cvasl.mold module

Copyright 2023 Netherlands eScience Center and the Amsterdam University Medical Center. Licensed under the Apache License, version 2.0. See LICENSE for details.

This file contains methods to normalize brain MRIs.

class cvasl.mold.NormedSliceViewer(volume, figsize=(10, 10))

Bases: object

A class to examine slices of MRIs, or other volumetric data, with normalizaiotn

plot_slice(z)
transpose(view)
class cvasl.mold.SliceViewer(volume, figsize=(10, 10))

Bases: object

A class to examine slices of MRIs, or other volumetric data

plot_slice(z)
transpose(view)
cvasl.mold.debias_folder(file_directory, algorithm, processed, force=False)

Debias function to perform bias field correction over an entire folder, through command_line. It does not return, files made are an artifact. Note this will only run on files with .gz at end of extension.

Parameters:

  • file_directory (str) – The string of the folder with files to hash

  • algorithm (algorithm) – algorithm e.g. N4_debias_sitk

  • processed (str) – folder where output images go

cvasl.mold.n4_debias_sitk(image_filename, iteration_vector=[20, 10, 10, 5], masking=True)

This is our implementation of sitk’s N4 debiasing algorithm. It is implemeted so the algorithm can be applied unformly from command line (eventually) Need to cite SITK

cvasl.mold.save_preprocessed(array, out_fname, force)

This function is written to be called by the cli module. It stores arrays in a directory.