Are you trying to view it in the volume or the surface? When I run freeview viewing the surface and load the label using the "Load Label" button (not File->LoadLabel), it works for me.
Can you try the tksurfer command below? It runs for me. You can ignore the warning about 0 nonzero vertices since they are all set to 1. tksurfer fsaverage lh inflated -label ~/tmp/lh_binarymap_area_covar8.label subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: /autofs/cluster/con_009/users/greve/ixi-subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/cluster/con_009/users/greve/ixi-subjects/ixi320/mri checking for nofix files in 'inflated' Reading image info (/autofs/cluster/con_009/users/greve/ixi-subjects/fsaverage) Reading /autofs/cluster/con_009/users/greve/ixi-subjects/fsaverage/mri/orig.mgz surfer: Reading header info from /autofs/cluster/con_009/users/greve/ixi-subjects/fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 surfer: curvature read: min=-0.673989 max=0.540227 surfer: single buffered window surfer: tkoInitWindow(fsaverage) setting percentile thresholds (-1.00, 0.00, 0.00) loading label /homes/4/greve/tmp/lh_binarymap_area_covar8.label reading white matter vertex locations... ******************** 0 nonzero vertices found ******************** label stat field identically zero - setting to 1 surfer: using interface /autofs/space/tanha_002/users/greve/fsdev.build/tktools/tksurfer.tcl Reading /autofs/space/tanha_002/users/greve/fsdev.build/tktools/tkm_common.tcl Reading /autofs/space/tanha_002/users/greve/fsdev.build/tktools/tkm_wrappers.tcl Reading /autofs/space/tanha_002/users/greve/fsdev.build/lib/tcl/fsgdfPlot.tcl Reading /autofs/space/tanha_002/users/greve/fsdev.build/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... On 07/15/2014 09:04 AM, Lars M. Rimol wrote: > Hi, > > I go to File -> Label -> load label and there I pick > lh_binarymap_area_covar8.label and then I get the error message: > > > % ******************** 0 nonzero vertices found ******************** > label stat field identically zero - setting to 1 > > > That's it! > > I don't know, but it seems to be saying that all vertices are zero, > doesn't it? > > When I cat the file, I see this: > > 163839 -34.195 -22.897 -24.093 0.0000000000 > > 163840 -34.295 -23.062 -23.449 0.0000000000 > > 163841 -35.093 -23.358 -22.788 0.0000000000 > > The leftmost column surely is vertex number, I don't know what the > next two are (if this were a volume, I'd say x,y,z coordinates) and if > the final column is the value of each vertex, I would have to agree > with tksurfer that there are no nonzero vertices. > > When I load the mgh file, thogh, it has some zero vertices and 98877 > that are 100, that is they are larger than 99.999999999999992. > > >> size(find(gt(testing,99.999999999999992))) > > ans = > > 98877 1 > > > Here's the code I used to make the binary map and save it as an mgh file: > > log10pID = significance threshold > > binaryVLBWlhcovar8(find(gt(binaryVLBWlhcovar8,log10pID))) = 100; > binaryVLBWlhcovar8(find(lt(binaryVLBWlhcovar8,log10pID))) = 0; > > fs_save_mgh(binaryVLBWlhcovar8,'lh_binarymap_area_covar8.mgh',mri); > > > So mri_cor2label must be changing some of these vertices from > 99.99999etc. to 0, right? > > > LMR > > > > On Mon, Jul 14, 2014 at 7:33 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > It loads ok for me both in 5.1 and 5.3. Can you give more info on > what is going wrong with tksurfer? > > > On 07/13/2014 05:35 AM, Lars M. Rimol wrote: > > Hi Doug, > > I'm having some problems with the label creation again. When I > run mri_cor2label, it seems OK (please see below), but when I > try to open it in tksurfer, it gives me an error message (bottom). > > Would you mind taking a look at this label to see what's wrong > with it? I'm attaching the binary mgh file and the label. NB! > The binary .mgh file is from matlab, where I have set all > suprathreshold vertices to 100 and all others to 0. Of course, > Matlab doesn't really do this, it sets them to somewhere close > to 99.999999999999992. I don't suppose I could use "greater > than 99" in mri_cor2label? > > ######### > creating label: > > [LMR in ~ ] mri_cor2label --i > > /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_pmaps/lh_binarymap_area_covar8.mgh > --id 100 --l > > /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_pmaps/lh_binarymap_area_covar8 > --surf fsaverage lh > $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ > Loading mri > > /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_pmaps/lh_binarymap_area_covar8.mgh > Loading /home/lmr/subjects/fsaverage/surf/lh.white > Scanning the volume > Found 98877 label voxels > Writing label file > > /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_pmaps/lh_binarymap_area_covar8 > Centroid: -28.93 -15.97 10.14 > mri_cor2label completed SUCCESSFULLY > > ####### > loading it in tksurfer: > > % ******************** 0 nonzero vertices found > ******************** > label stat field identically zero - setting to 1 > > > > Thank you! > > -- > yours, > > Lars M. Rimol, PhD > St. Olavs Hospital > Trondheim, > Norway > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > 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. > > > > > -- > yours, > > Lars M. Rimol, PhD > St. Olavs Hospital > Trondheim, > Norway -- 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
