[Loris-dev] Questions and errors uploading BIDS

[Morales Pinzon, Alfredo]

Hi Cécile,

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.