Fmriprep No BOLD images found for participant

1

I’m having issues with fmriprep getting the message “Exception: No BOLD images found for participant control01 and task . All workflows require BOLD images” when I run fmriprep.

Previously I’ve used 1.0.4 to preprocess my data, but went back, because I wanted to drop dummy scans and then apply fmriprep. I’ve used the two versions 1.1.2 and 1.1.4, which both give me the message “no bold images”

  • using singularity 2.5.2
  • Data is BIDS validated
  • Thought the dropping dummy scans was problematic, so tried two methods 1) nilearn 2) fsl-roi. Both work for the older ver-1.0.4, while not for the latest 1.1.4
  • Based on previous forums that discussed similar issued, I tried:
singularity exec ${MODULEDIR}/fmriprep_ver1.1.4-2018-08-06.img \
ls ${DATADIR}/Data/sourcedata_dropscans/

and get the correct subdirectories within sourcedata_dropscans

code that I’m running:

unset PYTHONPATH; singularity run  ${MODULEDIR}/fmriprep_ver1.1.4-2018-08-06.img \
${DATADIR}/Data/sourcedata_dropscans ${DATADIR}/Data/derivatives \
participant --participant_label ${SUBJ} \
--use-aroma --write-graph --ignore fieldmaps --fs-license-file ${DATADIR}/Data/license.txt \
-w ${DATADIR}/Data/derivatives/fmriprep/work/ \
--resource-monitor --low-mem

Thanks for all your help!

2

Could you post the output of:

singularity exec ${MODULEDIR}/fmriprep_ver1.1.4-2018-08-06.img \
    find ${DATADIR}/Data/sourcedata_dropscans/ -name "*_bold.*"

Cheers,
Oscar

3

Thanks for looking into this quickly. Below is the output:

