Subdivide Masks

pl-subdiv-minc is a ChRIS ds plugin which wraps mincresample. It increases the resolution of binary mask images using trilinear interpolation. This is useful for fetal brain MRI where the voxel sizes are very large relative to the shape of the mask.

See also: https://github.com/FNNDSC/ep-subdivide-mnc-methods

Installation

pl-subdiv-minc 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-subdiv-minc as a container:

apptainer exec docker://fnndsc/pl-subdiv-minc subdiv_mask [--args values...] input/ output/

To print its available options, run:

apptainer exec docker://fnndsc/pl-subdiv-minc subdiv_mask --help

Examples

Some example input MINC files can be found in the datalad repository here: https://github.com/FNNDSC/example_shapes/tree/master/minc

apptainer exec docker://fnndsc/pl-subdiv-minc:latest subdiv_mask incoming/ outgoing/

Get JSON Representation

Run chris_plugin_info to produce a JSON description of this plugin, which can be uploaded to a ChRIS Store.

docker run --rm localhost/fnndsc/pl-subdiv-minc:dev chris_plugin_info > chris_plugin_info.json