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/scripts/FreeSu > 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 <fis...@nmr.mgh.harvard.edu> > To: Antonin Skoch <a...@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 > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
