Hi all, I’m trying to open a couple aseg.mgz labels and color code them. I thought I’d do this by making my own ColorLUT table, setting the color of my regions, and then making every other region in the table be completely transparent by fiddling with the opacity value. I can’t figure out what number I want in the opacity column to make a region totally transparent, and on the wiki it says something about “255-alpha” for that column, but I don’t know what that means. In the opacity column I’ve tried values 0, 1, and 255, and it all looks the same (completely opaque) - anyone know what value I want there?
Attached is my ColorLUT table, which currently gives me yellow caudate and green amyg and hippo (what I want), and the rest of the aseg.mgz labels are all black (I’m trying to change all the black to 100% transparent so they don’t show up at all and all I see are my yellow and green regions). Thanks!! (If it’s relevant, I’m loading the fsaverage orig.mgz and aseg.mgz into freeview and loading my ColorLUT table onto the aseg.mgz there, because I can’t figure out how to get this working in tkmedit). Best, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Rm 2620A Charlestown, MA 02129 Phone: (617) 724-3283 Fax: (617) 726-4078
#$Id: FreeSurferColorLUT.txt,v 1.70.2.7 2012/08/27
17:20:08 nicks Exp $
#No. Label Name: R G B A
0 Unknown 0 0 0 255
1 Left-Cerebral-Exterior 0 0 0 255
2 Left-Cerebral-White-Matter 0 0 0 255
3 Left-Cerebral-Cortex 0 0 0 255
4 Left-Lateral-Ventricle 0 0 0 255
5 Left-Inf-Lat-Vent 0 0 0 255
6 Left-Cerebellum-Exterior 0 0 0 255
7 Left-Cerebellum-White-Matter 0 0 0 255
8 Left-Cerebellum-Cortex 0 0 0 255
9 Left-Thalamus 0 0 0 255
10 Left-Thalamus-Proper 0 0 0 255
11 Left-Caudate 220 216 20 255
12 Left-Putamen 0 0 0 255
13 Left-Pallidum 0 0 0 255
14 3rd-Ventricle 0 0 0 255
15 4th-Ventricle 0 0 0 255
16 Brain-Stem 0 0 0 255
17 Left-Hippocampus 0 225 0 255
18 Left-Amygdala 0 225 0 255
19 Left-Insula 0 0 0 255
20 Left-Operculum 0 0 0 255
21 Line-1 0 0 0 255
22 Line-2 0 0 0 255
23 Line-3 0 0 0 255
24 CSF 0 0 0 255
25 Left-Lesion 0 0 0 255
26 Left-Accumbens-area 0 0 0 255
27 Left-Substancia-Nigra 0 0 0 255
28 Left-VentralDC 0 0 0 255
29 Left-undetermined 0 0 0 255
30 Left-vessel 0 0 0 255
31 Left-choroid-plexus 0 0 0 255
32 Left-F3orb 0 0 0 255
33 Left-lOg 0 0 0 255
34 Left-aOg 0 0 0 255
35 Left-mOg 0 0 0 255
36 Left-pOg 0 0 0 255
37 Left-Stellate 0 0 0 255
38 Left-Porg 0 0 0 255
39 Left-Aorg 0 0 0 255
40 Right-Cerebral-Exterior 0 0 0 255
41 Right-Cerebral-White-Matter 0 0 0 255
42 Right-Cerebral-Cortex 0 0 0 255
