Atlas Conversion

This module enables the conversion of atlases in nifti format to Python & Blender readable *.obj files.

visualization.atlas_nifti_to_obj.conv_ewert(mat_path, nii_path, obj_path, slicer_path, seg_min_thresh=None, seg_max_thresh=None)

Extracts subcortical components from the Ewert 2017 atlas.

Parameters:

• mat_path (string) – Path to the atlas_index.mat file.

• nii_path (string) – Path to the to-be-converted nifti files.

• obj_path (String) – Path to place the output files.

• slicer_path (String) – Path to the 3dslicer binary/executable.

• seg_min_thresh (float) – Minimum value for automated segmentation

• seg_max_thresh (float) – Maximum value for automated segmentation