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/sc...
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