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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@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 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
