? (Right before the $dbh->do($query);
> print($centerID);
> print($query);
>
> Thank you!
>
> C?cile
>
> On Fri, Nov 26, 2021 at 10:55 AM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
> Hi C?cile,
>
> This is the branch that we are using in the IPMSA project:
>
> https://github.com/SPINEProject/Loris-MRI/tree/v23.0.3_IPMSA
> <https://secure-web.cisco.com/1_p5UjMqREHagXmmz7NxbZe91yrcn34HNneKcFN4qKhR9mT7798DmL7TgbLwjpDr1U0bQaX2Rdqcdu3-l5R95gEJ5AzIbYu4-psDEz9Gw3fmrcgxEel3V6rugNzEisR_jZbIG2f2KPrVumnb1MY-TJCYuPQqzVuM_3KHLYTzVKha7RbWAHq6GLefQmer8auU6BALsWue7RBcrrbG9kbGC-S-e1DZ-WP4gVNTDegrcGaghwyxclA9m6SZqs-OljIR6E7IViTaySgZuDnOp5meeyJlKdlksyj5cGVErq4YprL6I9uHWuLjB-06KBUFTBK6C1E38yyToTkJVVH-8LKRPKg/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Ftree%2Fv23.0.3_IPMSA>
>
> Best,
> Alfredo.
>
> On Nov 26, 2021, at 9:55 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> Could you point me to the version of the code you are using on GitHub so I
> can take a look at the correct MRI.pm file.
>
> Thank you!
>
> C?cile
>
> On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
> Hi C?cile,
>
> I?m getting the following error when inserting a minc file using the
> minc_insertion.pl
> <http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl>
> script:
>
> ===
> $ perl minc_insertion.pl
> <http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl>
> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc
> -verbose -acquisition_protocol t1c -create_minc_pics
>
> DBD::mysql::db do failed: Cannot add or update a child row: a foreign key
> constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1`
> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at
> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
> 1018.
>
> ERROR: Failed to insert record in table mri_scanner:
>
> The following database commands failed:
> PREPARE s FROM 'INSERT INTO mri_scanner
> (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
> SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
> 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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN
> KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
> ===
>
> Could you help me figuring out what is happening? Is there something I
> should add to the minc headers?
>
> 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 Mass General
> Brigham Compliance HelpLine at
> http://www.massgeneralbrigham.org/complianceline
> <http://secure-web.cisco.com/10DEfcj-Ova6W7NFLUPao--zc_ba_3Yk63CTqhSG5Ca4FJWekd8J8afbwCr_p31UYqWdlWd2rAqSBE3jLmNtkj6jzu0Deh3bP7WsUj3yX1B4Iv_RzcWr2nfZ7f8_OUQvlNL5D_jqwZyNdyv_JUiP0dLvm0NprWoJtFmmA4jwKQ4X8BKNoa6LBbiWMVYizEQDtUP5c9bc0XDPr-wYz3SlyBzIrLOxha8XYY4l8tLxS_skKp_uX_4jMesLtI_DCQza3WckhpQ7-43tcveIJ9vz-wKKRp31RbQkfDcbgexXsRG1oCpy-6zP8ggtvzNLZ0VSxSBDRZD7ti7dI0bPJXah5pg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
> . 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.
>
> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
>
> 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 Mass General
> Brigham Compliance HelpLine at
> http://www.massgeneralbrigham.org/complianceline
> <http://secure-web.cisco.com/1_sf0B_pY6Veyn85uEgw5ObBiM-QA382bc3nDvcSdrZOKA6no0I3vr4IK-5T3aDVnNH0xdP0QPSlWZoWkQ_GwFwWpmsSr4ck4dMGnU4VytPp-LDqG94cvmqnN5tL76lwADrn6xIQWpzuk5L8BVaZWrrrGjDSpYdGwV3AIPq2zzJhN9hBT5o5FBx0LlHEf-E7onD9zSqkkZiu9_atJraKUgpCCauEab0PbqWsTxYk0edTnIC6LbDq3t55qVy6FVWQybcR-n1rq2GND31ubWD7fk0h2dvddl4PnBk7PwnBZ6n6Q3S6lZvD9wWk_5ShEkjxI4GLdc2m60Frytk5an8XeeQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
> . 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.
>
> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
>
> 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 Mass General
> Brigham Compliance HelpLine at
> http://www.massgeneralbrigham.org/complianceline
> <http://secure-web.cisco.com/14m8jq3YFX-kL4WHSOD3NyklDH3_1jO6LrSN9gvfM5CyvUtE7cihaLOo51ulZdVQKgs5rOFUrgJxphRC2W3gjEcYsYyqJP3GlMV3sJHwLGLwsGvslUlp9df_5QkEDbk0OiO4v-SgA4uMhT6od0larJxEIegxbPKpy9GmlloLw6cDlPw0voUhi7Y0kxA_zjwDvxaVMhZ7RIpojsrcwl2crdOHamo_wQI9pz9cAU_qxwUGkhiSfwtcCe8i-UtBjbSEY9dM0SpejAYJqhqEpOK_aCqQ4_wOl8FxQWWNK2nOsD7QawkuH5liIxDIL5XojDqICa2oljEN17RtZIEy425vItA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
> . 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.
>
> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
>
> 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 Mass General
> Brigham Compliance HelpLine at
> http://www.massgeneralbrigham.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.
>
> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211129/df101a51/attachment-0001.html>

From oricod at ext.cnio.es  Mon Nov 29 08:51:59 2021
From: oricod at ext.cnio.es (=?iso-8859-1?Q?Rico=5FD=EDez=2EOlga?=)
Date: Mon, 29 Nov 2021 13:51:59 +0000
Subject: [Loris-dev] installation difficulties
Message-ID: <99B67BC1EEE7BC4E8F6D4B2EEC1F75A32A5E9D@DONAR.cnio.es>

Hello,

I am having some difficulties installing Loris.

The page that I have follow to install Loris is https://github.com/aces/Loris/blob/main/docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/01_LORIS_Install/Ubuntu/README.md

and also https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth

I have installed the versions on 0ubuntu0.20.04.1 for Linux on x86_64 ((Ubuntu)):
PHP 7.4.3
mysql  Ver 8.0.27
Composer version 2.1.11
Server version: Apache/2.4.41
npm 8.1.4
nodejs v10.19.0

But an error keep showing when i do the "make" (Posted bellow):

make
tools/gen-version.sh
npm install

> loris at 1.0.0 postinstall
> cd modules/electrophysiology_browser/jsx/react-series-data-viewer && npm install

up to date in 2.438s

up to date in 1m

314 packages are looking for funding
  run `npm fund` for details
npm run compile

> loris at 1.0.0 compile
> webpack

[webpack-cli] Invalid configuration object. Webpack has been initialized using a configuration object that does not match the API schema.
 - configuration[0].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[1].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[2].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[3].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[4].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[5].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[6].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[7].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[8].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[9].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[10].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[11].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[12].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[13].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[14].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[15].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[16].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[17].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[18].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[19].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[20].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[21].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[22].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[23].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[24].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[25].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[26].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[27].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[28].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[29].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[30].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[31].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[32].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[33].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[34].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[35].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[36].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[37].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[38].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[39].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
make: *** [Makefile:15: javascript] Error 2

What is going on?

Thanks in advance,
Olga





[Hazte Amigo del CNIO. M?s investigaci?n, menos c?ncer] <https://www.cnio.es/es/colaborar/comocolaborar.asp>

Fb Amigos del CNIO<https://www.facebook.com/AmigosdelCNIO/> |  Tw @CNIOStopCancer<https://twitter.com/CNIOStopCancer> |  Youtube canalcnio<https://www.youtube.com/canalcnio>


**ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protecci?n de los datos personales de las personas f?sicas, la informaci?n personal que nos pueda facilitar a trav?s de este correo electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de tramitar el objeto del presente correo electr?nico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no ser?n comunicados a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga exigido por una ley. Ud. podr? ejercer los derechos de acceso, rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer informaci?n adicional sobre el tratamiento de sus datos personales, puede consultar dicha informaci?n adicional en el siguiente enlace dentro de nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp

**LEGAL NOTICE**: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message.
Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211129/b1f8556b/attachment-0001.html>

From wangshen.mcin at gmail.com  Mon Nov 29 08:59:18 2021
From: wangshen.mcin at gmail.com (Shen Wang)
Date: Mon, 29 Nov 2021 08:59:18 -0500
Subject: [Loris-dev] installation difficulties
In-Reply-To: <99B67BC1EEE7BC4E8F6D4B2EEC1F75A32A5E9D@DONAR.cnio.es>
References: <99B67BC1EEE7BC4E8F6D4B2EEC1F75A32A5E9D@DONAR.cnio.es>
Message-ID: <CADM4SCz9JnDAAX7ivK-eeWFV6zkQzUGF4g6S4M4j-tXDHo31oQ@mail.gmail.com>

Hi Rico,
Please update your node js version  [NodeJS 16.10.0 (or higher)] ,  then
run "make" again.
I hope this will solve the problem.
Good luck
Best
Shen


On Mon, 29 Nov 2021 at 08:52, Rico_D?ez.Olga <oricod at ext.cnio.es> wrote:

