Hey again

sorry, I seem not to be able to accomplish this very simple thing!

First wrote out mask as .w file using vol2surf, but mri_cor2label couldn't read ('mri_read(): couldn't determine type of file ./rh.R2MaskBrain.w'). 

Then tried writing out as curv using the following command:

mri_vol2surf --mov  R2MaskBrain.nii.gz --reg register.dat --hemi $hemi --interp nearest --o ./$hemi.R2MaskBrain  --out_type curv  --projfrac 0.5

and got this error,

################

Writing to ./lh.R2MaskBrain

Dim: 152308 1 1

MRIwriteType(): code inconsistency (file type recognized but not caught)

ERROR: saving ./lh.R2MaskBrain

#####################

Bug, or user stupidity??? 

cheers,

Fred

On 14 Apr 2013, at 22:56, Douglas Greve <greve@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

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