fMRIprep-rodents error: (code: 53 - NO_T1W)

Software Support
1

Summary of what happened:

Run fMRIprep-rodents on simple dataset. Get error message saying:

1: [ERR] Dataset does not contain any T1w scans. (code: 53 - NO_T1W)

Which is indeed the case, since I am only using T2w. Unsure what to do. Tried simply switching the name of the anat file (see tree structure below). It then starts running, but I instead get the error:

FileNotFoundError: No T2w images found for subject sub-01

which I guess makes sense, but I am now stuck, and I don’t know what to do…

Command used (and if a helper script was used, a link to the helper script or the command generated):

docker run -ti --rm \
-e SUBJECTS_DIR=/tmp \
-v /Users/kelvin/Library/CloudStorage/OneDrive-DanmarksTekniskeUniversitet/Thesis/thesis_git/data/data_bids/rsfMRI_example_bids:/bids_dataset:ro \
-v /Users/kelvin/Library/CloudStorage/OneDrive-DanmarksTekniskeUniversitet/Thesis/thesis_git/data/data_processed:/outputs \
-v /Users/kelvin/Library/CloudStorage/OneDrive-DanmarksTekniskeUniversitet/Thesis/thesis_git/data/data_bids/work_dir:/work \
-v /Users/kelvin/.licences/freesurfer/license.txt:/opt/freesurfer/license.txt \
nipreps/fmriprep-rodents:fmri_prep_rodent \
/bids_dataset /outputs \
participant \
-w /work \

Version:

Latest docker image from docker hub

Environment (Docker, Singularity, custom installation):

docker

Data formatted according to a validatable standard? Please provide the output of the validator:

Passes tests on online BIDS-validator

Relevant log outputs (up to 20 lines):

.
├── dataset_description.json
├── participants.tsv
├── sub-01
│   ├── anat
│   │   └── sub-01_T2w.nii.gz
│   └── func
│       └── sub-01_task-rest_bold.nii.gz
└── task-rest_bold.json

Screenshots / relevant information:

2

If fmriprep-rodents accepts T2w images without T1w images, then it may be that it’s calling out to the BIDS validator incorrectly. (fMRIPrep requires T1w images.) Try --skip-bids-validation to see if it runs with T2w only.

3

thanks, will try that. Why does it require T1w?

4

fMRIPrep (for humans) assumes that there’s a T1w image. It just was never written to work with T2w-only datasets because they are extremely rare. fMRIPrep-rodents may have permitted T2w-only datasets (I’m only tangentially involved), but neglected to change the arguments to the BIDS validator.