Fetal CP Surface Extraction

Fetal brain cortical plate surface extraction using CIVET marching-cubes (sphere_mesh).

Abstract

pl-fetal-cp-surface-extract consumes binary volumetric .mnc brain masks to produce surfaces as .obj files with standard connectivity (81,920 triangles). This program is suitable for targeting the inner cortical plate surface (gray-white matter boundary) of high-quality human fetal brain MRI segmentation for subjects between 23-35 gestational weeks of age.

Background

Polygonal surface mesh representations of brain hemispheres are useful for measuring cortical thickness, image registration, and quantitative regional analysis.

Surface Extraction Algorithm

1. Proprocess mask using mincmorph to fill in disconnected voxels (improve mask quality)
2. Marching-cubes -> spherical topology surface mesh with unknown number of triangles
3. Sphere-to-sphere interpolation -> resample mesh to standard connectivity of 81,920 triangles, preserving morphology

Installation

pl-fetal-cp-surface-extract is a ChRIS plugin, meaning it can run from either within ChRIS or the command-line.

Usage

extract_cp reads mask files from an input directory and creates the resulting surface files in an output directory.

Input

Input files should be MINC .mnc files representing a mask of the white matter (WM) for a single brain hemisphere (either left or right). WM should be indicated by a value of 1, background value should be 0.

If the input directory contains multiple masks, they will all be processed individually and in parallel.

Options

--mincmorph-iterations

Number of mincmorph iterations to perform on the mask before marching-cubes. Use a larger value as a workaround for masks which have missing voxels. However, extremely bad masks will require external correction, for instance, using mincdefrag. Garbage in, garbage out.

extract_cp --mincmorph-iterations 10 /incoming /outgoing

--adapt_object_mesh

Arguments to pass to adapt_object_mesh, which does mesh smoothing. Use a larger value if the results are bumpy/voxelated in appearance.

extract_cp --adapt_object_mesh 1,100,1 /incoming /outgoing

--inflate_to_sphere_implicit

Arguments to pass to inflate_to_sphere_implicit. The default value (200, 200) should work for fetal brains. While it shouldn't be necessary, increasing the values shouldn't do any harm, and would help compensate for larger brain sizes.

Local Usage

To get started with local command-line usage, use Apptainer to run pl-fetal-cp-surface-extract as a container:

apptainer exec docker://fnndsc/pl-fetal-cp-surface-extract extract_cp input/ output/

To print its available options, run:

apptainer exec docker://fnndsc/pl-fetal-cp-surface-extract extract_cp --help

Suggested Software

Before pl-fetal-cp-surface-extract

• pl-nums2mask: create input masks

After pl-fetal-cp-surface-extract

• pl-surfdisterr: QC
• pl-smoothness-error: QC

Development

Instructions for developers.

Building

Build a local container image:

docker build -t localhost/fnndsc/pl-fetal-cp-surface-extract .

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-fetal-cp-surface-extract chris_plugin_info > chris_plugin_info.json

Local Test Run

Mount the source code extract_cp.py into a container to test changes without rebuild.

docker run --rm -it --userns=host -u $(id -u):$(id -g) \
    -v $PWD/extract_cp:/opt/conda/lib/python3.10/site-packages/extract_cp:ro \
    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
    localhost/fnndsc/pl-fetal-cp-surface-extract extract_cp /incoming /outgoing