> Hello,
>
> I am having some difficulties installing Loris.
>
> The page that I have follow to install Loris is
> https://github.com/aces/Loris/blob/main/docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/01_LORIS_Install/Ubuntu/README.md
>
> and also https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth
>
> I have installed the versions on 0ubuntu0.20.04.1 for Linux on x86_64
> ((Ubuntu)):
> PHP 7.4.3
> mysql  Ver 8.0.27
> Composer version 2.1.11
> Server version: Apache/2.4.41
> npm 8.1.4
> nodejs v10.19.0
>
> But an error keep showing when i do the "make" (Posted bellow):
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *make tools/gen-version.sh npm install > loris at 1.0.0 postinstall > cd
> modules/electrophysiology_browser/jsx/react-series-data-viewer && npm
> install up to date in 2.438s up to date in 1m 314 packages are looking for
> funding   run `npm fund` for details npm run compile > loris at 1.0.0 compile
> > webpack [webpack-cli] Invalid configuration object. Webpack has been
> initialized using a configuration object that does not match the API
> schema.  - configuration[0].node has an unknown property 'fs'. These
> properties are valid:    object { __dirname?, __filename?, global? }    ->
> Options object for node compatibility features.  - configuration[1].node
> has an unknown property 'fs'. These properties are valid:    object {
> __dirname?, __filename?, global? }    -> Options object for node
> compatibility features.  - configuration[2].node has an unknown property
> 'fs'. These properties are valid:    object { __dirname?, __filename?,
> global? }    -> Options object for node compatibility features.  -
> configuration[3].node has an unknown property 'fs'. These properties are
> valid:    object { __dirname?, __filename?, global? }    -> Options object
> for node compatibility features.  - configuration[4].node has an unknown
> property 'fs'. These properties are valid:    object { __dirname?,
> __filename?, global? }    -> Options object for node compatibility
> features.  - configuration[5].node has an unknown property 'fs'. These
> properties are valid:    object { __dirname?, __filename?, global? }    ->
> Options object for node compatibility features.  - configuration[6].node
> has an unknown property 'fs'. These properties are valid:    object {
> __dirname?, __filename?, global? }    -> Options object for node
> compatibility features.  - configuration[7].node has an unknown property
> 'fs'. These properties are valid:    object { __dirname?, __filename?,
> global? }    -> Options object for node compatibility features.  -
> configuration[8].node has an unknown property 'fs'. These properties are
> valid:    object { __dirname?, __filename?, global? }    -> Options object
> for node compatibility features.  - configuration[9].node has an unknown
> property 'fs'. These properties are valid:    object { __dirname?,
> __filename?, global? }    -> Options object for node compatibility
> features.  - configuration[10].node has an unknown property 'fs'. These
> properties are valid:    object { __dirname?, __filename?, global? }    ->
> Options object for node compatibility features.  - configuration[11].node
> has an unknown property 'fs'. These properties are valid:    object {
> __dirname?, __filename?, global? }    -> Options object for node
> compatibility features.  - configuration[12].node has an unknown property
> 'fs'. These properties are valid:    object { __dirname?, __filename?,
> global? }    -> Options object for node compatibility features.  -
> configuration[13].node has an unknown property 'fs'. These properties are
> valid:    object { __dirname?, __filename?, global? }    -> Options object
> for node compatibility features.  - configuration[14].node has an unknown
> property 'fs'. These properties are valid:    object { __dirname?,
> __filename?, global? }    -> Options object for node compatibility
> features.  - configuration[15].node has an unknown property 'fs'. These
> properties are valid:    object { __dirname?, __filename?, global? }    ->
> Options object for node compatibility features.  - configuration[16].node
> has an unknown property 'fs'. These properties are valid:    object {
> __dirname?, __filename?, global? }    -> Options object for node
> compatibility features.  - configuration[17].node has an unknown property
> 'fs'. These properties are valid:    object { __dirname?, __filename?,
> global? }    -> Options object for node compatibility features.  -
> configuration[18].node has an unknown property 'fs'. These properties are
> valid:    object { __dirname?, __filename?, global? }    -> Options object
> for node compatibility features.  - configuration[19].node has an unknown
> property 'fs'. These properties are valid:    object { __dirname?,
> __filename?, global? }    -> Options object for node compatibility
> features.  - configuration[20].node has an unknown property 'fs'. These
> properties are valid:    object { __dirname?, __filename?, global? }    ->
> Options object for node compatibility features.  - configuration[21].node
> has an unknown property 'fs'. These properties are valid:    object {
> __dirname?, __filename?, global? }    -> Options object for node
> compatibility features.  - configuration[22].node has an unknown property
> 'fs'. These properties are valid:    object { __dirname?, __filename?,
> global? }    -> Options object for node compatibility features.  -
> configuration[23].node has an unknown property 'fs'. These properties are
> valid:    object { __dirname?, __filename?, global? }    -> Options object
> for node compatibility features.  - configuration[24].node has an unknown
> property 'fs'. These properties are valid:    object { __dirname?,
> __filename?, global? }    -> Options object for node compatibility
> features.  - configuration[25].node has an unknown property 'fs'. These
> properties are valid:    object { __dirname?, __filename?, global? }    ->
> Options object for node compatibility features.  - configuration[26].node
> has an unknown property 'fs'. These properties are valid:    object {
> __dirname?, __filename?, global? }    -> Options object for node
> compatibility features.  - configuration[27].node has an unknown property
> 'fs'. These properties are valid:    object { __dirname?, __filename?,
> global? }    -> Options object for node compatibility features.  -
> configuration[28].node has an unknown property 'fs'. These properties are
> valid:    object { __dirname?, __filename?, global? }    -> Options object
> for node compatibility features.  - configuration[29].node has an unknown
> property 'fs'. These properties are valid:    object { __dirname?,
> __filename?, global? }    -> Options object for node compatibility
> features.  - configuration[30].node has an unknown property 'fs'. These
> properties are valid:    object { __dirname?, __filename?, global? }    ->
> Options object for node compatibility features.  - configuration[31].node
> has an unknown property 'fs'. These properties are valid:    object {
> __dirname?, __filename?, global? }    -> Options object for node
> compatibility features.  - configuration[32].node has an unknown property
> 'fs'. These properties are valid:    object { __dirname?, __filename?,
> global? }    -> Options object for node compatibility features.  -
> configuration[33].node has an unknown property 'fs'. These properties are
> valid:    object { __dirname?, __filename?, global? }    -> Options object
> for node compatibility features.  - configuration[34].node has an unknown
> property 'fs'. These properties are valid:    object { __dirname?,
> __filename?, global? }    -> Options object for node compatibility
> features.  - configuration[35].node has an unknown property 'fs'. These
> properties are valid:    object { __dirname?, __filename?, global? }    ->
> Options object for node compatibility features.  - configuration[36].node
> has an unknown property 'fs'. These properties are valid:    object {
> __dirname?, __filename?, global? }    -> Options object for node
> compatibility features.  - configuration[37].node has an unknown property
> 'fs'. These properties are valid:    object { __dirname?, __filename?,
> global? }    -> Options object for node compatibility features.  -
> configuration[38].node has an unknown property 'fs'. These properties are
> valid:    object { __dirname?, __filename?, global? }    -> Options object
> for node compatibility features.  - configuration[39].node has an unknown
> property 'fs'. These properties are valid:    object { __dirname?,
> __filename?, global? }    -> Options object for node compatibility
> features. make: *** [Makefile:15: javascript] Error 2*
>
> What is going on?
>
> Thanks in advance,
> Olga
>
>
>
>
> [image: Hazte Amigo del CNIO. M?s investigaci?n, menos c?ncer]
> <https://www.cnio.es/es/colaborar/comocolaborar.asp>
>
> *Fb* Amigos del CNIO <https://www.facebook.com/AmigosdelCNIO/> |  *Tw*
> @CNIOStopCancer <https://twitter.com/CNIOStopCancer> |  *Youtube*
> canalcnio <https://www.youtube.com/canalcnio>
>
>
> **ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros
> adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su
> destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro
> tipo de transmisi?n por parte de otra persona que no sea el destinatario.
> Si usted recibe por error este correo, se ruega comunicarlo al remitente y
> borrar el mensaje recibido.
> De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a
> la protecci?n de los datos personales de las personas f?sicas, la
> informaci?n personal que nos pueda facilitar a trav?s de este correo
> electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de
> tramitar el objeto del presente correo electr?nico. El tratamiento de sus
> datos personales se encuentra legitimado por ser necesario para gestionar
> el objeto del presente mensaje. Estos datos personales no ser?n comunicados
> a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga
> exigido por una ley. Ud. podr? ejercer los derechos de acceso,
> rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y
> oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029
> (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos
> en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer
> informaci?n adicional sobre el tratamiento de sus datos personales, puede
> consultar dicha informaci?n adicional en el siguiente enlace dentro de
> nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp
>
> **LEGAL NOTICE**: This email and any attached files may contain protected
> information for the sole use of its intended recipient or addressee. Anyone
> other than the intended recipient or addressee is strictly prohibited from
> distributing, reproducing or transmitting the email and its contents in any
> way. If you receive this email in error, please notify the sender and
> delete the message.
> Pursuant to the provisions of EU Regulation 2016/679 regarding the
> protection of personal data, any personal information you provide through
> this email will be registered by the CNIO Foundation in order to deal with
> content of this email. Your personal data must be processed in order to be
> able to deal with the content and purpose of this message. Your personal
> details will not be passed on to anyone else unless you authorise us to do
> so or we are required to do so by law. You may exercise your rights
> regarding access, rectification, suppression, limitation of processing,
> portability and opposition by writing to the following address: c/Melchor
> Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection
> Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If
> you require further information about the processing of your personal data,
> go to the following link on our webpage:
> https://www.cnio.es/es/privacidad/index.asp
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>


-- 
Shen Wang
Loris <https://github.com/aces/Loris>  Developer
Montreal Neurological Institute
McGill University
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211129/8262746d/attachment-0001.html>

