Re: [Freesurfer] resampling surfaces to native space, mri_surf2surf not scaling properly?

Try

mri_surf2surf --sval-xyz pial --reg resamp_brain.mgz.reg rawavg.mgz --tval resamp_lh_pial --tval-xyz --hemi lh --s 1158119_3_6

On 05/24/2013 04:42 PM, Gunter, Geoffrey wrote:

Hello,

I'm trying to resample Freesurfer output volumes and surfaces back into their native anatomical space using mri_vol2vol and mri_surf2surf. The volumes appear to be resampled correctly, their resolution and orientation match the original images'.

However, the resampled surfaces do not appear to have been transformed correctly by mri_surf2surf. When I visually compare them to the Freesurfer-space surfaces overlaid on the brain images in FreeView, TKMEdit, Paraview-CAWorks, etc., they seem to be identical to the un-transformed, Freesurfer-space surfaces. In addition, when I check the list of vertices for transformed and untransformed surfaces, the coordinates of each vertex are unchanged.

These are the commands that I'm using:

mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o
resamp_brain.mgz

mri_surf2surf --sval-xyz pial --reg resamp_brain.mgz.reg --tval
resamp_lh_pial --tval-xyz --hemi lh --s 1158119_3_6

The registration file, "resamp_brain.mgz.reg" looks like this:

subject-unknown
0.937500
0.937500
1.000000
1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
0.000000000000000e+00
0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
0.000000000000000e+00
0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
0.000000000000000e+00
0 0 0 1
round

My Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0

Could it be that mri_surf2surf is not applying scaling transformations correctly?

Thanks for your help, Geoff

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