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:do...@brainvis.wustl.edu] Sent: Tuesday, March 02, 2010 1:26 PM To: m...@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:fis...@nmr.mgh.harvard.edu] > Sent: Tuesday, March 02, 2010 12:38 PM > To: Douglas N Greve > Cc: m...@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:gr...@nmr.mgh.harvard.edu] >>> Sent: Tuesday, March 02, 2010 12:01 PM >>> To: m...@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. >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> 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 . 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