Thank you for your reply and giving your time. I am not be able to figure out where things are going wrong.
Then I followed the steps below of recon-all to create the apar+aseg.mgz file: recon-all -pial -subjid 100307 recon-all -cortribbon -subjid 100307 recon-all -parcstats -subjid 100307 recon-all -pctsurfcon -subjid 100307 recon-all -hyporelabel -subjid 100307 recon-all -aparc2aseg -subjid 100307
I am also putting the output mri_aparc2aseg from the recon-all.log file. ****************************************************************************************** @# AParc-to-ASeg aparc Mon Apr 10 22:18:54 BST 2017 /home/koushik/Parcellation/100307
mri_aparc2aseg --s 100307 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt
relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/koushik/Parcellation subject 100307 outvol /home/koushik/Parcellation/100307/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /home/koushik/Parcellation/100307/surf/lh.white
Reading lh pial surface /home/koushik/Parcellation/100307/surf/lh.pial
Loading lh annotations from /home/koushik/Parcellation/100307/label/lh.aparc.annot reading colortable from annotation file... colortable with 80 entries read (originally none)
Reading rh white surface /home/koushik/Parcellation/100307/surf/rh.white
Reading rh pial surface /home/koushik/Parcellation/100307/surf/rh.pial
Loading rh annotations from /home/koushik/Parcellation/100307/label/rh.aparc.annot reading colortable from annotation file... colortable with 80 entries read (originally none) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/koushik/Parcellation/100307/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from /home/koushik/Parcellation/100307/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; -------------------------
Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.15 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 103 rescaling Left_Cerebral_Cortex from 61 --> 76 rescaling Left_Lateral_Ventricle from 13 --> 22 rescaling Left_Inf_Lat_Vent from 34 --> 31 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 70 rescaling Left_Thalamus from 94 --> 102 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 86 rescaling Left_Putamen from 80 --> 92 rescaling Left_Pallidum from 98 --> 98 rescaling Third_Ventricle from 25 --> 39 rescaling Fourth_Ventricle from 22 --> 24 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 69 rescaling Left_Amygdala from 56 --> 72 rescaling CSF from 32 --> 56 rescaling Left_Accumbens_area from 62 --> 69 rescaling Left_VentralDC from 87 --> 89 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 75 rescaling Right_Lateral_Ventricle from 13 --> 22 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 70 rescaling Right_Thalamus_Proper from 85 --> 84 rescaling Right_Caudate from 62 --> 79 rescaling Right_Putamen from 80 --> 82 rescaling Right_Pallidum from 97 --> 96 rescaling Right_Hippocampus from 53 --> 68 rescaling Right_Amygdala from 55 --> 70 rescaling Right_Accumbens_area from 65 --> 77 rescaling Right_VentralDC from 86 --> 94 rescaling Fifth_Ventricle from 40 --> 47 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 54 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 503144 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 74 changed. pass 2: 4 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /home/koushik/Parcellation/100307/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Mon Apr 10 22:21:48 BST 2017 /home/koushik/Parcellation/100307 INFO: skipping a2009s aparc2aseg #----------------------------------------- #@# AParc-to-ASeg DKTatlas Mon Apr 10 22:21:48 BST 2017 /home/koushik/Parcellation/100307 INFO: skipping DKTatlas aparc2aseg
Started at Mon Apr 10 22:18:54 BST 2017 Ended at Mon Apr 10 22:21:48 BST 2017 #@#%# recon-all-run-time-hours 0.048 recon-all -s 100307 finished without error at Mon Apr 10 22:21:48 BST 2017
***************************
Thanks & regards
Sarbani ________________________________________ 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 18:14 To: Freesurfer support list Subject: Re: [Freesurfer] Implement my own parcellation on aparc+aseg.mgz file
ok, then what is the next step in your processing? And where does it go wrong? Does the annot display in the proper colors on the surface?
Sorry, I lost track of what was going on in your previous emails Bruce On Fri, 28 Apr 2017, Das S. wrote:
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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