unravel.image_tools.atlas.wireframe module#

Use atlas_wireframe (wf) from UNRAVEL to generate a thin wireframe image from an atlas NIfTI file.

Outputs:

  • path/atlas_img_W.nii.gz (Wireframe image)

  • path/atlas_img_W_IDs.nii.gz (Wireframe image with region IDs)

Note

  • Outlines are generated outside the regions and not inside smaller regions.

  • For regions at the surface of the brain, the outlines are internalized.

Usage:#

atlas_wireframe -i path.atlas.nii.gz [-wo path/atlas_img_W.nii.gz] [-id path/atlas_img_W_IDs.nii.gz] [-v]

unravel.image_tools.atlas.wireframe.parse_args()[source]#
unravel.image_tools.atlas.wireframe.process_intensity(args)[source]#

Process a single intensity: generate its binary mask, dilate, and find boundaries.

Parameters:

args (tuple) – A tuple containing the ndarray and the intensity value.

Returns a tuple with:

binary_mask (np.ndarray): A binary mask for the given intensity. boundary (np.ndarray): A binary boundary mask for the given intensity

unravel.image_tools.atlas.wireframe.generate_wireframe(atlas_ndarray, unique_intensities)[source]#

Generate a wireframe image of an atlas NIfTI file where outlines are outside the regions and not inside smaller regions.

Parameters:

  • atlas_ndarray (np.ndarray) – A 3D numpy array of an atlas NIfTI file.

  • unique_intensities (np.ndarray) – A list of unique intensity values in the atlas ndarray (sorted from smallest to largest regions)

Returns:

A binary wireframe image (1 = wireframe, 0 = background; uint8) wireframe_image_IDs (np.ndarray): A wireframe image with region IDs (uint16)

Return type:

wireframe_image (np.ndarray)

unravel.image_tools.atlas.wireframe.main()[source]#