CorpusCallosum.shape.postprocessing

CorpusCallosum.shape.postprocessing.check_area_changes(contours, threshold=0.3)

Check for large changes between consecutive CC areas and issue warnings.

Parameters:

contourslist[np.ndarray]

List of contours (2, N).

thresholdfloat, default=0.3

Threshold for relative change.

Returns:

bool

True if no large area changes are detected, False otherwise.

CorpusCallosum.shape.postprocessing.make_subdivision_mask(slice_shape, subdivision_lines, vox2ras, plot=False)

Create a mask for subdividing the corpus callosum based on split contours.

Parameters:

slice_shapepair of ints

Shape of the slice (rows, cols).

subdivision_lineslist[np.ndarray]

List of pairs of points defining the subdivision lines.

vox2rasAffineMatrix4x4

The vox2ras transformation matrix for the requested shape.

plotbool, default=False

Whether to plot the subdivision mask.

Returns:

np.ndarray

A mask of shape slice_shape where each pixel is labeled with a value from SUBSEGEMNT_LABELS indicating which subdivision segment it belongs to.

Notes

The function: 1. Creates coordinate grids for all points in the slice. 2. Initializes mask with first segment label. 3. For each subdivision line: - Tests which points lie to the right of the line. - Updates labels for those points.

CorpusCallosum.shape.postprocessing.offset_affine(offset)

Generate an affine transformation matrix that only constitutes an offset (vector).

Parameters:

offsetarray_like

A 3-dimensional offset vector (shape (3,)) to offset with.

Returns:

np.ndarray

Modified 4x4 affine transformation matrix with the specific offset.

Raises:

TypeError

If offset is not a

CorpusCallosum.shape.postprocessing.recon_cc_surf_measure(segmentation, slice_idx, slice_lia_vox2midslice_ras, ac_coords_vox, pc_coords_vox, num_thickness_points, subdivisions, subdivision_method, contour_smoothing)

Reconstruct surfaces and compute measures for a single slice for the corpus callosum.

Parameters:

segmentationnp.ndarray

3D segmentation array.

slice_idxint

Index of the slice to process.

slice_lia_vox2midslice_rasAffineMatrix4x4

4x4 affine transformation matrix.

ac_coords_voxnp.ndarray

AC voxel coordinates with shape (2,) containing its [y,x] positions.

pc_coords_voxnp.ndarray

PC voxel coordinates with shape (2,) containing its [y,x] positions.

num_thickness_pointsint

Number of points for thickness estimation.

subdivisionslist[float]

List of fractions for anatomical subdivisions.

subdivision_methodSubdivisionMethod

Method for contour subdivision (‘shape’, ‘vertical’, ‘angular’, or ‘eigenvector’).

contour_smoothingint

Gaussian sigma for contour smoothing.

Returns:

measuresCCMeasuresDict

Dictionary containing measurements.

contourCCContour

The contour object containing points, thickness values, and endpoint indices.

Raises:

ValueError

If no CC is found in the specified slice.

Notes

The function performs the following steps: 1. Extracts CC contour and identifies endpoints. 2. Converts coordinates to RAS space. 3. Calculates thickness profile using Laplace equation. 4. Computes shape metrics and subdivisions. 5. Generates visualization data.

CorpusCallosum.shape.postprocessing.recon_cc_surf_measures_multi(segmentation, slice_selection, upright_header, fsavg2midslab_vox2vox, fsavg_vox2ras, orig2fsavg_vox2vox, midslices, ac_coords_vox, pc_coords_vox, num_thickness_points, subdivisions, subdivision_method, contour_smoothing, subject_dir)

Surface reconstruction and metrics computation of corpus callosum slices based on selection mode.

Parameters:

segmentationnp.ndarray

3D segmentation array in LIA orientation.

slice_selectionstr

Which slices to process (‘middle’, ‘all’, or slice number).

upright_headerMGHHeader

The header of the upright image.

fsavg2midslab_vox2voxAffineMatrix4x4

The vox2vox transformation matrix from fsaverage (upright) space to the segmentation slab.

fsavg_vox2rasnp.ndarray

Base affine transformation matrix (fsaverage, upright space).

orig2fsavg_vox2voxAffineMatrix4x4

The transformation matrix from orig to fsaverage in voxel space.

midslicesnp.ndarray

Array of mid-sagittal slices.

ac_coords_voxnp.ndarray

AC voxel coordinates with shape (2,) containing its [y,x] positions.

pc_coords_voxnp.ndarray

PC voxel coordinates with shape (2,) containing its [y,x] positions.

num_thickness_pointsint

Number of points for thickness estimation.

subdivisionslist[float]

List of fractions for anatomical subdivisions.

subdivision_method‘shape’, ‘vertical’, ‘angular’, ‘eigenvector’

Method for contour subdivision.

contour_smoothingint

Gaussian sigma for contour smoothing.

subject_dirSubjectDirectory

The SubjectDirectory object managing file names in the subject directory.

Returns:

list of CCMeasuresDict

List of slice processing results.

list of concurrent.futures.Future

List of background IO processes.

list of CCContour

List of CC contours.

int

Number of failed slices.

CorpusCallosum.shape.postprocessing.subdivide_contour(midline_equi, subdivisions, ac_pt_acpc, contour_in_acpc_space, subdivision_method)

Subdivide the contour based on the subdivision method.

Parameters:

midline_equiPoints2dType

The midline equidistant points in ACPC space.

subdivisionslist[float]

The subdivisions.

ac_pt_acpcVector2d

The AC point in ACPC space (needed for eigenvector subdivision).

contour_in_acpc_spacePoints2dType

The contour in ACPC space.

subdivision_methodSubdivisionMethod

The subdivision method. One of “shape”, “vertical”, “angular”, or “eigenvector”.

Returns:

tuple[list[float], ContourList, np.ndarray, list[Points2dType]]

The areas, split contours, split points midline, and subdivision lines.

CorpusCallosum.shape.postprocessing.test_left_of_line(coords, line_start, line_end)

Test whether points in coords are to the left of the line (line_start->line_end).

Parameters:

coordsnp.ndarray

Array of coordinates of shape (…, N).

line_startarray_like

[x, y] coordinates of line start point (N,).

line_endarray_like

[x, y] coordinates of line end point (N,).

Returns:

np.ndarray

Boolean array where True means point is to the left of the line of shape coords.shape[:-1].