[MINC-users] label from 2 objects

[Simon Fristed Eskildsen]

Hi Mishkin,
I have put a 64 bit version here:
http://www.hst.aau.dk/~se/software/scan_surface_to_volume.bin64
It is dynamically linked to:
libhdf5-1.6.5.so.0 => /usr/lib/libhdf5-1.6.5.so.0 (0x00002b3c150c0000)
libnetcdf.so.3 => /usr/lib/libnetcdf.so.3 (0x00002b3c153e3000)
libm.so.6 => /lib/libm.so.6 (0x00002b3c15632000)
libc.so.6 => /lib/libc.so.6 (0x00002b3c158b4000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00002b3c15c06000)
libz.so.1 => /usr/lib/libz.so.1 (0x00002b3c15e21000)
/lib64/ld-linux-x86-64.so.2 (0x00002b3c14ea3000)

If it doesn't work I can try a static linking.

It only reads triangular polymeshes. It only evaluates the voxels touched by the mesh faces. I.e. you would probably combine it with surface_mask2 and minccalc to get a solid component with fuzzy edges.

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

> Hi Simon,
> Indeed I would be interested (I am on a 64 bit machine).
> Claude, do you happen to know how surface_mask2 handles voxels that
> are not completely bounded by the surface? is it a binary decision,
> or
> is there a threshold set somewhere?
> thanks,
> mishkin
> 
> 
> 
> On Fri, Feb 6, 2009 at 3:34 AM, Simon Fristed Eskildsen
> <se at hst.aau.dk> wrote:
> > 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
> >> >>
> >> >
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users