Yes, you just need to have it in the right format. I've attached an example.
On 08/24/2018 04:48 PM, miracle ozzoude wrote:
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Hello,
Can i specify a lookup table when using mri_gtmpvc? This is because I
have a non-freesurfer segmentation (MALPEM) and i would like to
perform partial volume on it without having to run freesurfer on the
subject for PET analysis. I have a lookup table for the segmentation.
I know mri_gtmpvc expects (?.ctab) file from the segmentation however,
it will require processing the subject with freesurfer and petsurfer.
I only want to use the partial volume command. How do I make it use
the lookup table i made rather than ?.ctab file?
Thank you.
Best,
Paul
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# TissueTypeSchema
#ctTType 0 unknown 0 0 0 0
#ctTType 1 cortex 205 62 78 0
#ctTType 2 subcort_gm 230 148 34 0
#ctTType 3 wm 0 255 0 0
#ctTType 4 csf 120 18 134 0
#ctTType 5 head 150 150 200 0
0 Unknown 0 0 0 0 0
2 Left-Cerebral-White-Matter 245 245 245 0 3
4 Left-Lateral-Ventricle 120 18 134 0 4
5 Left-Inf-Lat-Vent 196 58 250 0 4
7 Left-Cerebellum-White-Matter 220 248 164 0 3
8 Left-Cerebellum-Cortex 230 148 34 0 2
10 Left-Thalamus-Proper 0 118 14 0 2
11 Left-Caudate 122 186 220 0 2
12 Left-Putamen 236 13 176 0 2
13 Left-Pallidum 12 48 255 0 2
14 3rd-Ventricle 204 182 142 0 4
15 4th-Ventricle 42 204 164 0 4
16 Brain-Stem 119 159 176 0 3
17 Left-Hippocampus 220 216 20 0 2
18 Left-Amygdala 103 255 255 0 2
24 CSF 60 60 60 0 4
26 Left-Accumbens-area 255 165 0 0 2
28 Left-VentralDC 165 42 42 0 3
30 Left-vessel 160 32 240 0 4
31 Left-choroid-plexus 0 200 200 0 4
41 Right-Cerebral-White-Matter 245 245 245 0 3
43 Right-Lateral-Ventricle 120 18 134 0 4
44 Right-Inf-Lat-Vent 196 58 250 0 4
46 Right-Cerebellum-White-Matter 220 248 164 0 3
47 Right-Cerebellum-Cortex 230 148 34 0 2
49 Right-Thalamus-Proper 0 118 14 0 2
50 Right-Caudate 122 186 220 0 2
51 Right-Putamen 236 13 176 0 2
52 Right-Pallidum 13 48 255 0 2
53 Right-Hippocampus 220 216 20 0 2
54 Right-Amygdala 103 255 255 0 2
58 Right-Accumbens-area 255 165 0 0 2
60 Right-VentralDC 165 42 42 0 3
62 Right-vessel 160 32 240 0 4
63 Right-choroid-plexus 0 200 221 0 4
72 5th-Ventricle 120 190 150 0 4
80 non-WM-hypointensities 164 108 226 0 2
85 Optic-Chiasm 234 169 30 0 3
130 Air 147 19 173 0 5
165 Skull 120 120 120 0 5
172 Vermis 119 100 176 0 2
174 Pons 119 159 100 0 3
257 CSF-ExtraCerebral 60 60 60 0 4
258 Head-ExtraCerebral 150 150 200 0 5
1001 ctx-lh-bankssts 25 100 40 0 1
1002 ctx-lh-caudalanteriorcingulate 125 100 160 0 1
1003 ctx-lh-caudalmiddlefrontal 100 25 0 0 1
1005 ctx-lh-cuneus 220 20 100 0 1
1006 ctx-lh-entorhinal 220 20 10 0 1
