Usage

wrapper

meegpype-wrapper runs the meegpype pipelines inside the Docker / Apptainer image.

forward

usage: meegpype-wrapper forward [-h]
                                [--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                                [-w WORK_DIR] [--bem-method BEM_METHOD]
                                [--surface-src] [--volume-src] [--pos POS]
                                [--templateflow-dir TEMPLATEFLOW_DIR]
                                [--fs-license-file FS_LICENSE_FILE]
                                [--nprocs NPROCS] [--engine ENGINE]
                                bids_dir output_dir analysis_level

Positional Arguments

bids_dir

The root folder of a BIDS valid dataset.

output_dir

The output path for the outcomes of preprocessing and visual reports.

analysis_level

Possible choices: participant Processing stage to be run, only “participant” in the case of meegpype-forward.

Named Arguments

--participant-label, --participant_label

A space delimited list of participant identifiers or a single identifier (the sub- prefix can be removed).

-w, --work-dir

Path where intermediate results should be stored.

--bem-method

Method to use for BEM surface generation. Options: ‘basic’ or ‘refined’. Default is ‘basic’.

Default: 'basic'

--surface-src

Use a surface source distribution.

Default: False

--volume-src

Use a volumetric source distribution.

Default: False

--pos, --position

Positions to use for sources. A grid will be constructed with the spacing given by pos in mm, generating a volume source space

Default: 5

--templateflow-dir

Persistent folder used as TemplateFlow cache. Default is $TEMPLATEFLOW_HOME or ~/.cache/templateflow.

--fs-license-file

Path to FreeSurfer license key file.

--nprocs, --nthreads, --n_cpus, --n-cpus

Maximum number of threads across all processes.

Default: 1

--engine

Engine to use for running the pipeline. Can be ‘docker’ or ‘apptainer’. Default is ‘docker’.

Default: 'docker'