Re: [Freesurfer] TkSurfer and new color table. Mislabelling

[Pedro Paulo de Magalhães Oliveira Junior]

Thanks Douglas.

It did work using the color table with just the included labels (I had to
renumber the labels in the table)

For left:
1 ctx-lh-bankssts 255 42 0 0
2 ctx-lh-caudalmiddlefrontal 255 14 0 0
3 ctx-lh-entorhinal 255 17 0 0
4 ctx-lh-paracentral 255 43 0 0
5 ctx-lh-parstriangularis 255 15 0 0
6 ctx-lh-postcentral 255 14 0 0
7 ctx-lh-superiorfrontal 255 79 0 0
8 ctx-lh-frontalpole 255 17 0 0
9 ctx-lh-temporalpole 255 14 0 0

For right:
1 ctx-rh-bankssts 255 18 0 0
2 ctx-rh-isthmuscingulate 255 39 0 0
3 ctx-rh-medialorbitofrontal 255 60 0 0
4 ctx-rh-parstriangularis 255 13 0 0
5 ctx-rh-rostralanteriorcingulate 255 40 0 0
6 ctx-rh-superiorparietal 255 48 0 0
7 ctx-rh-frontalpole 255 106 0 0


On Thu, Jul 5, 2012 at 7:14 PM, Douglas N Greve
wrote:

> 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 <
>> 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
>> >>
>> >>
>> >>
>> 

Re: [Freesurfer] TkSurfer and new color table. Mislabelling

[Anderson Winkler]

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 
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

>> -- For mobile:
http://itunes.apple.com/br/artist/netfilter/id365306441
>>
>>
>>
>>
>
>
> ___
> Freesurfer mailing list
> 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 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html


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Re: [Freesurfer] TkSurfer and new color table. Mislabelling

[Douglas N Greve]

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 
> 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
> 
> >> -- For mobile:
> http://itunes.apple.com/br/artist/netfilter/id365306441
> >>
> >>
> >>
> >>
> >
> >
> > ___
> > Freesurfer mailing list
> > 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 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intende

Re: [Freesurfer] TkSurfer and new color table. Mislabelling

[Pedro Paulo de Magalhães Oliveira Junior]

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
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
> >>
> >>
> >>
> >>
> >
> >
> > ___
> > Freesurfer mailing list
> > 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
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> 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.
>
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.

Re: [Freesurfer] TkSurfer and new color table. Mislabelling

[Douglas N Greve]

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
>>
>>
>>
>>
>
>
> ___
> Freesurfer mailing list
> 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
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] TkSurfer and new color table. Mislabelling

[Bruce Fischl]

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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