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

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, map=None, mask=None, n_fibers=5, scale=1, other_maps=None)

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

  • map (str) – Path to dMRI map to control stopping criteria; usually an FA map. This map is stored under variable fa_n (n = 1, 2,…, n ) in .fib file. This maps is visualized by qa in DSI Studio. The peak amplitude response is used if no map is provided

  • 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)

  • scale (float; optional) – Affects overall size of odfs in .fib file. This only affects visualization. (Default: 1)

  • other_maps (list of str; optional) – List containing paths to other metrics maps to include into the .fib file for computing metrics values along tracks. The maps could be AD, AK, MK, AWF, etc. as long as they are the same size as SH coefficient file.

Return type

None, writes out file