1007 ctx-lh-fusiform 180 220 140 0 1
1008 ctx-lh-inferiorparietal 220 60 220 0 1
1009 ctx-lh-inferiortemporal 180 40 120 0 1
1010 ctx-lh-isthmuscingulate 140 20 140 0 1
1011 ctx-lh-lateraloccipital 20 30 140 0 1
1012 ctx-lh-lateralorbitofrontal 35 75 50 0 1
1013 ctx-lh-lingual 225 140 140 0 1
1014 ctx-lh-medialorbitofrontal 200 35 75 0 1
1015 ctx-lh-middletemporal 160 100 50 0 1
1016 ctx-lh-parahippocampal 20 220 60 0 1
1017 ctx-lh-paracentral 60 220 60 0 1
1018 ctx-lh-parsopercularis 220 180 140 0 1
1019 ctx-lh-parsorbitalis 20 100 50 0 1
1020 ctx-lh-parstriangularis 220 60 20 0 1
1021 ctx-lh-pericalcarine 120 100 60 0 1
1022 ctx-lh-postcentral 220 20 20 0 1
1023 ctx-lh-posteriorcingulate 220 180 220 0 1
1024 ctx-lh-precentral 60 20 220 0 1
1025 ctx-lh-precuneus 160 140 180 0 1
1026 ctx-lh-rostralanteriorcingulate 80 20 140 0 1
1027 ctx-lh-rostralmiddlefrontal 75 50 125 0 1
1028 ctx-lh-superiorfrontal 20 220 160 0 1
1029 ctx-lh-superiorparietal 20 180 140 0 1
1030 ctx-lh-superiortemporal 140 220 220 0 1
1031 ctx-lh-supramarginal 80 160 20 0 1
1032 ctx-lh-frontalpole 100 0 100 0 1
1033 ctx-lh-temporalpole 70 20 170 0 1
1034 ctx-lh-transversetemporal 150 150 200 0 1
1035 ctx-lh-insula 255 192 32 0 1
2001 ctx-rh-bankssts 25 100 40 0 1
2002 ctx-rh-caudalanteriorcingulate 125 100 160 0 1
2003 ctx-rh-caudalmiddlefrontal 100 25 0 0 1
2005 ctx-rh-cuneus 220 20 100 0 1
2006 ctx-rh-entorhinal 220 20 10 0 1
2007 ctx-rh-fusiform 180 220 140 0 1
2008 ctx-rh-inferiorparietal 220 60 220 0 1
2009 ctx-rh-inferiortemporal 180 40 120 0 1
2010 ctx-rh-isthmuscingulate 140 20 140 0 1
2011 ctx-rh-lateraloccipital 20 30 140 0 1
2012 ctx-rh-lateralorbitofrontal 35 75 50 0 1
2013 ctx-rh-lingual 225 140 140 0 1
2014 ctx-rh-medialorbitofrontal 200 35 75 0 1
2015 ctx-rh-middletemporal 160 100 50 0 1
2016 ctx-rh-parahippocampal 20 220 60 0 1
2017 ctx-rh-paracentral 60 220 60 0 1
2018 ctx-rh-parsopercularis 220 180 140 0 1
2019 ctx-rh-parsorbitalis 20 100 50 0 1
2020 ctx-rh-parstriangularis 220 60 20 0 1
2021 ctx-rh-pericalcarine 120 100 60 0 1
2022 ctx-rh-postcentral 220 20 20 0 1
2023 ctx-rh-posteriorcingulate 220 180 220 0 1
2024 ctx-rh-precentral 60 20 220 0 1
2025 ctx-rh-precuneus 160 140 180 0 1
2026 ctx-rh-rostralanteriorcingulate 80 20 140 0 1
2027 ctx-rh-rostralmiddlefrontal 75 50 125 0 1
2028 ctx-rh-superiorfrontal 20 220 160 0 1
2029 ctx-rh-superiorparietal 20 180 140 0 1
2030 ctx-rh-superiortemporal 140 220 220 0 1
2031 ctx-rh-supramarginal 80 160 20 0 1
2032 ctx-rh-frontalpole 100 0 100 0 1
2033 ctx-rh-temporalpole 70 20 170 0 1
2034 ctx-rh-transversetemporal 150 150 200 0 1
2035 ctx-rh-insula 255 192 32 0 1
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