How to use session label

Hi there,

I would like to run fMRIPrep on only one out of several sessions, but I cannot figure out how to define the session that should be run. So far I have tried the flags -s --session-label --session-id, but none of them seem to work. It says “unrecognized arguments: --session-label ses-T1” (for example).

I am trying to run the following command line (which works fine if I don’t use the session flag):
docker run --rm -e DOCKER_VERSION_8395080871=19.03.2 -v /home/jbruegge/freesurfer_liense_file/license.txt:/opt/freesurfer/license.txt:ro -v /data/TIMES/patients:/data:ro -v /data/TIMES/patients/derivatives/with_freesurfer:/out poldracklab/fmriprep:1.5.4 /data /out participant --participant_label sub-01 --session-label ses-T1 --output-spaces MNI152NLin6Asym fsaverage

I also tried this version (with all flags I mentioned above), but it also didn’t work. The error is exactly the same.:
docker run --rm -e DOCKER_VERSION_8395080871=19.03.2 -v /home/jbruegge/freesurfer_liense_file/license.txt:/opt/freesurfer/license.txt:ro -v /data/TIMES/patients:/data:ro -v /data/TIMES/patients/derivatives/with_freesurfer:/out poldracklab/fmriprep:1.5.4 /data /out participant --participant_label sub-01 session --session-label ses-T1 --output-spaces MNI152NLin6Asym fsaverage

So could you please tell me how to properly specify the session? Thank you!
Cheers,
Julia

1 Like

Hi @jbruegge

did you find a way to specify the session?

Best Regards,
Ana

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Hi @AnaTomomi

Back then I discovered that it was not implemented yet, so I gave up on it. Sorry to not be of more help!
Cheers,
Julia

You can try it with “–bids-filter-file” flag and specifying which session you would want to use in the json file for eg:

bids_filter_file.json:

{
“t1w”: {
“datatype”: “anat”,
“session”: “ses-T1”,
“acquisition”: null,
“suffix”: “T1w”
},
“bold”: {
“datatype”: “func”,
“session”: “ses-T1”,
“suffix”: “bold”
}
}