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
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