Hi Matt, I think that is all doable using mri_vol2surf, mri_surf2surf and mri_surf2vol. The deformation fields all live on the surface of the sphere, so there is no volumetric deformation to apply. It's also all subject to atlas. You could pick an individual subject and compose forward and inverse transforms to get to that space, but if all you want to do is map labels and scalars around I think Donna is right and you don't need to map surfaces at all.
Bruce On Tue, 2 Mar 2010, Matt Glasser wrote: > 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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