Hi Gary, don't load it as a label, load it as an overlay. Another thing
to note is that you should not specify both --projfrac and
--projfrac-max (or --projdist-max). In your first case, it won't make a
difference because --projfrac-max is last, but it will make a difference
in your second call below.
doug

On 09/09/2012 06:13 PM, Garikoitz Lerma Usabiaga wrote:

Dear freesurfers,
I am trying to create .mgh labels in order to obtain CT averages from
several subjects.

I register the ROI-s with bbregister and I get the .nii which renders
nicely in tksurfer:
/tksurfer Surfrend_Colin127 lh inflated /-overlay
/Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii -overlay-reg
/Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat
-fthresh 1



The problem arises when I try to use mri_vol2surf. I've been trying
with many different options, for example:

mri_vol2surf--mov
/Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii--reg
/Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat
--projfrac 0.5 --projfrac-max 0 1 .01--hemi lh--out
/Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh

or

mri_vol2surf --mov
/Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii--reg
/Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat
--projdist-max 0 1 0.1 --projfrac 1 --interp nearest --hemi lh --out
/Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh



When I try to visualize it with tksurfer, it gives me nothing:
/tksurfer Surfrend_Colin27 lh inflated -label/
/Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh -fthresh 1


How should I use mri_vol2surf in order to obtain results?
What are the alternatives in order to have surface labels?
Creating a label tracing the border of the .nii label in tksurfer  is
a posible solution?


Thank you very much for your attention,
Gari








[iMacGari:~] garikoitz% mri_vol2surf --mov
/Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii --reg
/Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat
--projfrac 0.5 --projfrac-max 0 1 .01 --hemi lh --out
/Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh
srcvol = /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii
srcreg =
/Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 1
INFO: float2int code = 0
Done loading volume
Reading surface
/Applications/freesurfer/subjects/Surfrend_Colin127/surf/lh.white
Done reading source surface
Reading thickness
/Applications/freesurfer/subjects/Surfrend_Colin127/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0 0 1
using old
2 0.01 0 1
using old
3 0.02 0 1
[...]
99 0.979999 0 1
using old
100 0.989999 0 1
using old
101 0.999999 0 1
using old
Done mapping volume to surface
Number of source voxels hit = 32875
Writing to /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh
Dim: 165607 1 1



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Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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