43 Right-Lateral-Ventricle 0 0 0 255
44 Right-Inf-Lat-Vent 0 0 0 255
45 Right-Cerebellum-Exterior 0 0 0 255
46 Right-Cerebellum-White-Matter 0 0 0 255
47 Right-Cerebellum-Cortex 0 0 0 255
48 Right-Thalamus 0 0 0 255
49 Right-Thalamus-Proper 0 0 0 255
50 Right-Caudate 220 216 20 255
51 Right-Putamen 0 0 0 255
52 Right-Pallidum 0 0 0 255
53 Right-Hippocampus 0 225 0 255
54 Right-Amygdala 0 225 0 255
55 Right-Insula 0 0 0 255
56 Right-Operculum 0 0 0 255
57 Right-Lesion 0 0 0 255
58 Right-Accumbens-area 0 0 0 255
59 Right-Substancia-Nigra 0 0 0 255
60 Right-VentralDC 0 0 0 255
61 Right-undetermined 0 0 0 255
62 Right-vessel 0 0 0 255
63 Right-choroid-plexus 0 0 0 255
64 Right-F3orb 0 0 0 255
65 Right-lOg 0 0 0 255
66 Right-aOg 0 0 0 255
67 Right-mOg 0 0 0 255
68 Right-pOg 0 0 0 255
69 Right-Stellate 0 0 0 255
70 Right-Porg 0 0 0 255
71 Right-Aorg 0 0 0 255
72 5th-Ventricle 0 0 0 255
73 Left-Interior 0 0 0 255
74 Right-Interior 0 0 0 255
# 0.98684210526316 0 0 0 255
77 WM-hypointensities 0 0 0 255
78 Left-WM-hypointensities 0 0 0 255
79 Right-WM-hypointensities 0 0 0 255
80 non-WM-hypointensities 0 0 0 255
81 Left-non-WM-hypointensities 0 0 0 255
82 Right-non-WM-hypointensities 0 0 0 255
83 Left-F1 0 0 0 255
84 Right-F1 0 0 0 255
85 Optic-Chiasm 0 0 0 255
192 Corpus_Callosum 0 0 0 255
0 0 0 255
86 Left_future_WMSA 0 0 0 255
87 Right_future_WMSA 0 0 0 255
88 future_WMSA 0 0 0 255
0 0 0 255
0 0 0 255
96 Left-Amygdala-Anterior 0 0 0 255
97 Right-Amygdala-Anterior 0 0 0 255
98 Dura 0 0 0 255
0 0 0 255
100 Left-wm-intensity-abnormality 0 0 0 255
101 Left-caudate-intensity-abnormality 0 0 0 255
102 Left-putamen-intensity-abnormality 0 0 0 255
103 Left-accumbens-intensity-abnormality 0 0 0 255
104 Left-pallidum-intensity-abnormality 0 0 0 255
105 Left-amygdala-intensity-abnormality 0 0 0 255
106 Left-hippocampus-intensity-abnormality 0 0 0 255
107 Left-thalamus-intensity-abnormality 0 0 0 255
108 Left-VDC-intensity-abnormality 0 0 0 255
109 Right-wm-intensity-abnormality 0 0 0 255
110 Right-caudate-intensity-abnormality 0 0 0 255
111 Right-putamen-intensity-abnormality 0 0 0 255
112 Right-accumbens-intensity-abnormality 0 0 0 255
113 Right-pallidum-intensity-abnormality 0 0 0 255
114 Right-amygdala-intensity-abnormality 0 0 0 255
115 Right-hippocampus-intensity-abnormality 0 0 0 255
116 Right-thalamus-intensity-abnormality 0 0 0 255
117 Right-VDC-intensity-abnormality 0 0 0 255
0 0 0 255
118 Epidermis 0 0 0 255
119 Conn-Tissue 0 0 0 255
120 SC-Fat-Muscle 0 0 0 255
121 Cranium 0 0 0 255
122 CSF-SA 0 0 0 255
123 Muscle 0 0 0 255
124 Ear 0 0 0 255
125 Adipose 0 0 0 255
