[Loris-dev] troubleshooting MRI upload via image uploader and registering instrument in backend

[Mouna Safi-Harab]

Hi Carolina,


I will try to address the first point, and let someone else in the Loris team address the second.


For the prod file error, I have seen this and it can be caused by multiple issues, so I will attempt to list a few possible causes, and hopefully one of them would resolve your problem (I am suspecting 1)b) could solve your issue):


1) environment file:

a) please confirm that the environment file (which is at /data/abcd/bin/mri/) includes the path to your dicom_archive directory:

export LORIS_CONFIG=/data/abcd/bin/mri/dicom-archive
b) source the environment file before running the pipeline:
(just type: source environment at the command line),
then type: echo $PATH to see if you get all the PATHS in the environment file sourced

2) permissions:
just make sure we have 770 permissions on the directories (recusrively) leading up to .loris_mri; and that they are owned by lorisadmin and groupowned by the front0end user (www-data). Then ensure a 640 permission on the prod file itself (with the same ownership and group ownership).

3) prod file customised routines:
If you edited the prod file, sometimes a syntax error in some of its project customizable routines could issue the error you are getting. Sp if for example you modified the getSubject() routine in the prod file, and opened a { and forgot to close it, you would get the error that the prod file is not readable...
You can send me your file separately (WITHOUT the database credentials) if you wish and I can check if this is the cause.

Let me know!

- Mouna

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Carolina Makowski <carolina.mak3 at gmail.com>
Sent: Friday, May 12, 2017 9:23:32 PM
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] troubleshooting MRI upload via image uploader and registering instrument in backend

Hi there,

I have two queries that are related to the imaging and behavioral domains of the database - please let me know if you would prefer that I separate the issues since they pertain to different aspects of the database, but for now I will put both issues here:

1) Failure uploading .tgz file through Image Uploader
Before getting to this point, we had completed everything outlined in the documentation online for the Imaging Database.
The tgz file I tried to upload was anonymized and the header/Patient Name was parsed accordingly, and the file did upload, but its status is marked as "Failure".
Next, we looked for the tgz file in the backend, and it does indeed appear in /data/incoming. We also followed all documentation in the Imaging Uploader documentation, changing the paths appropriately in the configuration module and updating the apache configuration file.
After running the imaging_upload_file.pl<http://imaging_upload_file.pl> script, we received the following error:

lorisadmin at abcd-dataweb:/data/abcd/bin/mri$ uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl/> -profile prod -verbose -upload_id 5 /data/incoming/NDARINV1ET4JE3B_174450_baselineyear1arm1_T1.tgz

    ERROR: You don't have a
    configuration file named 'prod' in:
    /data/abcd/bin/mri/dicom-archive/.loris_mri/

The prod file does indeed exist in that directory, and we have tried running this as root and lorisadmin, with appropriate permissions, and can access prod independently of this script. Has this error come up before in your experience?

2) Registering an instrument that was created using the Instrument Builder GUI.
I am having a bit of trouble following the documentation online for this. In particular, we are getting stuck in populating the test_subgroups table. According to the documentation online, this statement should apply to us (from section 3: populate test_names and test_subgroups tables): "For all *.linst instruments created via the Instrument Builder, sourcing the *.sql file takes care of this step". However, test_subgroups was not automatically populated (test_names was populated properly). We started delving into the "Instrument Coding Guide" documentation but I am under the impression that creation of an instrument through the instrument builder and using a linst file should bypass some of the steps that are required in this Instrument Coding Guide. Perhaps some clarification on the steps after building a linst file and after creating and adding the instrument table to the database would be helpful here.

Thanks in advance! I know I've been bombarding you guys with a lot of questions lately but I really appreciate the help :)

Have a nice weekend,
Carolina
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