BIDS_NiChart_DLMUSE: A BIDS-App wrapper for NiChart DLMUSE

About

This is a BIDS-App wrapper for NiChart DLMUSE, a tool for brain mask extraction, brain segmentation and getting ROI volumes.

Installation

BIDS_NiChart_DLMUSE can be installed using pip:

pip install ncdlmuse==<version>

Or using Docker:

docker pull cbica/ncdlmuse:<version>

Or using Singularity:

singularity build ncdlmuse.sif docker://cbica/ncdlmuse:<version>

Usage

Basic usage:

# participant-level analysis
# if no `--participant-label` is provided, run all
ncdlmuse bids_dir output_dir participant --device cuda

# group-level analysis
ncdlmuse bids_dir output_dir group

For more options:

ncdlmuse --help

More information and documentation can be found at https://cbica.github.io/NiChart_DLMUSE.

Using Singularity (Recommended):

# participant-level analysis
singularity run --nv --cleanenv \
       -B /path/to/bids/dir:/data:ro \
       -B /path/to/output/dir:/out \
       -B /path/to/work/dir:/work \
       ncdlmuse.sif \
            /data \
            /out \
            participant \
            --participant-label 01 \
            --session-id 1 \
            --device cuda \
            --work-dir /work \
            --stop-on-first-crash \
            --skip_bids_validation

# group-level analysis
singularity run --nv --cleanenv \
       -B /path/to/bids/dir:/data:ro \
       -B /path/to/output/dir:/out \
       -B /path/to/work/dir:/work \
       ncdlmuse.sif \
            /data \
            /out \
            group