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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