[vtkusers] Filling in blood vessels

[Gib Bogle]

Hi Mauro,

I've installed ITK and ITK-snap, and I can see that the tools I'm going to need 
are in these packages.  I've immediately encountered an issue I've never had to 
deal with - medical image formats.  Our images come from a multi-photon 
microscope, and are simply TIFFs.  ITK-snap requires the data to be in a DICOM 
volume (or some other special format like MetaImage).  I would have thought that 
it would be a simple matter to convert a stack of TIFF files into a DICOM 
volume, for example, but this doesn't seem to be the case.  Are you aware of a 
simple way to take a stack of TIFF files and convert it into a form readable by 
ITK-snap?

(I know that the ITK forum would be a better place to ask this, but I don't want 
to subscribe unless I need to.)

Thanks
Gib

On 19/12/2010 1:37 p.m., Mauro Maiorca wrote:
> Hi Gib,
>
> if I've understood correctly your problem, you want to segment ("fill
> in") the vessels then render the segmented image.
> VTK is great for rendering, but you might want to use ITK
> (www.itk.org) for segmentation (for just a threshold you can still use
> VTK - though).
> You might also want to have a look to ITK-snap
> (http://www.itksnap.org) and other VTK-related applications
> (http://www.vtk.org/VTK/resources/applications.html).
>
> cheers,
> Mauro
>
>
>
>
> On Sun, Dec 19, 2010 at 9:59 AM, Gib Bogle<g.bogle at auckland.ac.nz>  wrote:
>>
>> I've just started to become aware of the image-processing capabilities of VTK, and I'm wondering if I can use it for some tasks that I was expecting to use Amira for.  We are generating images in which the walls of blood vessels are stained, so that the vessels appear in 3D as tubes.  I believe the first processing step I need to make is to "fill in" the vessels, i.e. generate a thresholded 3D image in which the vessels appear solid.  Is this the kind of thing that VTK can handle?
>>
>> Thanks
>> Gib
>>
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