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 1Here'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 <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 greve@nmr.mgh.harvard.edu <mailto:greve@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
Hi Doug,
Yes that works! I'm viewing it on the surface.
LMR
On Tue, Jul 15, 2014 at 6:27 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
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 1Here'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 < 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 greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@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@nmr.mgh.harvard.edu
-
Douglas N Greve -
Lars M. Rimol