From AMORALESPINZON at BWH.HARVARD.EDU  Mon Jul 12 12:29:27 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Mon, 12 Jul 2021 16:29:27 +0000
Subject: [Loris-dev] Questions and errors uploading BIDS
Message-ID: <A142044A-2953-4B49-97E9-3BF869202F7B@bwh.harvard.edu>

Dear LorisDev team,

I am uploading a BIDS dataset in LORIS. I have the following questions and errors:

1. I added the file sub-<label>[_ses-<label>]_scans.tsv as suggested in the BIDS standard (https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file) to add the acquisition dates, do you take it into account to set the dates in LORIS? If not, how can I set the acquisition dates for the images in the session/visit?

2. I am doing the insertion visit by visit to be able to identify issues instead of running all the subjects at once. In this approach I get an error stating that the participants file (".../data/bids_imports/INFORMS_BIDSVersion_1.4.0/participants.tsv") is different from for every execution. Is there a way I can upload subject by subject without having this issue?

If l have to launch the whole dataset, is the bids script able to check what was already inserted in case there is an error and I have to it again?

3. After insertion of BIDS for a subject in a visit I cannot access the visit in the front end, I am getting a 500 error. Here is the error log in LORIS:

===
[Mon Jul 12 12:05:37.705967 2021] [php7:error] [pid 14497] [client 216.15.126.108:55424] PHP Fatal error:  Uncaught TypeError: Return value of Utility::getStageUsingCandID() must be of the type string, null returned in /var/www
/loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177): Utility::getStageUsingCandID('207019')\n#1 /var/www/loris/php/libraries/NDB_Page.class.inc(
707): LORIS\\instrument_list\\Instrument_List->setup()\n#2 /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234): NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3 /var/www/loris/src/Middleware/PageD
ecorationMiddleware.php(56): LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#4 /var/www/loris/php/libraries/NDB_Page.class.i
nc(692): LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#5 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(
137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on line 632, referer: https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/
===

Any ideas?

Thank you in advance for your help.

Best,
Alfredo.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the 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.
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From AMORALESPINZON at BWH.HARVARD.EDU  Thu Jul 15 15:33:57 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Thu, 15 Jul 2021 19:33:57 +0000
Subject: [Loris-dev] Questions and errors uploading BIDS
In-Reply-To: <A142044A-2953-4B49-97E9-3BF869202F7B@bwh.harvard.edu>
References: <A142044A-2953-4B49-97E9-3BF869202F7B@bwh.harvard.edu>
Message-ID: <36E88E76-4736-42BF-9905-F0FDD987915F@bwh.harvard.edu>

Hi C?cile,

Do you have any insights for these questions? I?m waiting some answers to be able to move forward.

Thank you in advance.

Best,
Alfredo.

> On Jul 12, 2021, at 12:29 PM, Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU> wrote:
> 
> Dear LorisDev team,
> 
> I am uploading a BIDS dataset in LORIS. I have the following questions and errors:
> 
> 1. I added the file sub-<label>[_ses-<label>]_scans.tsv as suggested in the BIDS standard (https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file) to add the acquisition dates, do you take it into account to set the dates in LORIS? If not, how can I set the acquisition dates for the images in the session/visit?
> 
> 2. I am doing the insertion visit by visit to be able to identify issues instead of running all the subjects at once. In this approach I get an error stating that the participants file (".../data/bids_imports/INFORMS_BIDSVersion_1.4.0/participants.tsv") is different from for every execution. Is there a way I can upload subject by subject without having this issue?
> 
> If l have to launch the whole dataset, is the bids script able to check what was already inserted in case there is an error and I have to it again?
> 
> 3. After insertion of BIDS for a subject in a visit I cannot access the visit in the front end, I am getting a 500 error. Here is the error log in LORIS:
> 
> ===
> [Mon Jul 12 12:05:37.705967 2021] [php7:error] [pid 14497] [client 216.15.126.108:55424] PHP Fatal error:  Uncaught TypeError: Return value of Utility::getStageUsingCandID() must be of the type string, null returned in /var/www
> /loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177): Utility::getStageUsingCandID('207019')\n#1 /var/www/loris/php/libraries/NDB_Page.class.inc(
> 707): LORIS\\instrument_list\\Instrument_List->setup()\n#2 /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234): NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3 /var/www/loris/src/Middleware/PageD
> ecorationMiddleware.php(56): LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#4 /var/www/loris/php/libraries/NDB_Page.class.i
> nc(692): LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#5 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(
> 137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on line 632, referer: https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/
> ===
> 
> Any ideas?
> 
> Thank you in advance for your help.
> 
> Best,
> Alfredo.

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the 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 cecile.madjar at mcin.ca  Thu Jul 15 17:23:31 2021
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Thu, 15 Jul 2021 17:23:31 -0400
Subject: [Loris-dev] Questions and errors uploading BIDS
In-Reply-To: <36E88E76-4736-42BF-9905-F0FDD987915F@bwh.harvard.edu>
References: <A142044A-2953-4B49-97E9-3BF869202F7B@bwh.harvard.edu>
 <36E88E76-4736-42BF-9905-F0FDD987915F@bwh.harvard.edu>
Message-ID: <CAMkiY3fPyON8j_dQ1NB5ndoC_hkmmYFZZ5wfiFswLf27GPeWVQ@mail.gmail.com>

Hi Alfredo,

Sorry for the delay, I had to take a deeper look at the code to answer some
of your questions. See below.

> 1. I added the file sub-<label>[_ses-<label>]_scans.tsv as suggested in
> the BIDS standard (
> https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file)
> to add the acquisition dates, do you take it into account to set the dates
> in LORIS? If not, how can I set the acquisition dates for the images in the
> session/visit?
>

Indeed, if you enter a date under an 'acq_time' column in the scans.tsv
file, it will add an entry in parameter_file for the scan_acquisition_time
parameter.


> >
> > 2. I am doing the insertion visit by visit to be able to identify issues
> instead of running all the subjects at once. In this approach I get an
> error stating that the participants file
> (".../data/bids_imports/INFORMS_BIDSVersion_1.4.0/participants.tsv") is
> different from for every execution. Is there a way I can upload subject by
> subject without having this issue?
>

yeah, this is a current limitation that this file keeps changing each time
you upload a new candidate. The pipeline was initially developed for
retrospective BIDS datasets. We would need to modify this part
<https://github.com/aces/Loris-MRI/blob/b5a6fc8cc3cf1fad50df21d9d87a284981705e3c/python/bids_import.py#L299>
for
prospective datasets so that instead of just trying to copy the
participants.tsv file, if it already exists, it would append a row into the
already existing file. You can find a fix for that in the following PR
https://github.com/aces/Loris-MRI/pull/645.


> >
> > If l have to launch the whole dataset, is the bids script able to check
> what was already inserted in case there is an error and I have to it again?
>

Yes, the pipeline is supposed to be smart enough to not reinsert something
that was previously inserted.


> >
> > 3. After insertion of BIDS for a subject in a visit I cannot access the
> visit in the front end, I am getting a 500 error. Here is the error log in
> LORIS:
> >
> > ===
> > [Mon Jul 12 12:05:37.705967 2021] [php7:error] [pid 14497] [client
> 216.15.126.108:55424] PHP Fatal error:  Uncaught TypeError: Return value
> of Utility::getStageUsingCandID() must be of the type string, null returned
> in /var/www
> > /loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0
> /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177):
> Utility::getStageUsingCandID('207019')\n#1
> /var/www/loris/php/libraries/NDB_Page.class.inc(
> > 707): LORIS\\instrument_list\\Instrument_List->setup()\n#2
> /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234):
> NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3
> /var/www/loris/src/Middleware/PageD
> > ecorationMiddleware.php(56):
> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest),
> Object(LORIS\\instrument_list\\Instrument_List))\n#4
> /var/www/loris/php/libraries/NDB_Page.class.i
> > nc(692):
> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest),
> Object(LORIS\\instrument_list\\Instrument_List))\n#5
> /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(
> > 137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on
> line 632, referer:
> https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/
> > ===
>

This might be due to the Current_stage not being set when creating the
visit via the bids_import.py script. Here is a PR to fix that issue next
time you import a new visit via bids_import.py:
https://github.com/aces/Loris-MRI/pull/644

Hope this helps,

C?cile
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From AMORALESPINZON at BWH.HARVARD.EDU  Thu Jul 15 17:33:31 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Thu, 15 Jul 2021 21:33:31 +0000
Subject: [Loris-dev] Questions and errors uploading BIDS
In-Reply-To: <CAMkiY3fPyON8j_dQ1NB5ndoC_hkmmYFZZ5wfiFswLf27GPeWVQ@mail.gmail.com>
References: <A142044A-2953-4B49-97E9-3BF869202F7B@bwh.harvard.edu>
 <36E88E76-4736-42BF-9905-F0FDD987915F@bwh.harvard.edu>
 <CAMkiY3fPyON8j_dQ1NB5ndoC_hkmmYFZZ5wfiFswLf27GPeWVQ@mail.gmail.com>
Message-ID: <CFA5093A-6593-47A3-9191-2AB7502C4A94@bwh.harvard.edu>

Hi C?cile,

Thank you for the answers. I will apply the patches and test.

Best,
Alfredo.

On Jul 15, 2021, at 5:23 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Sorry for the delay, I had to take a deeper look at the code to answer some of your questions. See below.

> 1. I added the file sub-<label>[_ses-<label>]_scans.tsv as suggested in the BIDS standard (https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file<https://secure-web.cisco.com/1RT0b_pDRzGh5oEnKt7wHclfIWMewUlzzoH-FStRocNdjI2mrpqsgr33eVaIS22zsvLSZ7Z8ugyaoZ07SHA_O7tObAB409DokII49oyHlFVQnGqaaxEoC_87rcI6ivzH41s36uv9R13FRzaiRJPDhbqmj3kt67BF36UEJp4e5xglyAHPcxx1DV8sf3sJ2TRBCKhNhHUWeRbPM9DdNrFxpoZzYHnN4xy-VMBRK5T9SF4afE6jv3tqdaKdfSYG2wDh-CWrIBbzyeSECIRnMYikelA/https%3A%2F%2Fbids-specification.readthedocs.io%2Fen%2Fstable%2F03-modality-agnostic-files.html%23scans-file>) to add the acquisition dates, do you take it into account to set the dates in LORIS? If not, how can I set the acquisition dates for the images in the session/visit?

Indeed, if you enter a date under an 'acq_time' column in the scans.tsv file, it will add an entry in parameter_file for the scan_acquisition_time parameter.

>
> 2. I am doing the insertion visit by visit to be able to identify issues instead of running all the subjects at once. In this approach I get an error stating that the participants file (".../data/bids_imports/INFORMS_BIDSVersion_1.4.0/participants.tsv") is different from for every execution. Is there a way I can upload subject by subject without having this issue?

yeah, this is a current limitation that this file keeps changing each time you upload a new candidate. The pipeline was initially developed for retrospective BIDS datasets. We would need to modify this part<https://secure-web.cisco.com/1FA74HdTiHzhrcJezSt2K6DKMGwP_wqxcdk1oXclu1U6jCz4rd2fSi-NwskWq_Qfb0p4MTUX6_XEbTFvgo_VxzSI4YiWtniz3W9Yi_Y_Yhd3GKBQD7kKnXK8l0jqEWj-6sZ77YTpIg9X5O235SfFeZ3JW3V5MFXQOH7vMnzgPDBS-6dsjvmCAtnAjP4DJoXkGwQ6VJLV21yWj9np6NfjWvjphVgXfpYnIoS4jb57yVl8xBW0ttGeejb-HEHsaZ-bNfre-16KCLmR-IJO3pZbnwg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fb5a6fc8cc3cf1fad50df21d9d87a284981705e3c%2Fpython%2Fbids_import.py%23L299> for prospective datasets so that instead of just trying to copy the participants.tsv file, if it already exists, it would append a row into the already existing file. You can find a fix for that in the following PR https://github.com/aces/Loris-MRI/pull/645<https://secure-web.cisco.com/1Tpg7v8DtF0HJJEnPZUNGN7gwCdF7vLrM19WZmYU8p4-riYcbJ1FVNYH0FGEvIBT0KwSYUMgtVeulxeEaGSohphmm0NQn8wIbxh5cSX4VwbKcKLhvQY1RtnS2SxEKUi4Pln5KHxRYDcVhz9sWnZ6EIhfZEDECvkuT2-zTt24B5MMeBduiQG8W3Pqa7Qr2oEjJW_m84bq0EVtbGQmu5ZVKytj8tPkwWAUE8gTEtLOb1DjwDX5O8y8EHAN_8lf2ZqJ9eojMRDufJj2QObf0g02n3Q/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F645>.

>
> If l have to launch the whole dataset, is the bids script able to check what was already inserted in case there is an error and I have to it again?

Yes, the pipeline is supposed to be smart enough to not reinsert something that was previously inserted.

>
> 3. After insertion of BIDS for a subject in a visit I cannot access the visit in the front end, I am getting a 500 error. Here is the error log in LORIS:
>
> ===
> [Mon Jul 12 12:05:37.705967 2021] [php7:error] [pid 14497] [client 216.15.126.108:55424<http://secure-web.cisco.com/1WYhYdfRTqaTteJ_4rndbHmww7uTfLympsocUwkjHV2oHQVOQ_ddIjv7AcfCoiP5cJIbw5iksCEFI9RVOxA3_lM6etO-PCaDz89PgNjaEjQPMC5dEfLOft3B7YhP7TCF4ISn-hvCOCFnhQqmRbs9zS1PRbVr6qe_Fra0AR2dZzskzHnYp2A_u29fTzE5u8vYJLMpl4t10wah4Bga-hhoD3gkgnRHVU5KAWy4uwX30Ma4tng8DnVlqBopiM9DpYE6ZEviZpdmHvWqJZxPHxbnHOw/http%3A%2F%2F216.15.126.108%3A55424>] PHP Fatal error:  Uncaught TypeError: Return value of Utility::getStageUsingCandID() must be of the type string, null returned in /var/www
> /loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177): Utility::getStageUsingCandID('207019')\n#1 /var/www/loris/php/libraries/NDB_Page.class.inc(
> 707): LORIS\\instrument_list\\Instrument_List->setup()\n#2 /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234): NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3 /var/www/loris/src/Middleware/PageD
> ecorationMiddleware.php(56): LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#4 /var/www/loris/php/libraries/NDB_Page.class.i
> nc(692): LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#5 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(
> 137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on line 632, referer: https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/<https://secure-web.cisco.com/1XkKe3e3JkFCEbEAQx3rrZ25ZCaDXFH7ViiHfRCVtt0ZTI9ckG_4i5CYOnY_Wv0SYfmdvUUZ0jQkdjvUgzKY9qJfqnqcVF_7n2nRaR-c1a4U_Y95LN-Dv96I8j-OBHltZ52DoTaYZ9RvB7YL9vP82yG9pUb2XlYJwK6xA6b2gGwhHhyqpdrPfRW0HZFx4__6pDI4CU5CQWx9_dteaDW3_xjntBo3296km9H-nJNiywrGrKtv_1pO6wCU5ygXs2bqXwZ9j7X4eILwCv0N7S7PlKA/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fcandidate_profile%2F207019%2F>
> ===

This might be due to the Current_stage not being set when creating the visit via the bids_import.py script. Here is a PR to fix that issue next time you import a new visit via bids_import.py: https://github.com/aces/Loris-MRI/pull/644<https://secure-web.cisco.com/1RuRCEtVgtWrK7Pm95g10P8zRltmw5fqwt4wM4vzTM2N7zp7p8HXJKNSQo5QSAfOa23ID04z8m13DojdlnneipDRp6yoYNUJIoorexU5ixp49Alwi5aaHokrOmz-gRnpRkrUxMNI04i2tsCDBAsyiwIBoMwgWyCGHg8asEvLiHrEcYtWAdRycS4UQ7Udt6hrVhp6DqF6kpBH3s4oWPPlFvnJ9CHywNOno0NqHI0zXVnlWI2BuIW0heLJeaDSyrvK-5FcYxqhfnBEJTq1hkNB-Jg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F644>

Hope this helps,

C?cile

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. 
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From AMORALESPINZON at BWH.HARVARD.EDU  Mon Jul 19 11:19:23 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Mon, 19 Jul 2021 15:19:23 +0000
Subject: [Loris-dev] Questions and errors uploading BIDS
In-Reply-To: <CAMkiY3fPyON8j_dQ1NB5ndoC_hkmmYFZZ5wfiFswLf27GPeWVQ@mail.gmail.com>
References: <A142044A-2953-4B49-97E9-3BF869202F7B@bwh.harvard.edu>
 <36E88E76-4736-42BF-9905-F0FDD987915F@bwh.harvard.edu>
 <CAMkiY3fPyON8j_dQ1NB5ndoC_hkmmYFZZ5wfiFswLf27GPeWVQ@mail.gmail.com>
Message-ID: <8EED5B04-BBAB-46DD-AD83-F9A830C5B6FE@BWH.HARVARD.EDU>

Hi C?cile,

I patched LORIS and inserted one visit.

Before moving forward I want to make sure the acquisition date was inserted, could you please tell me what is the ?ParameterFileID? for the acquisition date, I looked at the table parameter_file using one of the FileIDs from the last insertion but couldn't find the acquisition date. See the result of the query below.

2. The front-end is still crashing. This is the log:

===
[php7:error] [pid 32588] [client 155.33.137.12:23564] PHP Fatal error:  Uncaught TypeError: Return value of Utility::getStageUsingCandID() must be of the type string, null returned in /var/www/loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177): Utility::getStageUsingCandID('207019')\n#1 /var/www/loris/php/libraries/NDB_Page.class.inc(707): LORIS\\instrument_list\\Instrument_List->setup()\n#2 /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234): NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3 /var/www/loris/src/Middleware/PageDecorationMiddleware.php(56): LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#4 /var/www/loris/php/libraries/NDB_Page.class.inc(692): LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#5 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on line 632, referer: https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/
===

Happy to have a Zoom call if it helps.

Thank you for your help.

Best,
Alfredo.

