Command line interface

Snakebids helps build BIDS Apps with Snakemake

usage: funcmasker-flex [-h] [--workflow-mode] [--force-conversion]
                       [--retrofit] [--help-snakemake]
                       [--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                       [--exclude_participant_label EXCLUDE_PARTICIPANT_LABEL [EXCLUDE_PARTICIPANT_LABEL ...]]
                       [--derivatives DERIVATIVES [DERIVATIVES ...]]
                       [--filter-bold FILTER_BOLD [FILTER_BOLD ...]]
                       [--filter-mask FILTER_MASK [FILTER_MASK ...]]
                       [--wildcards-bold WILDCARDS_BOLD [WILDCARDS_BOLD ...]]
                       [--wildcards-mask WILDCARDS_MASK [WILDCARDS_MASK ...]]
                       [--path-bold PATH_BOLD] [--path-mask PATH_MASK]
                       bids_dir output_dir
                       {participant,train,evaluate,evaluate_rutherford}

STANDARD

Standard options for all snakebids apps

--workflow-mode, --workflow_mode, -W

Run Snakebids in Workflow mode. This will cause the entire Snakebids app, except for the results folder, to be copied into your output_dir. Snakemake will be run in this new child app, and results will be put in output_dir/results.

Default: False

--force-conversion, --force_conversion, -x

Force snakebids to convert a workflow output to a bidsapp output. conversion will delete all the files in the workflow snakebids app.

Default: False

--retrofit

Convert a legacy Snakebids output (Snakebids 0.3.x or lower) into bidsapp mode. This will delete any config files currently in the output.

Default: False

--help-snakemake, --help_snakemake

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

SNAKEBIDS

Options for snakebids app

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, train, evaluate, evaluate_rutherford

Level of the analysis that will be performed.

--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.

--derivatives

Path(s) to a derivatives dataset, for folder(s) that contains multiple derivatives datasets (default: False)

Default: False

BIDS FILTERS

Filters to customize PyBIDS get() as key=value pairs

--filter-bold, --filter_bold

(default: suffix=bold scope=raw extension=.nii.gz datatype=func)

--filter-mask, --filter_mask

(default: suffix=bold scope=derivatives extension=.nii.gz datatype=func)

INPUT WILDCARDS

File path entities to use as wildcards in snakemake

--wildcards-bold, --wildcards_bold

(default: subject session acquisition task run)

--wildcards-mask, --wildcards_mask

(default: subject session acquisition task 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-bold, --path_bold

--path-mask, --path_mask