For information about CVS itself, see its paper.
Usage:
usage: run.py [-h]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[--skullstrip] [--thresh [THRESH]] [--n4] [--cpus CPUS]
[--bids-filter-file FILE] [--skip_bids_validator] [-v]
bids_dir output_dir {participant,group}
CVS entrypoint script
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.
{participant,group} Level of the analysis that will be performed. Multiple
participant level analyses can be run independently
(in parallel) using the same output_dir.
optional arguments:
-h, --help show this help message and exit
--participant_label PARTICIPANT_LABEL [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.
--skullstrip Whether to skull strip inputs
--thresh [THRESH] Threshold for binary segmentation mask
--n4 Whether to N4 correct input
--cpus CPUS Number of CPUs to use
--bids-filter-file FILE
a JSON file describing custom BIDS input filters using
PyBIDS. For further details, please check out https://
fmriprep.readthedocs.io/en/latest/faq.html#how-do-I-
select-only-certain-files-to-be-input-to-fMRIPrep
--skip_bids_validator
Whether or not to perform BIDS dataset validation
-v, --version show program's version number and exit