===
select ParameterFileID,Value from parameter_file where FileID=428983;
+-----------------+----------------------------------------------------------------------------------------------------------------------------------+
| ParameterFileID | Value                                                                                                                            |
+-----------------+----------------------------------------------------------------------------------------------------------------------------------+
|       109949932 | MR                                                                                                                               |
|       109949967 | 130                                                                                                                              |
|       109949981 | 0.9765625                                                                                                                        |
|       109949977 | syngo_MR_A35_4VA35A                                                                                                              |
|       109949958 | 12:13:34.360020                                                                                                                  |
|       109949968 | t1_RIPOSIZ.                                                                                                                      |
|       109949973 | SK_SP_OSP                                                                                                                        |
|       109949962 | 2D                                                                                                                               |
|       109949960 | [0.999742, 0.000840254, 0.0226824, 1.88704e-10, 0.999315, -0.0370189]                                                            |
|       109949982 | 0.9765625                                                                                                                        |
|       109949975 | 5                                                                                                                                |
|       109949969 | CP_HeadArray                                                                                                                     |
|       109949965 | 70.3125                                                                                                                          |
|       109949966 | i                                                                                                                                |
|       109949945 | 0.187383                                                                                                                         |
|       109949978 | 3                                                                                                                                |
|       109949963 | 1.5                                                                                                                              |
|       109949976 | 3                                                                                                                                |
|       109949970 | 0.655                                                                                                                            |
|       109949964 | HFS                                                                                                                              |
|       109949974 | t1_RIPOSIZ.                                                                                                                      |
|       109949971 | SE                                                                                                                               |
|       109949956 | 99                                                                                                                               |
|       109949959 | 0.01                                                                                                                             |
|       109949930 | Siemens                                                                                                                          |
|       109949957 | 1                                                                                                                                |
|       109949983 | 2.9999998                                                                                                                        |
|       109949985 | 207019/sub-ANOM_ses-endoftreatment_ce-Gd_run-1_T1w_ZZZ_check.png                                                         |
|       109949972 | _tse2d1_5                                                                                                                        |
|       109949914 | 20140629                                                                                                                         |
|       109949915 | 99                                                                                                                               |
|       109949916 | 1                                                                                                                                |
|       109949917 | 12:13:34.360020                                                                                                                  |
|       109949918 | 256                                                                                                                              |
|       109949919 | dcm2niix                                                                                                                         |
|       109949920 | v1.0.20180622 (JP2:OpenJPEG) (JP-LS:CharLS) GCC7.3.0                                                                             |
|       109949921 | 0.01                                                                                                                             |
|       109949923 | 150                                                                                                                              |
|       109949924 | [0.999742, 0.000840254, 0.0226824, 1.88704e-10, 0.999315, -0.0370189]                                                            |
|       109949925 | ['ORIGINAL', 'PRIMARY', 'M', 'ND']                                                                                               |
|       109949926 | ROW                                                                                                                              |
|       109949928 | 2D                                                                                                                               |
|       109949929 | 1.5                                                                                                                              |
|       109949931 | Sonata                                                                                                                           |
|       109949933 | 1                                                                                                                                |
|       109949934 | HFS                                                                                                                              |
|       109949935 | 70.3125                                                                                                                          |
|       109949936 | i                                                                                                                                |
|       109949937 | 100                                                                                                                              |
|       109949938 | 0.55                                                                                                                             |
|       109949939 | 130                                                                                                                              |
|       109949940 | t1_RIPOSIZ.                                                                                                                      |
|       109949941 | %SiemensSeq%_tse                                                                                                                 |
|       109949942 | CP_HeadArray                                                                                                                     |
|       109949943 | 512                                                                                                                              |
|       109949944 | 0.655                                                                                                                            |
|       109949946 | SE                                                                                                                               |
|       109949947 | _tse2d1_5                                                                                                                        |
|       109949948 | SK_SP_OSP                                                                                                                        |
|       109949949 | t1_RIPOSIZ.                                                                                                                      |
|       109949950 | 5                                                                                                                                |
|       109949951 | [48, 57, 59, 361, 234, 67, -246, 256]                                                                                            |
|       109949952 | 3                                                                                                                                |
|       109949953 | syngo_MR_A35_4VA35A                                                                                                              |
|       109949954 | 3                                                                                                                                |
|       109949955 | 202.922                                                                                                                          |
|       109949961 | ['ORIGINAL', 'PRIMARY', 'M', 'ND']                                                                                               |
|       109949979 | bids_imports/INFORMS_BIDSVersion_1.4.0/sub-ANOM/ses-endoftreatment/anat/sub-ANOM_ses-endoftreatment_run-1_T1w.json     |
|       109949980 | 7655f29d97c14a6b88055f99c7879097650c31cafa7405a1ad3a93062d04669417f42b67c175e9ad904da1e1bb677b2fb6a44ed8b26af482a4d3c40498f284df |
|       109949984 | 3f487183fe830d801477568aec824c967a44d3bf3feb9cbd6575830d31b90b089cc625a037c487d3985fb10ee0a00f2eac824980955949c8955cdd304ea838b9 |
|       109949922 | 5                                                                                                                                |
|       109949927 | 1                                                                                                                                |
+-----------------+----------------------------------------------------------------------------------------------------------------------------------+
===

This is the content of the *_scan.tsv file:
===
filename        acq_time
anat/sub-ANOM_ses-endoftreatment_run-1_T1w.nii.gz  2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_ce-Gd_run-1_T1w.nii.gz    2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_run-1_FLAIR.nii.gz        2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_ce-Gd_run-2_T1w.nii.gz    2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_run-1_PD.nii.gz   2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_run-1_T2w.nii.gz  2014-06-29T00:00:00
===

On Jul 15, 2021, at 5:23 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Sorry for the delay, I had to take a deeper look at the code to answer some of your questions. See below.

> 1. I added the file sub-<label>[_ses-<label>]_scans.tsv as suggested in the BIDS standard (https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file<https://secure-web.cisco.com/1RT0b_pDRzGh5oEnKt7wHclfIWMewUlzzoH-FStRocNdjI2mrpqsgr33eVaIS22zsvLSZ7Z8ugyaoZ07SHA_O7tObAB409DokII49oyHlFVQnGqaaxEoC_87rcI6ivzH41s36uv9R13FRzaiRJPDhbqmj3kt67BF36UEJp4e5xglyAHPcxx1DV8sf3sJ2TRBCKhNhHUWeRbPM9DdNrFxpoZzYHnN4xy-VMBRK5T9SF4afE6jv3tqdaKdfSYG2wDh-CWrIBbzyeSECIRnMYikelA/https%3A%2F%2Fbids-specification.readthedocs.io%2Fen%2Fstable%2F03-modality-agnostic-files.html%23scans-file>) to add the acquisition dates, do you take it into account to set the dates in LORIS? If not, how can I set the acquisition dates for the images in the session/visit?

Indeed, if you enter a date under an 'acq_time' column in the scans.tsv file, it will add an entry in parameter_file for the scan_acquisition_time parameter.

>
> 2. I am doing the insertion visit by visit to be able to identify issues instead of running all the subjects at once. In this approach I get an error stating that the participants file (".../data/bids_imports/INFORMS_BIDSVersion_1.4.0/participants.tsv") is different from for every execution. Is there a way I can upload subject by subject without having this issue?

yeah, this is a current limitation that this file keeps changing each time you upload a new candidate. The pipeline was initially developed for retrospective BIDS datasets. We would need to modify this part<https://secure-web.cisco.com/1FA74HdTiHzhrcJezSt2K6DKMGwP_wqxcdk1oXclu1U6jCz4rd2fSi-NwskWq_Qfb0p4MTUX6_XEbTFvgo_VxzSI4YiWtniz3W9Yi_Y_Yhd3GKBQD7kKnXK8l0jqEWj-6sZ77YTpIg9X5O235SfFeZ3JW3V5MFXQOH7vMnzgPDBS-6dsjvmCAtnAjP4DJoXkGwQ6VJLV21yWj9np6NfjWvjphVgXfpYnIoS4jb57yVl8xBW0ttGeejb-HEHsaZ-bNfre-16KCLmR-IJO3pZbnwg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fb5a6fc8cc3cf1fad50df21d9d87a284981705e3c%2Fpython%2Fbids_import.py%23L299> for prospective datasets so that instead of just trying to copy the participants.tsv file, if it already exists, it would append a row into the already existing file. You can find a fix for that in the following PR https://github.com/aces/Loris-MRI/pull/645<https://secure-web.cisco.com/1Tpg7v8DtF0HJJEnPZUNGN7gwCdF7vLrM19WZmYU8p4-riYcbJ1FVNYH0FGEvIBT0KwSYUMgtVeulxeEaGSohphmm0NQn8wIbxh5cSX4VwbKcKLhvQY1RtnS2SxEKUi4Pln5KHxRYDcVhz9sWnZ6EIhfZEDECvkuT2-zTt24B5MMeBduiQG8W3Pqa7Qr2oEjJW_m84bq0EVtbGQmu5ZVKytj8tPkwWAUE8gTEtLOb1DjwDX5O8y8EHAN_8lf2ZqJ9eojMRDufJj2QObf0g02n3Q/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F645>.

>
> If l have to launch the whole dataset, is the bids script able to check what was already inserted in case there is an error and I have to it again?

Yes, the pipeline is supposed to be smart enough to not reinsert something that was previously inserted.

>
> 3. After insertion of BIDS for a subject in a visit I cannot access the visit in the front end, I am getting a 500 error. Here is the error log in LORIS:
>
> ===
> [Mon Jul 12 12:05:37.705967 2021] [php7:error] [pid 14497] [client 216.15.126.108:55424<http://secure-web.cisco.com/1WYhYdfRTqaTteJ_4rndbHmww7uTfLympsocUwkjHV2oHQVOQ_ddIjv7AcfCoiP5cJIbw5iksCEFI9RVOxA3_lM6etO-PCaDz89PgNjaEjQPMC5dEfLOft3B7YhP7TCF4ISn-hvCOCFnhQqmRbs9zS1PRbVr6qe_Fra0AR2dZzskzHnYp2A_u29fTzE5u8vYJLMpl4t10wah4Bga-hhoD3gkgnRHVU5KAWy4uwX30Ma4tng8DnVlqBopiM9DpYE6ZEviZpdmHvWqJZxPHxbnHOw/http%3A%2F%2F216.15.126.108%3A55424>] PHP Fatal error:  Uncaught TypeError: Return value of Utility::getStageUsingCandID() must be of the type string, null returned in /var/www
> /loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177): Utility::getStageUsingCandID('207019')\n#1 /var/www/loris/php/libraries/NDB_Page.class.inc(
> 707): LORIS\\instrument_list\\Instrument_List->setup()\n#2 /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234): NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3 /var/www/loris/src/Middleware/PageD
> ecorationMiddleware.php(56): LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#4 /var/www/loris/php/libraries/NDB_Page.class.i
> nc(692): LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#5 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(
> 137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on line 632, referer: https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/<https://secure-web.cisco.com/1XkKe3e3JkFCEbEAQx3rrZ25ZCaDXFH7ViiHfRCVtt0ZTI9ckG_4i5CYOnY_Wv0SYfmdvUUZ0jQkdjvUgzKY9qJfqnqcVF_7n2nRaR-c1a4U_Y95LN-Dv96I8j-OBHltZ52DoTaYZ9RvB7YL9vP82yG9pUb2XlYJwK6xA6b2gGwhHhyqpdrPfRW0HZFx4__6pDI4CU5CQWx9_dteaDW3_xjntBo3296km9H-nJNiywrGrKtv_1pO6wCU5ygXs2bqXwZ9j7X4eILwCv0N7S7PlKA/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fcandidate_profile%2F207019%2F>
> ===

This might be due to the Current_stage not being set when creating the visit via the bids_import.py script. Here is a PR to fix that issue next time you import a new visit via bids_import.py: https://github.com/aces/Loris-MRI/pull/644<https://secure-web.cisco.com/1RuRCEtVgtWrK7Pm95g10P8zRltmw5fqwt4wM4vzTM2N7zp7p8HXJKNSQo5QSAfOa23ID04z8m13DojdlnneipDRp6yoYNUJIoorexU5ixp49Alwi5aaHokrOmz-gRnpRkrUxMNI04i2tsCDBAsyiwIBoMwgWyCGHg8asEvLiHrEcYtWAdRycS4UQ7Udt6hrVhp6DqF6kpBH3s4oWPPlFvnJ9CHywNOno0NqHI0zXVnlWI2BuIW0heLJeaDSyrvK-5FcYxqhfnBEJTq1hkNB-Jg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F644>

Hope this helps,

C?cile

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From cecile.madjar at mcin.ca  Mon Jul 19 11:26:21 2021
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Mon, 19 Jul 2021 11:26:21 -0400
Subject: [Loris-dev] Questions and errors uploading BIDS
In-Reply-To: <8EED5B04-BBAB-46DD-AD83-F9A830C5B6FE@BWH.HARVARD.EDU>
References: <A142044A-2953-4B49-97E9-3BF869202F7B@bwh.harvard.edu>
 <36E88E76-4736-42BF-9905-F0FDD987915F@bwh.harvard.edu>
 <CAMkiY3fPyON8j_dQ1NB5ndoC_hkmmYFZZ5wfiFswLf27GPeWVQ@mail.gmail.com>
 <8EED5B04-BBAB-46DD-AD83-F9A830C5B6FE@BWH.HARVARD.EDU>
Message-ID: <CAMkiY3f8_bZxFJx8W5HFzzMPV8J_wB_BSPW=-ExmqA=WGSOdEA@mail.gmail.com>

Hi Alfredo,

For the acquisition date, try the following query:
SELECT pf.Value FROM parameter_file pf JOIN parameter_type pt USING
(ParameterTypeID) WHERE pt.Name="scan_acquisition_time" AND FileID=428983;

For 2., what does the following query return?
SELECT DISTINCT Current_stage FROM session WHERE CandID=207019;

