Command line interface
snakebids-app
usage: snakedwi [-h]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[--exclude_participant_label EXCLUDE_PARTICIPANT_LABEL [EXCLUDE_PARTICIPANT_LABEL ...]]
[--no_topup] [--no_bedpost] [--eddy_no_s2v] [--eddy_no_quad]
[--masking_method [{b0_BET,b0_SyN}]]
[--b0_bet_frac B0_BET_FRAC] [--use_gpu_eddy_container]
[--use_gpu_bedpost_container]
[--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.
- --no_topup
Disable topup (default: False)
Default: False
- --no_bedpost
Disable bedpost (default: False)
Default: False
- --eddy_no_s2v
Disables slice-to-volume in eddy. This option must be used if your dwi json does not include SliceTiming (default: False)
Default: False
- --eddy_no_quad
Disables eddy_quad QC report (default: False)
Default: False
- --masking_method
Possible choices: b0_BET, b0_SyN
Brain masking method to use (default: “b0_BET”)
Default: “b0_BET”
- --b0_bet_frac
BET fractional intensity threshold for b0 masking (default: 0.5)
Default: 0.5
- --use_gpu_eddy_container
Use GPU-based eddy container
Default: False
- --use_gpu_bedpost_container
Use GPU-based bedpost container
Default: False
- --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)