ComScan.nifti module

Author: Alexandre CARRE
Created on: Jan 14, 2021
ComScan.nifti.flatten_nifti_files(input_path, mask, output_flattened_array_path='flattened_array', dtype=<class 'numpy.float16'>, save=True, compress_save=True)[source]

Flattened list of nifti files to a flattened array [n_images, n_masked_voxels] and save to .npy or .npz if compressed

Parameters

  • input_path (List[str]) – List of nifti files path

  • mask (Union[str, ndarray]) – path of mask or array

  • output_flattened_array_path (str) – path of the output flattened array. No extension is needed. Will be save as .npy if no compression, else .npz

  • save (bool) – save the flattened array

  • dtype ([<class 'numpy.dtype'>, typing.Callable]) – dtype of the output flattened array. Default is float 16 to save memory

  • compress_save (bool) – If true compress the numpy array into .npz

Returns

flattened array [n_images, n_masked_voxels]