C?cile

On Mon, Jul 19, 2021 at 11:19 AM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi C?cile,
>
> I patched LORIS and inserted one visit.
>
> Before moving forward I want to make sure the acquisition date was
> inserted, could you please tell me what is the ?ParameterFileID? for the
> acquisition date, I looked at the table parameter_file using one of the
> FileIDs from the last insertion but couldn't find the acquisition date. See
> the result of the query below.
>
> 2. The front-end is still crashing. This is the log:
>
> ===
> [php7:error] [pid 32588] [client 155.33.137.12:23564] PHP Fatal error:
>  Uncaught TypeError: Return value of Utility::getStageUsingCandID() must be
> of the type string, null returned in
> /var/www/loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0
> /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177):
> Utility::getStageUsingCandID('207019')\n#1
> /var/www/loris/php/libraries/NDB_Page.class.inc(707):
> LORIS\\instrument_list\\Instrument_List->setup()\n#2
> /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234):
> NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3
> /var/www/loris/src/Middleware/PageDecorationMiddleware.php(56):
> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest),
> Object(LORIS\\instrument_list\\Instrument_List))\n#4
> /var/www/loris/php/libraries/NDB_Page.class.inc(692):
> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest),
> Object(LORIS\\instrument_list\\Instrument_List))\n#5
> /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(137):
> NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on line
> 632, referer:
> https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/
> ===
>
> Happy to have a Zoom call if it helps.
>
> Thank you for your help.
>
> Best,
> Alfredo.
>
> ===
> select ParameterFileID,Value from parameter_file where FileID=428983;
>
> +-----------------+----------------------------------------------------------------------------------------------------------------------------------+
> | ParameterFileID | Value
>                                                                            |
>
> +-----------------+----------------------------------------------------------------------------------------------------------------------------------+
> |       109949932 | MR
>                                                                           |
> |       109949967 | 130
>                                                                            |
> |       109949981 | 0.9765625
>                                                                            |
> |       109949977 | syngo_MR_A35_4VA35A
>                                                                            |
> |       109949958 | 12:13:34.360020
>                                                                            |
> |       109949968 | t1_RIPOSIZ.
>                                                                            |
> |       109949973 | SK_SP_OSP
>                                                                            |
> |       109949962 | 2D
>                                                                           |
> |       109949960 | [0.999742, 0.000840254, 0.0226824, 1.88704e-10,
> 0.999315, -0.0370189]
>      |
> |       109949982 | 0.9765625
>                                                                            |
> |       109949975 | 5
>                                                                            |
> |       109949969 | CP_HeadArray
>                                                                           |
> |       109949965 | 70.3125
>                                                                            |
> |       109949966 | i
>                                                                            |
> |       109949945 | 0.187383
>                                                                           |
> |       109949978 | 3
>                                                                            |
> |       109949963 | 1.5
>                                                                            |
> |       109949976 | 3
>                                                                            |
> |       109949970 | 0.655
>                                                                            |
> |       109949964 | HFS
>                                                                            |
> |       109949974 | t1_RIPOSIZ.
>                                                                            |
> |       109949971 | SE
>                                                                           |
> |       109949956 | 99
>                                                                           |
> |       109949959 | 0.01
>                                                                           |
> |       109949930 | Siemens
>                                                                            |
> |       109949957 | 1
>                                                                            |
> |       109949983 | 2.9999998
>                                                                            |
> |       109949985 |
> 207019/sub-ANOM_ses-endoftreatment_ce-Gd_run-1_T1w_ZZZ_check.png
>                                               |
> |       109949972 | _tse2d1_5
>                                                                            |
> |       109949914 | 20140629
>                                                                           |
> |       109949915 | 99
>                                                                           |
> |       109949916 | 1
>                                                                            |
> |       109949917 | 12:13:34.360020
>                                                                            |
> |       109949918 | 256
>                                                                            |
> |       109949919 | dcm2niix
>                                                                           |
> |       109949920 | v1.0.20180622 (JP2:OpenJPEG) (JP-LS:CharLS) GCC7.3.0
>                                                                           |
> |       109949921 | 0.01
>                                                                           |
> |       109949923 | 150
>                                                                            |
> |       109949924 | [0.999742, 0.000840254, 0.0226824, 1.88704e-10,
> 0.999315, -0.0370189]
>      |
> |       109949925 | ['ORIGINAL', 'PRIMARY', 'M', 'ND']
>                                                                           |
> |       109949926 | ROW
>                                                                            |
> |       109949928 | 2D
>                                                                           |
> |       109949929 | 1.5
>                                                                            |
> |       109949931 | Sonata
>                                                                           |
> |       109949933 | 1
>                                                                            |
> |       109949934 | HFS
>                                                                            |
> |       109949935 | 70.3125
>                                                                            |
> |       109949936 | i
>                                                                            |
> |       109949937 | 100
>                                                                            |
> |       109949938 | 0.55
>                                                                           |
> |       109949939 | 130
>                                                                            |
> |       109949940 | t1_RIPOSIZ.
>                                                                            |
> |       109949941 | %SiemensSeq%_tse
>                                                                           |
> |       109949942 | CP_HeadArray
>                                                                           |
> |       109949943 | 512
>                                                                            |
> |       109949944 | 0.655
>                                                                            |
> |       109949946 | SE
>                                                                           |
> |       109949947 | _tse2d1_5
>                                                                            |
> |       109949948 | SK_SP_OSP
>                                                                            |
> |       109949949 | t1_RIPOSIZ.
>                                                                            |
> |       109949950 | 5
>                                                                            |
> |       109949951 | [48, 57, 59, 361, 234, 67, -246, 256]
>                                                                            |
> |       109949952 | 3
>                                                                            |
> |       109949953 | syngo_MR_A35_4VA35A
>                                                                            |
> |       109949954 | 3
>                                                                            |
> |       109949955 | 202.922
>                                                                            |
> |       109949961 | ['ORIGINAL', 'PRIMARY', 'M', 'ND']
>                                                                           |
> |       109949979 |
> bids_imports/INFORMS_BIDSVersion_1.4.0/sub-ANOM/ses-endoftreatment/anat/sub-ANOM_ses-endoftreatment_run-1_T1w.json
>     |
> |       109949980 |
> 7655f29d97c14a6b88055f99c7879097650c31cafa7405a1ad3a93062d04669417f42b67c175e9ad904da1e1bb677b2fb6a44ed8b26af482a4d3c40498f284df
> |
> |       109949984 |
> 3f487183fe830d801477568aec824c967a44d3bf3feb9cbd6575830d31b90b089cc625a037c487d3985fb10ee0a00f2eac824980955949c8955cdd304ea838b9
> |
> |       109949922 | 5
>                                                                            |
> |       109949927 | 1
>                                                                            |
>
> +-----------------+----------------------------------------------------------------------------------------------------------------------------------+
> ===
>
> This is the content of the *_scan.tsv file:
> ===
> filename        acq_time
> anat/sub-ANOM_ses-endoftreatment_run-1_T1w.nii.gz  2014-06-29T00:00:00
> anat/sub-ANOM_ses-endoftreatment_ce-Gd_run-1_T1w.nii.gz
>  2014-06-29T00:00:00
> anat/sub-ANOM_ses-endoftreatment_run-1_FLAIR.nii.gz
>  2014-06-29T00:00:00
> anat/sub-ANOM_ses-endoftreatment_ce-Gd_run-2_T1w.nii.gz
>  2014-06-29T00:00:00
> anat/sub-ANOM_ses-endoftreatment_run-1_PD.nii.gz   2014-06-29T00:00:00
> anat/sub-ANOM_ses-endoftreatment_run-1_T2w.nii.gz  2014-06-29T00:00:00
> ===
>
> On Jul 15, 2021, at 5:23 PM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> Sorry for the delay, I had to take a deeper look at the code to answer
> some of your questions. See below.
>
> > 1. I added the file sub-<label>[_ses-<label>]_scans.tsv as suggested in
>> the BIDS standard (
>> https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file
>> <https://secure-web.cisco.com/1RT0b_pDRzGh5oEnKt7wHclfIWMewUlzzoH-FStRocNdjI2mrpqsgr33eVaIS22zsvLSZ7Z8ugyaoZ07SHA_O7tObAB409DokII49oyHlFVQnGqaaxEoC_87rcI6ivzH41s36uv9R13FRzaiRJPDhbqmj3kt67BF36UEJp4e5xglyAHPcxx1DV8sf3sJ2TRBCKhNhHUWeRbPM9DdNrFxpoZzYHnN4xy-VMBRK5T9SF4afE6jv3tqdaKdfSYG2wDh-CWrIBbzyeSECIRnMYikelA/https%3A%2F%2Fbids-specification.readthedocs.io%2Fen%2Fstable%2F03-modality-agnostic-files.html%23scans-file>)
>> to add the acquisition dates, do you take it into account to set the dates
>> in LORIS? If not, how can I set the acquisition dates for the images in the
>> session/visit?
>>
>
> Indeed, if you enter a date under an 'acq_time' column in the scans.tsv
> file, it will add an entry in parameter_file for the scan_acquisition_time
> parameter.
>
>
>> >
>> > 2. I am doing the insertion visit by visit to be able to identify
>> issues instead of running all the subjects at once. In this approach I get
>> an error stating that the participants file
>> (".../data/bids_imports/INFORMS_BIDSVersion_1.4.0/participants.tsv") is
>> different from for every execution. Is there a way I can upload subject by
>> subject without having this issue?
>>
>
> yeah, this is a current limitation that this file keeps changing each time
> you upload a new candidate. The pipeline was initially developed for
> retrospective BIDS datasets. We would need to modify this part
> <https://secure-web.cisco.com/1FA74HdTiHzhrcJezSt2K6DKMGwP_wqxcdk1oXclu1U6jCz4rd2fSi-NwskWq_Qfb0p4MTUX6_XEbTFvgo_VxzSI4YiWtniz3W9Yi_Y_Yhd3GKBQD7kKnXK8l0jqEWj-6sZ77YTpIg9X5O235SfFeZ3JW3V5MFXQOH7vMnzgPDBS-6dsjvmCAtnAjP4DJoXkGwQ6VJLV21yWj9np6NfjWvjphVgXfpYnIoS4jb57yVl8xBW0ttGeejb-HEHsaZ-bNfre-16KCLmR-IJO3pZbnwg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fb5a6fc8cc3cf1fad50df21d9d87a284981705e3c%2Fpython%2Fbids_import.py%23L299> for
> prospective datasets so that instead of just trying to copy the
> participants.tsv file, if it already exists, it would append a row into the
> already existing file. You can find a fix for that in the following PR
> https://github.com/aces/Loris-MRI/pull/645
> <https://secure-web.cisco.com/1Tpg7v8DtF0HJJEnPZUNGN7gwCdF7vLrM19WZmYU8p4-riYcbJ1FVNYH0FGEvIBT0KwSYUMgtVeulxeEaGSohphmm0NQn8wIbxh5cSX4VwbKcKLhvQY1RtnS2SxEKUi4Pln5KHxRYDcVhz9sWnZ6EIhfZEDECvkuT2-zTt24B5MMeBduiQG8W3Pqa7Qr2oEjJW_m84bq0EVtbGQmu5ZVKytj8tPkwWAUE8gTEtLOb1DjwDX5O8y8EHAN_8lf2ZqJ9eojMRDufJj2QObf0g02n3Q/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F645>
> .
>
>
>> >
>> > If l have to launch the whole dataset, is the bids script able to check
>> what was already inserted in case there is an error and I have to it again?
>>
>
> Yes, the pipeline is supposed to be smart enough to not reinsert something
> that was previously inserted.
>
>
>> >
>> > 3. After insertion of BIDS for a subject in a visit I cannot access the
>> visit in the front end, I am getting a 500 error. Here is the error log in
>> LORIS:
>> >
>> > ===
>> > [Mon Jul 12 12:05:37.705967 2021] [php7:error] [pid 14497] [client
>> 216.15.126.108:55424
>> <http://secure-web.cisco.com/1WYhYdfRTqaTteJ_4rndbHmww7uTfLympsocUwkjHV2oHQVOQ_ddIjv7AcfCoiP5cJIbw5iksCEFI9RVOxA3_lM6etO-PCaDz89PgNjaEjQPMC5dEfLOft3B7YhP7TCF4ISn-hvCOCFnhQqmRbs9zS1PRbVr6qe_Fra0AR2dZzskzHnYp2A_u29fTzE5u8vYJLMpl4t10wah4Bga-hhoD3gkgnRHVU5KAWy4uwX30Ma4tng8DnVlqBopiM9DpYE6ZEviZpdmHvWqJZxPHxbnHOw/http%3A%2F%2F216.15.126.108%3A55424>]
>> PHP Fatal error:  Uncaught TypeError: Return value of
>> Utility::getStageUsingCandID() must be of the type string, null returned in
>> /var/www
>> > /loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0
>> /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177):
>> Utility::getStageUsingCandID('207019')\n#1
>> /var/www/loris/php/libraries/NDB_Page.class.inc(
>> > 707): LORIS\\instrument_list\\Instrument_List->setup()\n#2
>> /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234):
>> NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3
>> /var/www/loris/src/Middleware/PageD
>> > ecorationMiddleware.php(56):
>> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest),
>> Object(LORIS\\instrument_list\\Instrument_List))\n#4
>> /var/www/loris/php/libraries/NDB_Page.class.i
>> > nc(692):
>> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest),
>> Object(LORIS\\instrument_list\\Instrument_List))\n#5
>> /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(
>> > 137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc
>> on line 632, referer:
>> https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/
>> <https://secure-web.cisco.com/1XkKe3e3JkFCEbEAQx3rrZ25ZCaDXFH7ViiHfRCVtt0ZTI9ckG_4i5CYOnY_Wv0SYfmdvUUZ0jQkdjvUgzKY9qJfqnqcVF_7n2nRaR-c1a4U_Y95LN-Dv96I8j-OBHltZ52DoTaYZ9RvB7YL9vP82yG9pUb2XlYJwK6xA6b2gGwhHhyqpdrPfRW0HZFx4__6pDI4CU5CQWx9_dteaDW3_xjntBo3296km9H-nJNiywrGrKtv_1pO6wCU5ygXs2bqXwZ9j7X4eILwCv0N7S7PlKA/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fcandidate_profile%2F207019%2F>
>> > ===
>>
>
> This might be due to the Current_stage not being set when creating the
> visit via the bids_import.py script. Here is a PR to fix that issue next
> time you import a new visit via bids_import.py:
> https://github.com/aces/Loris-MRI/pull/644
> <https://secure-web.cisco.com/1RuRCEtVgtWrK7Pm95g10P8zRltmw5fqwt4wM4vzTM2N7zp7p8HXJKNSQo5QSAfOa23ID04z8m13DojdlnneipDRp6yoYNUJIoorexU5ixp49Alwi5aaHokrOmz-gRnpRkrUxMNI04i2tsCDBAsyiwIBoMwgWyCGHg8asEvLiHrEcYtWAdRycS4UQ7Udt6hrVhp6DqF6kpBH3s4oWPPlFvnJ9CHywNOno0NqHI0zXVnlWI2BuIW0heLJeaDSyrvK-5FcYxqhfnBEJTq1hkNB-Jg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F644>
>
>
> Hope this helps,
>
> C?cile
>
>
> The information in this e-mail is intended only for the person to whom it
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From AMORALESPINZON at BWH.HARVARD.EDU  Mon Jul 19 11:41:41 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Mon, 19 Jul 2021 15:41:41 +0000
Subject: [Loris-dev] Questions and errors uploading BIDS
In-Reply-To: <CAMkiY3f8_bZxFJx8W5HFzzMPV8J_wB_BSPW=-ExmqA=WGSOdEA@mail.gmail.com>
References: <A142044A-2953-4B49-97E9-3BF869202F7B@bwh.harvard.edu>
 <36E88E76-4736-42BF-9905-F0FDD987915F@bwh.harvard.edu>
 <CAMkiY3fPyON8j_dQ1NB5ndoC_hkmmYFZZ5wfiFswLf27GPeWVQ@mail.gmail.com>
 <8EED5B04-BBAB-46DD-AD83-F9A830C5B6FE@BWH.HARVARD.EDU>
 <CAMkiY3f8_bZxFJx8W5HFzzMPV8J_wB_BSPW=-ExmqA=WGSOdEA@mail.gmail.com>
Message-ID: <B7DCD8E0-6D39-453A-99BB-5E1D4A13A8CF@bwh.harvard.edu>

Hi C?cile,

Thank you for the prompt reply. Here are the results for the queries:

===
SELECT pf.Value FROM parameter_file pf JOIN parameter_type pt USING (ParameterTypeID) WHERE pt.Name="scan_acquisition_time" AND FileID=428983;
Empty set (0.00 sec)
===

===
SELECT DISTINCT Current_stage FROM session WHERE CandID=207019;
+---------------+
| Current_stage |
+---------------+
| NULL          |
| Not Started   |
+---------------+
2 rows in set (0.01 sec)
===

As I said before, we can have a call if this makes things easier and faster.

Best,
Alfredo.

On Jul 19, 2021, at 11:26 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

For the acquisition date, try the following query:
SELECT pf.Value FROM parameter_file pf JOIN parameter_type pt USING (ParameterTypeID) WHERE pt.Name="scan_acquisition_time" AND FileID=428983;

For 2., what does the following query return?
SELECT DISTINCT Current_stage FROM session WHERE CandID=207019;

C?cile

On Mon, Jul 19, 2021 at 11:19 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I patched LORIS and inserted one visit.

Before moving forward I want to make sure the acquisition date was inserted, could you please tell me what is the ?ParameterFileID? for the acquisition date, I looked at the table parameter_file using one of the FileIDs from the last insertion but couldn't find the acquisition date. See the result of the query below.

2. The front-end is still crashing. This is the log:

===
[php7:error] [pid 32588] [client 155.33.137.12:23564<http://secure-web.cisco.com/1nROtbNw-Vzt6PDAU71bMpkZ2DX-C8_gGT7jPalLUwf7iW0vRUudY_S6vIhtCPN4YHMDNIlD9L_XfAEixBt2iRg_KHw6treMqgGID9xjB3xoxlLD2fhNblD3jlfGfUSZYqaMb2TZKSCJoVCGMoDx12cEmnzWRfPe2QxGRgwYHNP7Bf9SBcfWaAQ_ODCTQVBimXbr1NWavp5WNDM_hcGsLLupgF6xBbXBxr7s1e7BLCemInf4-AlIdok-y3-ZvC8BDdDbKsCs7sHYqn0gSK7YQsA/http%3A%2F%2F155.33.137.12%3A23564>] PHP Fatal error:  Uncaught TypeError: Return value of Utility::getStageUsingCandID() must be of the type string, null returned in /var/www/loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177): Utility::getStageUsingCandID('207019')\n#1 /var/www/loris/php/libraries/NDB_Page.class.inc(707): LORIS\\instrument_list\\Instrument_List->setup()\n#2 /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234): NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3 /var/www/loris/src/Middleware/PageDecorationMiddleware.php(56): LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#4 /var/www/loris/php/libraries/NDB_Page.class.inc(692): LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#5 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on line 632, referer: https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/<https://secure-web.cisco.com/1mVIQ6ONSXAF7-5MPbIxuWHNbxYUn-M6MiKm-VfZKDScn_0YJ02NPcV4p7rirYg2XnVfXdHzODTPAcrLuUItZ6KKzzEdJ2lQXp9ZTMufpswd6YsZlGwob5GriUoRzGl7WJKfUwk2hnizx5FQXgIT0jZjFQqSf0w-2sproV85wbmg5r4X4UtFMV9WCoOG__khDbsnWOcdGaPJHTS1tVcjVuS2tRv628XtslAP_5jnzzfTPMndhvwR3-tRMLUp_ptV7i_ww353-P3KHxecwTBVnXg/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fcandidate_profile%2F207019%2F>
===

Happy to have a Zoom call if it helps.

Thank you for your help.

Best,
Alfredo.

===
select ParameterFileID,Value from parameter_file where FileID=428983;
+-----------------+----------------------------------------------------------------------------------------------------------------------------------+
| ParameterFileID | Value                                                                                                                            |
+-----------------+----------------------------------------------------------------------------------------------------------------------------------+
|       109949932 | MR                                                                                                                               |
|       109949967 | 130                                                                                                                              |
|       109949981 | 0.9765625                                                                                                                        |
|       109949977 | syngo_MR_A35_4VA35A                                                                                                              |
|       109949958 | 12:13:34.360020                                                                                                                  |
|       109949968 | t1_RIPOSIZ.                                                                                                                      |
|       109949973 | SK_SP_OSP                                                                                                                        |
|       109949962 | 2D                                                                                                                               |
|       109949960 | [0.999742, 0.000840254, 0.0226824, 1.88704e-10, 0.999315, -0.0370189]                                                            |
|       109949982 | 0.9765625                                                                                                                        |
|       109949975 | 5                                                                                                                                |
|       109949969 | CP_HeadArray                                                                                                                     |
|       109949965 | 70.3125                                                                                                                          |
|       109949966 | i                                                                                                                                |
|       109949945 | 0.187383                                                                                                                         |
|       109949978 | 3                                                                                                                                |
|       109949963 | 1.5                                                                                                                              |
|       109949976 | 3                                                                                                                                |
|       109949970 | 0.655                                                                                                                            |
|       109949964 | HFS                                                                                                                              |
|       109949974 | t1_RIPOSIZ.                                                                                                                      |
|       109949971 | SE                                                                                                                               |
|       109949956 | 99                                                                                                                               |
|       109949959 | 0.01                                                                                                                             |
|       109949930 | Siemens                                                                                                                          |
|       109949957 | 1                                                                                                                                |
|       109949983 | 2.9999998                                                                                                                        |
|       109949985 | 207019/sub-ANOM_ses-endoftreatment_ce-Gd_run-1_T1w_ZZZ_check.png                                                         |
|       109949972 | _tse2d1_5                                                                                                                        |
|       109949914 | 20140629                                                                                                                         |
|       109949915 | 99                                                                                                                               |
|       109949916 | 1                                                                                                                                |
|       109949917 | 12:13:34.360020                                                                                                                  |
|       109949918 | 256                                                                                                                              |
|       109949919 | dcm2niix                                                                                                                         |
|       109949920 | v1.0.20180622 (JP2:OpenJPEG) (JP-LS:CharLS) GCC7.3.0                                                                             |
|       109949921 | 0.01                                                                                                                             |
|       109949923 | 150                                                                                                                              |
|       109949924 | [0.999742, 0.000840254, 0.0226824, 1.88704e-10, 0.999315, -0.0370189]                                                            |
|       109949925 | ['ORIGINAL', 'PRIMARY', 'M', 'ND']                                                                                               |
|       109949926 | ROW                                                                                                                              |
|       109949928 | 2D                                                                                                                               |
|       109949929 | 1.5                                                                                                                              |
|       109949931 | Sonata                                                                                                                           |
|       109949933 | 1                                                                                                                                |
|       109949934 | HFS                                                                                                                              |
|       109949935 | 70.3125                                                                                                                          |
|       109949936 | i                                                                                                                                |
|       109949937 | 100                                                                                                                              |
|       109949938 | 0.55                                                                                                                             |
|       109949939 | 130                                                                                                                              |
|       109949940 | t1_RIPOSIZ.                                                                                                                      |
|       109949941 | %SiemensSeq%_tse                                                                                                                 |
|       109949942 | CP_HeadArray                                                                                                                     |
|       109949943 | 512                                                                                                                              |
|       109949944 | 0.655                                                                                                                            |
|       109949946 | SE                                                                                                                               |
|       109949947 | _tse2d1_5                                                                                                                        |
|       109949948 | SK_SP_OSP                                                                                                                        |
|       109949949 | t1_RIPOSIZ.                                                                                                                      |
|       109949950 | 5                                                                                                                                |
|       109949951 | [48, 57, 59, 361, 234, 67, -246, 256]                                                                                            |
|       109949952 | 3                                                                                                                                |
|       109949953 | syngo_MR_A35_4VA35A                                                                                                              |
|       109949954 | 3                                                                                                                                |
|       109949955 | 202.922                                                                                                                          |
|       109949961 | ['ORIGINAL', 'PRIMARY', 'M', 'ND']                                                                                               |
|       109949979 | bids_imports/INFORMS_BIDSVersion_1.4.0/sub-ANOM/ses-endoftreatment/anat/sub-ANOM_ses-endoftreatment_run-1_T1w.json     |
|       109949980 | 7655f29d97c14a6b88055f99c7879097650c31cafa7405a1ad3a93062d04669417f42b67c175e9ad904da1e1bb677b2fb6a44ed8b26af482a4d3c40498f284df |
|       109949984 | 3f487183fe830d801477568aec824c967a44d3bf3feb9cbd6575830d31b90b089cc625a037c487d3985fb10ee0a00f2eac824980955949c8955cdd304ea838b9 |
|       109949922 | 5                                                                                                                                |
|       109949927 | 1                                                                                                                                |
+-----------------+----------------------------------------------------------------------------------------------------------------------------------+
===

This is the content of the *_scan.tsv file:
===
filename        acq_time
anat/sub-ANOM_ses-endoftreatment_run-1_T1w.nii.gz  2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_ce-Gd_run-1_T1w.nii.gz    2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_run-1_FLAIR.nii.gz        2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_ce-Gd_run-2_T1w.nii.gz    2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_run-1_PD.nii.gz   2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_run-1_T2w.nii.gz  2014-06-29T00:00:00
===

On Jul 15, 2021, at 5:23 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Sorry for the delay, I had to take a deeper look at the code to answer some of your questions. See below.

