What command are you using to visualize it? doug

On 10/09/2012 12:51 PM, Arnaud Guidon wrote:

Dear Freesurfer experts,

I'd like to transform a surface S to a native volume V which is not the original T1.

I first computed the transform V_to_orig.mat using flirt. Loading the resulting volume and the lh.pial showed satisfactory results in freeview.

Now I'd like to obtain the surface in the native volume. For this I tried applying the inverse of the flirt xform using mri_surf2surf:

tkregister2 --fsl orig_to_V.mat --mov orig.nii --targ V.nii.gz --reg orig_to_V.dat --noedit mri_surf2surf --sval-xyz pial --reg orig_to_V.dat --tval pial.native --tval-xyz --hemi lh --s subject

However the resulting surface is offset and orthogonal to the native volume.

Am I missing anything in the tkregister2 command?

Thanks for your help,

Arnaud

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