Thanks Donna for the explanation of my confusion.
I am wondering if there is any way I could make use of the Freesurfer registration and then get things into Caret where I could do what I want? For example, is there any way, given a registered and unregistered sphere of a given subject that we can figure out what the deformation map was?
If the above is not possible, is it possible to do the following in FreeSurfer? What I really need to be able to do is map some scalers/metrics from volume to white surface, then map from white surface to registered sphere, visualize them on a standard inflated surface (hopefully after averaging the scaler/metrics across several subjects) and draw some labels/paints, then map the labels/paints from the standard surface back to the individual white surface, and from the individual white surface back to the volume.
Thanks for everyone's help!
Matt.
-----Original Message----- From: Donna Dierker [mailto:donna@brainvis.wustl.edu] Sent: Tuesday, March 02, 2010 1:26 PM To: matt@ma-tea.com Cc: 'Bruce Fischl'; 'Douglas N Greve'; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Application of Default Surface Based Registration to Surfaces Other than the Sphere
Matt,
I think we just do things differently. We adopted Ziad Saad's concept of a standard mesh. (Before Ziad conceived it, we didn't do this, either.) But not everyone does this. My mental model of how others do things is poor. I recall using mrisp_paint to get some scalars on our PALS surfaces several years ago, with Bruce's help, but I didn't understand what I was doing.
One thing to realize is that usually people are interested in scalars associated with the surfaces (e.g., thickness, depth, fMRI intensities), rather than the surfaces themselves. I think you need the surfaces for your tractography stuff.
But if all you need is average metric data on average40, then I doubt you need the individual surfaces on a standard mesh.
Donna
On 03/02/2010 12:58 PM, Matt Glasser wrote:
Hi Doug and Bruce,
I am somewhat surprised by your responses, given that we do what I need
done
with Caret all the time. I wonder if I am not explaining myself clearly
or
not understanding your responses (Donna, perhaps you can help?). In
Caret,
one does a landmark-based registration of the sphere and generates a deformation map that is applied to all the other surfaces. Are you saying that there is no similar way to get a deformation map and apply it to the other surfaces?
I am just hoping to use the FreeSurfer registration because it is a little more automated than the Caret registration.
The end result is that I want to average some metric data from the volumes on the average surface.
Thanks and sorry for my lack of understanding,
Matt.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, March 02, 2010 12:38 PM To: Douglas N Greve Cc: matt@ma-tea.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Application of Default Surface Based
Registration
to Surfaces Other than the Sphere
Hi Matt,
you could use mri_surf2surf to map the fsaverage surface to any subject. We always avoid doing this as we want uniform sampling in the subject's space, and were willing to make the engineering more difficult to preserve
this.
cheers Bruce
On Tue, 2 Mar 2010, Douglas N Greve wrote:
Oh, that's not such an easy thing to do. We can only map values from one subject to another. I know what you are describing, and it would be nice to have. I'm not sure how possible it is as the density of the nodes changes from subject to subject at various locations in order to reflect the anatomy. I don't know if one surface will work for this (but maybe if it is higher res). Bruce might have more insight.
doug
Matt Glasser wrote:
Hi Doug,
Thanks for your response. How does one go about getting registered
white
matter surfaces then? I would like all of the surfaces to be registered
so
that they have the same number of nodes in the same places across
subjects.
Thanks,
Matt.
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tuesday, March 02, 2010 12:01 PM To: matt@ma-tea.com Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Application of Default Surface Based
Registration
to Surfaces Other than the Sphere
I'm not sure what you mean. When the sphere.reg is registered across subjects, it is sufficient to register the wm surfaces.
doug
Matt Glasser wrote:
Hi,
I am wondering if there is a way to apply the default surface based registration that is done during recon-all to surfaces other than the sphere so that the nodes are all lined up? I am wanting to have registered white matter surfaces that I can map data from the volume to the surface to and then average across subjects.
Thanks,
Matt.
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