> 1. I added the file sub-<label>[_ses-<label>]_scans.tsv as suggested in the BIDS standard (https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file<https://secure-web.cisco.com/1RT0b_pDRzGh5oEnKt7wHclfIWMewUlzzoH-FStRocNdjI2mrpqsgr33eVaIS22zsvLSZ7Z8ugyaoZ07SHA_O7tObAB409DokII49oyHlFVQnGqaaxEoC_87rcI6ivzH41s36uv9R13FRzaiRJPDhbqmj3kt67BF36UEJp4e5xglyAHPcxx1DV8sf3sJ2TRBCKhNhHUWeRbPM9DdNrFxpoZzYHnN4xy-VMBRK5T9SF4afE6jv3tqdaKdfSYG2wDh-CWrIBbzyeSECIRnMYikelA/https%3A%2F%2Fbids-specification.readthedocs.io%2Fen%2Fstable%2F03-modality-agnostic-files.html%23scans-file>) to add the acquisition dates, do you take it into account to set the dates in LORIS? If not, how can I set the acquisition dates for the images in the session/visit?

Indeed, if you enter a date under an 'acq_time' column in the scans.tsv file, it will add an entry in parameter_file for the scan_acquisition_time parameter.

>
> 2. I am doing the insertion visit by visit to be able to identify issues instead of running all the subjects at once. In this approach I get an error stating that the participants file (".../data/bids_imports/INFORMS_BIDSVersion_1.4.0/participants.tsv") is different from for every execution. Is there a way I can upload subject by subject without having this issue?

yeah, this is a current limitation that this file keeps changing each time you upload a new candidate. The pipeline was initially developed for retrospective BIDS datasets. We would need to modify this part<https://secure-web.cisco.com/1FA74HdTiHzhrcJezSt2K6DKMGwP_wqxcdk1oXclu1U6jCz4rd2fSi-NwskWq_Qfb0p4MTUX6_XEbTFvgo_VxzSI4YiWtniz3W9Yi_Y_Yhd3GKBQD7kKnXK8l0jqEWj-6sZ77YTpIg9X5O235SfFeZ3JW3V5MFXQOH7vMnzgPDBS-6dsjvmCAtnAjP4DJoXkGwQ6VJLV21yWj9np6NfjWvjphVgXfpYnIoS4jb57yVl8xBW0ttGeejb-HEHsaZ-bNfre-16KCLmR-IJO3pZbnwg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fb5a6fc8cc3cf1fad50df21d9d87a284981705e3c%2Fpython%2Fbids_import.py%23L299> for prospective datasets so that instead of just trying to copy the participants.tsv file, if it already exists, it would append a row into the already existing file. You can find a fix for that in the following PR https://github.com/aces/Loris-MRI/pull/645<https://secure-web.cisco.com/1Tpg7v8DtF0HJJEnPZUNGN7gwCdF7vLrM19WZmYU8p4-riYcbJ1FVNYH0FGEvIBT0KwSYUMgtVeulxeEaGSohphmm0NQn8wIbxh5cSX4VwbKcKLhvQY1RtnS2SxEKUi4Pln5KHxRYDcVhz9sWnZ6EIhfZEDECvkuT2-zTt24B5MMeBduiQG8W3Pqa7Qr2oEjJW_m84bq0EVtbGQmu5ZVKytj8tPkwWAUE8gTEtLOb1DjwDX5O8y8EHAN_8lf2ZqJ9eojMRDufJj2QObf0g02n3Q/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F645>.

>
> If l have to launch the whole dataset, is the bids script able to check what was already inserted in case there is an error and I have to it again?

Yes, the pipeline is supposed to be smart enough to not reinsert something that was previously inserted.

>
> 3. After insertion of BIDS for a subject in a visit I cannot access the visit in the front end, I am getting a 500 error. Here is the error log in LORIS:
>
> ===
> [Mon Jul 12 12:05:37.705967 2021] [php7:error] [pid 14497] [client 216.15.126.108:55424<http://secure-web.cisco.com/1WYhYdfRTqaTteJ_4rndbHmww7uTfLympsocUwkjHV2oHQVOQ_ddIjv7AcfCoiP5cJIbw5iksCEFI9RVOxA3_lM6etO-PCaDz89PgNjaEjQPMC5dEfLOft3B7YhP7TCF4ISn-hvCOCFnhQqmRbs9zS1PRbVr6qe_Fra0AR2dZzskzHnYp2A_u29fTzE5u8vYJLMpl4t10wah4Bga-hhoD3gkgnRHVU5KAWy4uwX30Ma4tng8DnVlqBopiM9DpYE6ZEviZpdmHvWqJZxPHxbnHOw/http%3A%2F%2F216.15.126.108%3A55424>] PHP Fatal error:  Uncaught TypeError: Return value of Utility::getStageUsingCandID() must be of the type string, null returned in /var/www
> /loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177): Utility::getStageUsingCandID('207019')\n#1 /var/www/loris/php/libraries/NDB_Page.class.inc(
> 707): LORIS\\instrument_list\\Instrument_List->setup()\n#2 /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234): NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3 /var/www/loris/src/Middleware/PageD
> ecorationMiddleware.php(56): LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#4 /var/www/loris/php/libraries/NDB_Page.class.i
> nc(692): LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#5 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(
> 137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on line 632, referer: https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/<https://secure-web.cisco.com/1XkKe3e3JkFCEbEAQx3rrZ25ZCaDXFH7ViiHfRCVtt0ZTI9ckG_4i5CYOnY_Wv0SYfmdvUUZ0jQkdjvUgzKY9qJfqnqcVF_7n2nRaR-c1a4U_Y95LN-Dv96I8j-OBHltZ52DoTaYZ9RvB7YL9vP82yG9pUb2XlYJwK6xA6b2gGwhHhyqpdrPfRW0HZFx4__6pDI4CU5CQWx9_dteaDW3_xjntBo3296km9H-nJNiywrGrKtv_1pO6wCU5ygXs2bqXwZ9j7X4eILwCv0N7S7PlKA/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fcandidate_profile%2F207019%2F>
> ===

This might be due to the Current_stage not being set when creating the visit via the bids_import.py script. Here is a PR to fix that issue next time you import a new visit via bids_import.py: https://github.com/aces/Loris-MRI/pull/644<https://secure-web.cisco.com/1RuRCEtVgtWrK7Pm95g10P8zRltmw5fqwt4wM4vzTM2N7zp7p8HXJKNSQo5QSAfOa23ID04z8m13DojdlnneipDRp6yoYNUJIoorexU5ixp49Alwi5aaHokrOmz-gRnpRkrUxMNI04i2tsCDBAsyiwIBoMwgWyCGHg8asEvLiHrEcYtWAdRycS4UQ7Udt6hrVhp6DqF6kpBH3s4oWPPlFvnJ9CHywNOno0NqHI0zXVnlWI2BuIW0heLJeaDSyrvK-5FcYxqhfnBEJTq1hkNB-Jg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F644>

Hope this helps,

C?cile

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From cecile.madjar at mcin.ca  Mon Jul 19 13:41:09 2021
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Mon, 19 Jul 2021 13:41:09 -0400
Subject: [Loris-dev] Questions and errors uploading BIDS
In-Reply-To: <B7DCD8E0-6D39-453A-99BB-5E1D4A13A8CF@bwh.harvard.edu>
References: <A142044A-2953-4B49-97E9-3BF869202F7B@bwh.harvard.edu>
 <36E88E76-4736-42BF-9905-F0FDD987915F@bwh.harvard.edu>
 <CAMkiY3fPyON8j_dQ1NB5ndoC_hkmmYFZZ5wfiFswLf27GPeWVQ@mail.gmail.com>
 <8EED5B04-BBAB-46DD-AD83-F9A830C5B6FE@BWH.HARVARD.EDU>
 <CAMkiY3f8_bZxFJx8W5HFzzMPV8J_wB_BSPW=-ExmqA=WGSOdEA@mail.gmail.com>
 <B7DCD8E0-6D39-453A-99BB-5E1D4A13A8CF@bwh.harvard.edu>
Message-ID: <CAMkiY3d0o34eZ5A9NN9RZX3UgcZz0MNLNNRtPfXULBhSqadsGg@mail.gmail.com>

Hi Alfredo,

The issue here is that the first session has a Current_stage set as NULL.
Maybe verify which session has Current_stage set to NULL. Maybe it comes
from an old import?

On Mon, Jul 19, 2021 at 11:41 AM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi C?cile,
>
> Thank you for the prompt reply. Here are the results for the queries:
>
> ===
> SELECT pf.Value FROM parameter_file pf JOIN parameter_type pt USING
> (ParameterTypeID) WHERE pt.Name="scan_acquisition_time" AND FileID=428983;
> Empty set (0.00 sec)
> ===
>
> ===
> SELECT DISTINCT Current_stage FROM session WHERE CandID=207019;
> +---------------+
> | Current_stage |
> +---------------+
> | NULL          |
> | Not Started   |
> +---------------+
> 2 rows in set (0.01 sec)
> ===
>
> As I said before, we can have a call if this makes things easier and
> faster.
>
> Best,
> Alfredo.
>
> On Jul 19, 2021, at 11:26 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> For the acquisition date, try the following query:
> SELECT pf.Value FROM parameter_file pf JOIN parameter_type pt USING
> (ParameterTypeID) WHERE pt.Name="scan_acquisition_time" AND FileID=428983;
>
> For 2., what does the following query return?
> SELECT DISTINCT Current_stage FROM session WHERE CandID=207019;
>
> C?cile
>
> On Mon, Jul 19, 2021 at 11:19 AM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Hi C?cile,
>>
>> I patched LORIS and inserted one visit.
>>
>> Before moving forward I want to make sure the acquisition date was
>> inserted, could you please tell me what is the ?ParameterFileID? for the
>> acquisition date, I looked at the table parameter_file using one of the
>> FileIDs from the last insertion but couldn't find the acquisition date. See
>> the result of the query below.
>>
>> 2. The front-end is still crashing. This is the log:
>>
>> ===
>> [php7:error] [pid 32588] [client 155.33.137.12:23564
>> <http://secure-web.cisco.com/1nROtbNw-Vzt6PDAU71bMpkZ2DX-C8_gGT7jPalLUwf7iW0vRUudY_S6vIhtCPN4YHMDNIlD9L_XfAEixBt2iRg_KHw6treMqgGID9xjB3xoxlLD2fhNblD3jlfGfUSZYqaMb2TZKSCJoVCGMoDx12cEmnzWRfPe2QxGRgwYHNP7Bf9SBcfWaAQ_ODCTQVBimXbr1NWavp5WNDM_hcGsLLupgF6xBbXBxr7s1e7BLCemInf4-AlIdok-y3-ZvC8BDdDbKsCs7sHYqn0gSK7YQsA/http%3A%2F%2F155.33.137.12%3A23564>]
>> PHP Fatal error:  Uncaught TypeError: Return value of
>> Utility::getStageUsingCandID() must be of the type string, null returned in
>> /var/www/loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0
>> /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177):
>> Utility::getStageUsingCandID('207019')\n#1
>> /var/www/loris/php/libraries/NDB_Page.class.inc(707):
>> LORIS\\instrument_list\\Instrument_List->setup()\n#2
>> /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234):
>> NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3
>> /var/www/loris/src/Middleware/PageDecorationMiddleware.php(56):
>> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest),
>> Object(LORIS\\instrument_list\\Instrument_List))\n#4
>> /var/www/loris/php/libraries/NDB_Page.class.inc(692):
>> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest),
>> Object(LORIS\\instrument_list\\Instrument_List))\n#5
>> /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(137):
>> NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on line
>> 632, referer:
>> https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/
>> <https://secure-web.cisco.com/1mVIQ6ONSXAF7-5MPbIxuWHNbxYUn-M6MiKm-VfZKDScn_0YJ02NPcV4p7rirYg2XnVfXdHzODTPAcrLuUItZ6KKzzEdJ2lQXp9ZTMufpswd6YsZlGwob5GriUoRzGl7WJKfUwk2hnizx5FQXgIT0jZjFQqSf0w-2sproV85wbmg5r4X4UtFMV9WCoOG__khDbsnWOcdGaPJHTS1tVcjVuS2tRv628XtslAP_5jnzzfTPMndhvwR3-tRMLUp_ptV7i_ww353-P3KHxecwTBVnXg/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fcandidate_profile%2F207019%2F>
>> ===
>>
>> Happy to have a Zoom call if it helps.
>>
>> Thank you for your help.
>>
>> Best,
>> Alfredo.
>>
>> ===
>> select ParameterFileID,Value from parameter_file where FileID=428983;
>>
>> +-----------------+----------------------------------------------------------------------------------------------------------------------------------+
>> | ParameterFileID | Value
>>                                                                            |
>>
>> +-----------------+----------------------------------------------------------------------------------------------------------------------------------+
>> |       109949932 | MR
>>
>> |
>> |       109949967 | 130
>>                                                                            |
>> |       109949981 | 0.9765625
>>                                                                            |
>> |       109949977 | syngo_MR_A35_4VA35A
>>                                                                            |
>> |       109949958 | 12:13:34.360020
>>                                                                            |
>> |       109949968 | t1_RIPOSIZ.
>>                                                                            |
>> |       109949973 | SK_SP_OSP
>>                                                                            |
>> |       109949962 | 2D
>>
>> |
>> |       109949960 | [0.999742, 0.000840254, 0.0226824, 1.88704e-10,
>> 0.999315, -0.0370189]
>>      |
>> |       109949982 | 0.9765625
>>                                                                            |
>> |       109949975 | 5
>>                                                                            |
>> |       109949969 | CP_HeadArray
>>
>> |
>> |       109949965 | 70.3125
>>                                                                            |
>> |       109949966 | i
>>                                                                            |
>> |       109949945 | 0.187383
>>
>> |
>> |       109949978 | 3
>>                                                                            |
>> |       109949963 | 1.5
>>                                                                            |
>> |       109949976 | 3
>>                                                                            |
>> |       109949970 | 0.655
>>                                                                            |
>> |       109949964 | HFS
>>                                                                            |
>> |       109949974 | t1_RIPOSIZ.
>>                                                                            |
>> |       109949971 | SE
>>
>> |
>> |       109949956 | 99
>>
>> |
>> |       109949959 | 0.01
>>
>> |
>> |       109949930 | Siemens
>>                                                                            |
>> |       109949957 | 1
>>                                                                            |
>> |       109949983 | 2.9999998
>>                                                                            |
>> |       109949985 |
>> 207019/sub-ANOM_ses-endoftreatment_ce-Gd_run-1_T1w_ZZZ_check.png
>>                                               |
>> |       109949972 | _tse2d1_5
>>                                                                            |
>> |       109949914 | 20140629
>>
>> |
>> |       109949915 | 99
>>
>> |
>> |       109949916 | 1
>>                                                                            |
>> |       109949917 | 12:13:34.360020
>>                                                                            |
>> |       109949918 | 256
>>                                                                            |
>> |       109949919 | dcm2niix
>>
>> |
>> |       109949920 | v1.0.20180622 (JP2:OpenJPEG) (JP-LS:CharLS) GCC7.3.0
>>
>> |
>> |       109949921 | 0.01
>>
>> |
>> |       109949923 | 150
>>                                                                            |
>> |       109949924 | [0.999742, 0.000840254, 0.0226824, 1.88704e-10,
>> 0.999315, -0.0370189]
>>      |
>> |       109949925 | ['ORIGINAL', 'PRIMARY', 'M', 'ND']
>>
>> |
>> |       109949926 | ROW
>>                                                                            |
>> |       109949928 | 2D
>>
>> |
>> |       109949929 | 1.5
>>                                                                            |
>> |       109949931 | Sonata
>>
>> |
>> |       109949933 | 1
>>                                                                            |
>> |       109949934 | HFS
>>                                                                            |
>> |       109949935 | 70.3125
>>                                                                            |
>> |       109949936 | i
>>                                                                            |
>> |       109949937 | 100
>>                                                                            |
>> |       109949938 | 0.55
>>
>> |
>> |       109949939 | 130
>>                                                                            |
>> |       109949940 | t1_RIPOSIZ.
>>                                                                            |
>> |       109949941 | %SiemensSeq%_tse
>>
>> |
>> |       109949942 | CP_HeadArray
>>
>> |
>> |       109949943 | 512
>>                                                                            |
>> |       109949944 | 0.655
>>                                                                            |
>> |       109949946 | SE
>>
>> |
>> |       109949947 | _tse2d1_5
>>                                                                            |
>> |       109949948 | SK_SP_OSP
>>                                                                            |
>> |       109949949 | t1_RIPOSIZ.
>>                                                                            |
>> |       109949950 | 5
>>                                                                            |
>> |       109949951 | [48, 57, 59, 361, 234, 67, -246, 256]
>>                                                                            |
>> |       109949952 | 3
>>                                                                            |
>> |       109949953 | syngo_MR_A35_4VA35A
>>                                                                            |
>> |       109949954 | 3
>>                                                                            |
>> |       109949955 | 202.922
>>                                                                            |
>> |       109949961 | ['ORIGINAL', 'PRIMARY', 'M', 'ND']
>>
>> |
>> |       109949979 |
>> bids_imports/INFORMS_BIDSVersion_1.4.0/sub-ANOM/ses-endoftreatment/anat/sub-ANOM_ses-endoftreatment_run-1_T1w.json
>>     |
>> |       109949980 |
>> 7655f29d97c14a6b88055f99c7879097650c31cafa7405a1ad3a93062d04669417f42b67c175e9ad904da1e1bb677b2fb6a44ed8b26af482a4d3c40498f284df
>> |
>> |       109949984 |
>> 3f487183fe830d801477568aec824c967a44d3bf3feb9cbd6575830d31b90b089cc625a037c487d3985fb10ee0a00f2eac824980955949c8955cdd304ea838b9
>> |
>> |       109949922 | 5
>>                                                                            |
>> |       109949927 | 1
>>                                                                            |
>>
>> +-----------------+----------------------------------------------------------------------------------------------------------------------------------+
>> ===
>>
>> This is the content of the *_scan.tsv file:
>> ===
>> filename        acq_time
>> anat/sub-ANOM_ses-endoftreatment_run-1_T1w.nii.gz  2014-06-29T00:00:00
>> anat/sub-ANOM_ses-endoftreatment_ce-Gd_run-1_T1w.nii.gz
>>  2014-06-29T00:00:00
>> anat/sub-ANOM_ses-endoftreatment_run-1_FLAIR.nii.gz
>>  2014-06-29T00:00:00
>> anat/sub-ANOM_ses-endoftreatment_ce-Gd_run-2_T1w.nii.gz
>>  2014-06-29T00:00:00
>> anat/sub-ANOM_ses-endoftreatment_run-1_PD.nii.gz   2014-06-29T00:00:00
>> anat/sub-ANOM_ses-endoftreatment_run-1_T2w.nii.gz  2014-06-29T00:00:00
>> ===
>>
>> On Jul 15, 2021, at 5:23 PM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>>
>>         External Email - Use Caution
>>
>> Hi Alfredo,
>>
>> Sorry for the delay, I had to take a deeper look at the code to answer
>> some of your questions. See below.
>>
>> > 1. I added the file sub-<label>[_ses-<label>]_scans.tsv as suggested in
>>> the BIDS standard (
>>> https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file
>>> <https://secure-web.cisco.com/1RT0b_pDRzGh5oEnKt7wHclfIWMewUlzzoH-FStRocNdjI2mrpqsgr33eVaIS22zsvLSZ7Z8ugyaoZ07SHA_O7tObAB409DokII49oyHlFVQnGqaaxEoC_87rcI6ivzH41s36uv9R13FRzaiRJPDhbqmj3kt67BF36UEJp4e5xglyAHPcxx1DV8sf3sJ2TRBCKhNhHUWeRbPM9DdNrFxpoZzYHnN4xy-VMBRK5T9SF4afE6jv3tqdaKdfSYG2wDh-CWrIBbzyeSECIRnMYikelA/https%3A%2F%2Fbids-specification.readthedocs.io%2Fen%2Fstable%2F03-modality-agnostic-files.html%23scans-file>)
>>> to add the acquisition dates, do you take it into account to set the dates
>>> in LORIS? If not, how can I set the acquisition dates for the images in the
>>> session/visit?
>>>
>>
>> Indeed, if you enter a date under an 'acq_time' column in the scans.tsv
>> file, it will add an entry in parameter_file for the scan_acquisition_time
>> parameter.
>>
>>
>>> >
>>> > 2. I am doing the insertion visit by visit to be able to identify
>>> issues instead of running all the subjects at once. In this approach I get
>>> an error stating that the participants file
>>> (".../data/bids_imports/INFORMS_BIDSVersion_1.4.0/participants.tsv") is
>>> different from for every execution. Is there a way I can upload subject by
>>> subject without having this issue?
>>>
>>
>> yeah, this is a current limitation that this file keeps changing each
>> time you upload a new candidate. The pipeline was initially developed for
>> retrospective BIDS datasets. We would need to modify this part
>> <https://secure-web.cisco.com/1FA74HdTiHzhrcJezSt2K6DKMGwP_wqxcdk1oXclu1U6jCz4rd2fSi-NwskWq_Qfb0p4MTUX6_XEbTFvgo_VxzSI4YiWtniz3W9Yi_Y_Yhd3GKBQD7kKnXK8l0jqEWj-6sZ77YTpIg9X5O235SfFeZ3JW3V5MFXQOH7vMnzgPDBS-6dsjvmCAtnAjP4DJoXkGwQ6VJLV21yWj9np6NfjWvjphVgXfpYnIoS4jb57yVl8xBW0ttGeejb-HEHsaZ-bNfre-16KCLmR-IJO3pZbnwg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fb5a6fc8cc3cf1fad50df21d9d87a284981705e3c%2Fpython%2Fbids_import.py%23L299> for
>> prospective datasets so that instead of just trying to copy the
>> participants.tsv file, if it already exists, it would append a row into the
>> already existing file. You can find a fix for that in the following PR
>> https://github.com/aces/Loris-MRI/pull/645
>> <https://secure-web.cisco.com/1Tpg7v8DtF0HJJEnPZUNGN7gwCdF7vLrM19WZmYU8p4-riYcbJ1FVNYH0FGEvIBT0KwSYUMgtVeulxeEaGSohphmm0NQn8wIbxh5cSX4VwbKcKLhvQY1RtnS2SxEKUi4Pln5KHxRYDcVhz9sWnZ6EIhfZEDECvkuT2-zTt24B5MMeBduiQG8W3Pqa7Qr2oEjJW_m84bq0EVtbGQmu5ZVKytj8tPkwWAUE8gTEtLOb1DjwDX5O8y8EHAN_8lf2ZqJ9eojMRDufJj2QObf0g02n3Q/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F645>
>> .
>>
>>
>>> >
>>> > If l have to launch the whole dataset, is the bids script able to
>>> check what was already inserted in case there is an error and I have to it
>>> again?
>>>
>>
>> Yes, the pipeline is supposed to be smart enough to not reinsert
>> something that was previously inserted.
>>
>>
>>> >
>>> > 3. After insertion of BIDS for a subject in a visit I cannot access
>>> the visit in the front end, I am getting a 500 error. Here is the error log
>>> in LORIS:
>>> >
>>> > ===
>>> > [Mon Jul 12 12:05:37.705967 2021] [php7:error] [pid 14497] [client
>>> 216.15.126.108:55424
>>> <http://secure-web.cisco.com/1WYhYdfRTqaTteJ_4rndbHmww7uTfLympsocUwkjHV2oHQVOQ_ddIjv7AcfCoiP5cJIbw5iksCEFI9RVOxA3_lM6etO-PCaDz89PgNjaEjQPMC5dEfLOft3B7YhP7TCF4ISn-hvCOCFnhQqmRbs9zS1PRbVr6qe_Fra0AR2dZzskzHnYp2A_u29fTzE5u8vYJLMpl4t10wah4Bga-hhoD3gkgnRHVU5KAWy4uwX30Ma4tng8DnVlqBopiM9DpYE6ZEviZpdmHvWqJZxPHxbnHOw/http%3A%2F%2F216.15.126.108%3A55424>]
>>> PHP Fatal error:  Uncaught TypeError: Return value of
>>> Utility::getStageUsingCandID() must be of the type string, null returned in
>>> /var/www
>>> > /loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0
>>> /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177):
>>> Utility::getStageUsingCandID('207019')\n#1
>>> /var/www/loris/php/libraries/NDB_Page.class.inc(
>>> > 707): LORIS\\instrument_list\\Instrument_List->setup()\n#2
>>> /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234):
>>> NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3
>>> /var/www/loris/src/Middleware/PageD
>>> > ecorationMiddleware.php(56):
>>> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest),
>>> Object(LORIS\\instrument_list\\Instrument_List))\n#4
>>> /var/www/loris/php/libraries/NDB_Page.class.i
>>> > nc(692):
>>> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest),
>>> Object(LORIS\\instrument_list\\Instrument_List))\n#5
>>> /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(
>>> > 137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc
>>> on line 632, referer:
>>> https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/
>>> <https://secure-web.cisco.com/1XkKe3e3JkFCEbEAQx3rrZ25ZCaDXFH7ViiHfRCVtt0ZTI9ckG_4i5CYOnY_Wv0SYfmdvUUZ0jQkdjvUgzKY9qJfqnqcVF_7n2nRaR-c1a4U_Y95LN-Dv96I8j-OBHltZ52DoTaYZ9RvB7YL9vP82yG9pUb2XlYJwK6xA6b2gGwhHhyqpdrPfRW0HZFx4__6pDI4CU5CQWx9_dteaDW3_xjntBo3296km9H-nJNiywrGrKtv_1pO6wCU5ygXs2bqXwZ9j7X4eILwCv0N7S7PlKA/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fcandidate_profile%2F207019%2F>
>>> > ===
>>>
>>
>> This might be due to the Current_stage not being set when creating the
>> visit via the bids_import.py script. Here is a PR to fix that issue next
>> time you import a new visit via bids_import.py:
>> https://github.com/aces/Loris-MRI/pull/644
>> <https://secure-web.cisco.com/1RuRCEtVgtWrK7Pm95g10P8zRltmw5fqwt4wM4vzTM2N7zp7p8HXJKNSQo5QSAfOa23ID04z8m13DojdlnneipDRp6yoYNUJIoorexU5ixp49Alwi5aaHokrOmz-gRnpRkrUxMNI04i2tsCDBAsyiwIBoMwgWyCGHg8asEvLiHrEcYtWAdRycS4UQ7Udt6hrVhp6DqF6kpBH3s4oWPPlFvnJ9CHywNOno0NqHI0zXVnlWI2BuIW0heLJeaDSyrvK-5FcYxqhfnBEJTq1hkNB-Jg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F644>
>>
>>
>> Hope this helps,
>>
>> C?cile
>>
>>
>> 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/12oS_QzclpiQcg_5CjSIubWkQntHnTzqFtBX6mIpa2UBfLh0PVFbNhw3IdXKR4AZ34z6Y4oONHxNl8RPg_-v5rbGH1bm25TzFr3nnHzzX-JiG9TdS5w_tGDS8dGTAdqHOqRD0y6Fn6ceB81q-IYVyZxyd-oWY8_bD4W7nK_hFDdMGi_GjLB5Qm-Opov0A6h0QkxNvnxJQpq85R1ace87QLIkJNTDBloRdcjKgYJm3NLT9JbBe-uOsotk5sBO21JKnuVHFKcIakn138zVhP4vF1A/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
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> The information in this e-mail is intended only for the person to whom it
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> Brigham Compliance HelpLine at
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From AMORALESPINZON at BWH.HARVARD.EDU  Mon Jul 19 15:07:33 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Mon, 19 Jul 2021 19:07:33 +0000
Subject: [Loris-dev] Questions and errors uploading BIDS
In-Reply-To: <CAMkiY3d0o34eZ5A9NN9RZX3UgcZz0MNLNNRtPfXULBhSqadsGg@mail.gmail.com>
References: <A142044A-2953-4B49-97E9-3BF869202F7B@bwh.harvard.edu>
 <36E88E76-4736-42BF-9905-F0FDD987915F@bwh.harvard.edu>
 <CAMkiY3fPyON8j_dQ1NB5ndoC_hkmmYFZZ5wfiFswLf27GPeWVQ@mail.gmail.com>
 <8EED5B04-BBAB-46DD-AD83-F9A830C5B6FE@BWH.HARVARD.EDU>
 <CAMkiY3f8_bZxFJx8W5HFzzMPV8J_wB_BSPW=-ExmqA=WGSOdEA@mail.gmail.com>
 <B7DCD8E0-6D39-453A-99BB-5E1D4A13A8CF@bwh.harvard.edu>
 <CAMkiY3d0o34eZ5A9NN9RZX3UgcZz0MNLNNRtPfXULBhSqadsGg@mail.gmail.com>
Message-ID: <BF655E11-66FE-4DC8-A419-C56862F54778@bwh.harvard.edu>

