Thanks Douglas. It did work using the color table with just the included labels (I had to renumber the labels in the table)
For left: 1 ctx-lh-bankssts 255 42 0 0 2 ctx-lh-caudalmiddlefrontal 255 14 0 0 3 ctx-lh-entorhinal 255 17 0 0 4 ctx-lh-paracentral 255 43 0 0 5 ctx-lh-parstriangularis 255 15 0 0 6 ctx-lh-postcentral 255 14 0 0 7 ctx-lh-superiorfrontal 255 79 0 0 8 ctx-lh-frontalpole 255 17 0 0 9 ctx-lh-temporalpole 255 14 0 0 For right: 1 ctx-rh-bankssts 255 18 0 0 2 ctx-rh-isthmuscingulate 255 39 0 0 3 ctx-rh-medialorbitofrontal 255 60 0 0 4 ctx-rh-parstriangularis 255 13 0 0 5 ctx-rh-rostralanteriorcingulate 255 40 0 0 6 ctx-rh-superiorparietal 255 48 0 0 7 ctx-rh-frontalpole 255 106 0 0 On Thu, Jul 5, 2012 at 7:14 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > 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<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<http://itunes.apple.com/br/artist/netfilter/id365306441> >> >> >> >> >> >> >> >> >> > >> > >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> > >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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> >> >> <http://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> >> >> <http://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:freesur...@nmr.mgh.** >> harvard.edu <Freesurfer@nmr.mgh.harvard.edu>> >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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<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> > >
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