so I can simply label the whole surface, if I'm confident? I don't know much about labels and how to make them (I use caret mainly, since I do monkey). I presume it's what one would imagine, and there's a way to figure it out.
On 20 July 2012 19:36, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Colin
the hires label is meant to be the portion of the surface that is far enough into the FOV/coil that you are confident of the data there.
cheers Bruce
On Fri, 20 Jul 2012, Colin Reveley wrote:
Hi -
I'm using freesurfer with an ex-vivo MTR of a monkey, at 0.25mm. unfortunately the data doesn't fit into 256^3, and anyway things are much faster, and decent results are to be had by downsampling to 0.5mm.
I did notice this mris_refine_surfaces. That looked great. I can fit 0.32mm into 256^3, so I did that, and called it 0.64mm, and treated it the same way I treated the 0.5mm (nu_correct etc etc) to get my "hires.mgz" for mris_refine_surfaces
then I noticed mris_refine_surfaces wants ?h_hires.label as well.
a) how would I make ?h_hires.label b) does my hires.mgz even have to be 256^3? If not, I could use the actual 250um data to refine the surface, and that would be nice. c) I don't suppose there would be any chance of not only using a hi res volume to refine the surfaces, but also upsampling the surfaces too? There is a reason I might want them upsampled. It would be nice for the ?h.white mesh to sort of approximately have a node for each voxel face. It's to do with more accurately mapping certain data in CARET later on.
I'd settle for just how to make ?h_hires.label and use mris_refine_surfaces though :)
cheers,
Colin
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