Hi C?cile,

Yes, I think two out of three visits had Current_stage NULL, what should value should it be? Is it enough to change it from NULL to ?something_else??

Does this impact the scan_acquisition_time?

Best,
Alfredo.

On Jul 19, 2021, at 1:41 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

The issue here is that the first session has a Current_stage set as NULL. Maybe verify which session has Current_stage set to NULL. Maybe it comes from an old import?

On Mon, Jul 19, 2021 at 11:41 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Thank you for the prompt reply. Here are the results for the queries:

===
SELECT pf.Value FROM parameter_file pf JOIN parameter_type pt USING (ParameterTypeID) WHERE pt.Name="scan_acquisition_time" AND FileID=428983;
Empty set (0.00 sec)
===

===
SELECT DISTINCT Current_stage FROM session WHERE CandID=207019;
+---------------+
| Current_stage |
+---------------+
| NULL          |
| Not Started   |
+---------------+
2 rows in set (0.01 sec)
===

As I said before, we can have a call if this makes things easier and faster.

Best,
Alfredo.

On Jul 19, 2021, at 11:26 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

For the acquisition date, try the following query:
SELECT pf.Value FROM parameter_file pf JOIN parameter_type pt USING (ParameterTypeID) WHERE pt.Name="scan_acquisition_time" AND FileID=428983;

For 2., what does the following query return?
SELECT DISTINCT Current_stage FROM session WHERE CandID=207019;

C?cile

On Mon, Jul 19, 2021 at 11:19 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I patched LORIS and inserted one visit.

Before moving forward I want to make sure the acquisition date was inserted, could you please tell me what is the ?ParameterFileID? for the acquisition date, I looked at the table parameter_file using one of the FileIDs from the last insertion but couldn't find the acquisition date. See the result of the query below.

2. The front-end is still crashing. This is the log:

===
[php7:error] [pid 32588] [client 155.33.137.12:23564<http://secure-web.cisco.com/1nROtbNw-Vzt6PDAU71bMpkZ2DX-C8_gGT7jPalLUwf7iW0vRUudY_S6vIhtCPN4YHMDNIlD9L_XfAEixBt2iRg_KHw6treMqgGID9xjB3xoxlLD2fhNblD3jlfGfUSZYqaMb2TZKSCJoVCGMoDx12cEmnzWRfPe2QxGRgwYHNP7Bf9SBcfWaAQ_ODCTQVBimXbr1NWavp5WNDM_hcGsLLupgF6xBbXBxr7s1e7BLCemInf4-AlIdok-y3-ZvC8BDdDbKsCs7sHYqn0gSK7YQsA/http%3A%2F%2F155.33.137.12%3A23564>] PHP Fatal error:  Uncaught TypeError: Return value of Utility::getStageUsingCandID() must be of the type string, null returned in /var/www/loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177): Utility::getStageUsingCandID('207019')\n#1 /var/www/loris/php/libraries/NDB_Page.class.inc(707): LORIS\\instrument_list\\Instrument_List->setup()\n#2 /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234): NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3 /var/www/loris/src/Middleware/PageDecorationMiddleware.php(56): LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#4 /var/www/loris/php/libraries/NDB_Page.class.inc(692): LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#5 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on line 632, referer: https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/<https://secure-web.cisco.com/1mVIQ6ONSXAF7-5MPbIxuWHNbxYUn-M6MiKm-VfZKDScn_0YJ02NPcV4p7rirYg2XnVfXdHzODTPAcrLuUItZ6KKzzEdJ2lQXp9ZTMufpswd6YsZlGwob5GriUoRzGl7WJKfUwk2hnizx5FQXgIT0jZjFQqSf0w-2sproV85wbmg5r4X4UtFMV9WCoOG__khDbsnWOcdGaPJHTS1tVcjVuS2tRv628XtslAP_5jnzzfTPMndhvwR3-tRMLUp_ptV7i_ww353-P3KHxecwTBVnXg/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fcandidate_profile%2F207019%2F>
===

Happy to have a Zoom call if it helps.

Thank you for your help.

Best,
Alfredo.

===
select ParameterFileID,Value from parameter_file where FileID=428983;
+-----------------+----------------------------------------------------------------------------------------------------------------------------------+
| ParameterFileID | Value                                                                                                                            |
+-----------------+----------------------------------------------------------------------------------------------------------------------------------+
|       109949932 | MR                                                                                                                               |
|       109949967 | 130                                                                                                                              |
|       109949981 | 0.9765625                                                                                                                        |
|       109949977 | syngo_MR_A35_4VA35A                                                                                                              |
|       109949958 | 12:13:34.360020                                                                                                                  |
|       109949968 | t1_RIPOSIZ.                                                                                                                      |
|       109949973 | SK_SP_OSP                                                                                                                        |
|       109949962 | 2D                                                                                                                               |
|       109949960 | [0.999742, 0.000840254, 0.0226824, 1.88704e-10, 0.999315, -0.0370189]                                                            |
|       109949982 | 0.9765625                                                                                                                        |
|       109949975 | 5                                                                                                                                |
|       109949969 | CP_HeadArray                                                                                                                     |
|       109949965 | 70.3125                                                                                                                          |
|       109949966 | i                                                                                                                                |
|       109949945 | 0.187383                                                                                                                         |
|       109949978 | 3                                                                                                                                |
|       109949963 | 1.5                                                                                                                              |
|       109949976 | 3                                                                                                                                |
|       109949970 | 0.655                                                                                                                            |
|       109949964 | HFS                                                                                                                              |
|       109949974 | t1_RIPOSIZ.                                                                                                                      |
|       109949971 | SE                                                                                                                               |
|       109949956 | 99                                                                                                                               |
|       109949959 | 0.01                                                                                                                             |
|       109949930 | Siemens                                                                                                                          |
|       109949957 | 1                                                                                                                                |
|       109949983 | 2.9999998                                                                                                                        |
|       109949985 | 207019/sub-ANOM_ses-endoftreatment_ce-Gd_run-1_T1w_ZZZ_check.png                                                         |
|       109949972 | _tse2d1_5                                                                                                                        |
|       109949914 | 20140629                                                                                                                         |
|       109949915 | 99                                                                                                                               |
|       109949916 | 1                                                                                                                                |
|       109949917 | 12:13:34.360020                                                                                                                  |
|       109949918 | 256                                                                                                                              |
|       109949919 | dcm2niix                                                                                                                         |
|       109949920 | v1.0.20180622 (JP2:OpenJPEG) (JP-LS:CharLS) GCC7.3.0                                                                             |
|       109949921 | 0.01                                                                                                                             |
|       109949923 | 150                                                                                                                              |
|       109949924 | [0.999742, 0.000840254, 0.0226824, 1.88704e-10, 0.999315, -0.0370189]                                                            |
|       109949925 | ['ORIGINAL', 'PRIMARY', 'M', 'ND']                                                                                               |
|       109949926 | ROW                                                                                                                              |
|       109949928 | 2D                                                                                                                               |
|       109949929 | 1.5                                                                                                                              |
|       109949931 | Sonata                                                                                                                           |
|       109949933 | 1                                                                                                                                |
|       109949934 | HFS                                                                                                                              |
|       109949935 | 70.3125                                                                                                                          |
|       109949936 | i                                                                                                                                |
|       109949937 | 100                                                                                                                              |
|       109949938 | 0.55                                                                                                                             |
|       109949939 | 130                                                                                                                              |
|       109949940 | t1_RIPOSIZ.                                                                                                                      |
|       109949941 | %SiemensSeq%_tse                                                                                                                 |
|       109949942 | CP_HeadArray                                                                                                                     |
|       109949943 | 512                                                                                                                              |
|       109949944 | 0.655                                                                                                                            |
|       109949946 | SE                                                                                                                               |
|       109949947 | _tse2d1_5                                                                                                                        |
|       109949948 | SK_SP_OSP                                                                                                                        |
|       109949949 | t1_RIPOSIZ.                                                                                                                      |
|       109949950 | 5                                                                                                                                |
|       109949951 | [48, 57, 59, 361, 234, 67, -246, 256]                                                                                            |
|       109949952 | 3                                                                                                                                |
|       109949953 | syngo_MR_A35_4VA35A                                                                                                              |
|       109949954 | 3                                                                                                                                |
|       109949955 | 202.922                                                                                                                          |
|       109949961 | ['ORIGINAL', 'PRIMARY', 'M', 'ND']                                                                                               |
|       109949979 | bids_imports/INFORMS_BIDSVersion_1.4.0/sub-ANOM/ses-endoftreatment/anat/sub-ANOM_ses-endoftreatment_run-1_T1w.json     |
|       109949980 | 7655f29d97c14a6b88055f99c7879097650c31cafa7405a1ad3a93062d04669417f42b67c175e9ad904da1e1bb677b2fb6a44ed8b26af482a4d3c40498f284df |
|       109949984 | 3f487183fe830d801477568aec824c967a44d3bf3feb9cbd6575830d31b90b089cc625a037c487d3985fb10ee0a00f2eac824980955949c8955cdd304ea838b9 |
|       109949922 | 5                                                                                                                                |
|       109949927 | 1                                                                                                                                |
+-----------------+----------------------------------------------------------------------------------------------------------------------------------+
===

This is the content of the *_scan.tsv file:
===
filename        acq_time
anat/sub-ANOM_ses-endoftreatment_run-1_T1w.nii.gz  2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_ce-Gd_run-1_T1w.nii.gz    2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_run-1_FLAIR.nii.gz        2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_ce-Gd_run-2_T1w.nii.gz    2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_run-1_PD.nii.gz   2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_run-1_T2w.nii.gz  2014-06-29T00:00:00
===

On Jul 15, 2021, at 5:23 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Sorry for the delay, I had to take a deeper look at the code to answer some of your questions. See below.

