"How much deformation" is a tricky subject, and we may very well mean something different than you do when you say it.
The short version: surface registration does not cause anatomical deformation. Any registered, resampled anatomical surface will still line up perfectly with the volume it started from. There is nothing like a volumetric warpfield for surface-based registration. However, we do in fact apply the FNIRT volumetric MNI registration warp to our surfaces, and we provide these surfaces in both subject structural space (in the T1w folder), and in MNI space (in the MNINonLinear folder). Because this is a volumetric registration, it does in fact cause anatomical deformation. You can measure this volume-registration-induced distortion on the surface, if you want, by comparing the anatomical surfaces (midthickness, etc) from the T1w and MNINonLinear folders to each other. The "spherical deformation" that we regularize during the surface registration (and which is captured by the MSMAll sphere surfaces) is really an artifact of keeping the registration from doing something silly - specifically, it is to prevent the registration from creating drastic changes in triangle density of the surface (which would lead to having too few datapoints in some locations, causing loss of detail). It is only a modification of the spherical coordinates, which are conceptually unrelated to the anatomical coordinates - the only purpose of the spherical coordinates is to make the surface-based registration easier to do. Tim On Tue, Nov 21, 2017 at 10:49 PM, Aaron C <[email protected]> wrote: > Hi Matt, > > Thank you for your reply. I am looking for the file which provides me with > the information to calculate how much deformation was done for some > subjects. Will it possible for me to compute the displacements of vertices > for the MSM-All registration using this file "${Subject}.L.sphere.MSMAll. > native.surf.gii"? Thank you. > > Aaron > ------------------------------ > *From:* Glasser, Matthew <[email protected]> > *Sent:* Sunday, November 19, 2017 10:47 PM > *To:* Aaron C; [email protected] > *Subject:* Re: [HCP-Users] A question about brain registration matrix > > This is a deformed spherical surface, not a warpfield or affine matrix as > you might be used to using, however, we do provide this: > > ${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject} > .L.sphere.MSMAll.native.surf.gii > ${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject} > .R.sphere.MSMAll.native.surf.gii > > What is it specifically that you need to do? > > Peace, > > Matt. > > From: <[email protected]> on behalf of Aaron C < > [email protected]> > Date: Sunday, November 19, 2017 at 9:38 PM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] A question about brain registration matrix > > Dear HCP experts, > > I have a question about the transformation matrix aligning the raw data to > the MSM-All registered data. Could I find the file of this matrix in the > preprocessed data? Thank you. > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
