Hi Karl

why is there any difference in either geometry or pixel values after converting back and forth? Can you send us your mri_convert command lines and screen output?

cheers Bruce On Wed, 5 Mar 2014, Koschutnig, Karl (karl.koschutnig@uni-graz.at) wrote:

Dear experts, our group decided to make all the white matter edits in brainvoyager (don't ask me why;-). So we converted the wm.mgz into nii and then into the brainvoyager format vmr, made the edits and the same way back into freesurfer. We started the recon-all -autorecon2-wm … and found massive reduction in the thickness. So far so bad. To figure out the problem we started at the beginning of the conversion-mess and converted the wm.mgz into wm.nii and back into wm.mgz and found nearly the same reduction in the thickness. Finally, here comes my question. Is it possible that due to interpolation errors in the mri_convert routine this reduction can be explained? PS: here is the output from mri_diff for the wm_orig.mgz and the converted one: Volumes differ in geometry row=1 col=1 diff=0.000000 (5.96046e-08) Please fin attached the reconstructed white matter surface (red = original, yellow = after converting the wm from nii in mgz and back)

thank you so much best Karl