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
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