<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Simon,<div class=""><br class=""></div><div class="">I think that it makes it past SetFrame and crashes on Update. Just to be sure, I put a debug message after SetFrame and it does make it to that point, so its got to be on the Update line.</div><div class=""><br class=""></div><div class="">— Matt</div><div class=""><br class=""><div apple-content-edited="true" class="">
<div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">__</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Matthew J. Riblett<br class="">Virginia Commonwealth University<br class="">Department of Radiation Oncology<br class="">Medical Physics Graduate Program<br class=""><br class="">Office: Sanger Hall, Room B1-013</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">401 College Street | P.O. Box 980058</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Richmond, Virginia 23298<br class=""><br class="">VCU Email:<span class="Apple-tab-span" style="white-space: pre;"> </span><span class="Apple-tab-span" style="white-space: pre;"> </span> <a href="mailto:riblettmj@vcu.edu" class="">riblettmj@vcu.edu</a><br class="">MCV Office Phone:<span class="Apple-tab-span" style="white-space: pre;"> </span> +1.804.628.4858</div></div><br class="Apple-interchange-newline">
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<br class=""><div><blockquote type="cite" class=""><div class="">On Feb 3, 2015, at 2:22 AM, Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" class="">simon.rit@creatis.insa-lyon.fr</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">That's weird because SetFrame does nothing else than change the value<br class="">of the member Frame. Are you sure it's on SetFrame that the crash<br class="">occurs?<br class=""><br class="">On Mon, Feb 2, 2015 at 7:44 PM, Matthew J. Riblett<br class=""><<a href="mailto:riblettmj@mymail.vcu.edu" class="">riblettmj@mymail.vcu.edu</a>> wrote:<br class=""><blockquote type="cite" class="">Simon,<br class=""><br class="">I rebuilt the rtkfdk app (actually all of RTK) in ‘Debug’ mode and with the<br class="">added debug line you suggested and it doesn’t look like the pointer is null.<br class="">Running it through gdb, I got the following info:<br class=""><br class="">m_Deformation=0x16ff820<br class=""><br class="">(gdb) x 0x16ff820<br class="">0x16ff820: 0x011c51d0<br class="">(gdb) x 0x011c51d0<br class="">0x11c51d0<br class=""><_ZTVN3rtk28CyclicDeformationImageFilterIN3itk5ImageINS1_6VectorIfLj3EEELj3EEEEE+16>:<br class="">0x005fb874<br class="">(gdb) x 0x005fb874<br class="">0x5fb874 <rtk::CyclicDeformationImageFilter<itk::Image<itk::Vector<float,<br class="">3u>, 3u> >::CreateAnother() const>: 0xe5894855<br class="">(gdb) x 0xe5894855<br class="">0xe5894855: Cannot access memory at address 0xe5894855<br class=""><br class="">I’m still waiting on the transformix DVF, but I’ll give that a try too when<br class="">its done.<br class=""><br class="">Thanks again!<br class=""><br class="">— Matt<br class=""><br class="">__<br class="">Matthew J. Riblett<br class="">Virginia Commonwealth University<br class="">Department of Radiation Oncology<br class="">Medical Physics Graduate Program<br class=""><br class="">Office: Sanger Hall, Room B1-013<br class="">401 College Street | P.O. Box 980058<br class="">Richmond, Virginia 23298<br class=""><br class="">VCU Email: <a href="mailto:riblettmj@vcu.edu" class="">riblettmj@vcu.edu</a><br class="">MCV Office Phone: +1.804.628.4858<br class=""><br class=""><br class=""><br class="">On Feb 2, 2015, at 1:16 PM, Matthew J. Riblett <<a href="mailto:riblettmj@mymail.vcu.edu" class="">riblettmj@mymail.vcu.edu</a>><br class="">wrote:<br class=""><br class="">Thanks for the quick reply Simon! I am using the rtkfdk app, and I will go<br class="">ahead and check to see if the pointer is null and let you know. My current<br class="">check is having transformix to generate a smaller DVF to see if that helps,<br class="">so the server is getting that done as we speak.