[Rtk-users] Trouble Reconstructing 3D CBCT using 4D DVF

[Matthew J. Riblett]

Hello RTK Users,

I’m just getting started using RTK as part of my graduate research and was hoping that someone might be able to help me sort out an issue I’ve been having reconstructing a 3D CBCT image dataset while applying a 4D deformation field — I’m reconstructing with ~2400 projections and the 4D DVF has been generated by transformix (.mhd format).  I followed, for the most part, the MCCBCTReconstruction example on the RTK Wiki.

While reconstructing, rtkfdk reads in all of the projections to memory, begins the ‘Reconstructing and Writing’ phase and proceeds for a few seconds before hanging — it doesn’t exit or fault, just drops to 0% CPU while retaining the projections in memory.  

By writing some basic debug messages into the source code, I’ve been able to determine that the issue lies somewhere at m_Deformation->Update() [Line 99 of code/rtkFDKWarpBackProjectionImageFilter.txx].  It appears that thread 0 makes it past the m_Deformation->SetFrame(iProj) line, but never makes it past the subsequent update.  I’m wondering if this has anything to do with the size of the DVF generated by transformix: approximately 4.0GB (512x100x512x10 image, 4-channels, FLOAT).

Just to provide a little more background information, I’m running RTK on a 32 core Sun Server (8x Quad-Core AMD Opteron 8356, 2.3Ghz) with 64GB of memory running Ubuntu 14.04.  RTK was built using the default ‘Release’ make configuration and linked to ITK 4.5.2.  Elastix and Transformix are both the latest version, 4.7.

Has anyone else run into a similar issue with reconstructing a similar image, or does anyone have any thoughts as to how to resolve this sort of issue?

Thanks in advance!

— Matt

__
Matthew J. Riblett
Virginia Commonwealth University
Department of Radiation Oncology
Medical Physics Graduate Program

Office:  Sanger Hall, Room B1-013
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VCU Email:		    riblettmj at vcu.edu <mailto:riblettmj at vcu.edu>
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