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
> >>
> >>
> >>
> >>
> >
> >
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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