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IDProjectCategoryView StatusDate SubmittedLast Update
0002007Slicer4Core: Building (CMake, Superbuild)public2012-05-09 10:092014-03-06 04:54
Reporterjcfr Assigned Tojcfr  
PrioritynormalSeverityminorReproducibilityhave not tried
Status closedResolutionfixed 
Product Version 
Target VersionSlicer 4.3.0Fixed in VersionSlicer 4.3.0 
Summary0002007: Build against ITKv4 and remove ITKv3
Description

Self described

TagsITKv4

Relationships

parent of 0002113 closedpohl Ensure EMSegment is compatible with ITKv4 
parent of 0002114 closedmccormic Ensure Slicer can be compiled against ITKv4 on both Windows 32 and 64 bit 
parent of 0002115 closedjcfr Mechanism to customize Slicer package name depending on build option 
parent of 0002116 closedjcfr Improve extension framework to differentiate extension build against different Slicer. 
parent of 0002729 closedmccormic Recent ITK changes may have broken Slicer4/ITKv4 - Slicer can't seem to read volumes 
parent of 0002800 closedhjmjohnson Create External_DWIConvert.cmake 
parent of 0002801 closedpieper Check Slicer packaging on Windows 32bit when built against ITKv4 
parent of 0002804 closedhjmjohnson Check Slicer packaging on MacOSX when built against ITKv4 
parent of 0002805 closedhjmjohnson Ensure the DCMTK external project of Slicer is used to build ITKv4 
parent of 0002806 closedjcfr Check that extensions can be built with Slicer ITKv4 
parent of 0002807 closedhjmjohnson itkTestMain.h is not available anymore in ITKv4. 
parent of 0002883 closedjcfr Fix FindDCMTK.cmake provided by ITKv4 
parent of 0002884 closedjcfr Windows / ITKv4 - When building, it complains with "illegal parameter from the moc.exe" 
related to 0001692 closedmccormic Implement a test named "py_SimpleITK_ImportTest" 
related to 0001693 closedmayeul.chassagnard Implement a test named "py_SimpleITK_SlicerPushPullTest" 
related to 0002879 closedpieper Unable to load dose volumes exported by Xio 

Activities

kikinis

kikinis

2012-05-27 02:38

developer   ~0004633

I do not know what version it is, but RSNA 2012 is the target date/event for Slicer 4 with ITK 4
jcfr

jcfr

2012-05-27 08:33

administrator   ~0004636

Re-targeted issues related to ITKv4 for Sept 1st release.
jcfr

jcfr

2012-06-28 06:58

administrator   ~0004960

From Hans - June 28 2012:

Done:
*
During Project Week we resolved the packaging issues.

  1. ITKv4 now supports runtime only installs. (Thanks Bill Lorensen)
  2. This required changes to both Slicer and ITKv4 (for complete
    compliance).
  3. The Slicer changes are checked into the repo.
  4. The ITKv4 changes are tested and merged into master branch of ITKv4
  5. BRAINSTools was cleaned up to support the COMPONENT Runtime Install
  6. Clean build process7. Remove configuration warnings about
    unnecessary/unused configuration commands
  7. Fix shared library linking for python on Mac for creating successful
    install
  8. Complete build success tested to respect superbuild requested compiler
    (set default CC=/dev/null and CXX=/dev/null to force errors)
  9. On Mac/Windows with case sensitive files system, CMAKE 2.8.9 is needed
    to build and install DCMTK from CTK
  10. Add and respect the ITK_LEGACY_REMOVE flag and verified that Slicer is
    not using any itkLegacyMacro code
  11. Fixed GrowCut bug exposed by ITKv4 (Thanks Jim and Brad Lowekamp)

==========
-- On Mac from a clean build from scratch we can produce a working .dmg
file that includes ITKv4 build and SimpleITK integration. This was
deployed and tested on Ron's laptop.
-- Windows build failed on Steve's "dirty" build environment, but
subsequently Brad Lowekamp reported unconfirmed successful "clean" windows
build.
-- Linux packaging not yet tested

==========
TODO:
-- More thorough testing of all compiler/platform options
-- Get nightly packages to build on the centralized robot build machines
-- Track down and fix regressions that may occur. (NOTE: In January Bill
Lorensen and I had both ITKv3 and ITKv4 builds passing the exactly the
same tests, so new regressions between ITKv3 and ITKv4 should be limited
to work done this spring).

Hans
pieper

pieper

2012-08-14 09:20

administrator   ~0005549

The following mail trail discusses issues with ITKv3 and recent versions of Xcode (clang-based). Take home message is that ITKv3 is not supported and we need to prioritize getting ITKv4 integrated as the default version.

On Tue, Aug 14, 2012 at 11:32 AM, Johnson, Hans J <hans-johnson@uiowa.edu> wrote:

I also think that python needs to be updated to 2.7, and numpy to little
more recent version for the clang-3.1 compiler to be happy even with ITKv4.

Kent and I are working on a clang improvement for SimpleITK as well.

Hans

On 8/14/12 10:19 AM, "Steve Pieper" <pieper@ibility.net> wrote:

Thanks, Hans - that makes perfect sense nd it adds urgency to our
move to ITKv4 in slicer.

I'll add a note to the slicer wiki.

-Steve

On Tue, Aug 14, 2012 at 11:14 AM, Johnson, Hans J
<hans-johnson@uiowa.edu> wrote:

Sorry Steve,

ITKv3 is definitely notmaintained any more, and will likely have
several
problems with clang.

I've made just a few easy fixes for ITKv3 to make it clang compatible,
but
decided to put my effots into ITKv4.

