nitools

Basic Neuroimaging functionality for Nifti, Gifti, Cifti Data structures. Basic useful functions missing from nibabel and nilearn

Installation

Over pip, you can install the package, using the command: pip install neuroimagingtools

Coordinate transforms and nifti (volume) utilities

• affine_transform: Affine Coordinate transform with individual x,y,z coordinates
• affine_transform_mat: Affine coordinate transform with coordinates in matrix format
• coords_to_linvidxs: Safe transform of coordinates to linear voxel indices
• euclidean_dist_sq: Squared Euclidean distance between coordinate pairs
• sample_img: Sample volume at arbitrary locations with nearest-neighbor or trilinear interpolation
• check_voxel_range: Check of voxel coordinates are within an image

Gifti Utilities

• make_func_gifti: Make a new functional giftiImage
• make_label_gifti: Make a new label giftiImage (with label table)
• get_gifti_column_names: Extract column names from gifti
• get_gifti_anatomical_struct: Extract Anatomical_structure_primary
• get_gifti_labels: Get label names and colors

Cifti Utilities

• join_giftis_to_cifti: Joins a left- and right-hemispheric Gifti into a single CIFTI
• split_cifti_to_giftis: Splits CIFTI into a left- and right-hemispheric Gifti
• volume_from_cifti: Extracts Nifti-volume data from a Cifti file
• surf_from_cifti: Extract the surface-based data from a Cifti file

Color utilities

• read_lut: Read a lookup table file
• save_lut: Save a lookup table file
• save_cmap: Save a FSLeyes colormap file

Border utilities

• Border: Border class
• Border.get_coords: Get coordinates for a border
• read_borders: Read a workbench border file
• save_borders: Save a workbench border file
• project_border: Project coordinates to a surface
• resample_border: Resample a border with regularly spacing

For documentation, see: https://nitools.readthedocs.io/en/latest/