> 1. I added the file sub-<label>[_ses-<label>]_scans.tsv as suggested in the BIDS standard (https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file<https://secure-web.cisco.com/1RT0b_pDRzGh5oEnKt7wHclfIWMewUlzzoH-FStRocNdjI2mrpqsgr33eVaIS22zsvLSZ7Z8ugyaoZ07SHA_O7tObAB409DokII49oyHlFVQnGqaaxEoC_87rcI6ivzH41s36uv9R13FRzaiRJPDhbqmj3kt67BF36UEJp4e5xglyAHPcxx1DV8sf3sJ2TRBCKhNhHUWeRbPM9DdNrFxpoZzYHnN4xy-VMBRK5T9SF4afE6jv3tqdaKdfSYG2wDh-CWrIBbzyeSECIRnMYikelA/https%3A%2F%2Fbids-specification.readthedocs.io%2Fen%2Fstable%2F03-modality-agnostic-files.html%23scans-file>) to add the acquisition dates, do you take it into account to set the dates in LORIS? If not, how can I set the acquisition dates for the images in the session/visit?

Indeed, if you enter a date under an 'acq_time' column in the scans.tsv file, it will add an entry in parameter_file for the scan_acquisition_time parameter.

>
> 2. I am doing the insertion visit by visit to be able to identify issues instead of running all the subjects at once. In this approach I get an error stating that the participants file (".../data/bids_imports/INFORMS_BIDSVersion_1.4.0/participants.tsv") is different from for every execution. Is there a way I can upload subject by subject without having this issue?

yeah, this is a current limitation that this file keeps changing each time you upload a new candidate. The pipeline was initially developed for retrospective BIDS datasets. We would need to modify this part<https://secure-web.cisco.com/1FA74HdTiHzhrcJezSt2K6DKMGwP_wqxcdk1oXclu1U6jCz4rd2fSi-NwskWq_Qfb0p4MTUX6_XEbTFvgo_VxzSI4YiWtniz3W9Yi_Y_Yhd3GKBQD7kKnXK8l0jqEWj-6sZ77YTpIg9X5O235SfFeZ3JW3V5MFXQOH7vMnzgPDBS-6dsjvmCAtnAjP4DJoXkGwQ6VJLV21yWj9np6NfjWvjphVgXfpYnIoS4jb57yVl8xBW0ttGeejb-HEHsaZ-bNfre-16KCLmR-IJO3pZbnwg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fb5a6fc8cc3cf1fad50df21d9d87a284981705e3c%2Fpython%2Fbids_import.py%23L299> for prospective datasets so that instead of just trying to copy the participants.tsv file, if it already exists, it would append a row into the already existing file. You can find a fix for that in the following PR https://github.com/aces/Loris-MRI/pull/645<https://secure-web.cisco.com/1Tpg7v8DtF0HJJEnPZUNGN7gwCdF7vLrM19WZmYU8p4-riYcbJ1FVNYH0FGEvIBT0KwSYUMgtVeulxeEaGSohphmm0NQn8wIbxh5cSX4VwbKcKLhvQY1RtnS2SxEKUi4Pln5KHxRYDcVhz9sWnZ6EIhfZEDECvkuT2-zTt24B5MMeBduiQG8W3Pqa7Qr2oEjJW_m84bq0EVtbGQmu5ZVKytj8tPkwWAUE8gTEtLOb1DjwDX5O8y8EHAN_8lf2ZqJ9eojMRDufJj2QObf0g02n3Q/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F645>.

>
> If l have to launch the whole dataset, is the bids script able to check what was already inserted in case there is an error and I have to it again?

Yes, the pipeline is supposed to be smart enough to not reinsert something that was previously inserted.

>
> 3. After insertion of BIDS for a subject in a visit I cannot access the visit in the front end, I am getting a 500 error. Here is the error log in LORIS:
>
> ===
> [Mon Jul 12 12:05:37.705967 2021] [php7:error] [pid 14497] [client 216.15.126.108:55424<http://secure-web.cisco.com/1WYhYdfRTqaTteJ_4rndbHmww7uTfLympsocUwkjHV2oHQVOQ_ddIjv7AcfCoiP5cJIbw5iksCEFI9RVOxA3_lM6etO-PCaDz89PgNjaEjQPMC5dEfLOft3B7YhP7TCF4ISn-hvCOCFnhQqmRbs9zS1PRbVr6qe_Fra0AR2dZzskzHnYp2A_u29fTzE5u8vYJLMpl4t10wah4Bga-hhoD3gkgnRHVU5KAWy4uwX30Ma4tng8DnVlqBopiM9DpYE6ZEviZpdmHvWqJZxPHxbnHOw/http%3A%2F%2F216.15.126.108%3A55424>] PHP Fatal error:  Uncaught TypeError: Return value of Utility::getStageUsingCandID() must be of the type string, null returned in /var/www
> /loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177): Utility::getStageUsingCandID('207019')\n#1 /var/www/loris/php/libraries/NDB_Page.class.inc(
> 707): LORIS\\instrument_list\\Instrument_List->setup()\n#2 /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234): NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3 /var/www/loris/src/Middleware/PageD
> ecorationMiddleware.php(56): LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#4 /var/www/loris/php/libraries/NDB_Page.class.i
> nc(692): LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#5 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(
> 137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on line 632, referer: https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/<https://secure-web.cisco.com/1XkKe3e3JkFCEbEAQx3rrZ25ZCaDXFH7ViiHfRCVtt0ZTI9ckG_4i5CYOnY_Wv0SYfmdvUUZ0jQkdjvUgzKY9qJfqnqcVF_7n2nRaR-c1a4U_Y95LN-Dv96I8j-OBHltZ52DoTaYZ9RvB7YL9vP82yG9pUb2XlYJwK6xA6b2gGwhHhyqpdrPfRW0HZFx4__6pDI4CU5CQWx9_dteaDW3_xjntBo3296km9H-nJNiywrGrKtv_1pO6wCU5ygXs2bqXwZ9j7X4eILwCv0N7S7PlKA/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fcandidate_profile%2F207019%2F>
> ===

This might be due to the Current_stage not being set when creating the visit via the bids_import.py script. Here is a PR to fix that issue next time you import a new visit via bids_import.py: https://github.com/aces/Loris-MRI/pull/644<https://secure-web.cisco.com/1RuRCEtVgtWrK7Pm95g10P8zRltmw5fqwt4wM4vzTM2N7zp7p8HXJKNSQo5QSAfOa23ID04z8m13DojdlnneipDRp6yoYNUJIoorexU5ixp49Alwi5aaHokrOmz-gRnpRkrUxMNI04i2tsCDBAsyiwIBoMwgWyCGHg8asEvLiHrEcYtWAdRycS4UQ7Udt6hrVhp6DqF6kpBH3s4oWPPlFvnJ9CHywNOno0NqHI0zXVnlWI2BuIW0heLJeaDSyrvK-5FcYxqhfnBEJTq1hkNB-Jg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F644>

Hope this helps,

C?cile

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From cecile.madjar at mcin.ca  Mon Jul 19 15:35:05 2021
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Mon, 19 Jul 2021 15:35:05 -0400
Subject: [Loris-dev] Questions and errors uploading BIDS
In-Reply-To: <BF655E11-66FE-4DC8-A419-C56862F54778@bwh.harvard.edu>
References: <A142044A-2953-4B49-97E9-3BF869202F7B@bwh.harvard.edu>
 <36E88E76-4736-42BF-9905-F0FDD987915F@bwh.harvard.edu>
 <CAMkiY3fPyON8j_dQ1NB5ndoC_hkmmYFZZ5wfiFswLf27GPeWVQ@mail.gmail.com>
 <8EED5B04-BBAB-46DD-AD83-F9A830C5B6FE@BWH.HARVARD.EDU>
 <CAMkiY3f8_bZxFJx8W5HFzzMPV8J_wB_BSPW=-ExmqA=WGSOdEA@mail.gmail.com>
 <B7DCD8E0-6D39-453A-99BB-5E1D4A13A8CF@bwh.harvard.edu>
 <CAMkiY3d0o34eZ5A9NN9RZX3UgcZz0MNLNNRtPfXULBhSqadsGg@mail.gmail.com>
 <BF655E11-66FE-4DC8-A419-C56862F54778@bwh.harvard.edu>
Message-ID: <CAMkiY3c5OYyMj-8jbvbVQRxyoR4jAzQmsC9JEMqM2rsWKnJVug@mail.gmail.com>

You can change the Current_stage to Not Started for those two visits then.

It should not be affecting the scan_acquisition_time since that information
is stored in parameter_file and not the session table.

