Package that provides tools for brain MRI Deep Learning pre-processing.

Note

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

brainprep.tbss.tbss_3_postreg(tbss_dir, use_fmrib58_fa_mean_and_skel=True)[source]¶

Use FSL tbss_3_postreg to apply the nonlinear transforms found in the previous stage to all subjects to bring them into standard space. Merge results into a single 4D image. Compute also a mean FA image and skeletonize it.

For more information, refer to: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS/UserGuide

Parameters:

tbss_dir : st

path to TBSS root directory.

use_fmrib58_fa_mean_and_skel : bool, default True

use the FMRIB58_FA mean FA image and its derived skeleton, instead of the mean of the subjects.

Returns:

all_fa : str

path to the subjects’ concatenated FA files in template space.

mean_fa str

path to the subjects’ mean FA.

mean_fa_mask : str

path to the brain mask of mean FA.

mean_fa_skel : str

path to the skeletonized mean FA.