Basic Neuroimaging functionality for Nifti, Gifti, Cifti Data structures. Basic useful functions missing from nibabel and nilearn
Over pip, you can install the package, using the command: pip install neuroimagingtools
- 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
- 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
- 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
- read_lut: Read a lookup table file
- save_lut: Save a lookup table file
- save_cmap: Save a FSLeyes colormap file
- 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/