<br class=""><br class="">You might also like to know that I’ve got RTK running on a Cray CX-1 (baby<br class="">supercomputer) sitting next to the aforementioned Sun x4600-M2. :)<br class=""><br class="">— Matt<br class=""><br class="">__<br class="">Matthew J. Riblett<br class="">Virginia Commonwealth University<br class="">Department of Radiation Oncology<br class="">Medical Physics Graduate Program<br class=""><br class="">Office: Sanger Hall, Room B1-013<br class="">401 College Street | P.O. Box 980058<br class="">Richmond, Virginia 23298<br class=""><br class="">VCU Email: <a href="mailto:riblettmj@vcu.edu" class="">riblettmj@vcu.edu</a><br class="">MCV Office Phone: +1.804.628.4858<br class=""><br class=""><br class=""><br class="">On Feb 2, 2015, at 12:19 PM, Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" class="">simon.rit@creatis.insa-lyon.fr</a>><br class="">wrote:<br class=""><br class="">Hi,<br class="">You're the first RTK user I know to use it on Sun! Nice!<br class="">If you've got 64 GB ram, that should be enough... although you could<br class="">ask elastix to generate a smaller DVF, RTK linearly interpolates<br class="">between vectors. You could even use B-spline coeffs directly but you'd<br class="">have to create a new DVF.<br class="">My guess is that there is a problem with the initialization of<br class="">m_Deformation since the line you mention is the first time it's ever<br class="">used in the class. Do you use the rtkfdk app? I would start by<br class="">checking that the pointer is not null before this line, sg like:<br class="">std::cout << "m_Deformation=" << m_Deformation.GetPointer() << std::endl;<br class="">If it equals 0, then there is something going with the deformation.<br class="">You can check it in the main app, rtkfdk.cxx.<br class="">Simon<br class=""><br class="">On Mon, Feb 2, 2015 at 6:03 PM, Matthew J. Riblett<br class=""><<a href="mailto:riblettmj@mymail.vcu.edu" class="">riblettmj@mymail.vcu.edu</a>> wrote:<br class=""><br class="">Hello RTK Users,<br class=""><br class="">I’m just getting started using RTK as part of my graduate research and was<br class="">hoping that someone might be able to help me sort out an issue I’ve been<br class="">having reconstructing a 3D CBCT image dataset while applying a 4D<br class="">deformation field — I’m reconstructing with ~2400 projections and the 4D DVF<br class="">has been generated by transformix (.mhd format). I followed, for the most<br class="">part, the MCCBCTReconstruction example on the RTK Wiki.<br class=""><br class="">While reconstructing, rtkfdk reads in all of the projections to memory,<br class="">begins the ‘Reconstructing and Writing’ phase and proceeds for a few seconds<br class="">before hanging — it doesn’t exit or fault, just drops to 0% CPU while<br class="">retaining the projections in memory.<br class=""><br class="">By writing some basic debug messages into the source code, I’ve been able to<br class="">determine that the issue lies somewhere at m_Deformation->Update() [Line 99<br class="">of code/rtkFDKWarpBackProjectionImageFilter.txx]. It appears that thread 0<br class="">makes it past the m_Deformation->SetFrame(iProj) line, but never makes it<br class="">past the subsequent update. I’m wondering if this has anything to do with<br class="">the size of the DVF generated by transformix: approximately 4.0GB<br class="">(512x100x512x10 image, 4-channels, FLOAT).<br class=""><br class="">Just to provide a little more background information, I’m running RTK on a<br class="">32 core Sun Server (8x Quad-Core AMD Opteron 8356, 2.3Ghz) with 64GB of<br class="">memory running Ubuntu 14.04. RTK was built using the default ‘Release’ make<br class="">configuration and linked to ITK 4.5.2. Elastix and Transformix are both the<br class="">latest version, 4.7.<br class=""><br class="">Has anyone else run into a similar issue with reconstructing a similar<br class="">image, or does anyone have any thoughts as to how to resolve this sort of<br class="">issue?<br class=""><br class="">Thanks in advance!<br class=""><br class="">— Matt<br class=""><br class="">__<br class="">Matthew J. Riblett<br class="">Virginia Commonwealth University<br class="">Department of Radiation Oncology<br class="">Medical Physics Graduate Program<br class=""><br class="">Office: Sanger Hall, Room B1-013<br class="">401 College Street | P.O. Box 980058<br class="">Richmond, Virginia 23298<br class=""><br class="">VCU Email: <a href="mailto:riblettmj@vcu.edu" class="">riblettmj@vcu.edu</a><br class="">MCV Office Phone: +1.804.628.4858<br class=""><br class=""><br class=""><br class="">_______________________________________________<br class="">Rtk-users mailing list<br class=""><a href="mailto:Rtk-users@public.kitware.com" class="">Rtk-users@public.kitware.com</a><br class="">http://public.kitware.com/mailman/listinfo/rtk-users<br class=""><br class=""><br class=""><br class=""></blockquote></div></blockquote></div><br class=""></div></body></html>