Is there a way to re-do the generation of the ribbon but generate it with a smaller voxel size? I've already had success resampling the T1.mgz to 0.25mm and using it as a template for mri_surf2vol with -- mkmask and --fillribbon, but the problem is that only projects out from the vertices, so the resulting ribbon is sparse and thready, and doesn't fill the whole cortical ribbon. (Likewise the ?h.ribbon.mgz file seems to be missing a lot of voxels in its interior.)

Ideally what I want is to be able to overlay the surfaces onto a volume of my chosen resolution, and then fill the voxels between the surface. I've been looking at matlab code, and found this program: http://tinyurl.com/2bbyap surface2volume.m which allegedly does what I want, but it doesn't actually seem to work right when I try it: I get only a few scattered voxels filled.

Does anyone have any idea of how to do this? Any help is greatly appreciated!

On May 3, 2007, at 10:31 AM, Bruce Fischl wrote:

Hi David,

we do generate such a thing called ?h.ribbon.mgz, but note that once you go back into the volume the topology is no longer preserved.

cheers, Bruce On Thu, 3 May 2007, David Perlman wrote:

...

I'm new to freesurfer, so I'm hoping this question isn't too obvious. I've searched the mailing list archives and the wiki but haven't found any leads.

I'm wondering if there's a way to generate a volume representation of the cortical sheet, based on the data from the white surface and the pial surface, so that the sheet will be guaranteed to have good topology, as well as retaining the proper thickness at each point? It seems like all the information for this is there already since we have the two surfaces, but I don't know how to go about figuring out how to convert it into volume data.

Here's a small image that might help give an idea of what I need: http://brainimaging.waisman.wisc.edu/~perlman/corticalsheet.png

In case you're curious, the reason I want this is because we're trying to test the novel method for cortical thickness measurement given in "Three-Dimensional Mapping of Cortical Thickness Using Laplace's Equation", Jones, Buchbinder and Aharon, Human Brain Mapping 11:12-32(2000).

-- -dave---------------------------------------------------------------- After all, it is not *that* inexpressible. -H.H. The Dalai Lama

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-- -dave---------------------------------------------------------------- Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe

Gheorghe has been working on a fix for this that will fill in all the holes, but I don't know the status. Gheorghe?

David Perlman wrote:

Is there a way to re-do the generation of the ribbon but generate it with a smaller voxel size? I've already had success resampling the T1.mgz to 0.25mm and using it as a template for mri_surf2vol with -- mkmask and --fillribbon, but the problem is that only projects out from the vertices, so the resulting ribbon is sparse and thready, and doesn't fill the whole cortical ribbon. (Likewise the ?h.ribbon.mgz file seems to be missing a lot of voxels in its interior.)

Ideally what I want is to be able to overlay the surfaces onto a volume of my chosen resolution, and then fill the voxels between the surface. I've been looking at matlab code, and found this program: http://tinyurl.com/2bbyap surface2volume.m which allegedly does what I want, but it doesn't actually seem to work right when I try it: I get only a few scattered voxels filled.

Does anyone have any idea of how to do this? Any help is greatly appreciated!

On May 3, 2007, at 10:31 AM, Bruce Fischl wrote:

...

Hi David,

we do generate such a thing called ?h.ribbon.mgz, but note that once you go back into the volume the topology is no longer preserved.

cheers, Bruce On Thu, 3 May 2007, David Perlman wrote:

...

I'm new to freesurfer, so I'm hoping this question isn't too obvious. I've searched the mailing list archives and the wiki but haven't found any leads.

I'm wondering if there's a way to generate a volume representation of the cortical sheet, based on the data from the white surface and the pial surface, so that the sheet will be guaranteed to have good topology, as well as retaining the proper thickness at each point? It seems like all the information for this is there already since we have the two surfaces, but I don't know how to go about figuring out how to convert it into volume data.

Here's a small image that might help give an idea of what I need: http://brainimaging.waisman.wisc.edu/~perlman/corticalsheet.png

In case you're curious, the reason I want this is because we're trying to test the novel method for cortical thickness measurement given in "Three-Dimensional Mapping of Cortical Thickness Using Laplace's Equation", Jones, Buchbinder and Aharon, Human Brain Mapping 11:12-32(2000).

-- -dave---------------------------------------------------------------- After all, it is not *that* inexpressible. -H.H. The Dalai Lama

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-- -dave---------------------------------------------------------------- Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe

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