126 Spinal-Cord 0 0 0 255
127 Soft-Tissue 0 0 0 255
128 Nerve 0 0 0 255
129 Bone 0 0 0 255
130 Air 0 0 0 255
131 Orbital-Fat 0 0 0 255
132 Tongue 0 0 0 255
133 Nasal-Structures 0 0 0 255
134 Globe 0 0 0 255
135 Teeth 0 0 0 255
136 Left-Caudate-Putamen 0 0 0 255
137 Right-Caudate-Putamen 0 0 0 255
138 Left-Claustrum 0 0 0 255
139 Right-Claustrum 0 0 0 255
140 Cornea 0 0 0 255
142 Diploe 0 0 0 255
143 Vitreous-Humor 0 0 0 255
144 Lens 0 0 0 255
145 Aqueous-Humor 0 0 0 255
146 Outer-Table 0 0 0 255
147 Inner-Table 0 0 0 255
148 Periosteum 0 0 0 255
149 Endosteum 0 0 0 255
150 R-C-S 0 0 0 255
151 Iris 0 0 0 255
152 SC-Adipose-Muscle 0 0 0 255
153 SC-Tissue 0 0 0 255
154 Orbital-Adipose 0 0 0 255
0 0 0 255
155 Left-IntCapsule-Ant 0 0 0 255
156 Right-IntCapsule-Ant 0 0 0 255
157 Left-IntCapsule-Pos 0 0 0 255
158 Right-IntCapsule-Pos 0 0 0 255
0 0 0 255
# These 0 0 0 255
159 Left-Cerebral-WM-unmyelinated 0 0 0 255
160 Right-Cerebral-WM-unmyelinated 0 0 0 255
161 Left-Cerebral-WM-myelinated 0 0 0 255
162 Right-Cerebral-WM-myelinated 0 0 0 255
163 Left-Subcortical-Gray-Matter 0 0 0 255
164 Right-Subcortical-Gray-Matter 0 0 0 255
165 Skull 0 0 0 255
166 Posterior-fossa 0 0 0 255
167 Scalp 0 0 0 255
168 Hematoma 0 0 0 255
169 Left-Basal-Ganglia 0 0 0 255
176 Right-Basal-Ganglia 0 0 0 255
0 0 0 255
# Label 0 0 0 255 Brainstem consituents
# No. 0 0 0 255 B A
170 brainstem 0 0 0 255
171 DCG 0 0 0 255
172 Vermis 0 0 0 255
173 Midbrain 0 0 0 255
174 Pons 0 0 0 255
175 Medulla 0 0 0 255
0 0 0 255
#176 Right-Basal-Ganglia 0 0 0 255 above
0 0 0 255
180 Left-Cortical-Dysplasia 0 0 0 255
181 Right-Cortical-Dysplasia 0 0 0 255
0 0 0 255
#192 Corpus_Callosum 0 0 0 255
193 Left-hippocampal_fissure 0 0 0 255
194 Left-CADG-head 0 0 0 255
195 Left-subiculum 0 0 0 255
196 Left-fimbria 0 0 0 255
197 Right-hippocampal_fissure 0 0 0 255
198 Right-CADG-head 0 0 0 255
199 Right-subiculum 0 0 0 255
200 Right-fimbria 0 0 0 255
201 alveus 0 0 0 255
202 perforant_pathway 0 0 0 255
203 parasubiculum 0 0 0 255
204 presubiculum 0 0 0 255
205 subiculum 0 0 0 255
206 CA1 0 0 0 255
207 CA2 0 0 0 255
208 CA3 0 0 0 255
209 CA4 0 0 0 255
210 GC-ML-DG 0 0 0 255
211 HATA 0 0 0 255
212 fimbria 0 0 0 255
213 lateral_ventricle 0 0 0 255
214 molecular_layer_HP 0 0 0 255
215 hippocampal_fissure 0 0 0 255
216 entorhinal_cortex 0 0 0 255
217 molecular_layer_subiculum 0 0 0 255
218 Amygdala 0 0 0 255
219 Cerebral_White_Matter 0 0 0 255
220 Cerebral_Cortex 0 0 0 255
221 Inf_Lat_Vent 0 0 0 255
222 Perirhinal 0 0 0 255
223 Cerebral_White_Matter_Edge 0 0 0 255
224 Background 0 0 0 255
225 Ectorhinal 0 0 0 255
