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

[Simon Rit]

Hi,
You're the first RTK user I know to use it on Sun! Nice!
If you've got 64 GB ram, that should be enough... although you could
ask elastix to generate a smaller DVF, RTK linearly interpolates
between vectors. You could even use B-spline coeffs directly but you'd
have to create a new DVF.
My guess is that there is a problem with the initialization of
m_Deformation since the line you mention is the first time it's ever
used in the class. Do you use the rtkfdk app? I would start by
checking that the pointer is not null before this line, sg like:
std::cout << "m_Deformation=" << m_Deformation.GetPointer() << std::endl;
If it equals 0, then there is something going with the deformation.
You can check it in the main app, rtkfdk.cxx.
Simon

On Mon, Feb 2, 2015 at 6:03 PM, Matthew J. Riblett
<riblettmj at mymail.vcu.edu> wrote:
> 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
> 401 College Street   |  P.O. Box 980058
> Richmond, Virginia 23298
>
> VCU Email:     riblettmj at vcu.edu
> MCV Office Phone:     +1.804.628.4858
>
>
>
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