cedalion.io.anatomy

Functions for reading and processing anatomical data.

Functions

cell_coordinates(mask, affine[, units])

Get the coordinates of each voxel in the transformed mask.

read_segmentation_masks(basedir[, mask_files])

Read segmentation masks from NIFTI files.
cedalion.io.anatomy.read_segmentation_masks(
basedir: str,
mask_files: Dict[str, str] = {'csf': 'csf.nii', 'gm': 'gm.nii', 'scalp': 'scalp.nii', 'skull': 'skull.nii', 'wm': 'wm.nii'},
) → Tuple[DataArray, ndarray][source]

Read segmentation masks from NIFTI files.

Parameters:

  • basedir (str) – Directory containing the mask files

  • mask_files (Dict[str, str]) – Dictionary mapping segmentation types to filenames

Returns:

  • masks (xr.DataArray): Concatenated segmentation masks with a new dimension segmentation_type.

  • affine (np.ndarray): Affine transformation matrix associated with the NIFTI files.

Return type:

Tuple[xr.DataArray, np.ndarray]

cedalion.io.anatomy.cell_coordinates(mask, affine, units='mm')[source]

Get the coordinates of each voxel in the transformed mask.

Parameters:

  • mask (xr.DataArray) – A binary mask of shape (i, j, k).

  • affine (np.ndarray) – Affine transformation matrix.

  • units (str) – Units of the output coordinates.

Returns:

Coordinates of the center of each voxel in the mask.

Return type:

xr.DataArray