Usage Notes

Command line interface

Evaluating the residual motion in fMRI connectome and visualize reports

usage: wonkyconn [-h] --phenotypes PHENOTYPES --atlas LABEL ATLAS_PATH [-v]
                 [--debug] [--light-mode] [--verbosity {0,1,2,3}] [--textual]
                 [--suppress-warnings]
                 bids_dir output_dir {group}

Positional Arguments

bids_dir

The directory with the input dataset (e.g. fMRIPrep derivative)formatted according to the BIDS standard

output_dir

The directory where the output files should be stored

analysis_level

Possible choices: group

Level of the analysis that will be performed. Only group level is available

Named Arguments

--phenotypes

Path to the phenotype file that has the columns participant_id, gender coded as M and F and age in years

--atlas

Specify the atlas label and the path to the atlas file (for example –atlas Schaefer2018 /path/to/atlas.nii.gz)

-v, --version

show program’s version number and exit

--debug

Default: False

--light-mode

Disable sex and age prediction to reduce runtime.

Default: False

--verbosity

Possible choices: 0, 1, 2, 3

Verbosity level.

Default: 2

--textual

Launch the Textual UI to configure and run wonkyconn.

Default: False

--suppress-warnings

Suppress Python RuntimeWarnings during processing.

Default: False