Hi Fred, why do you want to save it as a wfile? We're trying to phase
wfiles out. Can you use mgh format?
doug
On 4/15/13 12:56 PM, Fred Dick wrote:
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 <gr...@nmr.mgh.harvard.edu
<mailto: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
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