I would not trust ITKv3 with clang.

Hans

On 8/14/12 10:03 AM, "Steve Pieper" <pieper@ibility.net> wrote:

Hi Guys -

Should I interpret the silence as 'yes, ITKv3 may be broken on clang
because it's not tively maintained anymore' ?

Is there an itk version 3 dashboard?

Steve

On Sat, Aug 11, 2012 at 1:11 PM, Steve Pieper <pieper@ibility.net>
wrote:

Follow up: I do not get this crash with ITKv4 on clang.

On Sat, Aug 11, 2012 at 1:59 AM, Steve Pieper <pieper@ibility.net>
wrote:

Hi Hans, Brad, Jim -

I've noticed some strange crashes on a couple of my macs inside ITK
threading in CLI modules (see mail trail with Andrey below).

It seems that ITKv3 and clang are not working (I can't even build
ITKv3
with testing enabled [1]).

It is a 'known issue' ? I can't find any mention of such things on
the
ITK wiki. Is it just thatITKv3 is no longer supported?

I can move this question to the Insight-developers mailing list if
that's
a better forum, but I thought I would ask you guys first in case I
was
missing something obvious. I'm rying ITKv4 with clang to see if
that
fixes
the issue.

Thanks,
Steve

[1] http://open.cdash.org/buildSummary.php?buildid=2509334

---------- Forwarded message ----------
From: Steve Pieper <pieper@ibility.net>
Date: Sat, Aug 11, 2012 at 11:42 AM
Subject: Re: crop volume working for you on mac?
To: Andriy Fedorov <fedorov@bwh.harvard.edu>

It looks like the issue is that newer mac compilers (clang) lead to
crashes in crop volume while older ones (gcc) do not.

On my laptop and o common.bwh.harvard.edu I ave this compiler and I
get
the same kinds of crashes on both:

$ /usr/bin/c++ --version
Apple clang version 3.1 (tags/Appl/clang-318.0.61) (based on LLVM
3.1svn)
Target: x86_64-apple-darwin11.4.2
Thread model: posix

On glder.bwh.harvard.edu I have this compiler and I do not get a
crash:

$ /usr/bin/c++ --version
i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 (Based on Apple Inc.
build
5658) (LLVM build 2335.15.00)
Copyright (C) 2007 Free Software Foundation, Inc.
This is fee software; see the source for copying conditions. There
is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A ARTICULAR
PURPOSE.

Can you try this? I'm guessing you have gcc based compiler on your
laptop
and that's why it doesn't crash.

-Steve

On Sat, Aug 11, 2012 at 8:52 AM, Andriy Fedorov
<fedorov@bwh.harvard.edu>
wrote:

Steve, I'll test again today with nightly binaries on different
platforms.

On Sat, Aug 11, 2012 at 7:56 AM, Steve Pieper <pieper@ibility.net>
wrote:

Hmm, oky. I will try on other machines and try to get to the
ottom
of it.

I'm using a qt 4.8.1 binary download, but since th crash is in itk
it
shouldn't have any impact. It seemto be an itk threading issue.
I'm
using itkv3.

Thanks for checking,
-Steve

On Fri, Aug 10, 2012 at 8:33 PM, Andriy Fedorov
<fedoov@bwh.harvard.edu>
wrote:

Just tried that, no crash. I have it built in Debug mode, with Qt
built in ebug from source.

On Fri, Aug 10, 2012 at 8:05 PM, Andriy Fedorov
<fedorov@bwh.harvard.edu>
wrote:

Will do, but it will take me some time, beause I do not have
CLIs
built ... Will let you know.

On Fri, Aug 10, 212 at 7:45 PM, Steve Pieper
<pieper@ibility.net>
wrote:

Hi Andrey -

Can you check the crop volume module on your mac build? On my
laptop I
get
random cashes like the one pasted below. Sometimes it
happens
in
different
places, but it always crashes.

What I do:

  • download MRHead
  • put down and ROI (doesn't seem to matter where)
  • g to CropVolume
  • clickCrop! and the crash occurs in the resample code in the
    CLI.

I have tried a complete rebuild from scratch and this still
happens.
It
does NOT happen on linux though...

-Steve

Process: Slicer [64832]
Path:
/Users/USER/*/Slicer.app/Contents/MacOS/./Slicer
Identifier: ???
Verson: 4.1.0 (4.1.0-2012-08-10)
Code Type: X86-64 (Native)
Parent Process: Slicer [64831]

Date/Time: 2012-08-10 19:42:32.063 -0400
OS Version: Mac OS X 10.7.4 (11E2620)
Report Version: 9

Interval Since Last Report: 2036285 sec
Crashes Since Last Report: 49
Per-App Interval Since Last Report: 7670 sec
Per-App Crashes Since Last Report: 7
Anonymous UUID:
6240FD31-C1A2-414E-8258-B5B0A5E11E16

Crashed Thread: 18

Excepion Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000018

VM Regions Near 0x18:
-->
__TEXT 0000000100c87000-0000000100cad000 [
152K]
r-x/rwx SM=COW/Users/USER/*/Slicer.app/Contents/MacOS/Slicer

