[ITK Community] [Insight-users] Vesselness Memory Issue

[Bradley Lowekamp]

If you running some variant of linux you should be able to limit the memory used for a process. This may give you better behavior. Here may be a place to start:

http://stackoverflow.com/questions/4651234/linux-process-memory-limit

Brad

On Dec 11, 2013, at 1:45 PM, Ben Alpert <balpert at numira.com> wrote:

> Thanks for your help. I think breaking up the image into smaller blocks and running the filter on those is the way to go. The main problem is that I need to be able catch an exception when memory fails to allocate in order to then break up the image. I can’t take a chance of having my system freeze if the system happens to be low on memory. Do you happen to know why an exception isn’t thrown, and how can I fix this?
>  
> Thanks,
> Ben
>  
> From: Bradley Lowekamp [mailto:brad at lowekamp.net] 
> Sent: Monday, December 09, 2013 12:41 PM
> To: Ben Alpert
> Cc: insight-users at itk.org
> Subject: Re: [Insight-users] Vesselness Memory Issue
>  
> Hello,
>  
> You system lockup is likely due to memory exhaustion, and excessive thrashing. System lockup it typical of when running you of memory for an task.
>  
> I had a version of the MultiScaleHessian that was streamable. I haven't used it for a while not, and don't know what the state of it is after ITKv4.
> http://review.source.kitware.com/#/c/890/
>  
> You have a couple other options:
>  
> 1) Find smaller regions of interest. That is just don't run on the whole image at once.
> 2) For each scale stream your metric to disk. This is the way I recently did it. I was able to batch each scale out to a cluster node. And them perform on analysis on the scalar images in SimpleITK.
>  
> Those on my quick suggestions.
>  
> Good luck,
> Brad
>  
>  
> On Dec 9, 2013, at 2:20 PM, Ben Alpert <balpert at numira.com> wrote:
> 
> 
> Hi,
>  
> I have seen a few threads on this topic but I am still not sure what the best approach is. I am trying to enhance vessels using the MultiScaleHessianBasedMeasureImageFilter and Hessian3DToVesselnessMeasureImageFilter framework. When running the filters on a large enough volume, my system locks up, so there seems to be some exception handling issue since I would at least expect an error message in this case.
>  
> I understand that the HessianRecursiveGaussianImageFilter is not streamable and I have seen that a discrete version is available (https://github.com/blowekamp/itkLocalDiscreteHessian), but I am not sure how to integrate it with the MultiScaleHessian framework. Did anyone have any experience with this?
>  
> Also, other than for visualization/UI purposes, is there any advantage in using tubetk, as it is essentially built on itk?
>  
> Any help is appreciated.
> Thanks,
> Ben
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