[Freesurfer] Surfaces to *native* space

Dear all,

I think my issue is quite related to this one (if not duplicated, sorry in that case): https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/027622.h...

As Shani, I used bbregister to coregister diffusion images to anatomical:

bbregister --s OE0_T1 --mov DTI_b0_brain.nii.gz --reg dti2anat.dat --dti --init-fsl

Then, I visually checked the outcome and resampled the T1 to DTI space:

tkregister2 --mov DTI_b0.nii.gz --reg dti2anat.dat --surf mri_vol2vol --mov DTI_b0.nii.gz --targ OE0_T1/mri/T1.mgz --reg dti2anat.dat --o T1-to-DTI.nii.gz --inv tkregister2 --mov T1-to-DTI.nii.gz --targ DTI_b0.nii.gz --reg T1-to-DTI.nii.gz.reg

Everything looks fine, but I cannot get the pial and white surfaces into dti space (please note the --reg-inv param and the ref volume DTI_b0.nii.gz, that should be important IMHO):

mri_surf2surf --s OE0_T1 --sval-xyz white --reg-inv dti2anat.dat DTI_b0.nii.gz --tval lh.white.dti --tval-xyz --hemi lh

There seems to exist an orientation problem when trying to visualize the surface

tkmedit -f DTI_b0.nii.gz -surface lh.white.dti

I also applied the solution that Douglas recommended Shani, without good results :(.

Any light on this would be of the highest interest for me :D

Thanks, Oscar