From AMORALESPINZON at BWH.HARVARD.EDU  Mon Nov 29 13:30:40 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Mon, 29 Nov 2021 18:30:40 +0000
Subject: [Loris-dev] MINC insertion
In-Reply-To: <CAMkiY3erKTvEXScZofQeP-u2jFh4GK4gPEJnD7TgFuqsPYqSiQ@mail.gmail.com>
References: <DBD132E4-4075-42F5-82EA-62C4EA86A33A@mcgill.ca>
 <CAMkiY3fKNoN1U=t3mjM2VnOgWU56=0-YadQwLkc6xZOGUc-mvA@mail.gmail.com>
 <ED989A0A-3A12-4161-AF6A-8F7586F7DDFE@bwh.harvard.edu>
 <CAMkiY3eHjFAd1-bKdCx_5_k1nf2Mx_GCKDs2htAaTxxFoPqKhQ@mail.gmail.com>
 <63278E0B-C75D-467E-9A2C-579BC947EBC3@bwh.harvard.edu>
 <CAMkiY3fJcP0O=j++Rjjmymh9QqMofBY0NaTw0YH8GYTco7ZxSg@mail.gmail.com>
 <53B91CC9-99CE-4E76-A080-9E902115673A@bwh.harvard.edu>
 <CAMkiY3fUqgyP-BoFb71aOjBLfnPNRqt1UyQSEq6Q2TtObsNFoA@mail.gmail.com>
 <79E009D1-6AA8-4090-812A-F7405AE257C9@bwh.harvard.edu>
 <CAMkiY3eFwZbaCZXdBc-eS6Skp9-bSz5mHH6A2WwwS83_2WNmhg@mail.gmail.com>
 <94B44F39-0E17-4C7B-AE35-490F8BF95ABD@bwh.harvard.edu>
 <CAMkiY3erKTvEXScZofQeP-u2jFh4GK4gPEJnD7TgFuqsPYqSiQ@mail.gmail.com>
Message-ID: <E92E7EDA-FF77-41B1-82CD-1ABF0F0DFCCA@bwh.harvard.edu>

Hi C?cile,

Here is the results of the query:

===
mysql> SELECT * FROM psc WHERE CenterID=843 \G;
*************************** 1. row ***************************
  CenterID: 843
      Name: inf_0102
   PSCArea: NULL
   Address: NULL
      City: NULL
   StateID: NULL
       ZIP: NULL
    Phone1: NULL
    Phone2: NULL
  Contact1: NULL
  Contact2: NULL
     Alias: BGI
 MRI_alias: BGI
   Account: NULL
Study_site: Y
1 row in set (0.00 sec)
===

Alias and MRI_alias look fine. What should we look into now? We can debug over Zoom if that works for you.

Best,
Alfredo.

On Nov 29, 2021, at 8:40 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

I think we are indeed narrowing where the error happens. It looks like for some reason this getPSC<https://secure-web.cisco.com/1WKyW2D76xw9mcH7c3mrbUADimOSPIUAeml9rWivk7bItei0PlVHDbuGfrRpzeITWbL6b0Rr61uaOfjR-rrMpspUFVDp6AC5wXTy-v_mpx-SO9Fro3_O7WqkuAEbxZTWwVIvoAIdW5_K9PSX2xdI8_T64tIgsBc859NyIdKSuS4vJjdvc2VsaapiuHVAY8oaJ0x4ikpKSaiQocNEm2yqtX0tRI26lOCf1qGK5nam_R1310B5bXRHQRMJEmJ3EE9nx5WgxcJcOt078poMQe4krTe5X1yOWE9G3LauCi0VwvI_qoqKmqtkbU_6q0PES2OKttGDvMWpti_tEMV67ieEFVQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2Fv23.0.3_IPMSA%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm> function is returning "UNKN", 0. It might be related to the Alias or MRI_alias content of the psc table for CenterID 843.

What do you get when you run the following query?
SELECT * FROM psc WHERE CenterID=843;

In the Alias or MRI_alias column, you should be able to see BGI so that the scanner candidate can be identified with the proper site.

Let me know,

C?cile

On Sun, Nov 28, 2021 at 12:42 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Thank you, it looks like we?re getting closer to find a solution. Find the answers to your questions inline below.

Happy to debug over Zoom if it?s easier for you.

Best,
Alfredo.


On Nov 26, 2021, at 3:31 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

I notice that the CenterID for the site is 0. Do you have an entry in the psc table for a CenterID=0?
No, we don?t have it. The CenterID starts at 1.
===
select * from psc where CenterID=0;
Empty set (0.00 sec)
===

The problem here is that the data comes from a new scanner and the pipeline tries to first register a new candidate for the scanner (scanner candidate) before adding an entry in the mri_scanner table. To determine the site of the scanner, the pipeline uses the determinePSC<https://secure-web.cisco.com/1Dc-fajrB7Ud53q9lvqwcvWI66c8Sjd_VWPzsGJnI1xtsFo2tce71aRhvXOFAeXFyiXWHCRtrsuOUxz9FTymBxjmkO9QVm92NieBTkPQt3sHgPQQUT2j2bpLa-AQKrAp6CJLMFA3SshUHX9tSHCkDZl4-687CTtyUYa8o_QDxRn0UEiy6yqufe-DTaVIJxY2bFtGERf0kTxBUy4JaS_ZiEHYQ3uGUjy9x3F25dMV0RZ_8hv74gXSGJW3t7AJ2zm-stvAEvizinmIQrzN-OP0L0FTHPAmoHzn0NFzDCrYvCDnMCfBNCexzjhZ9JcsQSpQS_LK_oW8UEy8ObHNoEsbzKA/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRIProcessingUtility.pm%23L503> function of MRIProcessingUtility.pm (called by minc_insertion.pl<http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl> in line 454<https://secure-web.cisco.com/1UWbEiJQk9qeievujOxfe9vFYw_u8x2SaJKAYzS6WrKuX-cWcA62bpRkJ-fOL-6hCS2oSzF8ye-G99zRPL7lv-ggMi48rbGxbcOhqRu-S7FGWEZpc-vb_j_YA73XsG7Od4qBB98i5AMLyLXi5SZAwP5E_nbdjI626BeW24SmnD6Hd_MocuW8oOqNs4mTZSGh8EkMpO-BOuH4bMikoRDLakpW-VmFznZ130h0pg4vTAAfwsjwTvbjqHgFlzExIBUHDqgaeYpD5aWuC1jjiXxEy182es4Wv0VMpe5btqKR8f0VjaB-rl2G6tC0A8q5fHAfkY5fNxpYViSFAv6jJO-8F8w/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2Fminc_insertion.pl%23L454>). I would be curious to see what the $center_name and $centerID values returned are.
These are the returned values. Maybe we need to look deeper into this.
===
determinePSC->Center name: UNKN
determinePSC->Center ID: 0
===


Could you also copy the code you have in your prod file for the function getSubjectIDs?

You mean this file ?mri/dicom-archive/.loris_mri/prod?, right? Find the function enclosed.


Finally, could you check that the candidate BGI102001_207019 does have a RegistrationCenterID set and if there is already a screening session created in the session table, that the CenterID of that session has properly been set?


The candidate has a RegistrationCenterID (843):
===
select * from candidate where CandID=207019 \G;
*************************** 1. row ***************************
                  ID: 8974
              CandID: 207019
               PSCID: BGI102001
          ExternalID: NULL
                 DoB: 1969-05-15
                 EDC: NULL
                 Sex: Female
RegistrationCenterID: 843
RegistrationProjectID: 12
           Ethnicity: NULL
              Active: Y
         Date_active: 2021-05-27
        RegisteredBy: dataman
              UserID: dataman
     Date_registered: 2021-05-27
flagged_caveatemptor: false
      flagged_reason: NULL
       flagged_other: NULL
flagged_other_status: NULL
            Testdate: 2021-06-09 10:55:35
         Entity_type: Human
          ProbandSex: NULL
          ProbandDoB: NULL
                 DoD: NULL
1 row in set (0.00 sec)
===

The session with the proper values already exists:
===
mysql> select * from session where CandID=207019 and Visit_label="screening" \G;
*************************** 1. row ***************************
                 ID: 127260
             CandID: 207019
           CenterID: 843
            VisitNo: 1
        Visit_label: screening
       SubprojectID: 2
          Submitted: N
      Current_stage: Not Started
  Date_stage_change: NULL
          Screening: NULL
     Date_screening: NULL
              Visit: NULL
         Date_visit: NULL
           Approval: NULL
      Date_approval: NULL
             Active: Y
        Date_active: 2021-05-27
       RegisteredBy: dataman
             UserID: dataman
    Date_registered: 2021-05-27
           Testdate: 2021-06-10 18:35:41
   Hardcopy_request: -
        BVLQCStatus: NULL
          BVLQCType: NULL
     BVLQCExclusion: NULL
                QCd: NULL
          Scan_done: Y
        MRIQCStatus:
       MRIQCPending: N
MRIQCFirstChangeTime: NULL
MRIQCLastChangeTime: NULL
          MRICaveat: false
          ProjectID: 12
         languageID: 1
1 row in set (0.00 sec)
===

Thank you!

C?cile

On Fri, Nov 26, 2021 at 2:34 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Thank you for answer.

