Command line interface

usage: snakedwi [-h]
                [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                [--exclude_participant_label EXCLUDE_PARTICIPANT_LABEL [EXCLUDE_PARTICIPANT_LABEL ...]]
                [--output-spaces {T1w,dwi} [{T1w,dwi} ...]]
                [--skip-denoise SKIP_DENOISE] [--derivatives]
                [--masking-method [{b0_BET,b0_SyN,b0_synthstrip}]]
                [--b0-bet-frac B0_BET_FRAC]
                [--gradcorrect_coeffs GRADCORRECT_COEFFS]
                [--sdc_method {optimal,topup,sdcflow,synthsr,synb0,none}]
                [--sdc_method_alternate {sdcflow,synthsr,synb0}]
                [--use_eddy_s2v] [--use_eddy_gpu] [--skip_eddy_quad]
                [--slspec-txt SLSPEC_TXT]
                [--default-phase-encoding-direction {i,i-,j,j-,k,k-}]
                [--gradcorrect-skip-t1w] [--use_bedpost] [--use-bedpost-gpu]
                [--rigid-dwi-t1-init [{identity,image-centers}]]
                [--rigid_dwi_t1_iters RIGID_DWI_T1_ITERS]
                [--fs-license FS_LICENSE] [--version]
                [--filter-dwi ENTITY[:METHOD][=VALUE] [ENTITY[:METHOD][=VALUE]
                ...]] [--filter-T1w ENTITY[:METHOD][=VALUE]
                [ENTITY[:METHOD][=VALUE] ...]]
                [--wildcards-dwi WILDCARD [WILDCARD ...]]
                [--wildcards-T1w WILDCARD [WILDCARD ...]] [--path-dwi PATH]
                [--path-T1w PATH] [--pybidsdb-dir PATH] [--pybidsdb-reset]
                [--help-snakemake] [--force-output]
                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, --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, --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.

--output-spaces, --output_spaces

Possible choices: T1w, dwi

Output space(s) for the final preprocessed DWI data. Options are “T1w” (registered to T1w anatomical image) and “dwi” (native DWI space). Multiple spaces can be specified. If only “dwi” is selected, T1w images will not be required or processed. (default: [‘T1w’])

Default: ['T1w']

--skip-denoise, --skip_denoise

Skip the denoising step of the workflow. By default, denoising is performed if input diffusion data was acquired with at least 30 directions. (default: None)

--derivatives

Default: False

--masking-method, --masking_method

Possible choices: b0_BET, b0_SyN, b0_synthstrip

Brain masking method to use for b0 (default: ‘b0_synthstrip’)

Default: 'b0_synthstrip'

--b0-bet-frac, --b0_bet_frac

BET fractional intensity threshold for b0 masking (default: 0.5)

Default: 0.5

--gradcorrect_coeffs, --gradcorrect-coeffs

Path to file containing scanner specific gradient correction coefficients. Use this to enable gradient non-linearity correction. (default: None)

--sdc_method, --sdc-method

Possible choices: optimal, topup, sdcflow, synthsr, synb0, none

Set the susceptibility distortion correction (SDC) method to be used. By default, the optimal correction method is chosen based on the data available (“topup” if 2+ phase encoding directions or “synthsr” if single phase encoding direction). To skip SDC, set method to “none”. (default: ‘optimal’)

Default: 'optimal'

--sdc_method_alternate, --sdc-method-alternate

Possible choices: sdcflow, synthsr, synb0

Set alternate method to be used for single phase encoding SDC when “–sdc_method” is set to “optimal”, otherwise this flag is ignored. (default: ‘synthsr’)

Default: 'synthsr'

--use_eddy_s2v, --use-eddy-s2v

Enable slice-to-volume correction in Eddy. Your dwi json must either include SliceTiming information, or you must specify it with the –slspec-txt flag. If any subjects do not have this information, they will be run without slice-to-volume enabled. You must also use the –use_eddy_gpu option. (default: False)

Default: False

--use_eddy_gpu, --use-eddy-gpu

Use GPU-based version of eddy (must set container path in config)

Default: False

--skip_eddy_quad, --skip-eddy-quad

Disables eddy_quad QC report (default: False)

Default: False

--slspec-txt, --slspec_txt

Path to custom slspec txt file for use with eddy. Must use this if SliceTiming does not exist in the JSON (default: False)

Default: False

--default-phase-encoding-direction, --default_phase_encoding_direction

Possible choices: i, i-, j, j-, k, k-

Sets the PhaseEncodingDirection to use for dwi acquisitions where it is not specified in the JSON file. By default, none will be assumed, and the workflow will fail for subjects where this JSON tag is missing (default: ‘’)

Default: ''

--gradcorrect-skip-t1w, --gradcorrect_skip_t1w

Default: False

--use_bedpost, --use-bedpost

Enable bedpost (disabled by default)

Default: True

--use-bedpost-gpu, --use_bedpost_gpu

Use GPU-based version of bedpost (must set container path in config)

Default: False

--rigid-dwi-t1-init, --rigid_dwi_t1_init

Possible choices: identity, image-centers

Type of initialization to use for dwi to t1 rigid registration. (default: ‘identity’)

Default: 'identity'

--rigid_dwi_t1_iters, --rigid-dwi-t1-iters

Number of iterations to use at each multi-resolution stage for dwi to t1 rigid registration. (default: ‘50x50’)

Default: '50x50'

--fs-license, --fs_license

Path to the Freesurfer license file (needed for synb0 SDC method)

Default: False

--version

Print the version of snakedwi

--pybidsdb-dir, --pybidsdb_dir

Optional path to directory of SQLite databasefile for PyBIDS. If directory is passed and folder exists, indexing is skipped. If pybidsdb_reset is called, indexing will persist

--pybidsdb-reset, --pybidsdb_reset

Reindex existing PyBIDS SQLite database

Default: False

--help-snakemake, --help_snakemake

Options to Snakemake can also be passed directly at the command-line, use this to print Snakemake usage

--force-output, --force_output

Force output in a new directory that already has contents

Default: False

BIDS FILTERS

Update filters for input components. Each filter can be specified as a ENTITY=VALUE pair to select an value directly. To use regex filtering, ENTITY:match=REGEX or ENTITY:search=REGEX can be used for re.match() or re.search() respectively. Regex can also be used to select multiple values, e.g. ‘session:match=01|02’. ENTITY:required and ENTITY:none can be used to require or prohibit presence of an entity in selected paths, respectively. ENTITY:optional can be used to remove a filter.

--filter-dwi, --filter_dwi: (default: suffix=dwi extension=.nii.gz scope=raw invalid_filters=allow datatype=dwi)
--filter-T1w, --filter_T1w: (default: suffix=T1w extension=.nii.gz datatype=anat invalid_filters=allow)

INPUT WILDCARDS

Provide entities to be used as wildcards.

--wildcards-dwi, --wildcards_dwi: (default: subject session acquisition run direction)
--wildcards-T1w, --wildcards_T1w: (default: subject session acquisition run)

PATH OVERRIDE

Options for overriding BIDS by specifying absolute paths that include wildcards, e.g.: /path/to/my_data/{subject}/t1.nii.gz

--path-dwi, --path_dwi
--path-T1w, --path_T1w