Hope this helps,

C?cile

On Mon, Jul 19, 2021 at 3:07 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi C?cile,
>
> Yes, I think two out of three visits had Current_stage NULL, what should
> value should it be? Is it enough to change it from NULL to
> ?something_else??
>
> Does this impact the scan_acquisition_time?
>
> Best,
> Alfredo.
>
> On Jul 19, 2021, at 1:41 PM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> The issue here is that the first session has a Current_stage set as NULL.
> Maybe verify which session has Current_stage set to NULL. Maybe it comes
> from an old import?
>
> On Mon, Jul 19, 2021 at 11:41 AM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Hi C?cile,
>>
>> Thank you for the prompt reply. Here are the results for the queries:
>>
>> ===
>> SELECT pf.Value FROM parameter_file pf JOIN parameter_type pt USING
>> (ParameterTypeID) WHERE pt.Name="scan_acquisition_time" AND FileID=428983;
>> Empty set (0.00 sec)
>> ===
>>
>> ===
>> SELECT DISTINCT Current_stage FROM session WHERE CandID=207019;
>> +---------------+
>> | Current_stage |
>> +---------------+
>> | NULL          |
>> | Not Started   |
>> +---------------+
>> 2 rows in set (0.01 sec)
>> ===
>>
>> As I said before, we can have a call if this makes things easier and
>> faster.
>>
>> Best,
>> Alfredo.
>>
>> On Jul 19, 2021, at 11:26 AM, Cecile Madjar <cecile.madjar at mcin.ca>
>> wrote:
>>
>>         External Email - Use Caution
>>
>> Hi Alfredo,
>>
>> For the acquisition date, try the following query:
>> SELECT pf.Value FROM parameter_file pf JOIN parameter_type pt USING
>> (ParameterTypeID) WHERE pt.Name="scan_acquisition_time" AND FileID=428983;
>>
>> For 2., what does the following query return?
>> SELECT DISTINCT Current_stage FROM session WHERE CandID=207019;
>>
>> C?cile
>>
>> On Mon, Jul 19, 2021 at 11:19 AM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>>> Hi C?cile,
>>>
>>> I patched LORIS and inserted one visit.
>>>
>>> Before moving forward I want to make sure the acquisition date was
>>> inserted, could you please tell me what is the ?ParameterFileID? for the
>>> acquisition date, I looked at the table parameter_file using one of the
>>> FileIDs from the last insertion but couldn't find the acquisition date. See
>>> the result of the query below.
>>>
>>> 2. The front-end is still crashing. This is the log:
>>>
>>> ===
>>> [php7:error] [pid 32588] [client 155.33.137.12:23564
>>> <http://secure-web.cisco.com/1nROtbNw-Vzt6PDAU71bMpkZ2DX-C8_gGT7jPalLUwf7iW0vRUudY_S6vIhtCPN4YHMDNIlD9L_XfAEixBt2iRg_KHw6treMqgGID9xjB3xoxlLD2fhNblD3jlfGfUSZYqaMb2TZKSCJoVCGMoDx12cEmnzWRfPe2QxGRgwYHNP7Bf9SBcfWaAQ_ODCTQVBimXbr1NWavp5WNDM_hcGsLLupgF6xBbXBxr7s1e7BLCemInf4-AlIdok-y3-ZvC8BDdDbKsCs7sHYqn0gSK7YQsA/http%3A%2F%2F155.33.137.12%3A23564>]
>>> PHP Fatal error:  Uncaught TypeError: Return value of
>>> Utility::getStageUsingCandID() must be of the type string, null returned in
>>> /var/www/loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0
>>> /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177):
>>> Utility::getStageUsingCandID('207019')\n#1
>>> /var/www/loris/php/libraries/NDB_Page.class.inc(707):
>>> LORIS\\instrument_list\\Instrument_List->setup()\n#2
>>> /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234):
>>> NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3
>>> /var/www/loris/src/Middleware/PageDecorationMiddleware.php(56):
>>> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest),
>>> Object(LORIS\\instrument_list\\Instrument_List))\n#4
>>> /var/www/loris/php/libraries/NDB_Page.class.inc(692):
>>> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest),
>>> Object(LORIS\\instrument_list\\Instrument_List))\n#5
>>> /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(137):
>>> NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on line
>>> 632, referer:
>>> https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/
>>> <https://secure-web.cisco.com/1mVIQ6ONSXAF7-5MPbIxuWHNbxYUn-M6MiKm-VfZKDScn_0YJ02NPcV4p7rirYg2XnVfXdHzODTPAcrLuUItZ6KKzzEdJ2lQXp9ZTMufpswd6YsZlGwob5GriUoRzGl7WJKfUwk2hnizx5FQXgIT0jZjFQqSf0w-2sproV85wbmg5r4X4UtFMV9WCoOG__khDbsnWOcdGaPJHTS1tVcjVuS2tRv628XtslAP_5jnzzfTPMndhvwR3-tRMLUp_ptV7i_ww353-P3KHxecwTBVnXg/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fcandidate_profile%2F207019%2F>
>>> ===
>>>
>>> Happy to have a Zoom call if it helps.
>>>
>>> Thank you for your help.
>>>
>>> Best,
>>> Alfredo.
>>>
>>> ===
>>> select ParameterFileID,Value from parameter_file where FileID=428983;
>>>
>>> +-----------------+----------------------------------------------------------------------------------------------------------------------------------+
>>> | ParameterFileID | Value
>>>
>>>  |
>>>
>>> +-----------------+----------------------------------------------------------------------------------------------------------------------------------+
>>> |       109949932 | MR
>>>
>>> |
>>> |       109949967 | 130
>>>
>>>  |
>>> |       109949981 | 0.9765625
>>>
>>>  |
>>> |       109949977 | syngo_MR_A35_4VA35A
>>>
>>>  |
>>> |       109949958 | 12:13:34.360020
>>>
>>>  |
>>> |       109949968 | t1_RIPOSIZ.
>>>
>>>  |
>>> |       109949973 | SK_SP_OSP
>>>
>>>  |
>>> |       109949962 | 2D
>>>
>>> |
>>> |       109949960 | [0.999742, 0.000840254, 0.0226824, 1.88704e-10,
>>> 0.999315, -0.0370189]
>>>      |
>>> |       109949982 | 0.9765625
>>>
>>>  |
>>> |       109949975 | 5
>>>
>>>  |
>>> |       109949969 | CP_HeadArray
>>>
>>> |
>>> |       109949965 | 70.3125
>>>
>>>  |
>>> |       109949966 | i
>>>
>>>  |
>>> |       109949945 | 0.187383
>>>
>>> |
>>> |       109949978 | 3
>>>
>>>  |
>>> |       109949963 | 1.5
>>>
>>>  |
>>> |       109949976 | 3
>>>
>>>  |
>>> |       109949970 | 0.655
>>>
>>>  |
>>> |       109949964 | HFS
>>>
>>>  |
>>> |       109949974 | t1_RIPOSIZ.
>>>
>>>  |
>>> |       109949971 | SE
>>>
>>> |
>>> |       109949956 | 99
>>>
>>> |
>>> |       109949959 | 0.01
>>>
>>> |
>>> |       109949930 | Siemens
>>>
>>>  |
>>> |       109949957 | 1
>>>
>>>  |
>>> |       109949983 | 2.9999998
>>>
>>>  |
>>> |       109949985 |
>>> 207019/sub-ANOM_ses-endoftreatment_ce-Gd_run-1_T1w_ZZZ_check.png
>>>                                               |
>>> |       109949972 | _tse2d1_5
>>>
>>>  |
>>> |       109949914 | 20140629
>>>
>>> |
>>> |       109949915 | 99
>>>
>>> |
>>> |       109949916 | 1
>>>
>>>  |
>>> |       109949917 | 12:13:34.360020
>>>
>>>  |
>>> |       109949918 | 256
>>>
>>>  |
>>> |       109949919 | dcm2niix
>>>
>>> |
>>> |       109949920 | v1.0.20180622 (JP2:OpenJPEG) (JP-LS:CharLS) GCC7.3.0
>>>
>>> |
>>> |       109949921 | 0.01
>>>
>>> |
>>> |       109949923 | 150
>>>
>>>  |
>>> |       109949924 | [0.999742, 0.000840254, 0.0226824, 1.88704e-10,
>>> 0.999315, -0.0370189]
>>>      |
>>> |       109949925 | ['ORIGINAL', 'PRIMARY', 'M', 'ND']
>>>
>>> |
>>> |       109949926 | ROW
>>>
>>>  |
>>> |       109949928 | 2D
>>>
>>> |
>>> |       109949929 | 1.5
>>>
>>>  |
>>> |       109949931 | Sonata
>>>
>>> |
>>> |       109949933 | 1
>>>
>>>  |
>>> |       109949934 | HFS
>>>
>>>  |
>>> |       109949935 | 70.3125
>>>
>>>  |
>>> |       109949936 | i
>>>
>>>  |
>>> |       109949937 | 100
>>>
>>>  |
>>> |       109949938 | 0.55
>>>
>>> |
>>> |       109949939 | 130
>>>
>>>  |
>>> |       109949940 | t1_RIPOSIZ.
>>>
>>>  |
>>> |       109949941 | %SiemensSeq%_tse
>>>
>>> |
>>> |       109949942 | CP_HeadArray
>>>
>>> |
>>> |       109949943 | 512
>>>
>>>  |
>>> |       109949944 | 0.655
>>>
>>>  |
>>> |       109949946 | SE
>>>
>>> |
>>> |       109949947 | _tse2d1_5
>>>
>>>  |
>>> |       109949948 | SK_SP_OSP
>>>
>>>  |
>>> |       109949949 | t1_RIPOSIZ.
>>>
>>>  |
>>> |       109949950 | 5
>>>
>>>  |
>>> |       109949951 | [48, 57, 59, 361, 234, 67, -246, 256]
>>>
>>>  |
>>> |       109949952 | 3
>>>
>>>  |
>>> |       109949953 | syngo_MR_A35_4VA35A
>>>
>>>  |
>>> |       109949954 | 3
>>>
>>>  |
>>> |       109949955 | 202.922
>>>
>>>  |
>>> |       109949961 | ['ORIGINAL', 'PRIMARY', 'M', 'ND']
>>>
>>> |
>>> |       109949979 |
>>> bids_imports/INFORMS_BIDSVersion_1.4.0/sub-ANOM/ses-endoftreatment/anat/sub-ANOM_ses-endoftreatment_run-1_T1w.json
>>>     |
>>> |       109949980 |
>>> 7655f29d97c14a6b88055f99c7879097650c31cafa7405a1ad3a93062d04669417f42b67c175e9ad904da1e1bb677b2fb6a44ed8b26af482a4d3c40498f284df
>>> |
>>> |       109949984 |
>>> 3f487183fe830d801477568aec824c967a44d3bf3feb9cbd6575830d31b90b089cc625a037c487d3985fb10ee0a00f2eac824980955949c8955cdd304ea838b9
>>> |
>>> |       109949922 | 5
>>>
>>>  |
>>> |       109949927 | 1
>>>
>>>  |
>>>
>>> +-----------------+----------------------------------------------------------------------------------------------------------------------------------+
>>> ===
>>>
>>> This is the content of the *_scan.tsv file:
>>> ===
>>> filename        acq_time
>>> anat/sub-ANOM_ses-endoftreatment_run-1_T1w.nii.gz  2014-06-29T00:00:00
>>> anat/sub-ANOM_ses-endoftreatment_ce-Gd_run-1_T1w.nii.gz
>>>  2014-06-29T00:00:00
>>> anat/sub-ANOM_ses-endoftreatment_run-1_FLAIR.nii.gz
>>>  2014-06-29T00:00:00
>>> anat/sub-ANOM_ses-endoftreatment_ce-Gd_run-2_T1w.nii.gz
>>>  2014-06-29T00:00:00
>>> anat/sub-ANOM_ses-endoftreatment_run-1_PD.nii.gz   2014-06-29T00:00:00
>>> anat/sub-ANOM_ses-endoftreatment_run-1_T2w.nii.gz  2014-06-29T00:00:00
>>> ===
>>>
>>> On Jul 15, 2021, at 5:23 PM, Cecile Madjar <cecile.madjar at mcin.ca>
>>> wrote:
>>>
>>>         External Email - Use Caution
>>>
>>> Hi Alfredo,
>>>
>>> Sorry for the delay, I had to take a deeper look at the code to answer
>>> some of your questions. See below.
>>>
>>> > 1. I added the file sub-<label>[_ses-<label>]_scans.tsv as suggested
>>>> in the BIDS standard (
>>>> https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file
>>>> <https://secure-web.cisco.com/1RT0b_pDRzGh5oEnKt7wHclfIWMewUlzzoH-FStRocNdjI2mrpqsgr33eVaIS22zsvLSZ7Z8ugyaoZ07SHA_O7tObAB409DokII49oyHlFVQnGqaaxEoC_87rcI6ivzH41s36uv9R13FRzaiRJPDhbqmj3kt67BF36UEJp4e5xglyAHPcxx1DV8sf3sJ2TRBCKhNhHUWeRbPM9DdNrFxpoZzYHnN4xy-VMBRK5T9SF4afE6jv3tqdaKdfSYG2wDh-CWrIBbzyeSECIRnMYikelA/https%3A%2F%2Fbids-specification.readthedocs.io%2Fen%2Fstable%2F03-modality-agnostic-files.html%23scans-file>)
>>>> to add the acquisition dates, do you take it into account to set the dates
>>>> in LORIS? If not, how can I set the acquisition dates for the images in the
>>>> session/visit?
>>>>
>>>
>>> Indeed, if you enter a date under an 'acq_time' column in the scans.tsv
>>> file, it will add an entry in parameter_file for the scan_acquisition_time
>>> parameter.
>>>
>>>
>>>> >
>>>> > 2. I am doing the insertion visit by visit to be able to identify
>>>> issues instead of running all the subjects at once. In this approach I get
>>>> an error stating that the participants file
>>>> (".../data/bids_imports/INFORMS_BIDSVersion_1.4.0/participants.tsv") is
>>>> different from for every execution. Is there a way I can upload subject by
>>>> subject without having this issue?
>>>>
>>>
>>> yeah, this is a current limitation that this file keeps changing each
>>> time you upload a new candidate. The pipeline was initially developed for
>>> retrospective BIDS datasets. We would need to modify this part
>>> <https://secure-web.cisco.com/1FA74HdTiHzhrcJezSt2K6DKMGwP_wqxcdk1oXclu1U6jCz4rd2fSi-NwskWq_Qfb0p4MTUX6_XEbTFvgo_VxzSI4YiWtniz3W9Yi_Y_Yhd3GKBQD7kKnXK8l0jqEWj-6sZ77YTpIg9X5O235SfFeZ3JW3V5MFXQOH7vMnzgPDBS-6dsjvmCAtnAjP4DJoXkGwQ6VJLV21yWj9np6NfjWvjphVgXfpYnIoS4jb57yVl8xBW0ttGeejb-HEHsaZ-bNfre-16KCLmR-IJO3pZbnwg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fb5a6fc8cc3cf1fad50df21d9d87a284981705e3c%2Fpython%2Fbids_import.py%23L299> for
>>> prospective datasets so that instead of just trying to copy the
>>> participants.tsv file, if it already exists, it would append a row into the
>>> already existing file. You can find a fix for that in the following PR
>>> https://github.com/aces/Loris-MRI/pull/645
>>> <https://secure-web.cisco.com/1Tpg7v8DtF0HJJEnPZUNGN7gwCdF7vLrM19WZmYU8p4-riYcbJ1FVNYH0FGEvIBT0KwSYUMgtVeulxeEaGSohphmm0NQn8wIbxh5cSX4VwbKcKLhvQY1RtnS2SxEKUi4Pln5KHxRYDcVhz9sWnZ6EIhfZEDECvkuT2-zTt24B5MMeBduiQG8W3Pqa7Qr2oEjJW_m84bq0EVtbGQmu5ZVKytj8tPkwWAUE8gTEtLOb1DjwDX5O8y8EHAN_8lf2ZqJ9eojMRDufJj2QObf0g02n3Q/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F645>
>>> .
>>>
>>>
>>>> >
>>>> > If l have to launch the whole dataset, is the bids script able to
>>>> check what was already inserted in case there is an error and I have to it
>>>> again?
>>>>
>>>
>>> Yes, the pipeline is supposed to be smart enough to not reinsert
>>> something that was previously inserted.
>>>
>>>
>>>> >
>>>> > 3. After insertion of BIDS for a subject in a visit I cannot access
>>>> the visit in the front end, I am getting a 500 error. Here is the error log
>>>> in LORIS:
>>>> >
>>>> > ===
>>>> > [Mon Jul 12 12:05:37.705967 2021] [php7:error] [pid 14497] [client
>>>> 216.15.126.108:55424
>>>> <http://secure-web.cisco.com/1WYhYdfRTqaTteJ_4rndbHmww7uTfLympsocUwkjHV2oHQVOQ_ddIjv7AcfCoiP5cJIbw5iksCEFI9RVOxA3_lM6etO-PCaDz89PgNjaEjQPMC5dEfLOft3B7YhP7TCF4ISn-hvCOCFnhQqmRbs9zS1PRbVr6qe_Fra0AR2dZzskzHnYp2A_u29fTzE5u8vYJLMpl4t10wah4Bga-hhoD3gkgnRHVU5KAWy4uwX30Ma4tng8DnVlqBopiM9DpYE6ZEviZpdmHvWqJZxPHxbnHOw/http%3A%2F%2F216.15.126.108%3A55424>]
>>>> PHP Fatal error:  Uncaught TypeError: Return value of
>>>> Utility::getStageUsingCandID() must be of the type string, null returned in
>>>> /var/www
>>>> > /loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0
>>>> /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177):
>>>> Utility::getStageUsingCandID('207019')\n#1
>>>> /var/www/loris/php/libraries/NDB_Page.class.inc(
>>>> > 707): LORIS\\instrument_list\\Instrument_List->setup()\n#2
>>>> /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234):
>>>> NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3
>>>> /var/www/loris/src/Middleware/PageD
>>>> > ecorationMiddleware.php(56):
>>>> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest),
>>>> Object(LORIS\\instrument_list\\Instrument_List))\n#4
>>>> /var/www/loris/php/libraries/NDB_Page.class.i
>>>> > nc(692):
>>>> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest),
>>>> Object(LORIS\\instrument_list\\Instrument_List))\n#5
>>>> /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(
>>>> > 137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc
>>>> on line 632, referer:
>>>> https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/
>>>> <https://secure-web.cisco.com/1XkKe3e3JkFCEbEAQx3rrZ25ZCaDXFH7ViiHfRCVtt0ZTI9ckG_4i5CYOnY_Wv0SYfmdvUUZ0jQkdjvUgzKY9qJfqnqcVF_7n2nRaR-c1a4U_Y95LN-Dv96I8j-OBHltZ52DoTaYZ9RvB7YL9vP82yG9pUb2XlYJwK6xA6b2gGwhHhyqpdrPfRW0HZFx4__6pDI4CU5CQWx9_dteaDW3_xjntBo3296km9H-nJNiywrGrKtv_1pO6wCU5ygXs2bqXwZ9j7X4eILwCv0N7S7PlKA/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fcandidate_profile%2F207019%2F>
>>>> > ===
>>>>
>>>
>>> This might be due to the Current_stage not being set when creating the
>>> visit via the bids_import.py script. Here is a PR to fix that issue next
>>> time you import a new visit via bids_import.py:
>>> https://github.com/aces/Loris-MRI/pull/644
>>> <https://secure-web.cisco.com/1RuRCEtVgtWrK7Pm95g10P8zRltmw5fqwt4wM4vzTM2N7zp7p8HXJKNSQo5QSAfOa23ID04z8m13DojdlnneipDRp6yoYNUJIoorexU5ixp49Alwi5aaHokrOmz-gRnpRkrUxMNI04i2tsCDBAsyiwIBoMwgWyCGHg8asEvLiHrEcYtWAdRycS4UQ7Udt6hrVhp6DqF6kpBH3s4oWPPlFvnJ9CHywNOno0NqHI0zXVnlWI2BuIW0heLJeaDSyrvK-5FcYxqhfnBEJTq1hkNB-Jg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F644>
>>>
>>>
>>> Hope this helps,
>>>
>>> C?cile
>>>
>>>
>>> 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/12oS_QzclpiQcg_5CjSIubWkQntHnTzqFtBX6mIpa2UBfLh0PVFbNhw3IdXKR4AZ34z6Y4oONHxNl8RPg_-v5rbGH1bm25TzFr3nnHzzX-JiG9TdS5w_tGDS8dGTAdqHOqRD0y6Fn6ceB81q-IYVyZxyd-oWY8_bD4W7nK_hFDdMGi_GjLB5Qm-Opov0A6h0QkxNvnxJQpq85R1ace87QLIkJNTDBloRdcjKgYJm3NLT9JbBe-uOsotk5sBO21JKnuVHFKcIakn138zVhP4vF1A/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/115fegSDBx-RMF0OZa7z6f9XwFGUk4Xam4Sg3xrPrQuji2Bvh1lzopdqWHKdnV8zxQteTdJOU3ULO9w9ar4RPfujGMZNU4ZYBb_HGdeZJ0wf4RSY0bGkgL7GKZRGpDZSXpq8AaFc1gToO4pT-kmlfh92gKSzFA1YzUI_zbDopunD0mu6OjMATfN0ZNZIgVFbFJBejtS_KWpqpqE1IzO0K55Af2GEQ19VfRXJ8BT-tIHLbnb_pNiQeP6xHCAOajKtX3JkHm27p6yYfPjQz0c6pZA/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.
>
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From ayshjag at umich.edu  Mon Jul 19 15:57:15 2021
From: ayshjag at umich.edu (Ayshwarya Jagadeesan)
Date: Mon, 19 Jul 2021 15:57:15 -0400
Subject: [Loris-dev] Loris
Message-ID: <CACkoWBGMvrLn7d6v+ottRTL8i-OaYad3cbUHWuSarh36WeFqxQ@mail.gmail.com>

Hi,

I am trying to update from an very old version of Loris to newer version of
Loris. The newer version has lot of me functionalities. I tried following
the wiki documentation ,I was able to create the instruments, but was not
able to populate the instrument for the visit for a particular candidate.
I have a feel I am missing something.Any help would be greatly appreciated.
Thanks,
Ayshwarya.J
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From rogers at bic.mni.mcgill.ca  Mon Jul 19 16:10:35 2021
From: rogers at bic.mni.mcgill.ca (Christine Rogers)
Date: Mon, 19 Jul 2021 16:10:35 -0400
Subject: [Loris-dev] Loris
In-Reply-To: <CACkoWBGMvrLn7d6v+ottRTL8i-OaYad3cbUHWuSarh36WeFqxQ@mail.gmail.com>
References: <CACkoWBGMvrLn7d6v+ottRTL8i-OaYad3cbUHWuSarh36WeFqxQ@mail.gmail.com>
Message-ID: <CALbt7NBVrmT6MmPqXcOinCuwakB9eVpp953HXM-Y3QeJFALWAA@mail.gmail.com>

Hi Ayshwarya,
Thanks for reaching out, and glad to hear you're updating an existing LORIS
to include some of our new features.

Could you kindly let us know a few things to start  --
What version of LORIS did you upgrade from, and to?  (e.g .19.0.2 to 23.0.4
)

If you try running the *assign_missing_instruments.php *script (under the
tools directory), does it identify the missing instruments correctly?
If not, your battery may not be completely configured.  Let us know a
specific example and what output or error messaging you're seeing,
including in the apache error log.

In case you were wondering about the upgrade process, let us know --:
- Did you follow the release upgrade steps for each incremental release?
(this includes running patches, updating dependencies and sometimes
scripts). You'll likely want to note in particular any steps impacting
instrument battery definition.
- Have you updated php and run npm ?

Thanks,
Christine
on behalf of the LORIS team




On Mon, Jul 19, 2021 at 3:57 PM Ayshwarya Jagadeesan <ayshjag at umich.edu>
wrote:

> Hi,
>
> I am trying to update from an very old version of Loris to newer version
> of Loris. The newer version has lot of me functionalities. I tried
> following the wiki documentation ,I was able to create the instruments, but
> was not able to populate the instrument for the visit for a particular
> candidate.
> I have a feel I am missing something.Any help would be greatly appreciated.
> Thanks,
> Ayshwarya.J
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>


-- 
Research Project Officer
christine.rogers at mcgill.ca
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute-Hospital
McGill University | Montreal | Canada
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From rogers at bic.mni.mcgill.ca  Tue Jul 20 12:26:54 2021
From: rogers at bic.mni.mcgill.ca (Christine Rogers)
Date: Tue, 20 Jul 2021 12:26:54 -0400
Subject: [Loris-dev] Loris
In-Reply-To: <3f109c08b4794a6cb539db7e870242fd@med.umich.edu>
References: <CACkoWBGMvrLn7d6v+ottRTL8i-OaYad3cbUHWuSarh36WeFqxQ@mail.gmail.com>
 <CALbt7NBVrmT6MmPqXcOinCuwakB9eVpp953HXM-Y3QeJFALWAA@mail.gmail.com>
 <3f109c08b4794a6cb539db7e870242fd@med.umich.edu>
Message-ID: <CALbt7NB_M8b0cb0JVVVaiT0mLhHZ4LKpuZnKEdTpo9P-ywW-=w@mail.gmail.com>

Hi Ayshwarya,
I'm replying-all for community benefit, and so that team members can
provide additional answers --

It's great that you've already installed 22.0.1, and we recommend you
install the most recent release - 23.0.4 -  since we will support that best
for any questions you have.

To start, install 23.0.4 on your new VM.  Create a mysql dump of the old
database, copy that to the new VM, and source it there. Then follow the
release upgrade steps (as you found in our wiki page
<https://github.com/aces/Loris/wiki/Updating-your-LORIS>) and source
every release
upgrade patch <https://github.com/aces/Loris/tree/main/SQL/Release_patches> in
order to bring the old database up to date.  Please follow the Release notes
<https://github.com/aces/Loris/releases> along the way for any additional
steps or scripts.   It's also a good idea to double-check your dependency
versions --

Let us know if these are the steps you followed, and then send us
output/error messages you're getting. e.g. for the front end, please check
the apache error logs.

A few additional questions about the old project:
- How much data do you have?  ( both gb of imaging files, and number of
candidates/visits/instruments).
- Are there any code customizations
<https://github.com/aces/Loris/wiki/Code-Customization> in the
project/libraries and project/templates directory that override the LORIS
codebase?  This can include new modules or just changes to modules --
consult your project's specific documentation, so you can plan to update
these functionalities for the current LORIS architecture.

Best,
Christine







On Mon, Jul 19, 2021 at 4:30 PM Jagadeesan, Ayshwarya <ayshjag at med.umich.edu>
wrote:

> Hi Christine,
>
>
> Thank you for your reply.
>
>
> The old version I want to update is 14.12.1
>
> The new version is  the new LORIS ,that I hosted in a new server, the
> version Loris version is v22.0.1
>
> I tried '*assign_missing_instruments.php' * script. The script returns me
> nothing, since it is a brand new database.
>
>
> Please kindly let me know what should be done. Any video explanation will
> also help.
>
> Thanks,
>
> Ayshwarya.J
>
>
> ------------------------------
> *From:* Christine Rogers <rogers at bic.mni.mcgill.ca>
> *Sent:* Monday, July 19, 2021 4:10:35 PM
> *To:* Ayshwarya Jagadeesan
> *Cc:* loris-dev at bic.mni.mcgill.ca
> *Subject:* Re: [Loris-dev] Loris
>
> *External Email - Use Caution *
> Hi Ayshwarya,
> Thanks for reaching out, and glad to hear you're updating an existing
> LORIS to include some of our new features.
>
> Could you kindly let us know a few things to start  --
> What version of LORIS did you upgrade from, and to?  (e.g .19.0.2 to
> 23.0.4 )
>
> If you try running the *assign_missing_instruments.php *script (under the
> tools directory), does it identify the missing instruments correctly?
> If not, your battery may not be completely configured.  Let us know a
> specific example and what output or error messaging you're seeing,
> including in the apache error log.
>
> In case you were wondering about the upgrade process, let us know --:
> - Did you follow the release upgrade steps for each incremental release?
> (this includes running patches, updating dependencies and sometimes
> scripts). You'll likely want to note in particular any steps impacting
> instrument battery definition.
> - Have you updated php and run npm ?
>
> Thanks,
> Christine
> on behalf of the LORIS team
>
>
>
>
> On Mon, Jul 19, 2021 at 3:57 PM Ayshwarya Jagadeesan <ayshjag at umich.edu>
> wrote:
>
>> Hi,
>>
>> I am trying to update from an very old version of Loris to newer version
>> of Loris. The newer version has lot of me functionalities. I tried
>> following the wiki documentation ,I was able to create the instruments, but
>> was not able to populate the instrument for the visit for a particular
>> candidate.
>> I have a feel I am missing something.Any help would be greatly
>> appreciated.
>> Thanks,
>> Ayshwarya.J
>> _______________________________________________
>> Loris-dev mailing list
>> Loris-dev at bic.mni.mcgill.ca
>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>
>
>
> --
> Research Project Officer
> christine.rogers at mcgill.ca
> McGill Centre for Integrative Neuroscience | MCIN.ca
> Montreal Neurological Institute-Hospital
> McGill University | Montreal | Canada
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not
> be used for urgent or sensitive issues
>


-- 
Research Project Officer
christine.rogers at mcgill.ca
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute-Hospital
McGill University | Montreal | Canada
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From AMORALESPINZON at BWH.HARVARD.EDU  Fri Jul 23 10:57:55 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Fri, 23 Jul 2021 14:57:55 +0000
Subject: [Loris-dev] Questions and errors uploading BIDS
In-Reply-To: <CAMkiY3c5OYyMj-8jbvbVQRxyoR4jAzQmsC9JEMqM2rsWKnJVug@mail.gmail.com>
References: <A142044A-2953-4B49-97E9-3BF869202F7B@bwh.harvard.edu>
 <36E88E76-4736-42BF-9905-F0FDD987915F@bwh.harvard.edu>
 <CAMkiY3fPyON8j_dQ1NB5ndoC_hkmmYFZZ5wfiFswLf27GPeWVQ@mail.gmail.com>
 <8EED5B04-BBAB-46DD-AD83-F9A830C5B6FE@BWH.HARVARD.EDU>
 <CAMkiY3f8_bZxFJx8W5HFzzMPV8J_wB_BSPW=-ExmqA=WGSOdEA@mail.gmail.com>
 <B7DCD8E0-6D39-453A-99BB-5E1D4A13A8CF@bwh.harvard.edu>
 <CAMkiY3d0o34eZ5A9NN9RZX3UgcZz0MNLNNRtPfXULBhSqadsGg@mail.gmail.com>
 <BF655E11-66FE-4DC8-A419-C56862F54778@bwh.harvard.edu>
 <CAMkiY3c5OYyMj-8jbvbVQRxyoR4jAzQmsC9JEMqM2rsWKnJVug@mail.gmail.com>
Message-ID: <CBA46B74-F068-4598-B897-CE31C3014430@bwh.harvard.edu>

Hi C?cile,

I changed the Current_stage to Not Started for the visits that had it in NULL. Now I can see all the visits in the front-end. Thank you!

