cat-surf 1.0.1

Cython bindings to the CAT-Surface library (libCAT) for cortical surface analysis

cat-surf — Python bindings for CAT-Surface

cat-surf provides Python access to CAT-Surface, a mature C/C++ toolkit for surface-based neuroimaging analysis, focusing on the processing and analysis of cortical surface meshes.

CAT-Surface has been used internally for more than 10 years as part of CAT12, the SPM toolbox for computational anatomy. With this package, it is now distributed as an independent Python package for direct integration into external workflows to make CAT-Surface easier to use:

• in T1Prep workflows (currently relying on CAT-Surface binaries)
• in Python-based pipelines without subprocess-heavy wrappers
• in reproducible environments via published wheels

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Installation

pip install cat-surf

Pre-built wheels are available for:

• macOS — arm64 (Apple Silicon), x86_64 (Intel)
• Linux — x86_64, aarch64 (manylinux)
• Python 3.9 – 3.13

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Basic usage

import cat_surf

# Check version
print(cat_surf.__version__)

# Load a surface file (GIFTI, FreeSurfer, BIC/MNI formats)
vertices, faces = cat_surf.read_surface("lh.central.gii")

# Per-vertex area
area, total_area = cat_surf.get_area(vertices, faces)

# Euler characteristic
chi = cat_surf.euler_characteristic(vertices, faces)

# Smooth per-vertex data (heat kernel, FWHM in mm)
smoothed = cat_surf.smooth_heatkernel(vertices, faces, area, fwhm=20.0)

Surface operations

Function	Description
read_surface / write_surface	Multi-format surface I/O (GIFTI, FreeSurfer, BIC)
read_values / write_values	Per-vertex scalar I/O
get_area	Per-vertex and total surface area
get_area_normalized	Area normalized by a reference sphere
euler_characteristic	Topological integrity check
smooth_heatkernel	Heat-kernel smoothing of per-vertex data
smooth_mesh	Laplacian/Taubin mesh vertex smoothing
smoothed_curvatures	Mean curvature estimation
sulcus_depth	Sulcal depth via depth potential
reduce_mesh	Quadric mesh decimation
remove_intersections	Self-intersection repair
count_intersections	Count self-intersecting faces
surf_average	Vertex-wise averaging across surfaces
surf_to_sphere	Inflate surface to sphere
sphere_radius	Mean radius of a spherical surface
correct_thickness_folding	Folding-based thickness correction
point_distance	Vertex-to-surface point distances (symmetric)
point_distance_mean	Mean vertex-to-surface distance
hausdorff_distance	Hausdorff distance between two surfaces

Volume operations

Function	Description
vol_sanlm	Structure-adaptive non-local means denoising
vol_blood_vessel_correction	Blood vessel intensity correction
vol_thickness_pbt	Cortical thickness via projection-based method
vol_amap	Adaptive maximum a posteriori tissue segmentation
vol_marching_cubes	Isosurface extraction from a volume file

Conversion utilities

Function	Description
arrays_to_polygons	Convert NumPy vertex/face arrays to internal polygon mesh
polygons_to_arrays	Convert internal polygon mesh back to NumPy arrays

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Typical use cases

• Cortical mesh processing (resampling, smoothing, metrics)
• Thickness and folding related computations
• Volume-to-surface projection
• Denoising and volume preprocessing for structural MRI

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Citation / provenance

If you use this package in research, please cite Dahnke et al., 2013 and mention the cat-surf package version for reproducibility.

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Source

• Source: https://github.com/ChristianGaser/CAT-Surface