cbica/nichart_dlmuse repository overview

NiChart_DLMUSE processes T1 scans and performs automatic skull-stripping via DLICV and segmentation via DLMUSE. A CSV of regional volumes for each scan are also calculated and produced as DLMUSE_Volumes.csv.

A sample command is:

docker run -it --rm --gpus all --ipc=host -v /path/to/input:/input:ro -v /path/to/output:/output:rw cbica/nichart_dlmuse:1.0.10 -i /input -o /output -d cuda

Replace /path/to/input and /path/to/output with the real directories on your host machine. Input directory should contain T1 NIFTI (.nii.gz) scans.

--ipc=host is mandatory due to quirks of the containerized algorithm. --gpus all is mandatory if running with CUDA.