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

[Matthew J. Riblett]

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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto:riblettmj at vcu.edu>
>>> MCV Office Phone:     +1.804.628.4858
>>> 
>>> 
>>> 
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>>> Rtk-users mailing list
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>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>> 
> 

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