Hi Pedro,
Have a look at this article: http://brainder.org/2011/07/05/freesurfer-brains-in-arbitrary-colours I think this is the same you'd like to do (or you can change some steps easily). Hope it helps!
All the best,
Anderson
On 05/07/12 20:44, 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 <greve@nmr.mgh.harvard.edu mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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.
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