Application Specific Information:
objc[64832]: garbage collection is OFF

Thread 0:: Dispath queue: com.apple.main-thread
0 libvtkITK.dylib 0x000000010d1588e0
itk::Image<short,
3u>::GetPixel(itk::Index<3u> const&) const + 0
(itkImage.h:208)
1 libResampleScalarVectorDWIVoumeLib.dylib
0x000000013134592a
itk::LinearInterpolateImageFunction<itk::Image<short, 3u>,

double>::EvaluateOptimized(itk::LinearInterpolateImageFunction<itk::I
ma
ge<short,
3u>, doubl>::Dispatch<3u> const&, itk::ContinuousIndex<double,
3u>
const&)
const + 906 (itkOptLinearInterpolateImageFunction.h:257)
2 libResampleScalarVectorDWIVlumeLib.dylib 0x0000001313443e4
itk::LinearInterpolateImageFunction<itk::Image<short, 3u>,

double>::EvaluateAtContinuousIndex(itk::ContinuousIndex<double,
3u>
const&)
const + 36 (itkOptLinearInterpolateImageFunction.h:93)
3 libResampleScalarVectorDWIVolumeLib.dylib
0x0000000131341e25
itk::ResampleImageFilter<itk::Image<short, 3u>,
itk::Image<short,
3u>,
double>::LinearThreadedGenerateData(itk::ImageRegion<3u>
const&,
int) +
3605
(itkOptResampleImageFilter.txx:737)
4 libResampleScalarVectorDWIVolumeLib.dylib
0x000000013133b399
itk::ResampleImageFilter<itk::Image<short, 3u>,
itk::Imag<short,
3u>,
double>::ThreadedGenerateData(itk::ImageRegion<3u> const&,
int)
+
345
(itkOptResampleImageFilter.txx:255)
5 libvtkITK.dylib 0x000000010d0a8b2e
itk::ImageSource<itk::Image<short, 3u>
::ThreaderCallback(void) +
206
(itkImageSource.txx:296)
6 libITKCommon.3.20.dylib 0x0000000110c932d9
itk::MultiThreader::SingleMethodExecute() + 1033
(itkMultiThreader.cxx:393)
7 libvtkITK.dylib 0x000000010d0a89c0
itk::ImageSource<itk::Image<short, 3u> >::GenerateData() + 240
(itkImageSource.txx:244)
8 libITKCommon.3.20.dylib 0x0000000110cd5d33
itk::ProcessObject::UpdateOutputData(itk::DataObject) + 1267
(itkProcessObject.cxx:987)
9 libITKCommon.3.20.dylib 0x0000000110c6f85c
itk::DataObject::UpdateOutputData() + 172
(itkDataObject.cxx:423)
10 libMRMLCore.dylib 0x000000109f5c6d1
itk::ImageBase<3u>::UpdateOutputData() + 97
(itkImageBase.txx:292)
11 libITKCommon.3.20.dylib 0x0000000110c6f3e5
itk::Databject::Update() + 69 (itkDataObject.cxx:345)
12 libITKCommon.3.20.dylib 0x0000000110cd4fac
itk::ProcessObject::Update() + 76 (itkProcessObject.cxx:617)
13 libResampleScalarVectorDWIVolmeLib.dylib 0x00000001310ae61f
int
(anonymous namespace)::Rotate<short>((anonymus
namespace)::parameters&) +
2143 (ResampleScalarVectorDWIVolume.cxx:1224)
14 libResampleScalarVectorDWIVolumeLib.dylib
0x00000001310aa136
ModuleEntryPoint + 43958
(ResampleScalarVectorDWIVolume.cxx:1319)
15 libqSlicerBaseQTCLI.dylib 0x0000000100e20bdc
vtkSlicerCLIModuleLogic::ApplyTask(void*) + 5716
(vtkSlicerCLIModuleLogic.cxx:1576)
16 libqSlicerBaseQTCLI.dylib 0x0000000100e1456e

vtkSlicerCLIModuleLogic::ApplyAndWait(vtkMRMLCommandLineModuleNode*,
bool) +
158 (vtkSlicerCLIModuleLogic.cxx:332)
17 libvtkSlicerCropVolumeModuleLogic.dylib 0x000000011f174edc

vtkSlicerCropVolumeLogic::Apply(vtkMRMLCropVolumeParametersNode) +
4620
(vtkSlicerCropVolumeLogic.cxx:275)
18 libqSlicerCropVolumeModule.dylib 0x000000012281ddb
qSlicerCropVolumeModuleWidget::onApply() + 59
(qSlicerCropVolumeModuleWidget.cxx:184)
19 libqSlicerCropVolumeModule.dylib 0x0000000122c85c99
qSlicerCropVolueModuleWidget::qt_static_metacall(QObject,
QMetaObject::Call, int, void) + 233
(moc_qSlicerCropVolumeModuleWidget.cxx:71)
20 QtCore 0x000000010cbb022e
QMetaObject::activate(QObject, QMetaObject const, int,
void) +
1566
21 QtGui 0x000000010c427451
QAbstractButton::clicked(bool) + 49
22 QtGui 0x000000010c14a0d0
QAbstractButtonPrivate::emitClicked() + 64
23 QtGui 0x000000010c14b30a
QAbstractButtonPrivate::click() + 154
24 QtGui 0x000000010c14b561
QAbstractButton::mouseReleaseEvent(QMouseEvent) + 113
25 QtGui 0x000000010bdff651
QWidget:even(QEvent)

