DORIS: A diffusion MRI-based 10 tissue class deep learning segmentation algorithm tailored to improve anatomically-constrained tractography - Theaud, Guillaume; Edde, Manon; Dumont, Matthieu; Zotti, Clément; Zucchelli, Mauro; Deslauriers-Gauthier, Samuel; Deriche, Rachid; Jodoin, Pierre-Marc; Descoteaux, Maxime (Frontiers in Neuroimaging, 2022)
Modern tractography algorithms such as anatomically-constrained tractography (ACT) are based on segmentation maps of white matter (WM), gray matter (GM) and cerebrospinal fluid (CSF). These maps are generally estimated from a T1-weighted (T1w) image and then registered in diffusion weighted images (DWI) space. Registration of T1w to diffusion space and partial volume estimation are challenging and rarely voxel-perfect. Diffusion-based segmentation would thus potentially allow not to have higher quality anatomical priors injected in the tractography process. On the other hand, even if FA-based tractography is possible without T1 registration, the literature shows that this technique suffers from multiple issues such as holes in the tracking mask and a high proportion of generated broken and anatomically implausible streamlines. Therefore, there is an important need for a tissue segmentation algorithm that works directly in native diffusion space. We propose DORIS, a DWI-based deep learning segmentation algorithm based on a DenseUnet model. DORIS outputs 10 different tissue classes including WM, GM, CSF, ventricles and 6 other subcortical structures (putamen, pallidum, hippocampus, caudate, amygdala, thalamus). DORIS was trained and validated on a wide range of sujects, including 1000 individuals from 22 to 90 years old from clinical and research DWI acquisitions, from 5 public databases. In the absence of a "true" ground truth in diffusion space, DORIS used a silver standard strategy from Freesurfer output registered onto the DWI. This strategy is extensively evaluated and discussed in the current work. Segmentation maps provided by DORIS are quantitatively compared to Freesurfer and FSL-fast and the impacts on tractography evaluated. Overall, we show that DORIS is fast, accurate, and reproducible, and that DORIS-based tractograms produce bundles with a longer mean length and fewer anatomically implausible streamlines.