I included the following lines:

===
                  . " NOW(),   'NeuroDB::MRI', 'Scanner'          ) ";
+        print "\nCenter ID: " . $centerID . "\n\n";
+        print "\nQuery:" . $query . "\n\n";
         $dbh->do($query);
     }
===

And I got the following output:

===
perl minc_insertion.pl<http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc -verbose -acquisition_protocol t1c -create_minc_pics

log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-14-31-d7FH_S.log
    SELECT       ArchiveLocation     FROM       tarchive     WHERE       TarchiveID = (                      SELECT TarchiveID                      FROM tarchive_series                      WHERE SeriesUID=? AND EchoTime=?                    )
Center ID: 0


Query:INSERT INTO candidate (CandID,          PSCID,  RegistrationCenterID, Date_active,   Date_registered, UserID, Entity_type                       ) VALUES (442627, 'scanner',      0,  NOW(),    NOW(),   'NeuroDB::MRI', 'Scanner'          )

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1020.
ERROR: Failed to insert record in table mri_scanner:
The following database commands failed:
        PREPARE s FROM 'INSERT INTO mri_scanner (CandID,Model,Manufacturer,Serial_number,Software) VALUES (?,?,?,?,?)';
        SET @x1='442627', at x2='Sonata', at x3='Siemens', at x4='syngo_MR_2004A_4VA25A';
        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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

I think it?s important to mention that this candidate was created by the bids importing script. Maybe there is center associated with the candidates when using the bids script?

Let me know your thoughts.

Best,
Alfredo.

On Nov 26, 2021, at 11:13 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Thank you Alfredo.

I wonder whether the variable $centerID is null when provided to the query here<https://secure-web.cisco.com/1BZxp6fiw85BciAlo2QCPeT44gOAdEJUbAAAM3VJsTVYkl_27h-GCDhXtVO-8fh2ghdX3L0808bpAkrN-4-dTSIuf12yvdTBrdZ5Wl5YcKE3s4BTaFeJPBISOXE6-2TppWqpX8R4fldLsB6dpee4WAltjKy3u6ZJa01r-_Up1j5vB6cy_vbAyEgWl_Ft7ACUJ4VwQkwh01nnF8cpg5ePrLbF5bQw28VLFdg3Uo7dO81Ow5-zFCp5KKdHX0KX7vdIPmPuijtNDX9V5jT_YKMml5cX_tM2IVASxDa-wmo0JijRQ7k6oCTwK52FO0yRmVVeFj4108ZlyK2avqXijVKYreQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm%23L1012> in your case.

Could you add in MRI.pm line 1018 the following print statements and let me know what you get? (Right before the $dbh->do($query);
print($centerID);
print($query);

Thank you!

C?cile

On Fri, Nov 26, 2021 at 10:55 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

This is the branch that we are using in the IPMSA project:

https://github.com/SPINEProject/Loris-MRI/tree/v23.0.3_IPMSA<https://secure-web.cisco.com/1_p5UjMqREHagXmmz7NxbZe91yrcn34HNneKcFN4qKhR9mT7798DmL7TgbLwjpDr1U0bQaX2Rdqcdu3-l5R95gEJ5AzIbYu4-psDEz9Gw3fmrcgxEel3V6rugNzEisR_jZbIG2f2KPrVumnb1MY-TJCYuPQqzVuM_3KHLYTzVKha7RbWAHq6GLefQmer8auU6BALsWue7RBcrrbG9kbGC-S-e1DZ-WP4gVNTDegrcGaghwyxclA9m6SZqs-OljIR6E7IViTaySgZuDnOp5meeyJlKdlksyj5cGVErq4YprL6I9uHWuLjB-06KBUFTBK6C1E38yyToTkJVVH-8LKRPKg/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Ftree%2Fv23.0.3_IPMSA>

Best,
Alfredo.

On Nov 26, 2021, at 9:55 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Could you point me to the version of the code you are using on GitHub so I can take a look at the correct MRI.pm file.

Thank you!

C?cile

On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I?m getting the following error when inserting a minc file using the minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> script:

===
$ perl minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc  -verbose -acquisition_protocol t1c -create_minc_pics

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1018.

ERROR: Failed to insert record in table mri_scanner:

The following database commands failed:
PREPARE s FROM 'INSERT INTO mri_scanner (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

Could you help me figuring out what is happening? Is there something I should add to the minc headers?

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/10DEfcj-Ova6W7NFLUPao--zc_ba_3Yk63CTqhSG5Ca4FJWekd8J8afbwCr_p31UYqWdlWd2rAqSBE3jLmNtkj6jzu0Deh3bP7WsUj3yX1B4Iv_RzcWr2nfZ7f8_OUQvlNL5D_jqwZyNdyv_JUiP0dLvm0NprWoJtFmmA4jwKQ4X8BKNoa6LBbiWMVYizEQDtUP5c9bc0XDPr-wYz3SlyBzIrLOxha8XYY4l8tLxS_skKp_uX_4jMesLtI_DCQza3WckhpQ7-43tcveIJ9vz-wKKRp31RbQkfDcbgexXsRG1oCpy-6zP8ggtvzNLZ0VSxSBDRZD7ti7dI0bPJXah5pg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.


Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1_sf0B_pY6Veyn85uEgw5ObBiM-QA382bc3nDvcSdrZOKA6no0I3vr4IK-5T3aDVnNH0xdP0QPSlWZoWkQ_GwFwWpmsSr4ck4dMGnU4VytPp-LDqG94cvmqnN5tL76lwADrn6xIQWpzuk5L8BVaZWrrrGjDSpYdGwV3AIPq2zzJhN9hBT5o5FBx0LlHEf-E7onD9zSqkkZiu9_atJraKUgpCCauEab0PbqWsTxYk0edTnIC6LbDq3t55qVy6FVWQybcR-n1rq2GND31ubWD7fk0h2dvddl4PnBk7PwnBZ6n6Q3S6lZvD9wWk_5ShEkjxI4GLdc2m60Frytk5an8XeeQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.


Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/14m8jq3YFX-kL4WHSOD3NyklDH3_1jO6LrSN9gvfM5CyvUtE7cihaLOo51ulZdVQKgs5rOFUrgJxphRC2W3gjEcYsYyqJP3GlMV3sJHwLGLwsGvslUlp9df_5QkEDbk0OiO4v-SgA4uMhT6od0larJxEIegxbPKpy9GmlloLw6cDlPw0voUhi7Y0kxA_zjwDvxaVMhZ7RIpojsrcwl2crdOHamo_wQI9pz9cAU_qxwUGkhiSfwtcCe8i-UtBjbSEY9dM0SpejAYJqhqEpOK_aCqQ4_wOl8FxQWWNK2nOsD7QawkuH5liIxDIL5XojDqICa2oljEN17RtZIEy425vItA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.


Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1fFVWywiC_KI2wX-iM-iipSCRfAdgcr8caPgwKQ4dp_E6amXdXGc7f5R2bEhT0ZmPeCy6AXOIj0LWU8x0g9SAwx5xHb4GLCF-WQaSnrmTYPMha1wCzNZjbbBFCQIWFh-5N5ZGDPDOldyduZuC8MKXnKD0Q-W-6m3qAJrKOYtCur2SJ-tEq_MUeMO32jd104Mmv3FTkOUPxaDqSzIyJdrDtb-wImxqqblDaBhzm4JjA7RYkdtxpS9SlOO_KlPpmstVVrRotFCLSgjsT4iejspAR2jzTrd7Q6rQFUDBKugqnSW_Tn0i3OURMIorUsRwMg8dE6slT8k7I3iv88FTtVp8cA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.

Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211129/ff675562/attachment-0001.html>

From cecile.madjar at mcin.ca  Tue Nov 30 16:15:28 2021
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Tue, 30 Nov 2021 16:15:28 -0500
Subject: [Loris-dev] MINC insertion
In-Reply-To: <E92E7EDA-FF77-41B1-82CD-1ABF0F0DFCCA@bwh.harvard.edu>
References: <DBD132E4-4075-42F5-82EA-62C4EA86A33A@mcgill.ca>
 <CAMkiY3fKNoN1U=t3mjM2VnOgWU56=0-YadQwLkc6xZOGUc-mvA@mail.gmail.com>
 <ED989A0A-3A12-4161-AF6A-8F7586F7DDFE@bwh.harvard.edu>
 <CAMkiY3eHjFAd1-bKdCx_5_k1nf2Mx_GCKDs2htAaTxxFoPqKhQ@mail.gmail.com>
 <63278E0B-C75D-467E-9A2C-579BC947EBC3@bwh.harvard.edu>
 <CAMkiY3fJcP0O=j++Rjjmymh9QqMofBY0NaTw0YH8GYTco7ZxSg@mail.gmail.com>
 <53B91CC9-99CE-4E76-A080-9E902115673A@bwh.harvard.edu>
 <CAMkiY3fUqgyP-BoFb71aOjBLfnPNRqt1UyQSEq6Q2TtObsNFoA@mail.gmail.com>
 <79E009D1-6AA8-4090-812A-F7405AE257C9@bwh.harvard.edu>
 <CAMkiY3eFwZbaCZXdBc-eS6Skp9-bSz5mHH6A2WwwS83_2WNmhg@mail.gmail.com>
 <94B44F39-0E17-4C7B-AE35-490F8BF95ABD@bwh.harvard.edu>
 <CAMkiY3erKTvEXScZofQeP-u2jFh4GK4gPEJnD7TgFuqsPYqSiQ@mail.gmail.com>
 <E92E7EDA-FF77-41B1-82CD-1ABF0F0DFCCA@bwh.harvard.edu>
Message-ID: <CAMkiY3cKpqDwbpSxQKKtUir1Jvx9-ZwRn+PQ5DUp3kjZ0YLuxg@mail.gmail.com>

Hi Alfredo,

Sorry for the delay. Time flies quickly this week.

How about a Zoom call tomorrow (Wednesday) at 10:30AM or at 4PM?

Let me know if one of those times works for you.
Thanks!