${DATADIR}/Data/sourcedata_dropscans/sub-control13/func/sub-control13_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control13/func/sub-control13_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control13/func/sub-control13_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control13/func/sub-control13_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control13/func/sub-control13_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control13/func/sub-control13_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism04/func/sub-autism04_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism04/func/sub-autism04_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism04/func/sub-autism04_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism04/func/sub-autism04_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism04/func/sub-autism04_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism04/func/sub-autism04_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism13/func/sub-autism13_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism13/func/sub-autism13_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism13/func/sub-autism13_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism13/func/sub-autism13_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism13/func/sub-autism13_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism13/func/sub-autism13_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/task-pokertask_bold.json
${DATADIR}/Data/sourcedata_dropscans/sub-autism16/func/sub-autism16_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism16/func/sub-autism16_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism16/func/sub-autism16_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism16/func/sub-autism16_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism16/func/sub-autism16_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism16/func/sub-autism16_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control05/func/sub-control05_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control05/func/sub-control05_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control05/func/sub-control05_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control05/func/sub-control05_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control05/func/sub-control05_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control05/func/sub-control05_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control14/func/sub-control14_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control14/func/sub-control14_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control14/func/sub-control14_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control14/func/sub-control14_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control14/func/sub-control14_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control14/func/sub-control14_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism14/func/sub-autism14_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism14/func/sub-autism14_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism14/func/sub-autism14_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism14/func/sub-autism14_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism14/func/sub-autism14_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism14/func/sub-autism14_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism06/func/sub-autism06_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism06/func/sub-autism06_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism06/func/sub-autism06_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism06/func/sub-autism06_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism06/func/sub-autism06_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism06/func/sub-autism06_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism15/func/sub-autism15_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism15/func/sub-autism15_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism15/func/sub-autism15_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism15/func/sub-autism15_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism15/func/sub-autism15_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism15/func/sub-autism15_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control01/func/sub-control01_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control01/func/sub-control01_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control01/func/sub-control01_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control01/func/sub-control01_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control01/func/sub-control01_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control01/func/sub-control01_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism11/func/sub-autism11_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism11/func/sub-autism11_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism11/func/sub-autism11_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism11/func/sub-autism11_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism11/func/sub-autism11_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism11/func/sub-autism11_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism10/func/sub-autism10_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism10/func/sub-autism10_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism10/func/sub-autism10_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism10/func/sub-autism10_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism10/func/sub-autism10_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism10/func/sub-autism10_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control03/func/sub-control03_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control03/func/sub-control03_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control03/func/sub-control03_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control03/func/sub-control03_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control03/func/sub-control03_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control03/func/sub-control03_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control04/func/sub-control04_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control04/func/sub-control04_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control04/func/sub-control04_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control04/func/sub-control04_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control04/func/sub-control04_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control04/func/sub-control04_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism07/func/sub-autism07_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism07/func/sub-autism07_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism07/func/sub-autism07_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism07/func/sub-autism07_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism07/func/sub-autism07_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism07/func/sub-autism07_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control12/func/sub-control12_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control12/func/sub-control12_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control12/func/sub-control12_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control12/func/sub-control12_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control12/func/sub-control12_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control12/func/sub-control12_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism12/func/sub-autism12_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism12/func/sub-autism12_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism12/func/sub-autism12_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism12/func/sub-autism12_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism12/func/sub-autism12_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism12/func/sub-autism12_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control07/func/sub-control07_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control07/func/sub-control07_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control07/func/sub-control07_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control07/func/sub-control07_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control07/func/sub-control07_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control07/func/sub-control07_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control02/func/sub-control02_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control02/func/sub-control02_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control02/func/sub-control02_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control02/func/sub-control02_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control02/func/sub-control02_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control02/func/sub-control02_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism09/func/sub-autism09_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism09/func/sub-autism09_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism09/func/sub-autism09_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism09/func/sub-autism09_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism09/func/sub-autism09_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism09/func/sub-autism09_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control16/func/sub-control16_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control16/func/sub-control16_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control16/func/sub-control16_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control16/func/sub-control16_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control16/func/sub-control16_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control16/func/sub-control16_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism01/func/sub-autism01_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism01/func/sub-autism01_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism01/func/sub-autism01_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism01/func/sub-autism01_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism01/func/sub-autism01_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism01/func/sub-autism01_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control06/func/sub-control06_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control06/func/sub-control06_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control06/func/sub-control06_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control06/func/sub-control06_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control06/func/sub-control06_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control06/func/sub-control06_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism03/func/sub-autism03_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism03/func/sub-autism03_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism03/func/sub-autism03_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism03/func/sub-autism03_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism03/func/sub-autism03_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism03/func/sub-autism03_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism02/func/sub-autism02_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism02/func/sub-autism02_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism02/func/sub-autism02_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism02/func/sub-autism02_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism02/func/sub-autism02_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism02/func/sub-autism02_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control08/func/sub-control08_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control08/func/sub-control08_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control08/func/sub-control08_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control08/func/sub-control08_task-pokertask_run-01_bold.nii.gz
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${DATADIR}/Data/sourcedata_dropscans/sub-control08/func/sub-control08_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control10/func/sub-control10_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control10/func/sub-control10_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control10/func/sub-control10_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control10/func/sub-control10_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control10/func/sub-control10_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control10/func/sub-control10_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control11/func/sub-control11_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control11/func/sub-control11_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control11/func/sub-control11_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control11/func/sub-control11_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control11/func/sub-control11_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control11/func/sub-control11_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism05/func/sub-autism05_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism05/func/sub-autism05_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism05/func/sub-autism05_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism05/func/sub-autism05_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism05/func/sub-autism05_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism05/func/sub-autism05_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control09/func/sub-control09_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control09/func/sub-control09_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control09/func/sub-control09_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control09/func/sub-control09_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control09/func/sub-control09_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control09/func/sub-control09_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control15/func/sub-control15_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control15/func/sub-control15_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control15/func/sub-control15_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control15/func/sub-control15_task-pokertask_run-01_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control15/func/sub-control15_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-control15/func/sub-control15_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism08/func/sub-autism08_task-pokertask_run-02_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism08/func/sub-autism08_task-pokertask_run-06_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism08/func/sub-autism08_task-pokertask_run-04_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism08/func/sub-autism08_task-pokertask_run-03_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism08/func/sub-autism08_task-pokertask_run-05_bold.nii.gz
${DATADIR}/Data/sourcedata_dropscans/sub-autism08/func/sub-autism08_task-pokertask_run-01_bold.nii.gz
4

What is ${SUBJ} set to?

5

${SUBJ} is set by a wrapper script that feeds in sub-control01, sub-control02 … etc.

The error message reflects that the ${SUBJ} variables are passed on correctly:

Exception: No BOLD images found for participant control02 and task <all>. 
All workflows require BOLD images.
6

I’m befuddled why is this happening. Maybe the files are broken symlinks? Does the dataset pass the validator? could you show output of tree for a single subject?

