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 <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
    >>
    >>
    >>
    >>
    >
    >
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