use
tkmedit fsaverage orig.mgz -overlay teste_sig.mgz
doug
On 2/21/11 3:46 PM, Fernanda Palhano wrote:
Hi Bruce,
Thank you for the prompt reply.
I tried using mri_surf2vol :
mri_surf2vol --surfval
qdec/g1_g2_lh_06out/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh
--identity fsaverage --template fsaverage/mri/T1.mgz --hemi lh --o
teste_sig.mgz
gdiagno = -1
Using identity matrix for registration
Qa2v: SurfXYZ to VolCRS: ------------------------------
-1.000 0.000 0.000 128.000;
0.000 0.000 -1.000 128.000;
0.000 1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
--------------------------------------------------
subjects dir /Applications/freesurfer/subjects/dados_Riba/
surface value path
qdec/g1_g2_lh_06out/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh
hemi lh
mksurfmask 0
projfrac 0
outvol path teste_sig.mgz
template path fsaverage/mri/T1.mgz
------- Anat2Vol Registration (TkReg)----
1.000 0.000 0.000 0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
-----------------------------------------
height = 256
width = 256
depth = 256
xsize = 1.000000
ysize = 1.000000
zsize = 1.000000
cdc = -1.000000 0.000000 0.000000
rdc = 0.000000 0.000000 -1.000000
sdc = 0.000000 1.000000 0.000000
xyz0 = 0.000000 0.000000 0.000000
Gdiag_no -1
Reading surface
/Applications/freesurfer/subjects/dados_Riba//fsaverage/surf/lh.white
Done reading source surface
INFO: reading
qdec/g1_g2_lh_06out/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh
as MGH
Done loading source values (nvtxs = 163842)
INFO: mapping vertices to closest voxel
INFO: resampling surface to volume
INFO: sampled 73965 voxels in the volume
INFO: writing output volume to teste_sig.mgz
done
And then, use tkmedit to view it:
[Fernanda-Palhanos-Mac-Pro:freesurfer/subjects/dados_Riba]
fernandapalhano% tkmedit fsaverage teste_sig.mgz
mghRead(/Applications/freesurfer/subjects/dados_Riba//fsaverage/mri/teste_sig.mgz,
-1): could not open file
Error: Loading volume teste_sig.mgz
Couldn't read the anatomical volume.
Tkmedit couldn't read the volume you specified.
This could be because the image format wasn't recognized,
or it couldn't find the proper header,
or the file(s) were unreadable,
or it was the wrong size.
Am I using wrong parameters in mri_surf2vol?
Thanks again,
Fernanda
On Mon, Feb 21, 2011 at 5:30 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Fernanda
if that's a surface overlay you'll need to sample it into the
volume with mri_surf2vol
cheers
Bruce
On Mon, 21 Feb 2011, Fernanda Palhano wrote:
Hello,
Does anyone knows if is it possible to overlay the surface
file sig.mgh onto
a T1 vol?
I tried the command:
tkmedit fsaverage T1.mgz -fthresh 2 -fmax 5 -overlay
qdec/rh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh (where
2 and 5 were
the thresholds I used in qdec),
but it seems like I have only one point of the sig.mgh (in the
slice 128)
which is outside the volume.
There's another way to do this?
Thanks for the help!
Fernanda
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