I think we may have intended workbench-related things to go on hcp-users, but I'm not sure.
At any rate, -create-signed-distance-volume and -volume-math will allow you to do something like what you want. The first creates the signed distance function in whatever voxel grid you tell it to, as it takes a template volume to get the voxel grid. Make this for both white and pial surfaces, and then use -volume-math to threshold and "and" the results (via multiplication, like "(x > 0) * (y < 0)"). If you want voxels to be included/excluded by their centers, use a threshold of 0, or you can use something like half the voxel diagonal to exclude any voxel that could possibly have even a corner outside the ribbon (though that could exclude some voxels that are entirely inside the ribbon, as it doesn't actually do voxel/surface intersection, it just calculates signed distance at voxel centers). I think Matt has done this, but I don't recall what threshold he used. Tim On Wed, Oct 23, 2013 at 3:50 PM, Colin Reveley <[email protected]> wrote: > I think this one is for the caret list really. > > I wonder, is there a way using wb_command to generate a ribbon volume > suitable for myelin mapping, from a pair of surfaces? > > Unfortunately, caret "make segmentation from surface" seems to lack the > required precision. It seems I've been operating with that issue for a long > time without fully realising it. > > fressurfer mris_fill works very well. Unfortunately, the nature of the > data is such that generating conformed output and reslicing is not possible > without downsampling all the volumes to be mapped. And that basically won't > do it turns out. > > one can generate surface fills that are the exact minimum voxel dimensions > of the ribbon with mris_fill though. and they look great. Perfect. > > But I simply just cannot figure out how to resize that output and give it > the appropriate header so that it's the same size, shape, alignment as the > data volume to be mapped with caret and/or workbench myelin mapping. > > It strikes me that the 700um HCP structural pipeline or related primate > pipelines that deal with non-1mm data might in some way have addressed this > matter. > > It seems like the ribbon voxels are key here. I've traced my problems to > having an accurate ribbon. > > I can get one, but I can't figure out how to size and align it when I > can't use mris_fill -c > > best, > > Colin Reveley > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
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