7

Yes, I’ve validated through the webversion.
As for tree, if you’re referring to the subdirectory or files of a single subject, the output is below

sub-control01_task-pokertask_run-01_bold.nii.gz  sub-control01_task-pokertask_run-03_bold.nii.gz  sub-control01_task-pokertask_run-05_bold.nii.gz
sub-control01_task-pokertask_run-01_events.tsv   sub-control01_task-pokertask_run-03_events.tsv   sub-control01_task-pokertask_run-05_events.tsv
sub-control01_task-pokertask_run-02_bold.nii.gz  sub-control01_task-pokertask_run-04_bold.nii.gz  sub-control01_task-pokertask_run-06_bold.nii.gz
sub-control01_task-pokertask_run-02_events.tsv   sub-control01_task-pokertask_run-04_events.tsv   sub-control01_task-pokertask_run-06_events.tsv
8

So there are no anatomical (T1w) scans?

9

There are. My bad for leaving the anat folder out.
Here’s the complete subdirectory

sub-control01/anat/sub-control01_T1w.nii.gz

sub-control01/func/sub-control01_task-pokertask_run-01_bold.nii.gz  
sub-control01/func/sub-control01_task-pokertask_run-01_events.tsv  
sub-control01/func/sub-control01_task-pokertask_run-02_bold.nii.gz
sub-control01/func/sub-control01_task-pokertask_run-02_events.tsv
sub-control01/func/sub-control01_task-pokertask_run-03_bold.nii.gz
sub-control01/func/sub-control01_task-pokertask_run-03_events.tsv     
sub-control01/func/sub-control01_task-pokertask_run-04_bold.nii.gz
sub-control01/func/sub-control01_task-pokertask_run-04_events.tsv
sub-control01/func/sub-control01_task-pokertask_run-05_bold.nii.gz
sub-control01/func/sub-control01_task-pokertask_run-05_events.tsv
sub-control01/func/sub-control01_task-pokertask_run-06_bold.nii.gz
sub-control01/func/sub-control01_task-pokertask_run-06_events.tsv
10

Hi @hjung,

Could you run the following command?:

singularity exec ${MODULEDIR}/fmriprep_ver1.1.4-2018-08-06.img python -c "from fmriprep.utils.bids import collect_data; print(collect_data('<DATADIR>/Data/sourcedata_dropscans/', 'control01', None)[0])"

Please, make sure that you replace <DATADIR> with the full path stored in ${DATADIR} manually.

One impression I have is that the use of ${DATADIR} is obscuring the chase. I’m not sure whether the env variable is traversing into the container or resolved before that. I think it is being resolved, and thus I expected that the find command would have the ${DATADIR} resolved. Did you run the find from within the container?

Cheers,
Oscar

1 Like
11

Hi Oscar @oesteban

After running the command, I get

/usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
/usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
{'fmap': [], 'bold': [], 'sbref': [], 'flair': [], 't2w': [], 't1w': [], 'roi': []}

As for the env variables, the only env variable I have is ${SUBJ}.
${DATADIR} was simply to shortly represent the path, since it was too long. I am writing out $DATADIR manually in my original code. Apologies for the confusion.

When running the find command, I ran it on the HPC directly, not within the container. Also, all of the paths were spelled out manually, thus, there were no env variables for the find command.

Thanks for all your help!

Heejung

12

Sorry, I probably did not write the question correctly.

Did you run the find of the host system or the find of the container? In other words, did you run this:

find ${DATADIR}/Data/sourcedata_dropscans/ -name "*_bold.*"

or this

singularity exec ${MODULEDIR}/fmriprep_ver1.1.4-2018-08-06.img find ${DATADIR}/Data/sourcedata_dropscans/ -name "*_bold.*"

I would be interested in the output of the second, only. My suspicion is that you don’t have access to your BIDS data from within the container. Is it possible at all that ${DATADIR} is not bound within the container?

13

I ran the second command and below is the corresponding output. (I removed all of the misleading env variables.)

