Error running fmriprep: No BOLD images found for participant

1

Hello,

I’m attempting to run fmriprep for one participant on an HPC cluster, but am persistently getting the error: “Exception: No BOLD images found for participant 006 and task . All workflows require BOLD images.” I believe the dataset is BIDS valid; I converted the data to BIDS format using Heudiconv, and when I run a bids validator, I get one warning saying “Tabular file contains custom columns not described in a data dictionary.”

I’m using a script that loads all the programs needed to run fmriprep, and then runs fmriprep using the arguments passed to the script. So I’m executing the command:

source /gpfs/scratch/dpp5430/fmriprep_wrapper.sh /gpfs/scratch/dpp5430/Danieloutput /gpfs/scratch/dpp5430/fmriprepOut participant --participant_label 006

fmriprep_wrapper.sh is the script, Danieloutput is the BIDS directory, and fmriprepOut is my output directory.
In the script, fmriprep is being run with the statement:

fmriprep “$@”

When I echo “$@”, I get all the arguments as they’re supposed to appear.

Any thoughts on what could be happening?

Thanks!
Daniel

2

fMRIPrep did not find workable BOLD files for participant 006 - you could be pointing it to the wrong directory, your dataset is not BIDS-compliant or sub-006 doesn’t contain any bold data.

3

Thanks for the reply. I thought those might be issues, but the dataset is BIDS-compliant, and I’m pointing it to a directory with the dataset. A folder for sub-006 is at the top level of the directory, and it has BOLD data (nifti files). Is there anything else that could be going wrong?

4

It looks to me like fMRIPrep is looking for a particular task (''). Does fmriprep_wrapper.sh maybe require a task-id and default to None or an empty string?

1 Like
5

There was actually a typo in my original post. The error is “Exception: No BOLD images found for participant 006 and task all. All workflows require BOLD images.” The “all” has < > characters around it, but for some reason when I put those around it it no longer shows up in the post. I don’t think the fmriprep_wrapper.sh doesn’t require a task id - it just passes whatever arguments you give it to the fmriprep call. Sorry for the typo

6

What is the output of tree /gpfs/scratch/dpp5430/Danieloutput? (btw. this is a pretty suspicious name for an input folder).

7

Haha yeah that is a suspicious name - it’s named that because it’s the output of a conversion to BIDS. I don’t have tree installed, and I don’t think I have permission to; I’m running this on my university’s HPC network using a lab account. Is there any other way I can get you the info you’re looking for?

8

You can use find /gpfs/scratch/dpp5430/Danieloutput. It won’t be as pretty but it should show the necessary file structure.

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/gpfs/scratch/dpp5430/Danieloutput

/gpfs/scratch/dpp5430/Danieloutput/README

/gpfs/scratch/dpp5430/Danieloutput/sourcedata

/gpfs/scratch/dpp5430/Danieloutput/sourcedata/README

/gpfs/scratch/dpp5430/Danieloutput/sourcedata/sub-006

/gpfs/scratch/dpp5430/Danieloutput/sourcedata/sub-006/fmap

/gpfs/scratch/dpp5430/Danieloutput/sourcedata/sub-006/fmap/sub-006_dir-PA_epi.dicom.tgz

/gpfs/scratch/dpp5430/Danieloutput/sourcedata/sub-006/fmap/sub-006_dir-AP_epi.dicom.tgz

/gpfs/scratch/dpp5430/Danieloutput/sourcedata/sub-006/anat

/gpfs/scratch/dpp5430/Danieloutput/sourcedata/sub-006/anat/sub-006_T1w.dicom.tgz

/gpfs/scratch/dpp5430/Danieloutput/sourcedata/sub-006/func

/gpfs/scratch/dpp5430/Danieloutput/sourcedata/sub-006/func/sub-006_task-spottpav_run-01_sbref.dicom.tgz

/gpfs/scratch/dpp5430/Danieloutput/sourcedata/sub-006/func/sub-006_task-spottpit_run-01_sbref.dicom.tgz

/gpfs/scratch/dpp5430/Danieloutput/sourcedata/sub-006/func/sub-006_task-spottins_run-01_sbref.dicom.tgz

