Note

This page is a reference documentation. It only explains the function signature, and not how to use it. Please refer to the user guide for the big picture.

brainprep.interfaces.mgz_to_nii

brainprep.interfaces.mgz_to_nii(output_dir, entities)

Convert FreeSurfer images back to original Nifti space.

Convert FreeSurfer MGZ file in Nifti format and reslice the generated image as the ‘mri/rawavg.mgz’ image. A nearest neighbor interpolation is used. This includes the following images: - aparc+aseg - aparc.a2009s+aseg - aseg - wm - rawavg - ribbon - brain

Parameters:

output_dirDirectory

FreeSurfer working directory containing all the subjects.

entitiesdict

A dictionary of parsed BIDS entities including modality.

Returns:

images: tuple[File]

A tuple containing converted images. The images are returned in the following order: - aparc_aseg_file - aparc_a2009s_aseg_file - aseg_file - wm_file - rawavg_file - ribbon_file - brain_file