Installation

To install MEGPrep, you need to ensure that Docker are installed on your system. Please follow these steps for installation:

Install Docker

Install Docker according to your operating system. For detailed installation instructions, please visit the Docker official website.

Download MEGPrep Image

docker pull cmrlab/megprep:<version>

See the parameter description

docker run cmrlab/megprep:<version> -h Usage: /program/nextflow/run.sh [options] Options:

-c, --config

Specify the Nextflow config file (default: nextflow.config)

-i, --input

Specify the input directory

-o, --output

Specify the output directory(including report results.)

-r, --view-report

Run Streamlit to view the report (does not run Nextflow)

--fs_license_file

Specify the FreeSurfer license file

--fs_subjects_dir

Specify the FreeSurfer SUBJECTS_DIR directory containing processed T1 results

--t1_dir

Specify the T1 image directory

--t1_input_type

Specify the T1 input type

--anat_only

Run only the FreeSurfer related steps

--meg_only

Run only the MEG related steps

--resume

Resume the previous run(nextflow options)