neuroimagingtools 1.1.5

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/