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_1_preproc(tbss_dir, fa_file)[source]¶

Use FSL tbss_1_preproc to erode the FA images slightly and zero the end slices: to remove likely outliers from the diffusion tensor fitting.

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

Parameters:

tbss_dir : str

path to TBSS root directory containing all the FA *.nii.gz file to be processed.

fa_file : str

path to the FA file.

Returns:

fa_file : str

file with the preprocess Fractional Anisotropy (FA).

tbss_fa_dir : str

path to the subjects corrected FA files.

tbss_orig_dir : str

path to the copied subjects original FA files.