Hi Anna,
See attached.
Lilla
On Fri, 25 Oct 2019, Crawford, Anna wrote:
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Hello,
Just a quick question. We recently installed the new thalamus segmentation
subroutine. It’s really wonderful, and much promise to our work.
I can’t find a lookup table with the numerical labels from the FS output to the
thalamic nuclei. The numbers around between 8103-8133 on the right, and 8203
and 8233 on the left. Can you point me in the right direction for this?
For other FS segmented volumes I always use the following, but it doesn’t
include these thalamic subnuclei
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT
Thank you,
Anna
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#$Id: FreeSurferColorLUT.txt,v 1.105 2015/07/29 18:23:03 greve Exp $
#No. Label Name:R G B A
0 Unknown 0 0 0 0
1 Left-Cerebral-Exterior 70 130 180 0
2 Left-Cerebral-White-Matter 245 245 245 0
3 Left-Cerebral-Cortex205 62 78 0
4 Left-Lateral-Ventricle 120 18 134 0
5 Left-Inf-Lat-Vent 196 58 250 0
6 Left-Cerebellum-Exterior0 148 0 0
7 Left-Cerebellum-White-Matter220 248 164 0
8 Left-Cerebellum-Cortex 230 148 34 0
9 Left-Thalamus-unused0 118 14 0
10 Left-Thalamus 0 118 14 0
11 Left-Caudate122 186 220 0
12 Left-Putamen236 13 176 0
13 Left-Pallidum 12 48 255 0
14 3rd-Ventricle 204 182 142 0
15 4th-Ventricle 42 204 164 0
16 Brain-Stem 119 159 176 0
17 Left-Hippocampus220 216 20 0
18 Left-Amygdala 103 255 255 0
19 Left-Insula 80 196 98 0
20 Left-Operculum 60 58 210 0
21 Line-1 60 58 210 0
22 Line-2 60 58 210 0
23 Line-3 60 58 210 0
24 CSF 60 60 60 0
25 Left-Lesion 255 165 0 0
26 Left-Accumbens-area 255 165 0 0
27 Left-Substancia-Nigra 0 255 127 0
28 Left-VentralDC 165 42 42 0
29 Left-undetermined 135 206 235 0
30 Left-vessel 160 32 240 0
31 Left-choroid-plexus 0 200 200 0
32 Left-F3orb 100 50 100 0
33 Left-lOg135 50 74 0
34 Left-aOg122 135 50 0
35 Left-mOg51 50 135 0
36 Left-pOg74 155 60 0
37 Left-Stellate 120 62 43 0
38 Left-Porg 74 155 60 0
39 Left-Aorg 122 135 50 0
40 Right-Cerebral-Exterior 70 130 180 0
41 Right-Cerebral-White-Matter 245 245 245 0
42 Right-Cerebral-Cortex 205 62 78 0
43 Right-Lateral-Ventricle 120 18 134 0
44 Right-Inf-Lat-Vent 196 58 250 0
45 Right-Cerebellum-Exterior 0 148 0 0
46 Right-Cerebellum-White-Matter 220 248 164 0
47 Right-Cerebellum-Cortex 230 148 34 0
48 Right-Thalamus-unused 0 118 14 0
49 Right-Thalamus 0 118 14 0
50 Right-Caudate 122 186 220 0
51 Right-Putamen 236 13 176 0
52 Right-Pallidum 13 48 255 0
53 Right-Hippocampus 220 216 20 0
54 Right-Amygdala
