Tools for exporting DSIStudio-compatible outputs. Adapted from mattcieslak/dmri_convert/mrtrix_to_dsistudio.py to suit PyDesigner’s needs.

References:

1. https://github.com/mattcieslak/dmri_convert/blob/master/mrtrix_to_dsistudio.py

designer.tractography.dsistudio.convertLPS(input, output)

Converts a nifti file to LPS for compatibility with DSIStudio

Parameters

• input (str) – Path to input nifti file; must possess .nii extension

• output (str) – Path to output nifti file; must possess .nii extension

Returns

Return type

None, writes out file

designer.tractography.dsistudio.get_dsi_studio_ODF_geometry(odf_key)

Reads DSIStudio’s ODF geometry in odfs.mat

Parameters

odf_keys (str) – DSIStudio’s direction set to load

Returns

• odf_vertices (array_like(dtype=int)) – ODF vertices

• odf_faces (array_like(dtype=double)) – ODF faces

designer.tractography.dsistudio.makefib(input, output, mask=None, n_fibers=3)

Converts a NifTi .nii file containing sh coefficients to a DSI Studio fib file

This function uses sh2amp to get amplitude values for each direction in DSI Studio’s odf8 direction set. These values are masked and loaded into the “odfN” matrices in the fib file.

Parameters

• input (str) – Path to input nifti file containing SH coefficients

• output (str) – Path to output fib file; must end with .fib

• mask (str, optional) – Path to nifti file containing brain mask

• n_fibers (int, optional) – The maximum number ODF maxima to extract per voxel (Default: 3)

Returns

Return type

None, writes out file