/gpfs/scratch/dpp5430/Danieloutput/sourcedata/sub-006/func/sub-006_task-rest_run-01_sbref.dicom.tgz

/gpfs/scratch/dpp5430/Danieloutput/dataset_description.json

/gpfs/scratch/dpp5430/Danieloutput/sub-006

/gpfs/scratch/dpp5430/Danieloutput/sub-006/sub-006_scans.tsv

/gpfs/scratch/dpp5430/Danieloutput/sub-006/fmap

/gpfs/scratch/dpp5430/Danieloutput/sub-006/fmap/sub-006_dir-PA_epi.nii.gz

/gpfs/scratch/dpp5430/Danieloutput/sub-006/fmap/sub-006_dir-AP_epi.json

/gpfs/scratch/dpp5430/Danieloutput/sub-006/fmap/sub-006_dir-AP_epi.nii.gz

/gpfs/scratch/dpp5430/Danieloutput/sub-006/fmap/sub-006_dir-PA_epi.json

/gpfs/scratch/dpp5430/Danieloutput/sub-006/sub-006_scans.json

/gpfs/scratch/dpp5430/Danieloutput/sub-006/anat

/gpfs/scratch/dpp5430/Danieloutput/sub-006/anat/sub-006_T1w.json

/gpfs/scratch/dpp5430/Danieloutput/sub-006/anat/sub-006_T1w.nii.gz

/gpfs/scratch/dpp5430/Danieloutput/sub-006/func

/gpfs/scratch/dpp5430/Danieloutput/sub-006/func/sub-006_task-rest_run-01_sbref.json

/gpfs/scratch/dpp5430/Danieloutput/sub-006/func/sub-006_task-rest_run-01_sbref.nii.gz

/gpfs/scratch/dpp5430/Danieloutput/sub-006/func/sub-006_task-spottpav_run-01_sbref.json

/gpfs/scratch/dpp5430/Danieloutput/sub-006/func/sub-006_task-spottpit_run-01_sbref.json

/gpfs/scratch/dpp5430/Danieloutput/sub-006/func/sub-006_task-spottins_run-01_sbref.nii.gz

/gpfs/scratch/dpp5430/Danieloutput/sub-006/func/sub-006_task-spottpit_run-01_sbref.nii.gz

/gpfs/scratch/dpp5430/Danieloutput/sub-006/func/sub-006_task-spottins_run-01_sbref.json

/gpfs/scratch/dpp5430/Danieloutput/sub-006/func/sub-006_task-spottpav_run-01_sbref.nii.gz

/gpfs/scratch/dpp5430/Danieloutput/.heudiconv

/gpfs/scratch/dpp5430/Danieloutput/.heudiconv/006

/gpfs/scratch/dpp5430/Danieloutput/.heudiconv/006/info

/gpfs/scratch/dpp5430/Danieloutput/.heudiconv/006/info/006.auto.txt

/gpfs/scratch/dpp5430/Danieloutput/.heudiconv/006/info/temp_heur.py

/gpfs/scratch/dpp5430/Danieloutput/.heudiconv/006/info/006.edit.txt

/gpfs/scratch/dpp5430/Danieloutput/.heudiconv/006/info/dicominfo.tsv

/gpfs/scratch/dpp5430/Danieloutput/.heudiconv/006/info/filegroup.json

/gpfs/scratch/dpp5430/Danieloutput/.heudiconv/007

/gpfs/scratch/dpp5430/Danieloutput/.heudiconv/007/info

/gpfs/scratch/dpp5430/Danieloutput/.heudiconv/007/info/temp_heur.py

/gpfs/scratch/dpp5430/Danieloutput/.heudiconv/007/info/007.edit.txt

/gpfs/scratch/dpp5430/Danieloutput/.heudiconv/007/info/dicominfo.tsv

/gpfs/scratch/dpp5430/Danieloutput/.heudiconv/007/info/filegroup.json

/gpfs/scratch/dpp5430/Danieloutput/.heudiconv/007/info/007.auto.txt

/gpfs/scratch/dpp5430/Danieloutput/CHANGES

10

It doesn’t look like you have any functional data. Just single-band reference images.

1 Like
11

You’re right, I hadn’t noticed that. Thank you!

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