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)