[MINC-users] label from 2 objects

[Simon Fristed Eskildsen]

Hi Mishkin,
If interested, I have some code that calculates the inside fraction of every voxel w.r.t. some closed object. I.e. the output is fuzzy (or you may say PVE-like) hopefully solving the problems where the two surfaces are very close. The code is very beta, so no guarantees on the stability.

Simon
----- "Mishkin Derakhshan" <mishkind at gmail.com> wrote:

> Thanks Claude,
> Right after I sent the email I figured out in Display that I should
> 3D
> Fill each surface separately and then do some mincmath magic, but now
> I can automate the whole thing.
> thanks,
> mishkin
> 
> 
> On Thu, Feb 5, 2009 at 5:47 PM, Claude LEPAGE
> <claude at bic.mni.mcgill.ca> wrote:
> > Hi Mishkin,
> >
> > Try this:
> >
> >  scarus /home/claude > surface_mask2 -help
> > Command-specific options:
> >
> > Output options:
> >  -binary_mask: Create a binary output.
> > Generic options for all commands:
> >  -help:        Print summary of command-line options and abort
> >  -version:     Print version number of program and exit
> >
> > Usage: surface_mask2 in_volume.mnc surface.obj output.mnc
> >
> > Use the -binary_mask switch; repeat for the two surfaces. The
> > in_volume.mnc is your volume template for which you'd like the
> > voxelized surface to look like (use t1 image, for example).
> > Then use a little minccalc -expression ... to identify the region
> > in between. Of course, there are interpolation errors, but this
> > is as good as you can get. Beware that surfaces may intersect
> > or be very close to one another, possibly giving some holes in
> > the cortex sheet.
> >
> > Claude
> >
> >>
> >> Hi,
> >> I have two .obj files, and I'm assuming one is completely
> contained
> >> within the other. For example, a white matter surface and a grey
> >> matter surface for a single hemisphere.
> >> I'm interested in obtaining a mnc file that is a binary label that
> >> contains all the voxels between the two surfaces.
> >> My first attempt was to load things up in Display, scan the objects
> to
> >> volume and then use 3D Fill to get all the voxels in between,
> however,
> >> because the scanned objects sometimes touch on the volume, the 3D
> fill
> >> area, is not contiguous ie. i have lots of holes that i would need
> to
> >> fill manually.
> >> My next idea is to resample my volume to a 0.1 mm^3 grid and then
> try
> >> again, but I'm wondering if anyone has done something like this
> before
> >> and has a better solution.
> >>
> >> thanks,
> >> mishkin
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >
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