Yes there is embedded color file in my annot file. Here is the extract of lh.aparc.annot that I created.
koushik@koushik-DQ77MK:~/Parcellation/100307_old/100307/label$ mris_info lh.aparc.annot reading colortable from annotation file... colortable with 95 entries read (originally 100307/label/eq_parcellation_label/MyColorLUT.txt) 0 unknown 130 18 34 0 1 node-lh-1 70 130 180 0 2 node-lh-2 245 245 245 0 3 node-lh-3 205 62 78 0 4 node-lh-4 120 18 134 0 5 node-lh-5 196 58 250 0 6 node-lh-6 0 148 0 0 7 node-lh-7 220 248 164 0 8 node-lh-8 230 148 34 0 9 node-lh-9 0 118 14 0 10 node-lh-10 70 118 14 0 11 node-lh-11 122 186 220 0 12 node-lh-12 236 13 176 0 13 node-lh-13 12 48 255 0 14 node-lh-14 204 182 142 0 15 node-lh-15 42 204 164 0 16 node-lh-16 119 159 176 0 17 node-lh-17 220 216 20 0 18 node-lh-18 103 255 255 0 19 node-lh-19 80 196 98 0 20 node-lh-20 60 58 210 0 21 node-lh-21 160 58 210 0 22 node-lh-22 120 58 210 0 23 node-lh-23 40 58 210 0 24 node-lh-24 60 120 60 0 25 node-lh-25 255 100 0 0 26 node-lh-26 250 165 0 0 27 node-lh-27 0 255 127 0 28 node-lh-28 165 42 42 0 29 node-lh-29 135 206 235 0 30 node-lh-30 160 32 240 0 31 node-lh-31 0 200 200 0 32 node-lh-32 100 50 100 0 33 node-lh-33 135 50 74 0 34 node-lh-34 122 135 50 0 35 node-lh-35 51 50 135 0 36 node-lh-36 74 155 60 0 37 node-lh-37 120 62 43 0 38 node-lh-38 74 155 60 0 39 node-lh-39 122 135 50 0 40 node-lh-40 100 120 50 0 41 node-rh-1 70 130 180 0 42 node-rh-2 245 245 245 0 43 node-rh-3 205 62 78 0 44 node-rh-4 120 18 134 0 45 node-rh-5 196 58 250 0 46 node-rh-6 0 148 0 0 47 node-rh-7 220 248 164 0 48 node-rh-8 230 148 34 0 49 node-rh-9 0 118 14 0 50 node-rh-10 70 118 14 0 51 node-rh-11 122 186 220 0 52 node-rh-12 236 13 176 0 53 node-rh-13 12 48 255 0 54 node-rh-14 204 182 142 0 55 node-rh-15 42 204 164 0 56 node-rh-16 119 159 176 0 57 node-rh-17 220 216 20 0 58 node-rh-18 103 255 255 0 59 node-rh-19 80 196 98 0 60 node-rh-20 60 58 210 0 61 node-rh-21 160 58 210 0 62 node-rh-22 120 58 210 0 63 node-rh-23 40 58 210 0 64 node-rh-24 60 120 60 0 65 node-rh-25 255 100 0 0 66 node-rh-26 250 165 0 0 67 node-rh-27 0 255 127 0 68 node-rh-28 165 42 42 0 69 node-rh-29 135 206 235 0 70 node-rh-30 160 32 240 0 71 node-rh-31 0 200 200 0 72 node-rh-32 100 50 100 0 73 node-rh-33 135 50 74 0 74 node-rh-34 122 135 50 0 75 node-rh-35 51 50 135 0 76 node-rh-36 74 155 60 0 77 node-rh-37 120 62 43 0 78 node-rh-38 74 155 60 0 79 node-rh-39 122 135 50 0 80 node-rh-40 152 125 50 0 81 Left-Thalamus-Proper 0 118 14 255 82 Left-Caudate 122 186 220 255 83 Left-Putamen 236 13 176 255 84 Left-Pallidum 12 48 255 255 85 Left-Hippocampus 220 216 20 255 86 Left-Amygdala 103 255 255 255 87 Left-Accumbens-area 255 165 0 255 88 Right-Thalamus-Proper 0 118 14 255 89 Right-Caudate 122 186 220 255 90 Right-Putamen 236 13 176 255 91 Right-Pallidum 13 48 255 255 92 Right-Hippocampus 220 216 20 255 93 Right-Amygdala 103 255 255 255 94 Right-Accumbens-area 255 165 0 255
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 28 April 2017 15:35 To: Freesurfer support list Subject: Re: [Freesurfer] Implement my own parcellation on aparc+aseg.mgz file
Hi Das
can you check if there is an embedded colormap in your .annot file?You can do this by running mris_info on it.
cheers Bruce On Fri, 28 Apr 2017, Das S. wrote:
Hi I have create my own annot file and lookuptable for cortical parcellation. How I can implement my own parcellation in aparc+aseg.mgz file.
I am also stuck on how to update the FreeSurferColorLUT.txt file?
Please help. Thanks Sarbani
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