226 HP_tail 0 0 0 255
0 0 0 255
250 Fornix 0 0 0 255
251 CC_Posterior 0 0 0 255
252 CC_Mid_Posterior 0 0 0 255
253 CC_Central 0 0 0 255
254 CC_Mid_Anterior 0 0 0 255
255 CC_Anterior 0 0 0 255
0 0 0 255
# This 0 0 0 255 of voxel changes
256 Voxel-Unchanged 0 0 0 255
0 0 0 255
# lymph 0 0 0 255
331 Aorta 0 0 0 255
332 Left-Common-IliacA 0 0 0 255
333 Right-Common-IliacA 0 0 0 255
334 Left-External-IliacA 0 0 0 255
335 Right-External-IliacA 0 0 0 255
336 Left-Internal-IliacA 0 0 0 255
337 Right-Internal-IliacA 0 0 0 255
338 Left-Lateral-SacralA 0 0 0 255
339 Right-Lateral-SacralA 0 0 0 255
340 Left-ObturatorA 0 0 0 255
341 Right-ObturatorA 0 0 0 255
342 Left-Internal-PudendalA 0 0 0 255
343 Right-Internal-PudendalA 0 0 0 255
344 Left-UmbilicalA 0 0 0 255
345 Right-UmbilicalA 0 0 0 255
346 Left-Inf-RectalA 0 0 0 255
347 Right-Inf-RectalA 0 0 0 255
348 Left-Common-IliacV 0 0 0 255
349 Right-Common-IliacV 0 0 0 255
350 Left-External-IliacV 0 0 0 255
351 Right-External-IliacV 0 0 0 255
352 Left-Internal-IliacV 0 0 0 255
353 Right-Internal-IliacV 0 0 0 255
354 Left-ObturatorV 0 0 0 255
355 Right-ObturatorV 0 0 0 255
356 Left-Internal-PudendalV 0 0 0 255
357 Right-Internal-PudendalV 0 0 0 255
358 Pos-Lymph 0 0 0 255
359 Neg-Lymph 0 0 0 255
0 0 0 255
400 V1 0 0 0 255
401 V2 0 0 0 255
402 BA44 0 0 0 255
403 BA45 0 0 0 255
404 BA4a 0 0 0 255
405 BA4p 0 0 0 255
406 BA6 0 0 0 255
407 BA2 0 0 0 255
408 BA1_old 0 0 0 255
409 BAun2 0 0 0 255
410 BA1 0 0 0 255
411 BA2b 0 0 0 255
412 BA3a 0 0 0 255
413 BA3b 0 0 0 255
414 MT 0 0 0 255
415 AIPS_AIP_l 0 0 0 255
416 AIPS_AIP_r 0 0 0 255
417 AIPS_VIP_l 0 0 0 255
418 AIPS_VIP_r 0 0 0 255
419 IPL_PFcm_l 0 0 0 255
420 IPL_PFcm_r 0 0 0 255
421 IPL_PF_l 0 0 0 255
422 IPL_PFm_l 0 0 0 255
423 IPL_PFm_r 0 0 0 255
424 IPL_PFop_l 0 0 0 255
425 IPL_PFop_r 0 0 0 255
426 IPL_PF_r 0 0 0 255
427 IPL_PFt_l 0 0 0 255
428 IPL_PFt_r 0 0 0 255
429 IPL_PGa_l 0 0 0 255
430 IPL_PGa_r 0 0 0 255
431 IPL_PGp_l 0 0 0 255
432 IPL_PGp_r 0 0 0 255
433 Visual_V3d_l 0 0 0 255
434 Visual_V3d_r 0 0 0 255
435 Visual_V4_l 0 0 0 255
436 Visual_V4_r 0 0 0 255
437 Visual_V5_b 0 0 0 255
438 Visual_VP_l 0 0 0 255
439 Visual_VP_r 0 0 0 255
0 0 0 255
# wm 0 0 0 255
498 wmsa 0 0 0 255
499 other_wmsa 0 0 0 255
0 0 0 255
# HiRes 0 0 0 255
500 right_CA2_3 0 0 0 255
501 right_alveus 0 0 0 255
502 right_CA1 0 0 0 255
503 right_fimbria 0 0 0 255
504 right_presubiculum 0 0 0 255
505 right_hippocampal_fissure 0 0 0 255
506 right_CA4_DG 0 0 0 255
507 right_subiculum 0 0 0 255
508 right_fornix 0 0 0 255
0 0 0 255
550 left_CA2_3 0 0 0 255
551 left_alveus 0 0 0 255
