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?
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Pedro Paulo de Magalhães Oliveira Junior
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