The surface is created during recon-all. rawfunc2surf-sess resamples the volumetric fMRI onto the surface.
On 10/12/2017 01:42 PM, Alissa Stafford wrote: > Thanks Matt! Does rawfunc2surf-sess create the surface and smooth? > > From: <freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Matt > Glasser <m...@ma-tea.com <mailto:m...@ma-tea.com>> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Thursday, October 12, 2017 at 1:39 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto: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-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Alissa > Stafford <alissa.staff...@jhu.edu <mailto:alissa.staff...@jhu.edu>> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Thursday, October 12, 2017 at 12:29 PM > To: "Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>" > <Freesurfer@nmr.mgh.harvard.edu <mailto: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.edu > <mailto: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 > <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. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
