[slicer-users] VMTK centerlines and failure to allocate memory

Daniel Haehn haehn at bwh.harvard.edu
Mon Jun 14 14:06:33 EDT 2010

Hi julie,

I experienced out of memory errors when the input surface is very narrow at some points (f.e. due to stenosis). Maybe you can try to set the start and end fiducials closer together to try if it works at all on the model. If you would like to send me the segmented surface model, I would be happy to take a look.

Thank you for using VMTK in 3D Slicer.


Julie Rytlewski <j.rytlewski at gmail.com> wrote:

>I've been unable to successfully run the VMTK centerlines module on my 
>image stack--it stops about 40min to an hour into processing with a 
>"failure to locate [large number] of bytes." The data consists of 300 
>confocal microscopy images (Z-stack), approximately isotropic, 1024x1024 
>resolution, 8-bit grayscale. I've tried down-sampling to 512x512--that 
>didn't work. I tried taking an ROI from the 512x512 stack with the 
>volume cropping module--still didn't work. I've tried down-sampling the 
>ROI to somewhere near 256x256--nadda. I've tried deleting all previous 
>volumes and loading only the ones necessary for centerlines and that 
>didn't help. The vessel enhancement and level sets modules run just 
>fine. I'm running this on an iMac with 8GB of RAM.
>Are there other options to conserve memory? Or does this module have a 
>leak? I'm not convinced that this module is maxing out 8GB of memory... 
>or maybe it's not allocating enough to finish processing the data??
>Any help or advice would be very much appreciated.
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