Dear freesurfer expert,
We have preformed the full autorecon command using freesurfer and want to view the results in Slicer, When we load the pial surface onto slicer it doesn't seem to be coregister to the original MR image, how can we bring back the surface to the original native space or alternatively, how can we preforme the transformation on the original MRI so it will fit the surface that we gut. We found in the wiki a way to do that with volumes (mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz) but what about surface? We have also found the command mri_surf2surf, but not sure how to use it because we don't have surface in the native space?
thank you in advance Efrat
Hi Efrat Does it look ok in tkmedit or freeview? Cheers Bruce
On Feb 19, 2013, at 6:05 AM, Efrat Kliper e.kliper@gmail.com wrote:
Dear freesurfer expert,
We have preformed the full autorecon command using freesurfer and want to view the results in Slicer, When we load the pial surface onto slicer it doesn't seem to be coregister to the original MR image, how can we bring back the surface to the original native space or alternatively, how can we preforme the transformation on the original MRI so it will fit the surface that we gut. We found in the wiki a way to do that with volumes (mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz) but what about surface? We have also found the command mri_surf2surf, but not sure how to use it because we don't have surface in the native space?
thank you in advance Efrat _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
you can use mri_surf2surf, using the XYZ (--sval-xyz) as input, applying a transformation --reg, and spec XYZ as an output (--tval-xyz). You will need a registration matrix to map it from the surf coordinates to whatever coordinates slicer uses. doug
On 02/19/2013 06:05 AM, Efrat Kliper wrote:
Dear freesurfer expert, We have preformed the full autorecon command using freesurfer and want to view the results in Slicer, When we load the pial surface onto slicer it doesn't seem to be coregister to the original MR image, how can we bring back the surface to the original native space or alternatively, how can we preforme the transformation on the original MRI so it will fit the surface that we gut. We found in the wiki a way to do that with volumes (mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz) but what about surface? We have also found the command mri_surf2surf, but not sure how to use it because we don't have surface in the native space? thank you in advance Efrat
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Bruce Fischl -
Douglas N Greve -
Efrat Kliper