Dear Users,
Looking forward for Your support!
Summary of what happened:
I tried using heudiconv (instead Osirix + bids plugin) and I don’t understand why I can’t get the proper output. Problems:
- JSONs are missing at all.
- The program adds subject’s name at the beginning of the path automatically. I’d like ‘sub-name’ as it’s returned by the heuristic.
Command used (and if a helper script was used, a link to the helper script or the command generated):
docker run --user=(id -u):(id -g) -e “UID=(id -u)" -e "GID=(id -g)” --rm -t -v pwd:/base nipy/heudiconv:latest
-d /base/{subject}////.dcm -o /base/bids -f /base/code/heuristic.py -c dcm2niix -ss 01 -s xxx --anon-cmd /base/code/anon.py --minmeta
Version:
1.0.0 both from pip/conda and docker
Relevant log outputs (up to 20 lines):
tree bids
bids
└── xxx
└── sub-xxx
└── ses-01
├── anat
│ └── sub-xxx_ses-01_T1w.nii
├── fmap
│ └── sub-xxx_ses-01_dir-PA_epi.nii
└── func
├── sub-xxx_ses-01_task-fmri_run-01_bold.nii
└── sub-xxx_ses-01_task-fmri_run-02_bold.nii
7 directories, 4 files
Screenshots / relevant information:
INFO: [Node] Finished “convert”, elapsed time 0.198728s.
INFO: Adding “IntendedFor” to the fieldmaps in /base/bids/xxx/sub-B375_ses-01.
WARNING: We cannot add the IntendedFor field: no fmap/ in /base/bids/xxx/sub-xxx_ses-01
INFO: PROCESSING DONE: {‘subject’: ‘xxx’, ‘outdir’: ‘/base/bids/’, ‘session’: ‘01’}
anon.txt (377 Bytes)
heuristic.txt (2.0 KB)