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...surfer: using interface /autofs/space/tanha_002/users/greve/fsdev.build/tktools/tksurfer.tcl
******************** 0 nonzero vertices found ********************
label stat field identically zero - setting to 1
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
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>On Mon, Jul 14, 2014 at 7:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@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
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>
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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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--
yours,
Lars M. Rimol, PhD
St. Olavs Hospital
Trondheim,
Norway
--
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
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