Dear Bruce,

thank you very much for your time.

Concerning transformations, that is weird since I adopted my code from HCP pipelines

https://github.com/Washington-University/Pipelines/blob/master/FreeSurfer/scripts/FreeSurferHiresPial.sh

and there I think they use the surfaces precisely this way. They are using the surfaces generated by 1mm3 volumes as input and refine them by using co-registered higher resolution volumes. I use full-hires reconstruction, but for my safety and convenience I left the code with transformations, which (I thought) should do not any harm (there is not any resampling in my case).

I also checked the white and white.deformed processed by default HCP pipeline and they do NOT have the same ras2vox.

BTW, which transformation in mris_info is relevant for this case? I found several of them in mris_info:

talairch.xfm

surfaceRAS to talaraiched surfaceRAS

talairached surfaceRAS to surfaceRAS

Volume Geometry vox2ras

Volume Geometry vox2ras-tkr

Antonin

From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
To: Antonin Skoch <ansk@ikem.cz>
Sent: 11/23/2016 12:42 AM
Subject: Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement -issue with overlapping pial surfaces

yes, and I tracked it down and fixed it. BTW: don't use the
white.deformed surface - use the white one. You can't use one surface that
has been transformed (i.e. has a different ras2vox) and other surfaces that
have not (you can see this if you run mris_info on the surface files, the
ras2vox should match in all of them)

cheers
Bruce