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
${DATADIR}/Data/sourcedata_dropscans/sub-control08/func/sub-control08_task-pokertask_run-04_bold.nii.gz
${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


#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
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control03/func/sub-control03_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-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control04/func/sub-control04_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control04/func/sub-control04_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control04/func/sub-control04_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control04/func/sub-control04_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control04/func/sub-control04_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control04/func/sub-control04_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism07/func/sub-autism07_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism07/func/sub-autism07_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism07/func/sub-autism07_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism07/func/sub-autism07_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism07/func/sub-autism07_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism07/func/sub-autism07_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control12/func/sub-control12_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control12/func/sub-control12_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control12/func/sub-control12_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control12/func/sub-control12_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control12/func/sub-control12_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control12/func/sub-control12_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism12/func/sub-autism12_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism12/func/sub-autism12_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism12/func/sub-autism12_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism12/func/sub-autism12_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism12/func/sub-autism12_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism12/func/sub-autism12_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control07/func/sub-control07_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control07/func/sub-control07_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control07/func/sub-control07_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control07/func/sub-control07_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control07/func/sub-control07_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control07/func/sub-control07_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control02/func/sub-control02_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control02/func/sub-control02_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control02/func/sub-control02_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control02/func/sub-control02_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control02/func/sub-control02_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control02/func/sub-control02_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism09/func/sub-autism09_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism09/func/sub-autism09_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism09/func/sub-autism09_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism09/func/sub-autism09_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism09/func/sub-autism09_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism09/func/sub-autism09_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control16/func/sub-control16_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control16/func/sub-control16_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control16/func/sub-control16_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control16/func/sub-control16_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control16/func/sub-control16_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control16/func/sub-control16_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism01/func/sub-autism01_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism01/func/sub-autism01_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism01/func/sub-autism01_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism01/func/sub-autism01_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism01/func/sub-autism01_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism01/func/sub-autism01_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control06/func/sub-control06_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control06/func/sub-control06_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control06/func/sub-control06_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control06/func/sub-control06_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control06/func/sub-control06_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control06/func/sub-control06_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism03/func/sub-autism03_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism03/func/sub-autism03_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism03/func/sub-autism03_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism03/func/sub-autism03_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism03/func/sub-autism03_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism03/func/sub-autism03_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism02/func/sub-autism02_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism02/func/sub-autism02_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism02/func/sub-autism02_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism02/func/sub-autism02_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism02/func/sub-autism02_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism02/func/sub-autism02_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control08/func/sub-control08_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control08/func/sub-control08_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control08/func/sub-control08_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control08/func/sub-control08_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control08/func/sub-control08_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control08/func/sub-control08_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control10/func/sub-control10_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control10/func/sub-control10_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control10/func/sub-control10_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control10/func/sub-control10_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control10/func/sub-control10_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control10/func/sub-control10_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control11/func/sub-control11_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control11/func/sub-control11_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control11/func/sub-control11_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control11/func/sub-control11_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control11/func/sub-control11_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control11/func/sub-control11_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism05/func/sub-autism05_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism05/func/sub-autism05_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism05/func/sub-autism05_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism05/func/sub-autism05_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism05/func/sub-autism05_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism05/func/sub-autism05_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control09/func/sub-control09_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control09/func/sub-control09_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control09/func/sub-control09_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control09/func/sub-control09_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control09/func/sub-control09_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control09/func/sub-control09_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control15/func/sub-control15_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control15/func/sub-control15_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control15/func/sub-control15_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control15/func/sub-control15_task-pokertask_run-01_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control15/func/sub-control15_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-control15/func/sub-control15_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism08/func/sub-autism08_task-pokertask_run-02_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism08/func/sub-autism08_task-pokertask_run-06_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism08/func/sub-autism08_task-pokertask_run-04_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism08/func/sub-autism08_task-pokertask_run-03_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism08/func/sub-autism08_task-pokertask_run-05_bold.nii.gz
/work/ics/data/projects/snaglab/Projects/POKER.05/Data/sourcedata_dropscans/sub-autism08/func/sub-autism08_task-pokertask_run-01_bold.nii.gz

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']