Hello Bruce, Thank you very much. Can I still general cortical and subcortical maps with the Spherical warp of r/lh.white surface? If yes, please what are the steps to achieve this? can I still analyze it with mri_glm?
Best, Paul Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Saturday, October 14, 2017 11:27 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis Hi Paul if you use a property (like gm) to drive intersubject registration it then becomes difficult to also analyze it. If your warp was truly perfect you could just analyze the properties of the warp, but even then it is hard to localize effects (e.g. if you changed the smoothness of the warp field would the effect move somewhere else?). If the warp is not perfect then some of the effect is in your warp and some in the residual anatomical differences. There are lots of caveats like this you have to worry about. It's the reason we drive our spherical warp with the ?h.white surface. It is invariant to gm atrophy and so can be used to assess it without worrying about this kind of thing cheers Bruce On Fri, 13 Oct 2017, miracle ozzoude wrote: > Hello Bruce, > > Thank you for the response. I meant the latter ( making maps etc). I want to > do something similar to the subcortical volume based analysis on PETSurfer > page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why > should there be a problem with interpretation? > > Best, > Miracle > > Sent from my BlackBerry 10 smartphone. > Original Message > From: Bruce Fischl > Sent: Friday, October 13, 2017 6:53 PM > To: Freesurfer support list > Reply To: Freesurfer support list > Subject: Re: [Freesurfer] cortical/subcortical volume based analysis > > Hi Paul > > we typically do this type of analysis by looking at scatter plots of > structure volumes (e.g. hippocampus). Alternatively, you can make maps, > but that opens up all the problems/difficulties of interpretation of VBM. > Which did you mean? > cheers > Bruce > > On Fri, 13 Oct 2017, miracle ozzoude wrote: > >> Hello FreeSurfer experts, >> I want to perform a whole brain volume based group analysis for cortical and >> subcortical regions. >> That's something very similar to surface based group analysis for cortical >> thickness however, for >> volume. Is there a tutorial on how to do it? if yes, please can i get the >> link. If not, please can >> someone direct me how to go about doing it? My goal is to perform a group >> comparison between control >> and PD patients based on volume. Thank you very much. >> >> Best, >> Paul >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ 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.