C?cile

On Mon, Nov 29, 2021 at 1:30 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi C?cile,
>
> Here is the results of the query:
>
> ===
> mysql> SELECT * FROM psc WHERE CenterID=843 \G;
> *************************** 1. row ***************************
>   CenterID: 843
>       Name: inf_0102
>    PSCArea: NULL
>    Address: NULL
>       City: NULL
>    StateID: NULL
>        ZIP: NULL
>     Phone1: NULL
>     Phone2: NULL
>   Contact1: NULL
>   Contact2: NULL
>      Alias: BGI
>  MRI_alias: BGI
>    Account: NULL
> Study_site: Y
> 1 row in set (0.00 sec)
> ===
>
> Alias and MRI_alias look fine. What should we look into now? We can debug
> over Zoom if that works for you.
>
> Best,
> Alfredo.
>
> On Nov 29, 2021, at 8:40 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> I think we are indeed narrowing where the error happens. It looks like for
> some reason this getPSC
> <https://secure-web.cisco.com/1WKyW2D76xw9mcH7c3mrbUADimOSPIUAeml9rWivk7bItei0PlVHDbuGfrRpzeITWbL6b0Rr61uaOfjR-rrMpspUFVDp6AC5wXTy-v_mpx-SO9Fro3_O7WqkuAEbxZTWwVIvoAIdW5_K9PSX2xdI8_T64tIgsBc859NyIdKSuS4vJjdvc2VsaapiuHVAY8oaJ0x4ikpKSaiQocNEm2yqtX0tRI26lOCf1qGK5nam_R1310B5bXRHQRMJEmJ3EE9nx5WgxcJcOt078poMQe4krTe5X1yOWE9G3LauCi0VwvI_qoqKmqtkbU_6q0PES2OKttGDvMWpti_tEMV67ieEFVQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2Fv23.0.3_IPMSA%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm>
> function is returning "UNKN", 0. It might be related to the Alias or
> MRI_alias content of the psc table for CenterID 843.
>
> What do you get when you run the following query?
> SELECT * FROM psc WHERE CenterID=843;
>
> In the Alias or MRI_alias column, you should be able to see BGI so that
> the scanner candidate can be identified with the proper site.
>
> Let me know,
>
> C?cile
>
> On Sun, Nov 28, 2021 at 12:42 PM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Hi C?cile,
>>
>> Thank you, it looks like we?re getting closer to find a solution. Find
>> the answers to your questions inline below.
>>
>> Happy to debug over Zoom if it?s easier for you.
>>
>> Best,
>> Alfredo.
>>
>>
>> On Nov 26, 2021, at 3:31 PM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>>
>>         External Email - Use Caution
>>
>> Hi Alfredo,
>>
>> I notice that the CenterID for the site is 0. Do you have an entry in the
>> psc table for a CenterID=0?
>>
>> No, we don?t have it. The CenterID starts at 1.
>> ===
>> select * from psc where CenterID=0;
>> Empty set (0.00 sec)
>> ===
>>
>>
>> The problem here is that the data comes from a new scanner and the
>> pipeline tries to first register a new candidate for the scanner (scanner
>> candidate) before adding an entry in the mri_scanner table. To determine
>> the site of the scanner, the pipeline uses the determinePSC
>> <https://secure-web.cisco.com/1Dc-fajrB7Ud53q9lvqwcvWI66c8Sjd_VWPzsGJnI1xtsFo2tce71aRhvXOFAeXFyiXWHCRtrsuOUxz9FTymBxjmkO9QVm92NieBTkPQt3sHgPQQUT2j2bpLa-AQKrAp6CJLMFA3SshUHX9tSHCkDZl4-687CTtyUYa8o_QDxRn0UEiy6yqufe-DTaVIJxY2bFtGERf0kTxBUy4JaS_ZiEHYQ3uGUjy9x3F25dMV0RZ_8hv74gXSGJW3t7AJ2zm-stvAEvizinmIQrzN-OP0L0FTHPAmoHzn0NFzDCrYvCDnMCfBNCexzjhZ9JcsQSpQS_LK_oW8UEy8ObHNoEsbzKA/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRIProcessingUtility.pm%23L503>
>> function of MRIProcessingUtility.pm (called by minc_insertion.pl
>> <http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl>
>> in line 454
>> <https://secure-web.cisco.com/1UWbEiJQk9qeievujOxfe9vFYw_u8x2SaJKAYzS6WrKuX-cWcA62bpRkJ-fOL-6hCS2oSzF8ye-G99zRPL7lv-ggMi48rbGxbcOhqRu-S7FGWEZpc-vb_j_YA73XsG7Od4qBB98i5AMLyLXi5SZAwP5E_nbdjI626BeW24SmnD6Hd_MocuW8oOqNs4mTZSGh8EkMpO-BOuH4bMikoRDLakpW-VmFznZ130h0pg4vTAAfwsjwTvbjqHgFlzExIBUHDqgaeYpD5aWuC1jjiXxEy182es4Wv0VMpe5btqKR8f0VjaB-rl2G6tC0A8q5fHAfkY5fNxpYViSFAv6jJO-8F8w/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2Fminc_insertion.pl%23L454>).
>> I would be curious to see what the $center_name and $centerID values
>> returned are.
>>
>> These are the returned values. Maybe we need to look deeper into this.
>> ===
>> determinePSC->Center name: UNKN
>> determinePSC->Center ID: 0
>> ===
>>
>>
>> Could you also copy the code you have in your prod file for the function
>> getSubjectIDs?
>>
>>
>> You mean this file ?mri/dicom-archive/.loris_mri/prod?, right? Find the
>> function enclosed.
>>
>>
>> Finally, could you check that the candidate BGI102001_207019 does have a
>> RegistrationCenterID set and if there is already a screening session
>> created in the session table, that the CenterID of that session has
>> properly been set?
>>
>>
>> The candidate has a RegistrationCenterID (843):
>> ===
>> select * from candidate where CandID=207019 \G;
>> *************************** 1. row ***************************
>>                   ID: 8974
>>               CandID: 207019
>>                PSCID: BGI102001
>>           ExternalID: NULL
>>                  DoB: 1969-05-15
>>                  EDC: NULL
>>                  Sex: Female
>> RegistrationCenterID: 843
>> RegistrationProjectID: 12
>>            Ethnicity: NULL
>>               Active: Y
>>          Date_active: 2021-05-27
>>         RegisteredBy: dataman
>>               UserID: dataman
>>      Date_registered: 2021-05-27
>> flagged_caveatemptor: false
>>       flagged_reason: NULL
>>        flagged_other: NULL
>> flagged_other_status: NULL
>>             Testdate: 2021-06-09 10:55:35
>>          Entity_type: Human
>>           ProbandSex: NULL
>>           ProbandDoB: NULL
>>                  DoD: NULL
>> 1 row in set (0.00 sec)
>> ===
>>
>> The session with the proper values already exists:
>> ===
>> mysql> select * from session where CandID=207019 and
>> Visit_label="screening" \G;
>> *************************** 1. row ***************************
>>                  ID: 127260
>>              CandID: 207019
>>            CenterID: 843
>>             VisitNo: 1
>>         Visit_label: screening
>>        SubprojectID: 2
>>           Submitted: N
>>       Current_stage: Not Started
>>   Date_stage_change: NULL
>>           Screening: NULL
>>      Date_screening: NULL
>>               Visit: NULL
>>          Date_visit: NULL
>>            Approval: NULL
>>       Date_approval: NULL
>>              Active: Y
>>         Date_active: 2021-05-27
>>        RegisteredBy: dataman
>>              UserID: dataman
>>     Date_registered: 2021-05-27
>>            Testdate: 2021-06-10 18:35:41
>>    Hardcopy_request: -
>>         BVLQCStatus: NULL
>>           BVLQCType: NULL
>>      BVLQCExclusion: NULL
>>                 QCd: NULL
>>           Scan_done: Y
>>         MRIQCStatus:
>>        MRIQCPending: N
>> MRIQCFirstChangeTime: NULL
>> MRIQCLastChangeTime: NULL
>>           MRICaveat: false
>>           ProjectID: 12
>>          languageID: 1
>> 1 row in set (0.00 sec)
>> ===
>>
>> Thank you!
>>
>> C?cile
>>
>> On Fri, Nov 26, 2021 at 2:34 PM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>> Hi C?cile,
>>
>> Thank you for answer.
>>
>> I included the following lines:
>>
>> ===
>>                   . " NOW(),   'NeuroDB::MRI', 'Scanner'          ) ";
>> +        print "\nCenter ID: " . $centerID . "\n\n";
>> +        print "\nQuery:" . $query . "\n\n";
>>          $dbh->do($query);
>>      }
>> ===
>>
>> And I got the following output:
>>
>> ===
>> perl minc_insertion.pl
>> <http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl>
>> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc
>> -verbose -acquisition_protocol t1c -create_minc_pics
>>
>> log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is
>> /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-14-31-d7FH_S.log
>>     SELECT       ArchiveLocation     FROM       tarchive     WHERE
>> TarchiveID = (                      SELECT TarchiveID
>> FROM tarchive_series                      WHERE SeriesUID=? AND EchoTime=?
>>                   )
>> Center ID: 0
>>
>>
>> Query:INSERT INTO candidate (CandID,          PSCID,
>> RegistrationCenterID, Date_active,   Date_registered, UserID, Entity_type
>>                     ) VALUES (442627, 'scanner',      0,  NOW(),    NOW(),
>>   'NeuroDB::MRI', 'Scanner'          )
>>
>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign key
>> constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1`
>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at
>> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
