Doug, I did
mri_annotation2label --subject bert --hemi lh --outdir $SUBJECTS_DIR/bert/label mri_annotation2label --subject bert --hemi rh --outdir $SUBJECTS_DIR /bert/label And then mris_label2annot --s bert --hemi lh --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --l lh.bankssts.label --l lh.caudalmiddlefrontal.label --l lh.entorhinal.label --l lh.paracentral.label --l lh.parstriangularis.label --l lh.postcentral.label --l lh.superiorfrontal.label --l lh.frontalpole.label --l lh.temporalpole.label --a myannot and mris_label2annot --s bert --hemi rh --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --l rh.bankssts.label --l rh.isthmuscingulate.label --l rh.medialorbitofrontal.label --l rh.parstriangularis.label --l rh.rostralanteriorcingulate.label --l rh.superiorparietal.label --l rh.frontalpole.label --a myannot If this is the right procedure I guess I'll have to modify the existing annot in matlab because all the surface is being labelled as Unknown. Thanks PPJ On Thu, Jul 5, 2012 at 4:01 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > You can also break up the annot into labels ( mri_annotation2label) then > recombine them with a new color table with mris_label2annot. > doug > > On 07/05/2012 02:57 PM, Bruce Fischl wrote: > > Hi PPJ, > > > > I think the color lut is embedded in the aparc.annot. If you want to > > change it you have to change the one that's in the .annot. I would do > > it in matlab. > > > > cheers > > Bruce > > > > On Thu, 5 Jul 2012, Pedro Paulo de Magalhães Oliveira Junior wrote: > > > >> I'm trying to generate an image to a paper and I have to colorize > >> some areas of the cortex with specific > >> colors. > >> I have edited the FreeSurferColorLUT.txt changing the following lines: > >> 1001 ctx-lh-bankssts 255 42 0 0 > >> 1003 ctx-lh-caudalmiddlefrontal 255 14 0 0 > >> 1006 ctx-lh-entorhinal 255 17 0 0 > >> 1017 ctx-lh-paracentral 255 43 0 0 > >> 1020 ctx-lh-parstriangularis 255 15 0 0 > >> 1022 ctx-lh-postcentral 255 14 0 0 > >> 1028 ctx-lh-superiorfrontal 255 79 0 0 > >> 1032 ctx-lh-frontalpole 255 17 0 0 > >> 1033 ctx-lh-temporalpole 255 14 0 0 > >> 2001 ctx-rh-bankssts 255 18 0 0 > >> 2010 ctx-rh-isthmuscingulate 255 39 0 0 > >> 2014 ctx-rh-medialorbitofrontal 255 60 0 0 > >> 2020 ctx-rh-parstriangularis 255 13 0 0 > >> 2026 ctx-rh-rostralanteriorcingulate 255 40 0 0 > >> 2029 ctx-rh-superiorparietal 255 48 0 0 > >> 2032 ctx-rh-frontalpole 255 106 0 0 > >> > >> all other regions are 127 127 127 0 > >> > >> When I load the surface for some case with: > >> tksurfer bert lh pial -annot aparc -ctab FreeSurferColorLUT.txt > >> > >> I get the usual coloring scheme with the labels correct. TkSurfer > >> seems to be ignoring > >> FreeSurferColorLUT.txt, but the labels are placed in the right spots. > >> > >> When I try to manually force the FreeSurferColorLUT.txt I'm > >> visualizing an all grey image. And the surface is > >> completely mislabeled, there is a 4th ventricle in the surface, > >> putamen in the surface, etc. > >> > >> What am I doing wrong? > >> --------------------------------------------------------------------- > >> Pedro Paulo de Magalhães Oliveira Junior > >> Netfilter & SpeedComm Telecom-- www.netfilter.com.br > >> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 > >> > >> > >> > >> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > 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. > >
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