Regarding the scan_acquisition_time, would it be possible to debug it over a Zoom call. As I mentioned I have in place the file *_scans.tsv but the acquisition date is not in the database after insertion.

Best,
Alfredo.

On Jul 19, 2021, at 3:35 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

You can change the Current_stage to Not Started for those two visits then.

It should not be affecting the scan_acquisition_time since that information is stored in parameter_file and not the session table.

Hope this helps,

C?cile

On Mon, Jul 19, 2021 at 3:07 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Yes, I think two out of three visits had Current_stage NULL, what should value should it be? Is it enough to change it from NULL to ?something_else??

Does this impact the scan_acquisition_time?

Best,
Alfredo.

On Jul 19, 2021, at 1:41 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

The issue here is that the first session has a Current_stage set as NULL. Maybe verify which session has Current_stage set to NULL. Maybe it comes from an old import?

On Mon, Jul 19, 2021 at 11:41 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Thank you for the prompt reply. Here are the results for the queries:

===
SELECT pf.Value FROM parameter_file pf JOIN parameter_type pt USING (ParameterTypeID) WHERE pt.Name="scan_acquisition_time" AND FileID=428983;
Empty set (0.00 sec)
===

===
SELECT DISTINCT Current_stage FROM session WHERE CandID=207019;
+---------------+
| Current_stage |
+---------------+
| NULL          |
| Not Started   |
+---------------+
2 rows in set (0.01 sec)
===

As I said before, we can have a call if this makes things easier and faster.

Best,
Alfredo.

On Jul 19, 2021, at 11:26 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

For the acquisition date, try the following query:
SELECT pf.Value FROM parameter_file pf JOIN parameter_type pt USING (ParameterTypeID) WHERE pt.Name="scan_acquisition_time" AND FileID=428983;

For 2., what does the following query return?
SELECT DISTINCT Current_stage FROM session WHERE CandID=207019;

C?cile

On Mon, Jul 19, 2021 at 11:19 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I patched LORIS and inserted one visit.

Before moving forward I want to make sure the acquisition date was inserted, could you please tell me what is the ?ParameterFileID? for the acquisition date, I looked at the table parameter_file using one of the FileIDs from the last insertion but couldn't find the acquisition date. See the result of the query below.

2. The front-end is still crashing. This is the log:

===
[php7:error] [pid 32588] [client 155.33.137.12:23564<http://secure-web.cisco.com/1nROtbNw-Vzt6PDAU71bMpkZ2DX-C8_gGT7jPalLUwf7iW0vRUudY_S6vIhtCPN4YHMDNIlD9L_XfAEixBt2iRg_KHw6treMqgGID9xjB3xoxlLD2fhNblD3jlfGfUSZYqaMb2TZKSCJoVCGMoDx12cEmnzWRfPe2QxGRgwYHNP7Bf9SBcfWaAQ_ODCTQVBimXbr1NWavp5WNDM_hcGsLLupgF6xBbXBxr7s1e7BLCemInf4-AlIdok-y3-ZvC8BDdDbKsCs7sHYqn0gSK7YQsA/http%3A%2F%2F155.33.137.12%3A23564>] PHP Fatal error:  Uncaught TypeError: Return value of Utility::getStageUsingCandID() must be of the type string, null returned in /var/www/loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177): Utility::getStageUsingCandID('207019')\n#1 /var/www/loris/php/libraries/NDB_Page.class.inc(707): LORIS\\instrument_list\\Instrument_List->setup()\n#2 /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234): NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3 /var/www/loris/src/Middleware/PageDecorationMiddleware.php(56): LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#4 /var/www/loris/php/libraries/NDB_Page.class.inc(692): LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#5 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on line 632, referer: https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/<https://secure-web.cisco.com/1mVIQ6ONSXAF7-5MPbIxuWHNbxYUn-M6MiKm-VfZKDScn_0YJ02NPcV4p7rirYg2XnVfXdHzODTPAcrLuUItZ6KKzzEdJ2lQXp9ZTMufpswd6YsZlGwob5GriUoRzGl7WJKfUwk2hnizx5FQXgIT0jZjFQqSf0w-2sproV85wbmg5r4X4UtFMV9WCoOG__khDbsnWOcdGaPJHTS1tVcjVuS2tRv628XtslAP_5jnzzfTPMndhvwR3-tRMLUp_ptV7i_ww353-P3KHxecwTBVnXg/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fcandidate_profile%2F207019%2F>
===

Happy to have a Zoom call if it helps.

Thank you for your help.

Best,
Alfredo.

===
select ParameterFileID,Value from parameter_file where FileID=428983;
+-----------------+----------------------------------------------------------------------------------------------------------------------------------+
| ParameterFileID | Value                                                                                                                            |
+-----------------+----------------------------------------------------------------------------------------------------------------------------------+
|       109949932 | MR                                                                                                                               |
|       109949967 | 130                                                                                                                              |
|       109949981 | 0.9765625                                                                                                                        |
|       109949977 | syngo_MR_A35_4VA35A                                                                                                              |
|       109949958 | 12:13:34.360020                                                                                                                  |
|       109949968 | t1_RIPOSIZ.                                                                                                                      |
|       109949973 | SK_SP_OSP                                                                                                                        |
|       109949962 | 2D                                                                                                                               |
|       109949960 | [0.999742, 0.000840254, 0.0226824, 1.88704e-10, 0.999315, -0.0370189]                                                            |
|       109949982 | 0.9765625                                                                                                                        |
|       109949975 | 5                                                                                                                                |
|       109949969 | CP_HeadArray                                                                                                                     |
|       109949965 | 70.3125                                                                                                                          |
|       109949966 | i                                                                                                                                |
|       109949945 | 0.187383                                                                                                                         |
|       109949978 | 3                                                                                                                                |
|       109949963 | 1.5                                                                                                                              |
|       109949976 | 3                                                                                                                                |
|       109949970 | 0.655                                                                                                                            |
|       109949964 | HFS                                                                                                                              |
|       109949974 | t1_RIPOSIZ.                                                                                                                      |
|       109949971 | SE                                                                                                                               |
|       109949956 | 99                                                                                                                               |
|       109949959 | 0.01                                                                                                                             |
|       109949930 | Siemens                                                                                                                          |
|       109949957 | 1                                                                                                                                |
|       109949983 | 2.9999998                                                                                                                        |
|       109949985 | 207019/sub-ANOM_ses-endoftreatment_ce-Gd_run-1_T1w_ZZZ_check.png                                                         |
|       109949972 | _tse2d1_5                                                                                                                        |
|       109949914 | 20140629                                                                                                                         |
|       109949915 | 99                                                                                                                               |
|       109949916 | 1                                                                                                                                |
|       109949917 | 12:13:34.360020                                                                                                                  |
|       109949918 | 256                                                                                                                              |
|       109949919 | dcm2niix                                                                                                                         |
|       109949920 | v1.0.20180622 (JP2:OpenJPEG) (JP-LS:CharLS) GCC7.3.0                                                                             |
|       109949921 | 0.01                                                                                                                             |
|       109949923 | 150                                                                                                                              |
|       109949924 | [0.999742, 0.000840254, 0.0226824, 1.88704e-10, 0.999315, -0.0370189]                                                            |
|       109949925 | ['ORIGINAL', 'PRIMARY', 'M', 'ND']                                                                                               |
|       109949926 | ROW                                                                                                                              |
|       109949928 | 2D                                                                                                                               |
|       109949929 | 1.5                                                                                                                              |
|       109949931 | Sonata                                                                                                                           |
|       109949933 | 1                                                                                                                                |
|       109949934 | HFS                                                                                                                              |
|       109949935 | 70.3125                                                                                                                          |
|       109949936 | i                                                                                                                                |
|       109949937 | 100                                                                                                                              |
|       109949938 | 0.55                                                                                                                             |
|       109949939 | 130                                                                                                                              |
|       109949940 | t1_RIPOSIZ.                                                                                                                      |
|       109949941 | %SiemensSeq%_tse                                                                                                                 |
|       109949942 | CP_HeadArray                                                                                                                     |
|       109949943 | 512                                                                                                                              |
|       109949944 | 0.655                                                                                                                            |
|       109949946 | SE                                                                                                                               |
|       109949947 | _tse2d1_5                                                                                                                        |
|       109949948 | SK_SP_OSP                                                                                                                        |
|       109949949 | t1_RIPOSIZ.                                                                                                                      |
|       109949950 | 5                                                                                                                                |
|       109949951 | [48, 57, 59, 361, 234, 67, -246, 256]                                                                                            |
|       109949952 | 3                                                                                                                                |
|       109949953 | syngo_MR_A35_4VA35A                                                                                                              |
|       109949954 | 3                                                                                                                                |
|       109949955 | 202.922                                                                                                                          |
|       109949961 | ['ORIGINAL', 'PRIMARY', 'M', 'ND']                                                                                               |
|       109949979 | bids_imports/INFORMS_BIDSVersion_1.4.0/sub-ANOM/ses-endoftreatment/anat/sub-ANOM_ses-endoftreatment_run-1_T1w.json     |
|       109949980 | 7655f29d97c14a6b88055f99c7879097650c31cafa7405a1ad3a93062d04669417f42b67c175e9ad904da1e1bb677b2fb6a44ed8b26af482a4d3c40498f284df |
|       109949984 | 3f487183fe830d801477568aec824c967a44d3bf3feb9cbd6575830d31b90b089cc625a037c487d3985fb10ee0a00f2eac824980955949c8955cdd304ea838b9 |
|       109949922 | 5                                                                                                                                |
|       109949927 | 1                                                                                                                                |
+-----------------+----------------------------------------------------------------------------------------------------------------------------------+
===

This is the content of the *_scan.tsv file:
===
filename        acq_time
anat/sub-ANOM_ses-endoftreatment_run-1_T1w.nii.gz  2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_ce-Gd_run-1_T1w.nii.gz    2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_run-1_FLAIR.nii.gz        2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_ce-Gd_run-2_T1w.nii.gz    2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_run-1_PD.nii.gz   2014-06-29T00:00:00
anat/sub-ANOM_ses-endoftreatment_run-1_T2w.nii.gz  2014-06-29T00:00:00
===

On Jul 15, 2021, at 5:23 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Sorry for the delay, I had to take a deeper look at the code to answer some of your questions. See below.

> 1. I added the file sub-<label>[_ses-<label>]_scans.tsv as suggested in the BIDS standard (https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file<https://secure-web.cisco.com/1RT0b_pDRzGh5oEnKt7wHclfIWMewUlzzoH-FStRocNdjI2mrpqsgr33eVaIS22zsvLSZ7Z8ugyaoZ07SHA_O7tObAB409DokII49oyHlFVQnGqaaxEoC_87rcI6ivzH41s36uv9R13FRzaiRJPDhbqmj3kt67BF36UEJp4e5xglyAHPcxx1DV8sf3sJ2TRBCKhNhHUWeRbPM9DdNrFxpoZzYHnN4xy-VMBRK5T9SF4afE6jv3tqdaKdfSYG2wDh-CWrIBbzyeSECIRnMYikelA/https%3A%2F%2Fbids-specification.readthedocs.io%2Fen%2Fstable%2F03-modality-agnostic-files.html%23scans-file>) to add the acquisition dates, do you take it into account to set the dates in LORIS? If not, how can I set the acquisition dates for the images in the session/visit?

Indeed, if you enter a date under an 'acq_time' column in the scans.tsv file, it will add an entry in parameter_file for the scan_acquisition_time parameter.

>
> 2. I am doing the insertion visit by visit to be able to identify issues instead of running all the subjects at once. In this approach I get an error stating that the participants file (".../data/bids_imports/INFORMS_BIDSVersion_1.4.0/participants.tsv") is different from for every execution. Is there a way I can upload subject by subject without having this issue?

yeah, this is a current limitation that this file keeps changing each time you upload a new candidate. The pipeline was initially developed for retrospective BIDS datasets. We would need to modify this part<https://secure-web.cisco.com/1FA74HdTiHzhrcJezSt2K6DKMGwP_wqxcdk1oXclu1U6jCz4rd2fSi-NwskWq_Qfb0p4MTUX6_XEbTFvgo_VxzSI4YiWtniz3W9Yi_Y_Yhd3GKBQD7kKnXK8l0jqEWj-6sZ77YTpIg9X5O235SfFeZ3JW3V5MFXQOH7vMnzgPDBS-6dsjvmCAtnAjP4DJoXkGwQ6VJLV21yWj9np6NfjWvjphVgXfpYnIoS4jb57yVl8xBW0ttGeejb-HEHsaZ-bNfre-16KCLmR-IJO3pZbnwg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fb5a6fc8cc3cf1fad50df21d9d87a284981705e3c%2Fpython%2Fbids_import.py%23L299> for prospective datasets so that instead of just trying to copy the participants.tsv file, if it already exists, it would append a row into the already existing file. You can find a fix for that in the following PR https://github.com/aces/Loris-MRI/pull/645<https://secure-web.cisco.com/1Tpg7v8DtF0HJJEnPZUNGN7gwCdF7vLrM19WZmYU8p4-riYcbJ1FVNYH0FGEvIBT0KwSYUMgtVeulxeEaGSohphmm0NQn8wIbxh5cSX4VwbKcKLhvQY1RtnS2SxEKUi4Pln5KHxRYDcVhz9sWnZ6EIhfZEDECvkuT2-zTt24B5MMeBduiQG8W3Pqa7Qr2oEjJW_m84bq0EVtbGQmu5ZVKytj8tPkwWAUE8gTEtLOb1DjwDX5O8y8EHAN_8lf2ZqJ9eojMRDufJj2QObf0g02n3Q/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F645>.

>
> If l have to launch the whole dataset, is the bids script able to check what was already inserted in case there is an error and I have to it again?

Yes, the pipeline is supposed to be smart enough to not reinsert something that was previously inserted.

>
> 3. After insertion of BIDS for a subject in a visit I cannot access the visit in the front end, I am getting a 500 error. Here is the error log in LORIS:
>
> ===
> [Mon Jul 12 12:05:37.705967 2021] [php7:error] [pid 14497] [client 216.15.126.108:55424<http://secure-web.cisco.com/1WYhYdfRTqaTteJ_4rndbHmww7uTfLympsocUwkjHV2oHQVOQ_ddIjv7AcfCoiP5cJIbw5iksCEFI9RVOxA3_lM6etO-PCaDz89PgNjaEjQPMC5dEfLOft3B7YhP7TCF4ISn-hvCOCFnhQqmRbs9zS1PRbVr6qe_Fra0AR2dZzskzHnYp2A_u29fTzE5u8vYJLMpl4t10wah4Bga-hhoD3gkgnRHVU5KAWy4uwX30Ma4tng8DnVlqBopiM9DpYE6ZEviZpdmHvWqJZxPHxbnHOw/http%3A%2F%2F216.15.126.108%3A55424>] PHP Fatal error:  Uncaught TypeError: Return value of Utility::getStageUsingCandID() must be of the type string, null returned in /var/www
> /loris/php/libraries/Utility.class.inc:632\nStack trace:\n#0 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(177): Utility::getStageUsingCandID('207019')\n#1 /var/www/loris/php/libraries/NDB_Page.class.inc(
> 707): LORIS\\instrument_list\\Instrument_List->setup()\n#2 /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(234): NDB_Page->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#3 /var/www/loris/src/Middleware/PageD
> ecorationMiddleware.php(56): LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#4 /var/www/loris/php/libraries/NDB_Page.class.i
> nc(692): LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Laminas\\Diactoros\\ServerRequest), Object(LORIS\\instrument_list\\Instrument_List))\n#5 /var/www/loris/modules/instrument_list/php/instrument_list.class.inc(
> 137): NDB_Page->pro in /var/www/loris/php/libraries/Utility.class.inc on line 632, referer: https://ipmsa-loris.bic.mni.mcgill.ca/candidate_profile/207019/<https://secure-web.cisco.com/1XkKe3e3JkFCEbEAQx3rrZ25ZCaDXFH7ViiHfRCVtt0ZTI9ckG_4i5CYOnY_Wv0SYfmdvUUZ0jQkdjvUgzKY9qJfqnqcVF_7n2nRaR-c1a4U_Y95LN-Dv96I8j-OBHltZ52DoTaYZ9RvB7YL9vP82yG9pUb2XlYJwK6xA6b2gGwhHhyqpdrPfRW0HZFx4__6pDI4CU5CQWx9_dteaDW3_xjntBo3296km9H-nJNiywrGrKtv_1pO6wCU5ygXs2bqXwZ9j7X4eILwCv0N7S7PlKA/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fcandidate_profile%2F207019%2F>
> ===

This might be due to the Current_stage not being set when creating the visit via the bids_import.py script. Here is a PR to fix that issue next time you import a new visit via bids_import.py: https://github.com/aces/Loris-MRI/pull/644<https://secure-web.cisco.com/1RuRCEtVgtWrK7Pm95g10P8zRltmw5fqwt4wM4vzTM2N7zp7p8HXJKNSQo5QSAfOa23ID04z8m13DojdlnneipDRp6yoYNUJIoorexU5ixp49Alwi5aaHokrOmz-gRnpRkrUxMNI04i2tsCDBAsyiwIBoMwgWyCGHg8asEvLiHrEcYtWAdRycS4UQ7Udt6hrVhp6DqF6kpBH3s4oWPPlFvnJ9CHywNOno0NqHI0zXVnlWI2BuIW0heLJeaDSyrvK-5FcYxqhfnBEJTq1hkNB-Jg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F644>

Hope this helps,

C?cile

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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/1DuGeL6ukT-h5rrq0xxRXGA9OhaQ1ml18He9vyWuEEo6NnR3iTE5ZoIN5VgKkSlmL7h1LH3Ga75RFJNERZkLAz3zewuS2qhCrAIXqy4ZXTNVlA4loK8X6q3ILBHSzIZdi3i0E5JQzbZu29cj6sbcYEow9fVyh-zccYRbPVIIzZUGgDnExYl4cr0_O9Yw6LpJ28qIRDdvip2cAIBbemL5dr3k3v6gwx1C7QEIsvmZI8u1X0bBV5qe7AEYs4X3eCPVzcpAJ1tIawvW0SYqbzZDwOA/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. 
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