>> 1020.
>> ERROR: Failed to insert record in table mri_scanner:
>> The following database commands failed:
>>         PREPARE s FROM 'INSERT INTO mri_scanner
>> (CandID,Model,Manufacturer,Serial_number,Software) VALUES (?,?,?,?,?)';
>>         SET
>> @x1='442627', at x2='Sonata', at x3='Siemens', at x4='syngo_MR_2004A_4VA25A';
>>         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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN
>> KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
>> ===
>>
>> I think it?s important to mention that this candidate was created by the
>> bids importing script. Maybe there is center associated with the candidates
>> when using the bids script?
>>
>> Let me know your thoughts.
>>
>> Best,
>> Alfredo.
>>
>> On Nov 26, 2021, at 11:13 AM, Cecile Madjar <cecile.madjar at mcin.ca>
>> wrote:
>>
>>         External Email - Use Caution
>>
>> Thank you Alfredo.
>>
>> I wonder whether the variable $centerID is null when provided to the
>> query here
>> <https://secure-web.cisco.com/1BZxp6fiw85BciAlo2QCPeT44gOAdEJUbAAAM3VJsTVYkl_27h-GCDhXtVO-8fh2ghdX3L0808bpAkrN-4-dTSIuf12yvdTBrdZ5Wl5YcKE3s4BTaFeJPBISOXE6-2TppWqpX8R4fldLsB6dpee4WAltjKy3u6ZJa01r-_Up1j5vB6cy_vbAyEgWl_Ft7ACUJ4VwQkwh01nnF8cpg5ePrLbF5bQw28VLFdg3Uo7dO81Ow5-zFCp5KKdHX0KX7vdIPmPuijtNDX9V5jT_YKMml5cX_tM2IVASxDa-wmo0JijRQ7k6oCTwK52FO0yRmVVeFj4108ZlyK2avqXijVKYreQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm%23L1012>
>> in your case.
>>
>> Could you add in MRI.pm line 1018 the following print statements and let
>> me know what you get? (Right before the $dbh->do($query);
>> print($centerID);
>> print($query);
>>
>> Thank you!
>>
>> C?cile
>>
>> On Fri, Nov 26, 2021 at 10:55 AM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>> Hi C?cile,
>>
>> This is the branch that we are using in the IPMSA project:
>>
>> https://github.com/SPINEProject/Loris-MRI/tree/v23.0.3_IPMSA
>> <https://secure-web.cisco.com/1_p5UjMqREHagXmmz7NxbZe91yrcn34HNneKcFN4qKhR9mT7798DmL7TgbLwjpDr1U0bQaX2Rdqcdu3-l5R95gEJ5AzIbYu4-psDEz9Gw3fmrcgxEel3V6rugNzEisR_jZbIG2f2KPrVumnb1MY-TJCYuPQqzVuM_3KHLYTzVKha7RbWAHq6GLefQmer8auU6BALsWue7RBcrrbG9kbGC-S-e1DZ-WP4gVNTDegrcGaghwyxclA9m6SZqs-OljIR6E7IViTaySgZuDnOp5meeyJlKdlksyj5cGVErq4YprL6I9uHWuLjB-06KBUFTBK6C1E38yyToTkJVVH-8LKRPKg/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Ftree%2Fv23.0.3_IPMSA>
>>
>> Best,
>> Alfredo.
>>
>> On Nov 26, 2021, at 9:55 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>>
>>         External Email - Use Caution
>>
>> Hi Alfredo,
>>
>> Could you point me to the version of the code you are using on GitHub so
>> I can take a look at the correct MRI.pm file.
>>
>> Thank you!
>>
>> C?cile
>>
>> On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>> Hi C?cile,
>>
>> I?m getting the following error when inserting a minc file using the
>> minc_insertion.pl
>> <http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl>
>> script:
>>
>> ===
>> $ perl minc_insertion.pl
>> <http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl>
>> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc
>> -verbose -acquisition_protocol t1c -create_minc_pics
>>
>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign key
>> constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1`
>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at
>> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
>> 1018.
>>
>> ERROR: Failed to insert record in table mri_scanner:
>>
>> The following database commands failed:
>> PREPARE s FROM 'INSERT INTO mri_scanner
>> (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
>> SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
>> 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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN
>> KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
>> ===
>>
>> Could you help me figuring out what is happening? Is there something I
>> should add to the minc headers?
>>
>> 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 Mass General
>> Brigham Compliance HelpLine at
>> http://www.massgeneralbrigham.org/complianceline
>> <http://secure-web.cisco.com/10DEfcj-Ova6W7NFLUPao--zc_ba_3Yk63CTqhSG5Ca4FJWekd8J8afbwCr_p31UYqWdlWd2rAqSBE3jLmNtkj6jzu0Deh3bP7WsUj3yX1B4Iv_RzcWr2nfZ7f8_OUQvlNL5D_jqwZyNdyv_JUiP0dLvm0NprWoJtFmmA4jwKQ4X8BKNoa6LBbiWMVYizEQDtUP5c9bc0XDPr-wYz3SlyBzIrLOxha8XYY4l8tLxS_skKp_uX_4jMesLtI_DCQza3WckhpQ7-43tcveIJ9vz-wKKRp31RbQkfDcbgexXsRG1oCpy-6zP8ggtvzNLZ0VSxSBDRZD7ti7dI0bPJXah5pg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>> . 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.
>>
>> Please note that this e-mail is not secure (encrypted).  If you do not
>> wish to continue communication over unencrypted e-mail, please notify the
>> sender of this message immediately.  Continuing to send or respond to
>> e-mail after receiving this message means you understand and accept this
>> risk and wish to continue to communicate over unencrypted e-mail.
>>
>>
>> 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 Mass General
>> Brigham Compliance HelpLine at
>> http://www.massgeneralbrigham.org/complianceline
>> <http://secure-web.cisco.com/1_sf0B_pY6Veyn85uEgw5ObBiM-QA382bc3nDvcSdrZOKA6no0I3vr4IK-5T3aDVnNH0xdP0QPSlWZoWkQ_GwFwWpmsSr4ck4dMGnU4VytPp-LDqG94cvmqnN5tL76lwADrn6xIQWpzuk5L8BVaZWrrrGjDSpYdGwV3AIPq2zzJhN9hBT5o5FBx0LlHEf-E7onD9zSqkkZiu9_atJraKUgpCCauEab0PbqWsTxYk0edTnIC6LbDq3t55qVy6FVWQybcR-n1rq2GND31ubWD7fk0h2dvddl4PnBk7PwnBZ6n6Q3S6lZvD9wWk_5ShEkjxI4GLdc2m60Frytk5an8XeeQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>> . 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.
>>
>> Please note that this e-mail is not secure (encrypted).  If you do not
>> wish to continue communication over unencrypted e-mail, please notify the
>> sender of this message immediately.  Continuing to send or respond to
>> e-mail after receiving this message means you understand and accept this
>> risk and wish to continue to communicate over unencrypted e-mail.
>>
>>
>> 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 Mass General
>> Brigham Compliance HelpLine at
>> http://www.massgeneralbrigham.org/complianceline
>> <http://secure-web.cisco.com/14m8jq3YFX-kL4WHSOD3NyklDH3_1jO6LrSN9gvfM5CyvUtE7cihaLOo51ulZdVQKgs5rOFUrgJxphRC2W3gjEcYsYyqJP3GlMV3sJHwLGLwsGvslUlp9df_5QkEDbk0OiO4v-SgA4uMhT6od0larJxEIegxbPKpy9GmlloLw6cDlPw0voUhi7Y0kxA_zjwDvxaVMhZ7RIpojsrcwl2crdOHamo_wQI9pz9cAU_qxwUGkhiSfwtcCe8i-UtBjbSEY9dM0SpejAYJqhqEpOK_aCqQ4_wOl8FxQWWNK2nOsD7QawkuH5liIxDIL5XojDqICa2oljEN17RtZIEy425vItA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>> . 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.
>>
>> Please note that this e-mail is not secure (encrypted).  If you do not
>> wish to continue communication over unencrypted e-mail, please notify the
>> sender of this message immediately.  Continuing to send or respond to
>> e-mail after receiving this message means you understand and accept this
>> risk and wish to continue to communicate over unencrypted e-mail.
>>
>>
>> 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 Mass General
>> Brigham Compliance HelpLine at
>> http://www.massgeneralbrigham.org/complianceline
>> <http://secure-web.cisco.com/1fFVWywiC_KI2wX-iM-iipSCRfAdgcr8caPgwKQ4dp_E6amXdXGc7f5R2bEhT0ZmPeCy6AXOIj0LWU8x0g9SAwx5xHb4GLCF-WQaSnrmTYPMha1wCzNZjbbBFCQIWFh-5N5ZGDPDOldyduZuC8MKXnKD0Q-W-6m3qAJrKOYtCur2SJ-tEq_MUeMO32jd104Mmv3FTkOUPxaDqSzIyJdrDtb-wImxqqblDaBhzm4JjA7RYkdtxpS9SlOO_KlPpmstVVrRotFCLSgjsT4iejspAR2jzTrd7Q6rQFUDBKugqnSW_Tn0i3OURMIorUsRwMg8dE6slT8k7I3iv88FTtVp8cA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>> . 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.
>>
>> Please note that this e-mail is not secure (encrypted).  If you do not
>> wish to continue communication over unencrypted e-mail, please notify the
>> sender of this message immediately.  Continuing to send or respond to
>> e-mail after receiving this message means you understand and accept this
>> risk and wish to continue to communicate over unencrypted e-mail.
>>
>
> 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 Mass General
> Brigham Compliance HelpLine at
> http://www.massgeneralbrigham.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.
>
> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211130/4610021d/attachment-0001.html>

