TOADS and LesionTOADS are software packages that perform brain tissue class segmentation from structural MRI images. Lesion-TOADS assigns each voxel to one of 13 different tissue classes (TOADS assigns only 12, since it doesn’t look for lesions). A key of the meaning of each numerical label is surprisingly difficult to find, so here they are. (Thanks to Danny Reich for sharing these with me!)
0 way outside the brain
1 outside the brain
5 sulcal/cisternal CSF
6 ventricles
10 lesions
14 cerebellar cortical gray matter
15 cerebral cortical gray matter
16 caudate
17 thalamus
18 putamen
22 brainstem
24 cerebellar white matter
25 cerebral white matter
Here’s an example segmentation and T1-weighted image of the brain of a multiple sclerosis (MS) patient, visualized using MIPAV (source: Shiee et al. 2012). You can see all the tissue classes except the cerebellar gray and white matter. Cerebral white matter (25) is shown in white, and cerebral cortical gray matter (15) is shown in orange along the outer border of the cerebral white matter. CSF can be seen in dark red on the edge of the brain (5) and in the ventricles (6). Deep gray matter structures are inside the white matter, close to the ventricles, and are shown in shades of yellow-orange, with the putamen (18) in the lightest shade, the thalamus (17) in the next-lightest shade, and the caudate (16) in the darkest shade. Finally, lesions (10) are shown in red.
Mandy Mejia 