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> 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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