From AMORALESPINZON at BWH.HARVARD.EDU  Tue Nov 30 23:19:52 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Wed, 1 Dec 2021 04:19:52 +0000
Subject: [Loris-dev] MINC insertion
In-Reply-To: <CAMkiY3cKpqDwbpSxQKKtUir1Jvx9-ZwRn+PQ5DUp3kjZ0YLuxg@mail.gmail.com>
References: <DBD132E4-4075-42F5-82EA-62C4EA86A33A@mcgill.ca>
 <CAMkiY3fKNoN1U=t3mjM2VnOgWU56=0-YadQwLkc6xZOGUc-mvA@mail.gmail.com>
 <ED989A0A-3A12-4161-AF6A-8F7586F7DDFE@bwh.harvard.edu>
 <CAMkiY3eHjFAd1-bKdCx_5_k1nf2Mx_GCKDs2htAaTxxFoPqKhQ@mail.gmail.com>
 <63278E0B-C75D-467E-9A2C-579BC947EBC3@bwh.harvard.edu>
 <CAMkiY3fJcP0O=j++Rjjmymh9QqMofBY0NaTw0YH8GYTco7ZxSg@mail.gmail.com>
 <53B91CC9-99CE-4E76-A080-9E902115673A@bwh.harvard.edu>
 <CAMkiY3fUqgyP-BoFb71aOjBLfnPNRqt1UyQSEq6Q2TtObsNFoA@mail.gmail.com>
 <79E009D1-6AA8-4090-812A-F7405AE257C9@bwh.harvard.edu>
 <CAMkiY3eFwZbaCZXdBc-eS6Skp9-bSz5mHH6A2WwwS83_2WNmhg@mail.gmail.com>
 <94B44F39-0E17-4C7B-AE35-490F8BF95ABD@bwh.harvard.edu>
 <CAMkiY3erKTvEXScZofQeP-u2jFh4GK4gPEJnD7TgFuqsPYqSiQ@mail.gmail.com>
 <E92E7EDA-FF77-41B1-82CD-1ABF0F0DFCCA@bwh.harvard.edu>
 <CAMkiY3cKpqDwbpSxQKKtUir1Jvx9-ZwRn+PQ5DUp3kjZ0YLuxg@mail.gmail.com>
Message-ID: <MN2PR04MB616084F0AB13FA4BC5B23C988F689@MN2PR04MB6160.namprd04.prod.outlook.com>

Hi C?cile,

Thank you. 4pm works. I?ll send a send in a separate email.

Best,
Alfredo.



Get Outlook for iOS<https://aka.ms/o0ukef>
________________________________
From: Cecile Madjar <cecile.madjar at mcin.ca>
Sent: Tuesday, November 30, 2021 4:15:28 PM
To: Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU>
Cc: loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>; Sridar Narayanan <sridar.narayanan at mcgill.ca>; Rozie Arnaoutelis <rozie.arnaoutelis at mcgill.ca>; Douglas Arnold, Dr. <douglas.arnold at mcgill.ca>; Guttmann, Charles,M.D. <guttmann at bwh.harvard.edu>; Istvan Akos Imre Morocz, Dr <istvan.morocz at mcgill.ca>; Samir Das <samirdas99 at gmail.com>
Subject: Re: [Loris-dev] MINC insertion


        External Email - Use Caution

Hi Alfredo,

Sorry for the delay. Time flies quickly this week.

How about a Zoom call tomorrow (Wednesday) at 10:30AM or at 4PM?

Let me know if one of those times works for you.
Thanks!

C?cile

On Mon, Nov 29, 2021 at 1:30 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Here is the results of the query:

===
mysql> SELECT * FROM psc WHERE CenterID=843 \G;
*************************** 1. row ***************************
  CenterID: 843
      Name: inf_0102
   PSCArea: NULL
   Address: NULL
      City: NULL
   StateID: NULL
       ZIP: NULL
    Phone1: NULL
    Phone2: NULL
  Contact1: NULL
  Contact2: NULL
     Alias: BGI
 MRI_alias: BGI
   Account: NULL
Study_site: Y
1 row in set (0.00 sec)
===

Alias and MRI_alias look fine. What should we look into now? We can debug over Zoom if that works for you.

Best,
Alfredo.

On Nov 29, 2021, at 8:40 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

I think we are indeed narrowing where the error happens. It looks like for some reason this getPSC<https://secure-web.cisco.com/1WKyW2D76xw9mcH7c3mrbUADimOSPIUAeml9rWivk7bItei0PlVHDbuGfrRpzeITWbL6b0Rr61uaOfjR-rrMpspUFVDp6AC5wXTy-v_mpx-SO9Fro3_O7WqkuAEbxZTWwVIvoAIdW5_K9PSX2xdI8_T64tIgsBc859NyIdKSuS4vJjdvc2VsaapiuHVAY8oaJ0x4ikpKSaiQocNEm2yqtX0tRI26lOCf1qGK5nam_R1310B5bXRHQRMJEmJ3EE9nx5WgxcJcOt078poMQe4krTe5X1yOWE9G3LauCi0VwvI_qoqKmqtkbU_6q0PES2OKttGDvMWpti_tEMV67ieEFVQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2Fv23.0.3_IPMSA%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm> function is returning "UNKN", 0. It might be related to the Alias or MRI_alias content of the psc table for CenterID 843.

What do you get when you run the following query?
SELECT * FROM psc WHERE CenterID=843;

In the Alias or MRI_alias column, you should be able to see BGI so that the scanner candidate can be identified with the proper site.

Let me know,

C?cile

On Sun, Nov 28, 2021 at 12:42 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Thank you, it looks like we?re getting closer to find a solution. Find the answers to your questions inline below.

Happy to debug over Zoom if it?s easier for you.

Best,
Alfredo.


On Nov 26, 2021, at 3:31 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

I notice that the CenterID for the site is 0. Do you have an entry in the psc table for a CenterID=0?
No, we don?t have it. The CenterID starts at 1.
===
select * from psc where CenterID=0;
Empty set (0.00 sec)
===

The problem here is that the data comes from a new scanner and the pipeline tries to first register a new candidate for the scanner (scanner candidate) before adding an entry in the mri_scanner table. To determine the site of the scanner, the pipeline uses the determinePSC<https://secure-web.cisco.com/1Dc-fajrB7Ud53q9lvqwcvWI66c8Sjd_VWPzsGJnI1xtsFo2tce71aRhvXOFAeXFyiXWHCRtrsuOUxz9FTymBxjmkO9QVm92NieBTkPQt3sHgPQQUT2j2bpLa-AQKrAp6CJLMFA3SshUHX9tSHCkDZl4-687CTtyUYa8o_QDxRn0UEiy6yqufe-DTaVIJxY2bFtGERf0kTxBUy4JaS_ZiEHYQ3uGUjy9x3F25dMV0RZ_8hv74gXSGJW3t7AJ2zm-stvAEvizinmIQrzN-OP0L0FTHPAmoHzn0NFzDCrYvCDnMCfBNCexzjhZ9JcsQSpQS_LK_oW8UEy8ObHNoEsbzKA/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRIProcessingUtility.pm%23L503> function of MRIProcessingUtility.pm (called by minc_insertion.pl<http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl> in line 454<https://secure-web.cisco.com/1UWbEiJQk9qeievujOxfe9vFYw_u8x2SaJKAYzS6WrKuX-cWcA62bpRkJ-fOL-6hCS2oSzF8ye-G99zRPL7lv-ggMi48rbGxbcOhqRu-S7FGWEZpc-vb_j_YA73XsG7Od4qBB98i5AMLyLXi5SZAwP5E_nbdjI626BeW24SmnD6Hd_MocuW8oOqNs4mTZSGh8EkMpO-BOuH4bMikoRDLakpW-VmFznZ130h0pg4vTAAfwsjwTvbjqHgFlzExIBUHDqgaeYpD5aWuC1jjiXxEy182es4Wv0VMpe5btqKR8f0VjaB-rl2G6tC0A8q5fHAfkY5fNxpYViSFAv6jJO-8F8w/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2Fminc_insertion.pl%23L454>). I would be curious to see what the $center_name and $centerID values returned are.
These are the returned values. Maybe we need to look deeper into this.
===
determinePSC->Center name: UNKN
determinePSC->Center ID: 0
===


Could you also copy the code you have in your prod file for the function getSubjectIDs?

You mean this file ?mri/dicom-archive/.loris_mri/prod?, right? Find the function enclosed.


Finally, could you check that the candidate BGI102001_207019 does have a RegistrationCenterID set and if there is already a screening session created in the session table, that the CenterID of that session has properly been set?


