[MINC-users] label from 2 objects

[Mishkin Derakhshan]

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
>> >>
>> >
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