  • 2369
    26 QtGui 0x000000010c14a358
    QAbstractButton::event(QEvent) + 40
    27 QtGui 0x000000010c1e5d55
    QPushButton:event(QEvent    ) + 69
    28 QtGui 0x000000010bda793d
    QApplicationPrivate::notify_helper(QObject, QEvent) + 189
    9 QtGui 0x000000010bde2f0
    QApplication::notify(QObject, QEvent) + 2384
    30 QtCore 0x000000010cb9817c
    QCoreApplication::notifyInternal(QObject, QEvent) + 124
    31 QtGui 0x000000010bdac12d
    QApplicationPrivate::sendMouseEvent(QWidget    , QMouseEvent,
    QWidget    ,
    QWidget*, QWidget*, QPointer<QWidget>&, bool) + 333
    32 QtGui 0x000000010bd5b985
    qt_mac_handleMouseEvent(NSEvent    , QEvent::Type,
    Qt::MouseButton,
    QWidget*) +
    741
    33 com.apple.AppKit 0x00007fff9959340e
    -[NSWidow
    sendEvent:]
  • 6504
    34 QtGui 0x000000010bd0a37
    -[QCocoaWindow
    sendEvent:] + 87
    35 com.apple.AppKit 0x00007fff9952ca55
    -[NSApplication
    sendEvent:] + 5593
    36 QtGui 0x000000010bd55b24
    -[QNSApplication
    sendEvent:] + 84
    7 com.apple.AppKit 0x00007fff994c30c6
    -[NSApplication
    run] +
    555
    38 QtGui 0x000000010bd60900

QEventDispatcherMac::processEvents(QFlags<QEventLoop::ProcessEventsFl
ag
) +
1824
39 QtCore 0x000000010cb97094

QEventLoop::processvents(QFlags<QEventLoop::ProcessEventsFlag>) +
68
40 QtCore 0x000000010cb97444
QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 324
41 QtCore 0x000000010cb99b2c
QCoreApplication::exec() + 188
42 0x000000010ca4e6b
(anonymous
namespace)::SlicerAppMain(int, char**) + 4283 (Main.cxx:365)
43 0x0000000100ca3da2 main +
34
(Main.cxx:397)
44 0x0000000100ca3d74 start +
52

Thread 1:: Dispatch queue: com.apple.libdispatch-manager
0 libsystem_kernel.dylib 0x00007fff98c217e6 kevent +
10
1 libdispatch.dylib 0x00007fff8e69578a
_dispatch_mgr_invoke
923
2 libdispatch.dylib 0x00007fff8e6941a
_dispatc_mgr_thread +
54

hread 2:
0 libsystem_kernel.dylib 0x00007fff98c21af2 read +
10
1 libCTKCore.0.1.dylib 0x00000001088bb4d8
ctkFDHandler::run() +
72 (ctkErrorLogFDMessageHandler.cpp:193)
2 QtCore 0x000000010ca835ba
QThreadPrivate::start(void*) + 298
3 libsystem_c.dylib 0x00007fff985f28bf
_pthread_start
+
335
4 libsystem_c.dylib 0x00007fff985f5b75
thread_start +
13

Thread 3:
0 libsystem_kernel.dylib 0x00007fff98c21af2 read +
10
1 libCKCore.0.1.dylib 0x00000001088bb4d8
ctkFDHandler::run() +
72 (ctkErrorLogFDMessageHandler.cpp:193)
2 QtCore 0x000000010ca835ba
QThreadPrivate::start(void*) + 298
3 libsystem_c.dylib 0x00007fff985f28bf
_pthread_start
+
335
4 libsystem_c.dylib 0x00007fff985f5b75
thread_start +
13

Thread 4:
0 libsystem_kernel.dylib 0x00007fff98c20e42
__semwait_signal

  • 10
    1 libsystem_c.dylib 0x00007fff9a8dea
    nanosleep +
    164
    2 libsystem_c.dylib 0x00007fff985a8bb5 usleep +
    53
    3 libitksys.3.20.dylib 0x0000000112846f5
    itksys::SystemTools::Delay(unsigned int) + 117
    (SystemTools.cxx:4088)
    4 libSlicerBaseLgic.dylib 0x0000000105586988
    vtkSlicerpplicationLogic::ProcessProcessingTasks() + 568
    (vtkSlicerAppicationLogic.cxx:473)
    5 libSlicerBaseLoc.dylib 0x00000001055864b6
    vtkSlicerApplicationLogic::ProcessingThreaderCallback(void*) +
    54
    (vtkSlicerApplicationLogic.cxx:425)
    6 libsystem_c.dylib 0x00007ff985f28bf
    _pthread_start

  • 335
    7 libsystem_c.dylib 0x00007fff985f5b75
    thread_start +
    13

Thread 5:
0 libsystem_kernel.dylib 0x00007fff98c20e42
__semwait_sigal

  • 10
    1 libsystem_c.dylib 0x00007fff985a8dea
    nanosleep +
    164
    2 libsystem_c.dylib 0x00007fff985a8bb5 usleep +
    53
    3 libitksys.3.20.dylib 0x00000001112846f5
    itksys::SystemTools::Delay(unsigned int) + 117
    (SystemTools.cxx:4088)
    4 libSlicerBaseLogic.dylib 0x0000000105586c18
    vtkSlicerApplicationLogic::ProcessNetworkingTasks() + 568
    (vtkSlicerApplicationLogic.cxx:547)
    5 libSlicerBaseLogic.dylib 0x0000000105586506
    vtkSlicerApplicationLogic::NetworkingThreaderCallback(void*) +
    54
    (vtkSlicerApplicationLogic.cxx:501)
    6 libsystem_c.dylib 0x00007fff985f28bf
    _pthread_start

