On Mon, Feb 21, 2011 at 6:01 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

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 <fischl@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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