Segmentation of intrinsically very low contrast magnetic resonance brain images using tensor-based DTI registration

Background: In patients with hypomyelinating leukodystrophies, contrast of T1-weighted brain MRI is very low due to the lack of myelin, preventing a reliable segmentation. In diffusion tensor images the contrast is higher, thanks to anisotropy and orientation of white matter (WM) tracts. We aimed to develop and assess a tensor-guided atlas-based segmentation method suitable for segmentation of very low contrast images. Methods: 17 control subjects (mean age 8.0 yrs (SD 8.0)) and 27 subjects with hypomyelinating leukodystrophies (mean age 10.7 yrs (SD 10.2)) were included. DTI and 3D T1 images were segmented using a DTI-TK tensor-guided IIT-atlas-based segmentation method. For the control subjects, these segmentations were compared with a conventional segmentation of their 3D T1-weighted images. A qualitative visual assessment and a quantitative assessment using DTI metrics was performed to assess the patient segmentations. Results: In control subjects, the tensor-based method performed as can be expected for atlas-based segmentation methods, with Dice coefficients of 0.65, 0.72, 0.81 and 0.86 for cortical grey matter (GM), WM, deep grey matter (DGM), and thalamus, respectively. In patients with hypomyelination the visual assessment showed anatomically adequate segmentations. All tissue-specific DTI metrics differed between patients and controls. Patients with hypomyelination had reduced FA and increased mean, axial and radial diffusivities, not only in total WM, but also in the corticospinal tracts, optic radiations and thalamus. Conclusion: Even in the absence of normal myelin, the presence and direction of axons allowed tensor-based registration and thereby atlas-based segmentation. We showed the applicability of the segmentation method in the context of quantitative MRI, allowing for whole-brain or regional tissue-specific and tract-specific analyses of very low contrast images.