[vmtk-users] dealing with large data

[Joong-Ho W. <jh...@st...>]

Hi Luca,

Thanks for the notice. I will use 3.0.1 next time I compile VMTK (hope 
it's not too soon :) ).

Now I'm working on real datasets. They are scans of abdominal aorta and 
iliac arteries. Each dataset is made of 600-1000+ dicom files.

As you may have guessed, there is a memory problem. vmtkimagereader 
couldn't read more than 495 slices. So I dropped some chunks and was 
able to load them. VOI selector worked well, and the next task is level 
set segmentation.

It seem to be working, but after segmenting the first branch, when I 
tried initial segmentation, VMTK reported out of memory and nothing 
happened. That same thing happened even though I save the first 
segmentation and continued segmentation using -levelsetsfile option.

My desktop has 2GB of memory, and this is the physical limit of the 
hardware. Maybe the only solution is to split them into several parts 
and merge the results.

So I wonder if it is possible:

1. merge segmentation files off-line, that is, outside of 
vmtklevelsetsegmentation.

2. merge centerlines

It seems 2 should be enough for my purpose, but when I tested with 
splitting, the origins didn't match. It appears that vmtkimagereader has 
-origin option, but they are not for dicom format.

Could you figure out a solution? Thanks.

Regards,

    Joong-Ho.



Luca Antiga wrote:
> Hi Joong-Ho, 
>  after checking with Luis Ibanez, I found out that the problem has been 
> fixed in the current ITK stable version (3.0.1)
> I compile it and I confirm that the problem is gone.
> Ciao
> 
> Luca
>