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

[Simon Rit]

That's weird because SetFrame does nothing else than change the value
of the member Frame. Are you sure it's on SetFrame that the crash
occurs?

On Mon, Feb 2, 2015 at 7:44 PM, Matthew J. Riblett
<riblettmj at mymail.vcu.edu> wrote:
> Simon,
>
> I rebuilt the rtkfdk app (actually all of RTK) in ‘Debug’ mode and with the
> added debug line you suggested and it doesn’t look like the pointer is null.
> Running it through gdb, I got the following info:
>
> m_Deformation=0x16ff820
>
> (gdb) x 0x16ff820
> 0x16ff820:      0x011c51d0
> (gdb) x 0x011c51d0
> 0x11c51d0
> <_ZTVN3rtk28CyclicDeformationImageFilterIN3itk5ImageINS1_6VectorIfLj3EEELj3EEEEE+16>:
> 0x005fb874
> (gdb) x 0x005fb874
> 0x5fb874 <rtk::CyclicDeformationImageFilter<itk::Image<itk::Vector<float,
> 3u>, 3u> >::CreateAnother() const>:   0xe5894855
> (gdb) x 0xe5894855
> 0xe5894855:     Cannot access memory at address 0xe5894855
>
> I’m still waiting on the transformix DVF, but I’ll give that a try too when
> its done.
>
> Thanks again!
>
> — 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
>
>
>
> On Feb 2, 2015, at 1:16 PM, Matthew J. Riblett <riblettmj at mymail.vcu.edu>
> wrote:
>
> Thanks for the quick reply Simon!  I am using the rtkfdk app, and I will go
> ahead and check to see if the pointer is null and let you know.  My current
> check is having transformix to generate a smaller DVF to see if that helps,
> so the server is getting that done as we speak.
>
> You might also like to know that I’ve got RTK running on a Cray CX-1 (baby
> supercomputer) sitting next to the aforementioned Sun x4600-M2.  :)
>
> — 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
>
>
>
> On Feb 2, 2015, at 12:19 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
> wrote:
>
> 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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