  • 335
    7 libsystem_c.dylib 0x00007fff985f5b75
    thread_start +
    13

Thread 6:
0 libsystem_kernel.dylib 0x00007fff98c20bca
__psynch_cvwait +
10
1 libsystem_c.dylib 0x00007fff985f6274
_pthread_cond_wait
+
840
2 QtWebKit 0x0000000103b15855
WTF::TCMalloc_PageHeap::scavengerThread() + 117
3 QtWebKit 0x0000000103b15ae9
WTF::TCMalloc_PageHeap::runSavengerThread(void*) + 9
4 libsystem_c.dylib 0x00007fff985f28bf
_pthread_start
+
335
5 libsystem_c.dylib 0x00007fff985f5b75
thread_start +
13

Thread 7:
0 libsystem_kernel.dylib 0x00007fff98c2df2 __select

  • 10
    1 QtCore 0x000000010cbc8cce
    qt_safe_select(int,
    fd_set, fd_set, fd_set, timeval const) + 142
    2 QtCore 0x000000010cbcd0a3

QEventDispatcherUNIXPrivate::doSelect(QFlags<QEventLoop::ProcessEvent
sF
lag>,
timeval*) + 435
3 QtCore 0x000000010cbcd572

QEventDispatcherUNIX::processEvents(QFlags<QEventLoop::ProcessEventsF
la
g>) +
178
4 QtCore 0x000000010cb97094

EventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) +

68
5 QtCore 0x000000010cb97444
QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 324
6 QtCore 0x000000010ca7ff08
QThread::exec() +
312
7 QtCore 0x000000010ca835ba
QThreadPrivate::start(void*) + 28
8 libsyste_c.dylib 0x00007fff985f28bf
_pthread_start
+
335
9 libsystem_c.dylib 0x00007fff985f5b75
thread_start +
13

Thread 8:
0 libsystem_kernel.dylib 0x00007fff98c217e6 kevent +
10
1 QtCore 0x000000010cbb39
QKqueueFileSystemWatcherEngine::run() + 153
2 QtCore 0x000000010ca835ba
QThreadPrivate::start(void*) + 298
3 libsystem_c.dylib 0x00007fff985f28bf
_pthread_start
+
335
4 libsystem_c.dylib 0x00007fff985f5b75
thread_start +
13

Thread 9:
0 libsystem_kernel.dylib 0x00007fff98c20df2 __select

  • 10
    1 QtCore 0x000000010cb6b6b0
    QProcessManager::run()
  • 96
    2 QtCore 0x000000010ca835ba
    QThreadPrivate::start(void*) + 298
    3 libsystem_c.dylib 0x00007fff985f28bf
    _pthread_start

  • 335
    4 libsystem_c.dylib 0x00007fff985f5b75
    thread_start +
    13

Thread 10:: com.apple.CFSocket.private
0 libsystem_kernel.dylib 0x00007fff98c20df2 __select

  • 10
    1 com.apple.CoreFoundation 0x00007fff8f23fc8b
    __CFSocketManager

  • 1355
    2 libsystem_c.dylib 0x00007fff985f8bf
    _pthread_start

  • 335
    3 libsystem_c.dylib 0x00007fff985f5b75
    thread_start +
    13

Thread 11:
0 libsystem_kernel.dylib 0x00007fff98c21192
__workq_kernreturn +
10
1 libsyste_c.dylib 0x00007fff985f4594
_pthread_wqthread

  • 758
    2 libsystem_c.dylib 0x00007fff985f5b85
    start_wqthread

  • 13

Thread 12:
0 libResampleScalarVecorDWIVolumeLib.dylib
0x0000000131345697
itk::LinearInterpolateImageFunction<itk::Image<short, 3u>,

double>::EvaluateOptimized(itk::LinearInterpolateImageFunction<itk::I
ma
ge<short,
3u>, double>::Dispatch<3u> const&,
itk::ContinuousIndex<double,
3u>
const&)
const + 247 (itkOptLinearInterpolateImageFunction.h:235)
1 libResampleScalarVectorDWIVolumeLib.dylib
0x00000001313443e4
itk::LinarInterpolateImageFunction<itk::Image<short, 3u>,

double>::EvaluateAtContinuousIndex(itk::ContinuousIndex<double,
3u>
const&)
const + 36 (itkOptLinearInterpolateImageFunction.h:93)
2 libResampleScalarVectorDWIVolumeLib.dylib
0x0000000131341e25
itk::ResampleImageFilter<itk::Image<short, 3u>,
itk::Image<short,
3u>,
double>::LinearThreadedGenerateData(itk::ImageRegion<3u>
const&,
int) +
3605
(itkOptResampleImageFilter.txx:737)
3 libResampleScalarVectorDWIVolumeLibdylib
0x000000013133b399
itk::ResampleImageFilter<itk::Image<short, 3u>,
itk::Image<short,
3u>,
double>::ThreadedGenerateData(itk::ImageRegion<3u>const&,
int)
+
345
(itkOptResampleImageFlter.txx:255)
4 libvtkITK.dylib 0x000000010d0a8b2e
itk::ImageSource<itk::Image<short, 3u>
::ThreaderCallback(void) +
206
(itkImageSource.txx:296)
5 libITKCommon.3.20.dylib 0x0000000110c94dd6
itk::MultiThreader::SingleMethodProxy(void) + 22
(itkMultiThreader.cxx:853)
6 libsystem_c.dylib 0x00007fff985f28bf
_pthread_start
+
335
7 libsystem_c.dylib 0x00007fff985f5b75
thread_start +
13

