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