neuroimagingtools 1.1.4

Neuroimaging analysis tools

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_image: Sample a 3d volume at arbitrary locations with nearest-neighbor or trilinear interpolation

• sample_images: Samples a set of 3d or 4d volumes at arbitrary locations efficiently

• check_voxel_range: Check of voxel coordinates are within an image

• deform_image: Moves a volume image according to a deformation field

• change_nifti_numformat: Adjusts the numerical format of a Nifti image

• get_mask_coords: Extracts the voxel coordinates from a mask 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/