TOADS and Lesion-TOADS Tissue Class Key

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.

Screen Shot 2014-10-09 at 3.01.31 PM

Screen Shot 2014-10-09 at 3.16.47 PM


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