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
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