[Insight-users] Lack of memory for segmentation; SetNumberOfThreads

Kevin H. Hobbs kevin.hobbs.1 at ohiou.edu
Wed Jan 25 10:53:07 EST 2006

On Wed, 2006-01-25 at 14:26 +0000, Atwood, Robert C wrote:
> Thanks,Jim, for the clarification. I was seeing that 'threading' was
> happening when I expected 'streaming', this gives me the correct names
> to use!  Also I did not realize that it requied a separate filter to
> enable streaming. In the original suggestion I thought that you meant
> any of the filters that support streaming needed to be downstream. 
> However, the StreamingPage.html seems to not have any text on it? I
> tried Firefox and also Microsoft Internet Explorer browsers in case it
> was a browser problem, but all I see is the image illustrating the
> concept but no text explaining how to use it. 
> I have tried it now in what appears to be the correct way , also I
> changed to GradientAnisotropicDiffusion which seems to be streamable and
> gives similar results for my purposes. 
> Unfortunately I still cannot process an image of greater than 1 gb on a
> 2gb memory node it cannot allocate the memory for the output image, so
> it seems that the biggest image is half the memory, to enable the
> original and the final whole images to be in memory despite having some
> swap space set up? Does this make sense?
> Thanks
> Robert

As I recall, there are no streaming ITK file readers or writers. So
you'll have 1GByte buffers on both ends of your pipeline. That's all
your RAM right there if both ends are the same size image. You may be
able to squeak by on swap space, but that's SLOW. It's a particular pain
if the image is bigger than your RAM + swap.  Then you can't even read
it, the program just errors out at the first attempt to allocate memory.

VTK however does have streaming readers and writers. I was told a while
back ( But I can't find that e-mail ) to try those on both ends of the
pipeline with VTK to ITK and ITK to VTK filters.  I never got around to
it though.
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