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
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
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
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.eduwrote:
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 greve@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.
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 >> >> >> >> > > > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu <mailto:greve@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.
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 greve@nmr.mgh.harvard.eduwrote:
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.**edugreve@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<http://itunes.apple.com/br/artist/netfilter/id365306441> >> >> >> >> > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@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> <http://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> <http://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 Freesurfer@nmr.mgh.harvard.edu>
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Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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 <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 >> >> >> >> > > > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu <mailto:greve@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.
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Anderson Winkler -
Bruce Fischl -
Douglas N Greve -
Pedro Paulo de Magalhães Oliveira Junior