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

[Christine Rogers]

Hi Carolina,
Happy to address your second question -- thanks for catching that omission
in the wiki, not sure why we haven't found this gap before in the LINST
documentation - I've added notes to update this.

note: Test subgroups do apply to LINST instruments exactly as they apply to
PHP-coded instruments.

Test subgroups are simply used to organize the list of instruments
displayed in any given timepoint into blocks of related instruments.
Typically, it's useful to visually break down a long list of instruments in
a visit into categories such as (e.g.) "Developmental" measures, then
"Communication" tests, followed by "Medical/Family History" questionnaires,
etc.

To define these test_subgroups, use a MySQL insert statement to add each to
the *test_subgroups* table, e.g.: To display 'Developmental' instruments
first in order within each timepoint page:

> INSERT INTO *test_subgroups* (Subgroup_name, group_order) VALUES
> ('Developmental', '1');


Next, associate each instruments to a subgroup, by updating the *test_names*
table to populate the Sub_group field. (I'm assuming your instruments
already exist in *test_names*; note only one subgroup per instrument is
best.)

e.g. To add the Vineland II (testname: 'vabs2') to the 'Developmental'
measures subgroup :

UPDATE *test_names* SET Sub_group =
>      (SELECT ID FROM *test_subgroups*
>          WHERE Subgroup_name = 'Developmental')
> WHERE Test_name = 'vabs2' ;


Hope this helps --
cheers,
Christine

On Fri, May 12, 2017 at 9:23 PM, Carolina Makowski <carolina.mak3 at gmail.com>
wrote:

> 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 script, we received the
> following error:
>
> lorisadmin at abcd-dataweb:/data/abcd/bin/mri$ uploadNeuroDB/imaging_upload_f
> ile.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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>


-- 

christine.rogers at mcgill.ca
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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