The candidate has a RegistrationCenterID (843):
===
select * from candidate where CandID=207019 \G;
*************************** 1. row ***************************
                  ID: 8974
              CandID: 207019
               PSCID: BGI102001
          ExternalID: NULL
                 DoB: 1969-05-15
                 EDC: NULL
                 Sex: Female
RegistrationCenterID: 843
RegistrationProjectID: 12
           Ethnicity: NULL
              Active: Y
         Date_active: 2021-05-27
        RegisteredBy: dataman
              UserID: dataman
     Date_registered: 2021-05-27
flagged_caveatemptor: false
      flagged_reason: NULL
       flagged_other: NULL
flagged_other_status: NULL
            Testdate: 2021-06-09 10:55:35
         Entity_type: Human
          ProbandSex: NULL
          ProbandDoB: NULL
                 DoD: NULL
1 row in set (0.00 sec)
===

The session with the proper values already exists:
===
mysql> select * from session where CandID=207019 and Visit_label="screening" \G;
*************************** 1. row ***************************
                 ID: 127260
             CandID: 207019
           CenterID: 843
            VisitNo: 1
        Visit_label: screening
       SubprojectID: 2
          Submitted: N
      Current_stage: Not Started
  Date_stage_change: NULL
          Screening: NULL
     Date_screening: NULL
              Visit: NULL
         Date_visit: NULL
           Approval: NULL
      Date_approval: NULL
             Active: Y
        Date_active: 2021-05-27
       RegisteredBy: dataman
             UserID: dataman
    Date_registered: 2021-05-27
           Testdate: 2021-06-10 18:35:41
   Hardcopy_request: -
        BVLQCStatus: NULL
          BVLQCType: NULL
     BVLQCExclusion: NULL
                QCd: NULL
          Scan_done: Y
        MRIQCStatus:
       MRIQCPending: N
MRIQCFirstChangeTime: NULL
MRIQCLastChangeTime: NULL
          MRICaveat: false
          ProjectID: 12
         languageID: 1
1 row in set (0.00 sec)
===

Thank you!

C?cile

On Fri, Nov 26, 2021 at 2:34 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Thank you for answer.

I included the following lines:

===
                  . " NOW(),   'NeuroDB::MRI', 'Scanner'          ) ";
+        print "\nCenter ID: " . $centerID . "\n\n";
+        print "\nQuery:" . $query . "\n\n";
         $dbh->do($query);
     }
===

And I got the following output:

===
perl minc_insertion.pl<http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc -verbose -acquisition_protocol t1c -create_minc_pics

log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-14-31-d7FH_S.log
    SELECT       ArchiveLocation     FROM       tarchive     WHERE       TarchiveID = (                      SELECT TarchiveID                      FROM tarchive_series                      WHERE SeriesUID=? AND EchoTime=?                    )
Center ID: 0


Query:INSERT INTO candidate (CandID,          PSCID,  RegistrationCenterID, Date_active,   Date_registered, UserID, Entity_type                       ) VALUES (442627, 'scanner',      0,  NOW(),    NOW(),   'NeuroDB::MRI', 'Scanner'          )

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1020.
ERROR: Failed to insert record in table mri_scanner:
The following database commands failed:
        PREPARE s FROM 'INSERT INTO mri_scanner (CandID,Model,Manufacturer,Serial_number,Software) VALUES (?,?,?,?,?)';
        SET @x1='442627', at x2='Sonata', at x3='Siemens', at x4='syngo_MR_2004A_4VA25A';
        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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

I think it?s important to mention that this candidate was created by the bids importing script. Maybe there is center associated with the candidates when using the bids script?

Let me know your thoughts.

Best,
Alfredo.

On Nov 26, 2021, at 11:13 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Thank you Alfredo.

I wonder whether the variable $centerID is null when provided to the query here<https://secure-web.cisco.com/1BZxp6fiw85BciAlo2QCPeT44gOAdEJUbAAAM3VJsTVYkl_27h-GCDhXtVO-8fh2ghdX3L0808bpAkrN-4-dTSIuf12yvdTBrdZ5Wl5YcKE3s4BTaFeJPBISOXE6-2TppWqpX8R4fldLsB6dpee4WAltjKy3u6ZJa01r-_Up1j5vB6cy_vbAyEgWl_Ft7ACUJ4VwQkwh01nnF8cpg5ePrLbF5bQw28VLFdg3Uo7dO81Ow5-zFCp5KKdHX0KX7vdIPmPuijtNDX9V5jT_YKMml5cX_tM2IVASxDa-wmo0JijRQ7k6oCTwK52FO0yRmVVeFj4108ZlyK2avqXijVKYreQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm%23L1012> in your case.

Could you add in MRI.pm line 1018 the following print statements and let me know what you get? (Right before the $dbh->do($query);
print($centerID);
print($query);

Thank you!

C?cile

On Fri, Nov 26, 2021 at 10:55 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

This is the branch that we are using in the IPMSA project:

https://github.com/SPINEProject/Loris-MRI/tree/v23.0.3_IPMSA<https://secure-web.cisco.com/1_p5UjMqREHagXmmz7NxbZe91yrcn34HNneKcFN4qKhR9mT7798DmL7TgbLwjpDr1U0bQaX2Rdqcdu3-l5R95gEJ5AzIbYu4-psDEz9Gw3fmrcgxEel3V6rugNzEisR_jZbIG2f2KPrVumnb1MY-TJCYuPQqzVuM_3KHLYTzVKha7RbWAHq6GLefQmer8auU6BALsWue7RBcrrbG9kbGC-S-e1DZ-WP4gVNTDegrcGaghwyxclA9m6SZqs-OljIR6E7IViTaySgZuDnOp5meeyJlKdlksyj5cGVErq4YprL6I9uHWuLjB-06KBUFTBK6C1E38yyToTkJVVH-8LKRPKg/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Ftree%2Fv23.0.3_IPMSA>

Best,
Alfredo.

On Nov 26, 2021, at 9:55 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Could you point me to the version of the code you are using on GitHub so I can take a look at the correct MRI.pm file.

Thank you!

C?cile

On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I?m getting the following error when inserting a minc file using the minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> script:

===
$ perl minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc  -verbose -acquisition_protocol t1c -create_minc_pics

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1018.

ERROR: Failed to insert record in table mri_scanner:

The following database commands failed:
PREPARE s FROM 'INSERT INTO mri_scanner (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
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 (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

Could you help me figuring out what is happening? Is there something I should add to the minc headers?

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/10DEfcj-Ova6W7NFLUPao--zc_ba_3Yk63CTqhSG5Ca4FJWekd8J8afbwCr_p31UYqWdlWd2rAqSBE3jLmNtkj6jzu0Deh3bP7WsUj3yX1B4Iv_RzcWr2nfZ7f8_OUQvlNL5D_jqwZyNdyv_JUiP0dLvm0NprWoJtFmmA4jwKQ4X8BKNoa6LBbiWMVYizEQDtUP5c9bc0XDPr-wYz3SlyBzIrLOxha8XYY4l8tLxS_skKp_uX_4jMesLtI_DCQza3WckhpQ7-43tcveIJ9vz-wKKRp31RbQkfDcbgexXsRG1oCpy-6zP8ggtvzNLZ0VSxSBDRZD7ti7dI0bPJXah5pg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.


Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1_sf0B_pY6Veyn85uEgw5ObBiM-QA382bc3nDvcSdrZOKA6no0I3vr4IK-5T3aDVnNH0xdP0QPSlWZoWkQ_GwFwWpmsSr4ck4dMGnU4VytPp-LDqG94cvmqnN5tL76lwADrn6xIQWpzuk5L8BVaZWrrrGjDSpYdGwV3AIPq2zzJhN9hBT5o5FBx0LlHEf-E7onD9zSqkkZiu9_atJraKUgpCCauEab0PbqWsTxYk0edTnIC6LbDq3t55qVy6FVWQybcR-n1rq2GND31ubWD7fk0h2dvddl4PnBk7PwnBZ6n6Q3S6lZvD9wWk_5ShEkjxI4GLdc2m60Frytk5an8XeeQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.


Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/14m8jq3YFX-kL4WHSOD3NyklDH3_1jO6LrSN9gvfM5CyvUtE7cihaLOo51ulZdVQKgs5rOFUrgJxphRC2W3gjEcYsYyqJP3GlMV3sJHwLGLwsGvslUlp9df_5QkEDbk0OiO4v-SgA4uMhT6od0larJxEIegxbPKpy9GmlloLw6cDlPw0voUhi7Y0kxA_zjwDvxaVMhZ7RIpojsrcwl2crdOHamo_wQI9pz9cAU_qxwUGkhiSfwtcCe8i-UtBjbSEY9dM0SpejAYJqhqEpOK_aCqQ4_wOl8FxQWWNK2nOsD7QawkuH5liIxDIL5XojDqICa2oljEN17RtZIEy425vItA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.


Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1fFVWywiC_KI2wX-iM-iipSCRfAdgcr8caPgwKQ4dp_E6amXdXGc7f5R2bEhT0ZmPeCy6AXOIj0LWU8x0g9SAwx5xHb4GLCF-WQaSnrmTYPMha1wCzNZjbbBFCQIWFh-5N5ZGDPDOldyduZuC8MKXnKD0Q-W-6m3qAJrKOYtCur2SJ-tEq_MUeMO32jd104Mmv3FTkOUPxaDqSzIyJdrDtb-wImxqqblDaBhzm4JjA7RYkdtxpS9SlOO_KlPpmstVVrRotFCLSgjsT4iejspAR2jzTrd7Q6rQFUDBKugqnSW_Tn0i3OURMIorUsRwMg8dE6slT8k7I3iv88FTtVp8cA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.


Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/14gGcX-ZD6Amc10oWq9YHUYDZwfI3Ra0YaIetGnqyBxDXjW2fkG07-SpnWf6ZWiMMuWxnSoLULOR9NMLOcJiMgBuZCcIt0RYXiMw3EibvjtSF-QMJ3sGSOAMIROOiVMwlt5nrV2O7wLJlh3xOKBlVMU7fcJsx9UxZkRIrvXGY3If6E2iTE4UQ5ZI1j6xGWgdYq5ff8qBRME2FK0lFmNWaFYVTYkmphxy8dXKWJMPtlpfY2km6XVTFG28sO33tQBCVVJ-jGy9f7bMO8sAj6sP8h9mT1Mrv2oq5fwVO8Zx6Ec1j9vTarLT6L_MOVQWPA1YvjGshE6gRajrWQAAwcQfw-w/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.


Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20211201/04ffc170/attachment-0001.html>