Dear Freesurfer experts,
I have made a parcellation of the white matter surface outside of freesurfer in volumes. I convert the volume labels to surface labels. I have now a lot of surface labels (~500 for each hemisphere) which I want to concatenate to an annotation file for easier visualization. When I use mris_label2annot to perform this operation I get a lot of warnings: "WARNING: vertex 6021 maps to multiple labels! (overwriting)", and the result does not look right. When I load some of the single labels into freeview or tksurfer they look fine. Does anyone know how to perform this operation? How do I avoid the warnings?
I do the operations (volume labels-->surface labels-->annotation) on each hemisphere separately, but I have some regions located in both hemispheres. Is it then possible to keep the whole region the same color across hemispheres during the operations?
Best, Karen
Hi Karen What do you mean the results don't look right? Can you send an image? Cheers Bruce
On Jun 19, 2014, at 9:41 AM, Karen Marie Sandø Ambrosen kmsa@dtu.dk wrote:
Dear Freesurfer experts,
I have made a parcellation of the white matter surface outside of freesurfer in volumes. I convert the volume labels to surface labels. I have now a lot of surface labels (~500 for each hemisphere) which I want to concatenate to an annotation file for easier visualization. When I use mris_label2annot to perform this operation I get a lot of warnings: "WARNING: vertex 6021 maps to multiple labels! (overwriting)", and the result does not look right. When I load some of the single labels into freeview or tksurfer they look fine. Does anyone know how to perform this operation? How do I avoid the warnings?
I do the operations (volume labels-->surface labels-->annotation) on each hemisphere separately, but I have some regions located in both hemispheres. Is it then possible to keep the whole region the same color across hemispheres during the operations?
Best, Karen _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
When I input all the labels in the mris_label2annot command I get the result shown in: H09_copy_AllLabels2annot.png and it gives a lot of warnings: "Warning: vertex 142382 with annotation ffffffff - out of range!". The command I use looks like: mris_label2annot --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --l label1 --l label2 ... --labeln --s H09_copy --a output_annotation --h lh When I run the command I get a lot of warnings: "WARNING: vertex 139930 maps to multiple labels! (overwriting)".
In comparison if I create an annotation using only, e.g., the first 10 labels I get the result shown in: H09_copy_10Labels2annot.png and I don't get any warnings. If I create an annotation using the first 100 labels I get the result shown in: H09_copy_100Labels2annot.png and I get warnings similar to when I use all the labels.
I hope this makes the problem more clear.
Best, Karen
On 06/20/2014 04:02 AM, Bruce Fischl wrote:
Hi Karen What do you mean the results don't look right? Can you send an image? Cheers Bruce
On Jun 19, 2014, at 9:41 AM, Karen Marie Sandø Ambrosen kmsa@dtu.dk wrote:
Dear Freesurfer experts,
I have made a parcellation of the white matter surface outside of freesurfer in volumes. I convert the volume labels to surface labels. I have now a lot of surface labels (~500 for each hemisphere) which I want to concatenate to an annotation file for easier visualization. When I use mris_label2annot to perform this operation I get a lot of warnings: "WARNING: vertex 6021 maps to multiple labels! (overwriting)", and the result does not look right. When I load some of the single labels into freeview or tksurfer they look fine. Does anyone know how to perform this operation? How do I avoid the warnings?
I do the operations (volume labels-->surface labels-->annotation) on each hemisphere separately, but I have some regions located in both hemispheres. Is it then possible to keep the whole region the same color across hemispheres during the operations?
Best, Karen _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Don't use FreeSurferColorLUT.txt, you need to create your own color table whose format is like FreeSurferColorLUT.txt doug
On 06/20/2014 03:49 AM, Karen Marie Sandø Ambrosen wrote:
Hi Bruce,
When I input all the labels in the mris_label2annot command I get the result shown in: H09_copy_AllLabels2annot.png and it gives a lot of warnings: "Warning: vertex 142382 with annotation ffffffff - out of range!". The command I use looks like: mris_label2annot --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --l label1 --l label2 ... --labeln --s H09_copy --a output_annotation --h lh When I run the command I get a lot of warnings: "WARNING: vertex 139930 maps to multiple labels! (overwriting)".
In comparison if I create an annotation using only, e.g., the first 10 labels I get the result shown in: H09_copy_10Labels2annot.png and I don't get any warnings. If I create an annotation using the first 100 labels I get the result shown in: H09_copy_100Labels2annot.png and I get warnings similar to when I use all the labels.
I hope this makes the problem more clear.
Best, Karen
On 06/20/2014 04:02 AM, Bruce Fischl wrote:
Hi Karen What do you mean the results don't look right? Can you send an image? Cheers Bruce
On Jun 19, 2014, at 9:41 AM, Karen Marie Sandø Ambrosen kmsa@dtu.dk wrote:
Dear Freesurfer experts,
I have made a parcellation of the white matter surface outside of freesurfer in volumes. I convert the volume labels to surface labels. I have now a lot of surface labels (~500 for each hemisphere) which I want to concatenate to an annotation file for easier visualization. When I use mris_label2annot to perform this operation I get a lot of warnings: "WARNING: vertex 6021 maps to multiple labels! (overwriting)", and the result does not look right. When I load some of the single labels into freeview or tksurfer they look fine. Does anyone know how to perform this operation? How do I avoid the warnings?
I do the operations (volume labels-->surface labels-->annotation) on each hemisphere separately, but I have some regions located in both hemispheres. Is it then possible to keep the whole region the same color across hemispheres during the operations?
Best, Karen _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
We do not have a way to resolve the overlapping problem. That is something you will have to figure out. You should be able to keep the colors the same by specifying the entries in the color table doug
On 6/19/14 3:41 PM, Karen Marie Sandø Ambrosen wrote:
Dear Freesurfer experts,
I have made a parcellation of the white matter surface outside of freesurfer in volumes. I convert the volume labels to surface labels. I have now a lot of surface labels (~500 for each hemisphere) which I want to concatenate to an annotation file for easier visualization. When I use mris_label2annot to perform this operation I get a lot of warnings: "WARNING: vertex 6021 maps to multiple labels! (overwriting)", and the result does not look right. When I load some of the single labels into freeview or tksurfer they look fine. Does anyone know how to perform this operation? How do I avoid the warnings?
I do the operations (volume labels-->surface labels-->annotation) on each hemisphere separately, but I have some regions located in both hemispheres. Is it then possible to keep the whole region the same color across hemispheres during the operations?
Best, Karen _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Douglas N Greve
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Karen Marie Sandø Ambrosen