Hi Pedro Paulo, it is not quite the right procedure, but I'm surprised that it gave unknown for all labels. Try modifying the colortable.txt such that the first entry is the name and color for your first label, etc. doug
On 07/05/2012 03:44 PM, Pedro Paulo de Magalhães Oliveira Junior wrote: > 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 <mailto: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 > <http://www.netfilter.com.br> > >> -- For mobile: > http://itunes.apple.com/br/artist/netfilter/id365306441 > >> > >> > >> > >> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > -- 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