Thread 13:
0 libMRMLCore.dylib 0x0000000109f591b0
itk::Idex<3u>::operator[](unsigned int) + 0 (itkIndex.h:210)
1 libResampleScalarVectorDWIVolumeLib.dylib
0x0000000131345890
itk::LinearInterpolateImageFunction<itk::Image<short, 3u>,

double>::EvaluateOptimized(itk::LinearInterpolateImageFunction<itk::I
ma
ge<short,
3u>, double>::Dispatch<3u> const&, itk::ContinuousIndex<double,
3u>
const&)
const + 752 (itkOptLinearInterpolateImageFunction.h:249)
2 libResampleScalarVectorDWIVolumeLib.dylib
0x00000001313443e4
itk::LinearInterpolateImageFunction<itk::Image<short, 3u>,
double>::EvaluateAtContinuousIndex(itk::ContnuousIndex<double,
3u>
const&)
const + 36 (itkOptLiearInterpolateImageFunction.h:93)
3 libResampleScalarVectorDWIVolumeLib.dylib
0x0000000131341e25
itk::ResampleImageFilter<itk::Image<short, 3u>,
itk::Image<short,
3u>,
double>::LinearThreadedGenerateData(itk::ImageRegion<3u>
const&,
int) +
3605
(itkOptResampleImageFilter.txx:737)
4 libResampleScalarVectorDWIVolumeLib.dylib
0x000000013133b399
itk::ResampleImageFilter<itk::Image<short, 3u>,
itk::Image<short,
3u>,
double>::ThreadedGenerateData(itk::ImageRegion<3u> const&,
int)
+
345
(itkOptResampleImageFilter.txx:255)
5 libvtkITK.dylib 0x000000010d0a8b2e
itk::ImageSource<itk::Image<short, 3u>
::ThreaderCallback(void) +
206
(itkImageSource.txx:296)
6 libITKCommon.3.20.dylib 0x0000000110c94dd6
itk::MultiThreader::SingeMethodProxy(void) + 22
(itkMultiThreader.cxx:853)
7 libsystem_c.dylib 0x00007fff985f28bf
_pthread_start
+
335
8 libsystem_c.dylib 0x00007fff985f5b75
thread_sart +
13

Thread 14:
0 libMRMLCore.dylib 0x0000000109f07fc8
itk::Index<3u>::operator[](unsigned int) const + 8
(itkIndex.h:216)
1 libMRMLCore.dylib 0x0000000109f5b5b7
itk::ImageHelper<3u,
2u>::CmputeOffsetInner(itk::Index<3u> const&, itk::Index<3u>
const&,
long
const, long&, itk::Concept::Detail::UniqueType_bool<false>
const&)
+
55
(itkImageHelper.h:127)
2 libMRMLCore.dylib 0x0000000109f5b571
itk::ImageHelper<3u,
3u>::ComputeOffset(itk::Index<3u> const&, itk::Index<3u>
const&,
long
const, long&) + 49 (itkImageHelper.h:119)
3 libMRMLCore.dylib 0x0000000109f5b42f
itk::ImageBase<3u>::ComputeOffset(itk::Index<3u> const&) const

  • 95
    (itkImageBase.h:290)
    4 libvtkITK.dylib 0x000000010d158907
    itk::Image<short,
    3u>::GetPixel(itk::Index<3u> const&) const+ 39
    (itkImage.h:209)
    5 libResampleScalarVectorDWIVolumeLib.dylib
    0x000000013134682f
    i::LinearInterpolateImageFunction<itk::Image<short, 3,

double>::EvaluateOptimized(itk::LinearInterpolateImageFunction<itk::I
ma
ge<short,
3u>, double>::Dispatch<3u> const&,
itk::ContinuousIndex<double,
3u>
const&)
const + 4751 (itkOptLinearInterpolateImageFunction.h:436)
6 libResampleScalarVectorDWIVolumLib.dylib
0x00000001313443e4
itk::LinearInterpolateImageFunction<itk::Image<short, 3u>,

double>::EvaluateAtContinuousIndex(itk::ContinuousIndex<double,
3u>
const&)
cnst + 36 (itkOptLinearInterpolateImageFunction.h:3)
7 libResampleScalarVectorDWIVolumeLib.dylib
0x0000000131341e25
itk::ResampleImageFilter<itk::Image<short, 3u>,
itk::Image<short,
3u>,
double>::LinearThreadedGenerateData(itk::ImageRegion<3u>
const&,
int) +
3605
(itkOptResampleImageFilter.txx:737)
8 libResampleScalarVectorDWIVolueLib.dylib
0x000000013133b399
itk::ResampleImageFilter<itk::Image<short, 3u,
itk::Image<short,
3u>,
double>::ThreadedGenerateData(itk::ImageRegion<3u> const&,
int)
+
345
(itkOptResampleImageFilter.txx:255)
9 libvtkITK.dylib 0x000000010d0a8b2e
itk::ImageSource<itk::Image<shor, 3u>
::ThreaderCallback(void) +
206
(itkImageSource.txx:296)
10 libITKCommon.3.20.dylib 0x0000000110c94dd6
itk::MultiThreader::SingleMethodProxy(void) + 22
(itkMultiThreader.cxx:853)
11 libsystem_c.dylib 0x00007fff985f28bf
_pthread_start
+
335
12 libsystem_dylib 0x00007fff985f5b75
thread_start +
13

Thread 15:
0 libvtkITK.dylib 0x000000010d158c28
itk::ImportImageContainer<unsigned long,
short>::operator[](unsigned>>>>>> >> >> long) +
8 (itkImportImageContainer.h:78)
1 libvtkITK.dylib 0x000000010d158929
itk::Image<short,
3u>::GetPixel(itk::Index<3u> const&) const + 73
(itkImage.h:210)
2 libResampleScalarVectorDWIVolumeLib.dylib
0x000000013134592a
itk::LinearInterpolateImageFunction<itk::Image<short, 3u>,

double>::EvaluateOptimized(itk::LinearInterpolateImageFunction<itk:I
ma
ge<short,

