LGD White Matter Masking

pl-lgd-hemis is a ChRIS ds plugin which creates left and right hemisphere white matter masks from segmentations.

Its hard-coded mappings are as follows:

anatomical region	mapped classification
cortical plate	grey matter
CSF	CSF
brain stem	CSF
midbrain	CSF
cerebellum	CSF
Clear Label	background
everything else	white matter

Installation

pl-lgd-hemis is a ChRIS plugin, meaning it can run from either within ChRIS or the command-line.

Local Usage

To get started with local command-line usage, use Apptainer (a.k.a. Singularity) to run pl-lgd-hemis as a container:

apptainer exec docker://fnndsc/pl-lgd-hemis lgd_hemis input/ output/

To print its available options, run:

apptainer exec docker://fnndsc/pl-lgd-hemis lgd_hemis --help

lgd_hemis requires two positional arguments: a directory containing input data, and a directory where to create output data.

The input directory is expected to contain subject folders where each folder contains exactly two MINC volumes: segmentation and T1/T2 image. For each subject folder input, an output folder is created containing wm_left.mnc and wm_right.mnc.