the vox2ras. Not sure about the HCP pipeline. They use a deprecated version of FS, but in any case what you had would not work as the ?h.pial surface didn't match the ?h.white.deformed one. If you also deformed the pial it would be ok

On Wed, 23 Nov 2016, Antonin Skoch wrote:

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... rferHiresPial.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