Thanks Matt! Does rawfunc2surf-sess create the surface and smooth?
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Matt Glasser <matt@ma-tea.commailto:matt@ma-tea.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, October 12, 2017 at 1:39 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] volume vs surface-based and surface smoothing
Volume-based registration is fine with subject as you have the same brain that you are registering (ideally such registrations are 6 DOF rigid registrations and any image distortions are corrected for). Surface-based registration is better when comparing across subjects due to the variability in cortical folding patterns and locations of areas relative to folds across subjects. Smoothing is best done on the surface if it is done at all. Smoothing in the volume harms one’s spatial localization precision much more than smoothing on the surface for an equivalent FWMH in mm. It is worth keeping in mind that smoothing on the surface does still blur across cortical areal boundaries, however, so for many analyses it may be better to average within cortical areas rather than to smooth a lot.
Peace,
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alissa Stafford <alissa.stafford@jhu.edumailto:alissa.stafford@jhu.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, October 12, 2017 at 12:29 PM To: "Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] volume vs surface-based and surface smoothing
Hello,
I am trying to understand the preprocessing functions to successfully complete surface-based analysis. I am confused about what is happening on the volume level and when exactly the surface is being created. My questions revolve around register-sess and rawfunc2surf-sess.
Registration has 2 parts: 1: the native anatomical space is registered with the fsaverage space. This is happening during recon-all. 2: native functional data is registered with the native anatomical data. This is happening during register-sess in preprocess-sess. Aren’t these both volume-based registrations? If not when are the surfaces created? My concern is that it is volume-based and I was under the impression from this article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , that all registrations should be done on the surface.
I am also confused about rawfunc2surf-sess. I believe up until this function in preprocess-sess, everything has been done in the volume so this is the first step that is done in the surface, is that correct? And then does this do smoothing? I realized it has a fwhm input option so it must smooth. So is this where the functional data is now expressed in the surface and it also smooths? Or does surfsmooth-sess need to be run in addition to rawfunc2surf-sess?
I basically just want to be making sure I understand when registration is volume-based or surface-based and when it’s appropriate to use volume-based. And I was using the rawfunc2surf function assuming it was for smoothing, but I am not so sure if this only creates the surface or also smooths.
Thanks, Alissa _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.