3u>, double::Dispatch<3u> const&,
itk::ContinuousIndex<double,
3u>
const&)
const + 906 (itkOptLinearInterpolateImageFunction.h:257)
3 libResampleScalarVectorDWIVolumeLib.dylib
0x00000001313443e4
itk::LinearInterpolateImageFunction<itk::Image<short, 3u>,
double>::EvaluateAtCotinuousIndex(itk::ContinuousIndex<double,
3u>
const&)
const + 36 (itkOptLinearInterpolateImageFuntion.h:93)
4 libResampleScalarVectorDWIVolumeLib.dylib
0x0000000131341e25
itk::ResampeImageFilter<itk::Image<short, 3u>,
itk::Image<short,
3u>,
double>::LinearThreadedGenerateData(itk::ImageRegion<3u>
const&,
int) +
3605
(itkOptResampleImageFilter.txx:737)
5 libResampleScalarVectorDWIVolumeLib.dylib
0x000000013133b399
itk::ResampleImageFilter<itk::Image<short, 3u>,
itk::Image<short,
3u>,
double>::ThreadedGenerateData(itk::ImageRegion<3u> const&, int)
+
345
(itkOptResampleImageFilter.txx:255)
6 libvtkITK.dylib 0x000000010d0a8b2e
itk::ImageSource<itk::Image<short, 3u>
::ThreaderCallback(void) +
206
(itkImageSource.txx:296)
7 libITKCommon.3.20.dylib 0x0000000110c94dd6
itk::MultiThreader::SingleMethodProxy(void) + 22
(itkMultiThreader.cxx:853)
8 libsystem_c.dylib x00007fff985f28bf
_pthread_start
+
335
9 libsystem_c.dylib 0x00007fff985f5b75
thread_start +
13

Thread 16:
0 libResampleScalarVectorDWIVolumeLib.dylib
0x000000013134450d
itk::ImageFunction<itk::Image<short, 3u>, double,
double>::IsInsideBuffer(itk::ContinuousIndex<double, 3u>
const&)
const

  • 93
    (itkImageFuction.h:160)
    1 libResampleScalarVectorDWIVolumeLib.dylib
    0x0000000131341d42
    itk::ResampleImageFilter<itk::Image<short, 3u>,
    itk::Image<short,
    3u>,
    double>::LiearThreadedGenerateData(itk::ImageRegion<3u>
    const&,
    int) +
    3378
    (itkOptResampleImageFilter.txx:725)
    2 libResampleScalarVectorDWIVolumeLib.dylib
    0x000000013133b399
    itk::ResampleImageFilter<itk::Image<short, 3u>,
    itk::Image<short,
    3u>,
    double>::ThreadedGenerateData(itk::ImageRegion<3u> const&,
    int)

  • 345
    (itkOptResampleImageFilter.txx:25)
    3 libvtkITK.dylib 0x000000010d0a8b2e
    itk::ImageSource<itk::Image<short, 3u>
    ::ThreaderCallback(void) +
    206
    (itkImageSource.txx:296)
    4 libITKCommon.3.20.dylib 0x0000000110c94dd6
    itk::MultiThreader::SingleMethodProxy(void    ) + 22
    (itkMultiThreader.cxx:853)
    5 libsystem_c.dylib 0x00007fff985f28bf
    _pthread_start

  • 335
    6 libsystem_c.dylib 0x00007fff985f5b75
    thread_start +
    13

Thread 17:
0 libResampleScalarVectorDWIVolumeLib.dylib
0x000000013134562b
itk::LinearInterpolateImageFunction<itk::Image<short, 3u>,

double>::EvaluateOptimized(itk::LinearInterpolateImageFunction<itk::I
ma
ge<short,
3u>, double>::Dispatch<3u> const&,
itk::ContinuousIndex<double,
3u>
const&)
const + 139 (itkOptLinearInterpolateImageFunction.h:231)
1 libResampleScalarVectorDWIVolumeLib.dylib
0x00000001313443e4
itk::LinearInterpolateImageFunction<itk::Image<short, 3u>,

double>::EvaluateAtContinuousIndex(itk::ContinuousIndex<double,
3u>
const&)
const + 36 (itkOptLinearInterpolateImageFunction.h:93)
2 libResampleScalarVectorDWIVolumeLib.dylib
0x0000000131341e25
itk::ResampleImageFilter<itk::Image<short, 3u>,
itk::Image<short,
3u>,
double>::LinearThreadedGenerateData(itk::ImageRegion<3u>
const&,
int) +
3605
(itkOptResampleImageFilter.txx:737)
3 libResampleScalarVectorDWIVolumeLib.dylib
0x000000013133b399
itk::ResampleImageFilter<itk::Image<short, 3u>,
itk::Image<short,
3u>,
double>::ThreadedGenerateData(itk::ImageRegion<3u> const&,
int)
+
345
(itkOptResampleImageFilter.txx:255)
4 libvtkITK.dylib 0x000000010d0a8b2e
itk::ImageSource<itk::Image<short, 3u>
::ThreaderCallback(void) +
206
(itkImageSource.txx:296)
5 libITKCommon.3.20.dylib 0x0000000110c94dd6
itk::MultiThreader::SingleMethodProxy(void) + 22
(itkMultiThreader.cxx:853)
6 libsystem_c.dylib 0x00007fff985f28bf
_pthread_start
+
335
7 libsystem_c.dylib 0x00007fff985f5b75
thread_start +
13

