Based on the documentation, I’m running this command:
docker run -i --rm \
-v /Volumes/Data/Research/fmri/fmri_rep_sup:/bids_dataset \
-v /Volumes/Data/Research/fmri/fmri_rep_sup/output:/output \
bids/mrtrix3_connectome \
/bids_dataset /output preproc --participant_label 01
And this is my data structure for sub-01 within the folder I’ve pointed bids_dataset to:
sub-01
├── anat
│ ├── sub-01_T1w.json
│ └── sub-01_T1w.nii
├── dwi
│ ├── sub-01_dwi.bval
│ ├── sub-01_dwi.bvec
│ ├── sub-01_dwi.json
│ └── sub-01_dwi.nii
├── fmap
│ ├── sub-01_magnitude1.json
│ ├── sub-01_magnitude1.nii
│ ├── sub-01_phasediff.json
│ └── sub-01_phasediff.nii
└── func
├── sub-01_task-ao_run-01_bold.json
├── sub-01_task-ao_run-01_bold.nii
├── sub-01_task-ao_run-01_events.tsv
├── sub-01_task-ao_run-02_bold.json
├── sub-01_task-ao_run-02_bold.nii
├── sub-01_task-ao_run-02_events.tsv
├── sub-01_task-ao_run-03_bold.json
├── sub-01_task-ao_run-03_bold.nii
├── sub-01_task-ao_run-03_events.tsv
├── sub-01_task-ao_run-04_bold.json
├── sub-01_task-ao_run-04_bold.nii
└── sub-01_task-ao_run-04_events.tsv
Yet, MRtrix3 complains that the fmap folder isn’t present.
mrtrix3_connectome.py: Commencing execution for session: 'sub-01'
mrtrix3_connectome.py: Generated scratch directory: /mrtrix3_connectome.py-tmp-VS3ZOU/
mrtrix3_connectome.py: Importing DWI data into scratch directory
Command: mrconvert /bids_dataset/sub-01/dwi/sub-01_dwi.nii /mrtrix3_connectome.py-tmp-VS3ZOU/dwi1.mif -fslgrad /bids_dataset/sub-01/dwi/sub-01_dwi.bvec /bids_dataset/sub-01/dwi/sub-01_dwi.bval -json_import /bids_dataset/sub-01/dwi/sub-01_dwi.json
mrtrix3_connectome.py: Importing fmap data into scratch directory
mrtrix3_connectome.py: [ERROR] Inadequate data for pre-processing of session "sub-01": No phase-encoding contrast in input DWIs, and no fmap/ directory, so EPI distortion correction cannot be performed
Thanks for any suggestions!