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

The problem is with the way you are creating the registration matrix, use this instead

tkregister2 --mov rawavg.mgz --targ orig.mgz --regheader --noedit --reg resamp_brain.mgz.reg

doug

On 05/28/2013 11:19 AM, Gunter, Geoffrey wrote:

Thanks for your response, Douglas.

I tried your suggestion, it doesn't appear to have changed the transformation at all though. There is still no scaling being applied to the surface.

Is there anything else I can try to fix this problem?

Thanks, Geoff ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, May 24, 2013 5:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: 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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