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.workflow.prequal.brainprep_prequal(dwi, bvec, bval, pe, readout_time, output_dir, t1=None)[source]¶

Define the dMRI pre-processing workflow.

Parameters:

dwi : str

path to the diffusion weighted image.

bvec:

path to the bvec file.

bval:

path to the bval file.

pe : str

the de phase encoding direction (i, i-, j, j-, k, k-).

readout_time : str

readout time of the dwi image.

output_dir : str

path to the output directory.

t1 : str, default None

path to the t1 image in case of synb0 use.

Notes

In order to use the synb0 feature you must bind your freesurfer license as such: -B /path/to/freesurfer/license.txt:/APPS/freesurfer/license.txt