Command line interface¶
snakebids-app
usage: hippunfold [-h]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[--exclude_participant_label EXCLUDE_PARTICIPANT_LABEL [EXCLUDE_PARTICIPANT_LABEL ...]]
[--derivatives DERIVATIVES [DERIVATIVES ...]]
[--bet_frac BET_FRAC]
[--filter_dwi FILTER_DWI [FILTER_DWI ...]]
[--filter_t1w FILTER_T1W [FILTER_T1W ...]]
bids_dir output_dir {participant}
Positional Arguments¶
- bids_dir
The directory with the input dataset formatted according to the BIDS standard.
- output_dir
The directory where the output files should be stored. If you are running group level analysis this folder should be prepopulated with the results of the participant level analysis.
- analysis_level
Possible choices: participant
Level of the analysis that will be performed.
Named Arguments¶
- --participant_label
The label(s) of the participant(s) that should be analyzed. The label corresponds to sub-<participant_label> from the BIDS spec (so it does not include “sub-“). If this parameter is not provided all subjects should be analyzed. Multiple participants can be specified with a space separated list.
- --exclude_participant_label
The label(s) of the participant(s) that should be excluded. The label corresponds to sub-<participant_label> from the BIDS spec (so it does not include “sub-“). If this parameter is not provided all subjects should be analyzed. Multiple participants can be specified with a space separated list.
- --derivatives
Path(s) to a derivatives dataset, for folder(s) that contains multiple derivatives datasets (default: False)
Default: False
- --bet_frac
Specify custom template
- --filter_dwi
Filters (PyBIDS) for dwi, where FILTER_DWI is key=value pair(s) (default: suffix=dwi extension=.nii.gz scope=raw invalid_filters=allow datatype=dwi)
- --filter_t1w
Filters (PyBIDS) for t1w, where FILTER_T1W is key=value pair(s) (default: suffix=T1w extension=.nii.gz scope=raw datatype=anat invalid_filters=allow space=None)