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
<gr...@nmr.mgh.harvard.edu <mailto: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
<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
gr...@nmr.mgh.harvard.edu <mailto:gr...@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.
_______________________________________________
Freesurfer mailing list
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.
_______________________________________________
Freesurfer mailing list
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.
