cat-surf 1.0.9

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	Mirrors
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	CAT_SurfArea
get_area_normalized	Area normalized by a reference sphere	CAT_SurfArea -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 (QEM) mesh decimation (aggressiveness, preserve_sharp)	CAT_SurfReduce
remove_intersections	Self-intersection repair (MeshFix)	CAT_SurfRemoveIntersections
count_intersections	Count self-intersecting faces	CAT_SurfRemoveIntersections -count
surf_average	Vertex-wise averaging across surfaces (return_rms for std dev)	CAT_SurfAverage
surf_to_sphere	Inflate surface to sphere	CAT_Surf2Sphere
sphere_radius	Mean radius of a spherical surface	—
correct_thickness_folding	Folding-based thickness correction (slope, max_dist clipping)	CAT_SurfCorrectThicknessFolding
point_distance	Linked vertex distance between two meshes	CAT_SurfDistance -link
point_distance_mean	Mean (Tfs) vertex distance	CAT_SurfDistance -mean
hausdorff_distance	Hausdorff distance between two surfaces	—
resample_to_sphere	Resample surface/values onto a target sphere	CAT_SurfResample
surf_deform	Deform a surface toward a volume isovalue	CAT_SurfDeform
surf_to_pial_white	Estimate pial + white surfaces from a central surface	CAT_Surf2PialWhite
central_to_pial	Generate a pial surface from central + thickness	—
surf_warp	DARTEL-based spherical registration	CAT_SurfWarp

Volume operations

Function	Description	Mirrors
vol_sanlm	Structure-adaptive non-local means denoising	CAT_VolSanlm
vol_blood_vessel_correction	Blood vessel intensity correction	CAT_VolBloodVesselCorrection
vol_thickness_pbt	Cortical thickness via projection-based method	CAT_VolThicknessPbt
vol_amap	Adaptive maximum a posteriori tissue segmentation	CAT_VolAmap (core only)
vol_marching_cubes	Isosurface extraction with genus-0 topology correction	CAT_VolMarchingCubes
vol2surf	Map a volume to a surface along inward normals	CAT_Vol2Surf

Volume input convention

Every volume-consuming function accepts three input forms interchangeably:

import cat_surf, nibabel as nib
import numpy as np

# 1. file path
v, f = cat_surf.vol_marching_cubes("brain.nii.gz", threshold=0.5)

# 2. (ndarray, affine) tuple — supply a 4×4 RAS+ affine
v, f = cat_surf.vol_marching_cubes((array, affine), threshold=0.5)

# 3. any nibabel-image-like object (.affine + .get_fdata())
v, f = cat_surf.vol_marching_cubes(nib.load("brain.nii.gz"), threshold=0.5)

The data is auto-converted to float32 (matching the C library's expectation), and 4-D series default to the middle frame. No copy is made if the array is already float32/Fortran-order. Internally a minimal nifti_image is built from the affine — only the fields libCAT actually reads (dims, voxel sizes, sto_xyz).

Registration

Function	Description
bbreg	Full BBR pipeline: optional NMI init → boundary-based surface registration
bbreg_detect_contrast	Auto-detect T1/FLAIR vs T2/BOLD from WM/GM intensity ratio
volume_register_nmi	Cross-modal rigid registration via Normalised Mutual Information (≈ mri_coreg)
volume_register_robust	Same-modality rigid registration via Tukey biweight M-estimation (≈ mri_robust_register)

Basic BBR usage

import cat_surf
import nibabel as nib

# Load surfaces (GIFTI or any format supported by cat_surf.read_surface)
lh_verts, lh_faces = cat_surf.read_surface("lh.white.surf.gii")
rh_verts, rh_faces = cat_surf.read_surface("rh.white.surf.gii")

# Full pipeline: NMI init from T1w reference, then BBR
matrix, cost = cat_surf.bbreg(
    "bold_mean.nii.gz",
    lh_surface=(lh_verts, lh_faces),
    rh_surface=(rh_verts, rh_faces),
    ref_file="T1w.nii.gz",     # NMI initialisation
    verbose=True,
)
print(f"BBR cost: {cost:.4f}")
print("EPI → T1 matrix:\n", matrix)

# Save the 4×4 transform for use with FSL / ANTs
import numpy as np
np.savetxt("epi_to_t1.txt", matrix)

Standalone volume registration

# Cross-modal (EPI ↔ T1w) — NMI
matrix, nmi = cat_surf.volume_register_nmi("T1w.nii.gz", "bold_mean.nii.gz")

# Same-modality (T1w ↔ T1w) — robust IRLS
matrix, res = cat_surf.volume_register_robust("t1_ref.nii.gz", "t1_moving.nii.gz")

Contrast auto-detection

# 0 = T1/FLAIR, 1 = T2/BOLD, -1 = undetermined
contrast = cat_surf.bbreg_detect_contrast(
    "bold_mean.nii.gz",
    lh_surface=(lh_verts, lh_faces),
    rh_surface=(rh_verts, rh_faces),
)

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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cat_surf.cli — drop-in replacement for the CAT binaries

The cat_surf.cli subpackage mirrors the CAT_* command-line binaries one-to-one: same names (snake_case, CAT_ prefix dropped), same positional argument order, same option semantics and defaults. Each function reads its inputs from disk, calls the in-memory numpy wrapper, and writes the outputs — ideal for porting shell scripts to Python.

from cat_surf import cli

# CAT_VolMarchingCubes brain.nii.gz brain.gii -thresh 0.5
cli.vol_marching_cubes("brain.nii.gz", "brain.gii", threshold=0.5)

# CAT_Surf2PialWhite central.gii thickness.txt labels.nii pial.gii white.gii
cli.surf2pial_white("central.gii", "thickness.txt", "labels.nii",
                    "pial.gii", "white.gii")

# CAT_SurfDistance -mean surf1.gii surf2.gii out.txt
cli.surf_distance("surf1.gii", "surf2.gii", "out.txt", mode="mean")

# CAT_VolSanlm in.nii out.nii -strength 1.0
cli.vol_sanlm("in.nii", "out.nii", strength=1.0)

The full mapping:

CAT binary	cat_surf.cli.<name>
CAT_Surf2PialWhite	surf2pial_white
CAT_Surf2Sphere	surf2sphere
CAT_SurfArea	surf_area
CAT_SurfAverage	surf_average
CAT_SurfCorrectThicknessFolding	surf_correct_thickness_folding
CAT_SurfDeform	surf_deform
CAT_SurfDistance	surf_distance
CAT_SurfReduce	surf_reduce
CAT_SurfRemoveIntersections	surf_remove_intersections
CAT_SurfResample	surf_resample
CAT_SurfWarp	surf_warp
CAT_Vol2Surf	vol2surf
CAT_VolAmap	vol_amap
CAT_VolBloodVesselCorrection	vol_blood_vessel_correction
CAT_VolMarchingCubes	vol_marching_cubes
CAT_VolSanlm	vol_sanlm
CAT_VolThicknessPbt	vol_thickness_pbt

For composable in-memory pipelines, prefer the lower-level cat_surf API directly — the CLI shims are just thin convenience wrappers.

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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