[BUG] Participant_label flag is ignored when running docker

[monique2208]

Is there an existing issue for this?

• I have searched the existing issues

Operating system

• Linux
• Mac
• Windows

Operating system version

Windows 11

SPM 12 version

• 7771
• 7487
• 7219

Platform

• MATLAB
• Octave

Platform version

Latest docker image

bidspm version

v3.1.0

bidspm branch / commit number

No response

Expected Behavior

When I add the participant_label flag to my command I expect to run only the participants I specified. But the flag is not passed on the bidspm function.

BIDS stats model

No response

Current Behavior & Error message

All participant data is processed and I do not get any error messages or warnings related to the participant flag.

Anything else?

I have tried out the participant flag with the actions smooth and stats.

[github-actions]

Thank you for your issue. Give us a little time to review it.

PS. You might want to check the FAQ if you haven't done so already.

This is an automated reply, generated by FAQtory

[Remi-Gau]

Very possible that some flags of the CLI are not properly passed to MAtlab or Octave.

Will double check.

Thanks for opening an issue.

[Remi-Gau]

Trying to reproduce on the main branch.

Running this on some of the data in the 'demos/openneuro/inputs/ds000001'.

bidspm inputs/ds000001 outputs/ds000001/derivatives subject \
    --action preprocess \
    --task balloonanalogrisktask \
    --fwhm 8 \
    --participant_label 01 02 03

Command constructed:

 addpath('/home/remi/github/cpp-lln-lab/bidspm'); % I just added this (so you may not have it)
 bidspm();
 bidspm('/home/remi/github/cpp-lln-lab/bidspm/demos/openneuro/inputs/ds000001', ...
                         '/home/remi/github/cpp-lln-lab/bidspm/demos/openneuro/outputs/ds000001/derivatives', ...
                         'subject', ...
                         'action', 'preprocess', ...
                         'verbosity', 2, ...
                         'space', { 'IXI549Space' }, ...
                         'task', { 'balloonanalogrisktask' }, ...
                         'fwhm', [8.0], ...
                         'participant_label', { '01', '02', '03' });
 exit;

And then some of the workflow indeed say that they will work on just 3 subjects.

[16:41:29] bidspm - INFO                                getData
WILL WORK ON SUBJECTS
        - 01
        - 02
        - 03


[16:41:29] bidspm - INFO                                printWorkflowName
WORKFLOW: SPATIAL PREPROCESSING

Did you have this bug for the preprocess action too?

I assumed you did: just want to make sure.

[Remi-Gau]

just to know.

what was the command you passed to the docker image and what command was constructed and passed to bidspm?

[monique2208]

I ran the following in docker command:

docker run --rm -it -v .\ds003126_3sub_test:/bids -v .\ds003126_3sub_test\derivatives\bidspm-preproc:/prep:ro -v .\ds003126_3sub_test:/out -v .\ds003126_3sub_test\derivatives\models\model-defaultRead_smdl.json:/model:ro cpplab/bidspm /bids /out dataset --action stats --participant_label 047EPKL014010 --task read --model /model --preproc_dir /prep --space MNI152NLin2009cAsym --skip_validation

and the following was passed to bidspm:

Running the following command:

 bidspm();
 bidspm('/bids', ...
                         '/out', ...
                         'subject', ...
                         'action', 'stats', ...
                         'verbosity', 2, ...
                         'space', { 'MNI152NLin2009cAsym' }, ...
                         'task', { 'read' }, ...
                         'fwhm', 6.0, ...
                         'skip_validation', true, ...
                         'preproc_dir', '/prep', ...
                         'model_file', '/model');
 exit;

[Remi-Gau]

OK thanks

will keep digging

[Remi-Gau]

OK trying on stats

running this:

bidspm demos/openneuro/inputs/ds000001 demos/openneuro/outputs/ds000001/derivatives subject \
    --action stats \
    --preproc_dir demos/openneuro/outputs/ds000001/derivatives/bidspm-preproc \
    --task balloonanalogrisktask \
    --model_file demos/openneuro/models/model-balloonanalogrisktaskDefault_smdl.json \
    --fwhm 8 \
    --participant_label 01 02

gives this

bidspm();
bidspm('/home/remi/github/cpp-lln-lab/bidspm/demos/openneuro/inputs/ds000001', ...
                         '/home/remi/github/cpp-lln-lab/bidspm/demos/openneuro/outputs/ds000001/derivatives', ...
                         'subject', ...
                         'action', 'stats', ...
                         'verbosity', 2, ...
                         'space', { 'IXI549Space' }, ...
                         'fwhm', [8.0], ...
                         'participant_label', { '01', '02' }, ...
                         'preproc_dir', '/home/remi/github/cpp-lln-lab/bidspm/demos/openneuro/outputs/ds000001/derivatives/bidspm-preproc', ...
                         'model_file', '/home/remi/github/cpp-lln-lab/bidspm/demos/openneuro/models/model-balloonanalogrisktaskDefault_smdl.json');
 exit;

and runs on the requested subjects.

Next thing to try for me: try to reproduce with the latest stable docker image.