/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control13/func/sub-control13_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control13/func/sub-control13_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control13/func/sub-control13_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control13/func/sub-control13_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control13/func/sub-control13_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control13/func/sub-control13_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism04/func/sub-autism04_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism04/func/sub-autism04_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism04/func/sub-autism04_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism04/func/sub-autism04_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism04/func/sub-autism04_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism04/func/sub-autism04_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism13/func/sub-autism13_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism13/func/sub-autism13_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism13/func/sub-autism13_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism13/func/sub-autism13_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism13/func/sub-autism13_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism13/func/sub-autism13_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/task-pokertask_bold.json
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism16/func/sub-autism16_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism16/func/sub-autism16_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism16/func/sub-autism16_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism16/func/sub-autism16_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism16/func/sub-autism16_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism16/func/sub-autism16_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control05/func/sub-control05_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control05/func/sub-control05_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control05/func/sub-control05_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control05/func/sub-control05_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control05/func/sub-control05_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control05/func/sub-control05_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control14/func/sub-control14_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control14/func/sub-control14_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control14/func/sub-control14_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control14/func/sub-control14_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control14/func/sub-control14_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control14/func/sub-control14_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism14/func/sub-autism14_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism14/func/sub-autism14_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism14/func/sub-autism14_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism14/func/sub-autism14_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism14/func/sub-autism14_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism14/func/sub-autism14_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism06/func/sub-autism06_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism06/func/sub-autism06_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism06/func/sub-autism06_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism06/func/sub-autism06_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism06/func/sub-autism06_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism06/func/sub-autism06_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism15/func/sub-autism15_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism15/func/sub-autism15_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism15/func/sub-autism15_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism15/func/sub-autism15_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism15/func/sub-autism15_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism15/func/sub-autism15_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control01/func/sub-control01_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control01/func/sub-control01_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control01/func/sub-control01_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control01/func/sub-control01_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control01/func/sub-control01_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control01/func/sub-control01_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism11/func/sub-autism11_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism11/func/sub-autism11_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism11/func/sub-autism11_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism11/func/sub-autism11_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism11/func/sub-autism11_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism11/func/sub-autism11_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism10/func/sub-autism10_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism10/func/sub-autism10_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism10/func/sub-autism10_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism10/func/sub-autism10_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism10/func/sub-autism10_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism10/func/sub-autism10_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control03/func/sub-control03_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control03/func/sub-control03_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control03/func/sub-control03_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control03/func/sub-control03_task-pokertask_run-05_bold.nii.gz
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I’m not sure if I understand what “$DATADIR not bound within the container” means.

14

Basically, you just confirmed that fMRIPrep (and the container around it) have access to /work/ics/data/projects/snaglab/Projects/POKER.05/.

The working directory where you ran find is the same you were using to run fMRIPrep, correct?

15

Correct, I ran find in the directory where I ran my fmriprep scripts.

16

I bet POKER.05 is confusing pybids! Could you try renaming it to POKER05 (without the dot)?

17

I was hoping that was the fix, but didn’t work. I have the same error message

/usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
/usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
/usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
/usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
Process Process-2:
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 93, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 542, in build_workflow
    ignore_aroma_err=opts.ignore_aroma_denoising_errors,
  File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 210, in init_fmriprep_wf
    ignore_aroma_err=ignore_aroma_err)
  File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 377, in init_single_subject_wf
    subject_id, task_id if task_id else '<all>'))
Exception: No BOLD images found for participant control01 and task <all>. All workflows require BOLD images.

I wonder why I have these error messages, when the same dataset works for ver 1.0.4.

18

Let’s see whether pybids is not reading the data structure or it is fMRIPrep mishandling the query:

singularity exec ${MODULEDIR}/fmriprep_ver1.1.4-2018-08-06.img python -c "from bids.grabbids import BIDSLayout; print(BIDSLayout('/work/ics/data/projects/snaglab/Projects/POKER.05').get(type=['T1w', 'bold'], return_type='id', target='subject'))"
19

Hi @hjung, did the command I posted give any interesting output?

20

Hi @oesteban

I ran the code as you suggested, and below is the output. (Note: for the print(BIDSLayout( )) part, I changed it to ~/POKER.05/Data/sourcedata_dropscans, instead of ~/POKER.05)

singularity exec /work/ics/data/projects/snaglab/modules/fmriprep_ver1.1.4-2018-08-06.img python -c "from bids.grabbids import BIDSLayout; print(BIDSLayout('/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans').get(type=['T1w', 'bold'], return_type='id', target='subject'))"

output:

/usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
/usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
['autism01', 'autism02', 'autism03', 'autism04', 'autism05', 'autism06', 'autism07', 'autism08', 'autism09', 'autism10', 'autism11', 'autism12', 'autism13', 'autism14', 'autism15', 'autism16', 'control01', 'control02', 'control03', 'control04', 'control05', 'control06', 'control07', 'control08', 'control09', 'control10', 'control11', 'control12', 'control13', 'control14', 'control15', 'control16']