Dear all
I am painting some higher-res anatomical data from a volume to a surface, and want to use a mask that excludes the vessels. (The same data but 1x1x1 conformed were used to create the surface).
I've created a binary label in the same space
mri_cor2label --i ./R2Mask.nii.gz --l ./R2s.label --id 1
made sure that it looks ok when I read in hi-res to tkmedit and display label,
then ran mri_vol2surf
mri_vol2surf --mov ./sPQ07082012-0009-00001-000208-01_R1.nii --reg register.dat --surf-fwhm 4 --hemi $hemi --projfrac $frac --interp trilinear --out_type w --mask R2s.label --o ./dancar-0.5-lh.w
And got the output (pasted below), showing that the output is all zero.
Output is fine without label, or with -cortex.
I've also tried this with a conformed version of the label (also verified in tkmedit) and have had the same thing. (I thought maybe it was applying it to orig vol, which I admit would be strange).
(I noticed someone had a similar issue a couple of years ago, but it involved a surface rather than volume label, and looked like it had been resolved).
Am running current stable version on Mountain Lion.
Thanks for any pointers,
best, Fred
########################################################## masking output with label R2s.label INFO: output format is paint srcvol = ./sPQ07082012-0009-00001-000208-01_R1.nii srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label R2s.label Reading surface /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.white Done reading source surface Reading thickness /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 108676 Surface smoothing by fwhm = 4 (n=10) Masking with R2s.label Warning: all vertex values are zero
Hi Fred, that mask is an inclusive mask, not an exclusive mask. Try inverting you mask. doug
On 4/14/13 4:31 PM, Fred Dick wrote:
Dear all
I am painting some higher-res anatomical data from a volume to a surface, and want to use a mask that excludes the vessels. (The same data but 1x1x1 conformed were used to create the surface).
I've created a binary label in the same space
mri_cor2label --i ./R2Mask.nii.gz --l ./R2s.label --id 1
made sure that it looks ok when I read in hi-res to tkmedit and display label,
then ran mri_vol2surf
mri_vol2surf --mov ./sPQ07082012-0009-00001-000208-01_R1.nii --reg
register.dat --surf-fwhm 4 --hemi $hemi --projfrac $frac --interp trilinear --out_type w --mask R2s.label --o ./dancar-0.5-lh.w
And got the output (pasted below), showing that the output is all zero.
Output is fine without label, or with -cortex.
I've also tried this with a conformed version of the label (also verified in tkmedit) and have had the same thing. (I thought maybe it was applying it to orig vol, which I admit would be strange).
(I noticed someone had a similar issue a couple of years ago, but it involved a surface rather than volume label, and looked like it had been resolved).
Am running current stable version on Mountain Lion.
Thanks for any pointers,
best, Fred
########################################################## masking output with label R2s.label INFO: output format is paint srcvol = ./sPQ07082012-0009-00001-000208-01_R1.nii srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label R2s.label Reading surface /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.white Done reading source surface Reading thickness /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 108676 Surface smoothing by fwhm = 4 (n=10) Masking with R2s.label Warning: all vertex values are zero
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Fred Dick