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 >>> <k...@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 -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
