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)