552 left_CA1 0 0 0 255
553 left_fimbria 0 0 0 255
554 left_presubiculum 0 0 0 255
555 left_hippocampal_fissure 0 0 0 255
556 left_CA4_DG 0 0 0 255
557 left_subiculum 0 0 0 255
558 left_fornix 0 0 0 255
0 0 0 255
600 Tumor 0 0 0 255
0 0 0 255
0 0 0 255
# Cerebellar 0 0 0 255 (matches labels
in cma.h)
#No. Label 0 0 0 255 A
601 Cbm_Left_I_IV 0 0 0 255
602 Cbm_Right_I_IV 0 0 0 255
603 Cbm_Left_V 0 0 0 255
604 Cbm_Right_V 0 0 0 255
605 Cbm_Left_VI 0 0 0 255
606 Cbm_Vermis_VI 0 0 0 255
607 Cbm_Right_VI 0 0 0 255
608 Cbm_Left_CrusI 0 0 0 255
609 Cbm_Vermis_CrusI 0 0 0 255
610 Cbm_Right_CrusI 0 0 0 255
611 Cbm_Left_CrusII 0 0 0 255
612 Cbm_Vermis_CrusII 0 0 0 255
613 Cbm_Right_CrusII 0 0 0 255
614 Cbm_Left_VIIb 0 0 0 255
615 Cbm_Vermis_VIIb 0 0 0 255
616 Cbm_Right_VIIb 0 0 0 255
617 Cbm_Left_VIIIa 0 0 0 255
618 Cbm_Vermis_VIIIa 0 0 0 255
619 Cbm_Right_VIIIa 0 0 0 255
620 Cbm_Left_VIIIb 0 0 0 255
621 Cbm_Vermis_VIIIb 0 0 0 255
622 Cbm_Right_VIIIb 0 0 0 255
623 Cbm_Left_IX 0 0 0 255
624 Cbm_Vermis_IX 0 0 0 255
625 Cbm_Right_IX 0 0 0 255
626 Cbm_Left_X 0 0 0 255
627 Cbm_Vermis_X 0 0 0 255
628 Cbm_Right_X 0 0 0 255
0 0 0 255
# Cerebellar 0 0 0 255
640 Cbm_Right_I_V_med 0 0 0 255
641 Cbm_Right_I_V_mid 0 0 0 255
642 Cbm_Right_VI_med 0 0 0 255
643 Cbm_Right_VI_mid 0 0 0 255
644 Cbm_Right_VI_lat 0 0 0 255
645 Cbm_Right_CrusI_med 0 0 0 255
646 Cbm_Right_CrusI_mid 0 0 0 255
647 Cbm_Right_CrusI_lat 0 0 0 255
648 Cbm_Right_CrusII_med 0 0 0 255
649 Cbm_Right_CrusII_mid 0 0 0 255
650 Cbm_Right_CrusII_lat 0 0 0 255
651 Cbm_Right_7med 0 0 0 255
652 Cbm_Right_7mid 0 0 0 255
653 Cbm_Right_7lat 0 0 0 255
654 Cbm_Right_8med 0 0 0 255
655 Cbm_Right_8mid 0 0 0 255
656 Cbm_Right_8lat 0 0 0 255
657 Cbm_Right_PUNs 0 0 0 255
658 Cbm_Right_TONs 0 0 0 255
659 Cbm_Right_FLOs 0 0 0 255
660 Cbm_Left_I_V_med 0 0 0 255
661 Cbm_Left_I_V_mid 0 0 0 255
662 Cbm_Left_VI_med 0 0 0 255
663 Cbm_Left_VI_mid 0 0 0 255
664 Cbm_Left_VI_lat 0 0 0 255
665 Cbm_Left_CrusI_med 0 0 0 255
666 Cbm_Left_CrusI_mid 0 0 0 255
667 Cbm_Left_CrusI_lat 0 0 0 255
668 Cbm_Left_CrusII_med 0 0 0 255
669 Cbm_Left_CrusII_mid 0 0 0 255
670 Cbm_Left_CrusII_lat 0 0 0 255
671 Cbm_Left_7med 0 0 0 255
672 Cbm_Left_7mid 0 0 0 255
673 Cbm_Left_7lat 0 0 0 255
674 Cbm_Left_8med 0 0 0 255
675 Cbm_Left_8mid 0 0 0 255
676 Cbm_Left_8lat 0 0 0 255
677 Cbm_Left_PUNs 0 0 0 255
678 Cbm_Left_TONs 0 0 0 255
679 Cbm_Left_FLOs 0 0 0 255
0 0 0 255
701 CSF-FSL-FAST 0 0 0 255
702 GrayMatter-FSL-FAST 0 0 0 255
703 WhiteMatter-FSL-FAST 0 0 0 255
0 0 0 255
999 SUSPICIOUS 0 0 0 255
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