Ah, OK, makes sense - should have guessed, sorry, vol2surf behaved so agreeably with the vertex-free mask!
Shall make that surf mask now, thanks much, Fred On 14 Apr 2013, at 22:56, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > > Oh, the label should be a surface label. mri_cor2label creates a volume label > (basically it just means that each label point corresponds to a 1mm3 cube > instead of a verex -- the vertex numbers should all be -1). Try running > vol2surf on the mask (using nearest interp) to create a surface mask. Then > create a surface label with mri_cor2label using the --surf option. > doug > > > > > On 4/14/13 5:01 PM, Fred Dick wrote: >> Hi Doug >> >> I've actually tried both inclusive and exclusive and have failed - just >> checked again in tkmedit that the label was coming up correctly and it was. >> >> Just to double-check - the label should be in the space of the --mov, right? >> >> Thanks! >> >> Fred >> >> >> >> 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 >> >> --regregister.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 >> >> >> > > > 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. >
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