Thread 18 Crashed:
0 libunwind.dylib 0x00007fff9aa680ce
_Unwind_Resume
+
27
1 libvtkITK.dylib 0x000000010d0a8baa
itk::ImageSource<itk::Image<short, 3u>
::ThreaderCallback(void) +
330
2 libITKCommon.3.20.dylib 0x0000000110c94dd6
itk::MultiThreader::SingleMethodProxy(void) + 22
(itkMultiThreader.cxx:853)
3 libsystem_c.dylib 0x00007fff985f28bf
_pthread_start
+
335
4 libsystem_c.dylib 0x00007fff985f5b75
thread_start +
13

Thread 18 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000000000008 rcx:
0x0000000099651db0
rdx: 0x00007fb499651db0
rdi: 0x000000013d5939d8 rsi: 0x00007fff9aa680ce rbp:
0x000000013d593de0
rsp: 0x000000013d5939d0
r8: 0x000000013d5932e0 r9: 0x000000010e37b3d0 r10:
0x0000000000078000
r11: 0x0000000110cdd800
r12: 0x000000000001006b r13: 0x000000013d594000 r14:
0x00007fb4935ca7c0
r15: 0x0000000110c94dc0
rip: 0x00007fff9aa680ce rfl: 0x0000000000010246 cr2:
0x0000000000000018
Logical CPU: 7

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jcfr

jcfr

2012-11-19 12:22

administrator   ~0007325

Last edited: 2012-11-19 12:23

From Williams, Norman K:

The game plan is this:

  1. Get Slicer building ITK4 as part of its SuperBuild, using
    USE_SYSTEM_DCMTK
  2. Then take out the DCMTKImageIO stuff in the DWIConvert program, which
    is the program I worked on that refactors DicomToNrrdConvertor using DCMTK
    instead of GDCM. That program currently includes its own itkDCMTKImageIO
    source.
jcfr

jcfr

2013-02-12 06:38

administrator   ~0007892

See r21688 - http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=21688
jcfr

jcfr

2013-03-06 18:00

administrator   ~0008093

Slicer is now successfully build and packaged against ITKv4
jcfr

jcfr

2014-03-06 04:53

administrator   ~0010779

Closing resolved issues that have not been updated in more than 3 months

Issue History

Date Modified Username Field Change
2012-05-09 10:09 jcfr New Issue
2012-05-09 10:09 jcfr Status new => assigned
2012-05-09 10:09 jcfr Assigned To => jcfr
2012-05-09 10:09 jcfr Target Version => Slicer 4.3.0
2012-05-09 10:10 jcfr Summary Official build of Slicer build against ITKv4 => Build against ITKv4 and remove ITKv3
2012-05-23 15:14 jcfr Relationship added parent of 0002113
2012-05-23 15:17 jcfr Relationship added child of 0002107
2012-05-23 15:18 jcfr Relationship deleted child of 0002107
2012-05-23 15:18 jcfr Relationship added parent of 0002114
2012-05-23 15:25 jcfr Relationship added parent of 0001692
2012-05-23 15:25 jcfr Relationship added parent of 0001693
2012-05-23 15:28 jcfr Relationship added parent of 0002115
2012-05-23 15:33 jcfr Relationship added parent of 0002116
2012-05-27 02:38 kikinis Note Added: 0004633
2012-05-27 08:32 jcfr Target Version Slicer 4.3.0 => Slicer 4.2.0 - Sept 1st 2012
2012-05-27 08:33 jcfr Note Added: 0004636
2012-06-28 06:58 jcfr Note Added: 0004960
2012-08-14 09:20 pieper Note Added: 0005549
2012-08-20 10:06 jcfr Target Version Slicer 4.2.0 - Feature freeze Sept 1st 2012 => Slicer 4.2.5
2012-08-21 09:39 jcfr Target Version Slicer 4.2.5 => Slicer 4.3.0
2012-11-05 08:22 jcfr Relationship added parent of 0002729
2012-11-19 12:22 jcfr Note Added: 0007325
2012-11-19 12:23 jcfr Note Edited: 0007325
2012-11-30 09:35 jcfr Tag Attached: ITKv4
2012-11-30 09:39 jcfr Relationship added parent of 0002800
2012-11-30 09:42 jcfr Relationship added parent of 0002801
2012-11-30 09:44 jcfr Relationship added parent of 0002804
2012-11-30 09:47 jcfr Relationship added parent of 0002805
2012-11-30 09:50 jcfr Relationship added child of 0002806
2012-11-30 10:07 jcfr Relationship added parent of 0002807
2013-01-23 12:36 pieper Relationship added related to 0002879
2013-01-24 05:45 jcfr Relationship added parent of 0002883
2013-01-24 05:49 jcfr Relationship added parent of 0002884
2013-02-12 06:38 jcfr Note Added: 0007892
2013-02-13 13:38 jcfr Relationship replaced parent of 0002806
2013-03-06 17:59 jcfr Relationship replaced related to 0001692
2013-03-06 17:59 jcfr Relationship replaced related to 0001693
2013-03-06 18:00 jcfr Note Added: 0008093
2013-03-06 18:00 jcfr Status assigned => resolved
2013-03-06 18:00 jcfr Fixed in Version => Slicer 4.3.0
2013-03-06 18:00 jcfr Resolution open => fixed
2014-03-06 04:53 jcfr Note Added: 0010779
2014-03-06 04:54 jcfr Status resolved => closed