[MINC-users] label from 2 objects

[Mishkin Derakhshan]

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
>>
>