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_4_prestats(tbss_dir, threshold=0.2)[source]¶

Use FSL tbss_4_prestats to thresholds the mean FA skeleton image at the chosen threshold, create a distance map, and project the FA data onto the mean FA skeleton. To be used before any voxelwise cross-subject stats.

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

Parameters:

tbss_dir : str

path to TBSS root directory.

threshold : float, default 0.2

threshold applied to the mean FA skeleton.

Returns:

all_fa_skeletonized : str

path to the subjects’ concatenated skeletonized FA.

mean_fa_skel_mask : str

path to the binary skeleton mask.

mean_fa_skel_mask_dst : str

path to the distance map created from the skeleton mask.

thresh_file : str

text file indicating threshold used.