8.2.1. Parcellations#

Provide functions for parcellation.

junifer.data.parcellations.list_parcellations()#

List all the available parcellations.

Returns:

list of str: A list with all available parcellations.

junifer.data.parcellations.load_parcellation(name, parcellations_dir=None, resolution=None, path_only=False)#

Load a brain parcellation (including a label file).

If it is a built-in parcellaions and file is not present in the parcellations_dir directory, it will be downloaded.

Parameters:

namestr: The name of the parcellation. Check valid options by calling junifer.data.parcellations.list_parcellations().
parcellations_dirstr or pathlib.Path, optional: Path where the parcellations files are stored. The default location is “$HOME/junifer/data/parcellations” (default None).
resolutionfloat, optional: The desired resolution of the parcellation to load. If it is not available, the closest resolution will be loaded. Preferably, use a resolution higher than the desired one. By default, will load the highest one (default None).
path_onlybool, optional: If True, the parcellation image will not be loaded (default False).

Returns:

Nifti1Image or None: Loaded parcellation image.
list of str: Parcellation labels.
pathlib.Path: File path to the parcellation image.

junifer.data.parcellations.register_parcellation(name, parcellation_path, parcels_labels, overwrite=False)#

Parameters:

namestr: The name of the parcellation.
parcellation_pathstr or pathlib.Path: The path to the parcellation file.
parcels_labelslist of str: The list of labels for the parcellation.
overwritebool, optional: If True, overwrite an existing parcellation with the same name. Does not apply to built-in parcellations (default False).

Raises:

ValueError: If the parcellation name is already registered and overwrite is set to False or if the parcellation name is a built-in parcellation.

8.2.2. Coordinates#

Provide functions for list of coordinates.

junifer.data.coordinates.list_coordinates()#

List all the available coordinates lists (VOIs).

Returns:

list of str: A list with all available coordinates names.

junifer.data.coordinates.load_coordinates(name)#

Load coordinates.

Parameters:

namestr: The name of the coordinates.

Returns:

numpy.ndarray: The coordinates.
list of str: The names of the VOIs.

junifer.data.coordinates.register_coordinates(name, coordinates, voi_names, overwrite=False)#

Parameters:

namestr: The name of the coordinates.
coordinatesnumpy.ndarray: The coordinates.
voi_nameslist of str: The names of the VOIs.
overwritebool, optional: If True, overwrite an existing list of coordinates with the same name. Does not apply to built-in coordinates (default False).

8.2.3. Masks#

Provide functions for masks.

junifer.data.masks.list_masks()#

List all the available masks.

Returns:

list of str: A list with all available masks names.

junifer.data.masks.load_mask(name, resolution=None, path_only=False)#

Load mask.

Parameters:

namestr: The name of the mask.
resolutionfloat, optional: The desired resolution of the mask to load. If it is not available, the closest resolution will be loaded. Preferably, use a resolution higher than the desired one. By default, will load the highest one (default None).
path_onlybool, optional: If True, the mask image will not be loaded (default False).

Returns:

Nifti1Image or None: Loaded mask image.
pathlib.Path: File path to the mask image.

junifer.data.masks.register_mask(name, mask_path, overwrite=False)#

Parameters:

namestr: The name of the mask.
mask_pathstr or pathlib.Path: The path to the mask file.
overwritebool, optional: If True, overwrite an existing mask with the same name. Does not apply to built-in mask (default False).

Raises:

ValueError: If the mask name is already registered and overwrite is set to False or if the mask name is a built-in mask.