I wasn't able to reproduce this on a current build (r24903) so I suspect it was the same issue as $4139, which was recently resolved.

Happens for me on r24901 (latest nightly build on the web site right now). Think this was fixed last night? Is there a way to pull down r24903 to try on my machine without waiting until tomorrow?

The issue isn't in the 4.5.0-1 release. Other than waiting until tomorrow you would need to build from source. It was just fixed 16 hours ago.

Sorry to report that r24903 doesn't resolve this bug. I just pulled it down and tried again:

• loaded an nnrd volume file and h5 transform matrix
• used Resample Scalar/Vector/DWI Volume module to apply the transform (which worked just file)
• hit File>Close Scene
• crash (console output below)

I should say, this doesn't seem to be restricted to the Resample plugin -- it happens periodically with lots of the modules. In fact if I just do:

• load volume
• median filter
• close scene

It crashes as well. I don't think this is actually new -- it's been happening for a while with the stable release (for me), but I just got in the habit of frequent saves.. But it's a pain because the startup time is so long (at least under linux).

-------------------- console output --------------------------

2016-01-29 09:46:38
Slicer version ...........: 4.5.0-2016-01-28 (revision 24903) linux-amd64 - installed
Operating system .........: Linux / 3.11-2-amd64 / 0000001 SMP Debian 3.11.8-1 (2013-11-13) - 64-bit
Memory ...................: 7940 MB physical, 7999 MB virtual
CPU ......................: GenuineIntel 2.826 MHz, 1 cores
Developer mode enabled ...: yes
Prefer executable CLI ....: no
Additional module paths ..: (none)
Number of registered modules: 141
Number of instantiated modules: 141
When loading module "CLIEventTest" , the dependency "CLI4Test" failed to be loaded.
Initializing terminology mapping for map file /auto/share/MRI-tools/Slicer-4.5.0-2016-01-28-linux-amd64/share/Slicer-4.5/ColorFiles/Terminology//GenericAnatomyColors-SNOMED.csv
288 terms were read for Slicer LUT GenericAnatomyColors
GetSliceIntersectionsVisibility: no scene

When loading module "TwoCLIsInARowTest" , the dependency "CLI4Test" failed to be loaded.
When loading module "TwoCLIsInParallelTest" , the dependency "CLI4Test" failed to be loaded.
Number of loaded modules: 138
Switch to module: "Welcome"
Loaded volume from file: /auto/home/mazer/MRI/bert/bert-unbias.nrrd. Dimensions: 256x256x176. Number of components: 1. Pixel type: float.

"Volume" Reader has successfully read the file "/auto/home/mazer/MRI/bert/bert-unbias.nrrd"
CreateVTKTransformFromITK - SetVTKLinearTransformFromITK conversionSuccess:1
CreateVTKTransformFromITK - SetVTKLinearTransformFromITK conversionSuccess:1
"Transform" Reader has successfully read the file "/auto/home/mazer/MRI/bert/tostax.h5"
Switch to module: "Transforms"
Switch to module: "BRAINSResample"
Switch to module: "ResampleScalarVectorDWIVolume"
Found SharedObject Module
ModuleType: SharedObjectModule
Resample Scalar/Vector/DWI Volume command line:

slicer:0x7fcaec1d34e0 --processinformationaddress 0x8680010 --transformationFile /tmp/Slicer/BFACE_vtkMRMLLinearTransformNodeE.mat --hfieldtype h-Field --interpolation linear --transform_order output-to-input --image_center input --spacing 0,0,0 --size 0,0,0 --direction_matrix 0,0,0,0,0,0,0,0,0 --number_of_thread 0 --default_pixel_value 0 --window_function c --spline_order 3 --transform_matrix 1,0,0,0,1,0,0,0,1,0,0,0 --transform a slicer:0x1bb8220#vtkMRMLScalarVolumeNode1 slicer:0x1bb8220#vtkMRMLScalarVolumeNode2

error: [/auto/share/MRI-tools/Slicer-4.5.0-2016-01-28-linux-amd64/./bin/SlicerApp-real] exit abnormally - Report the problem.

Okay, I was able to reproduce this with the current nightly build and got the stack trace below. It's something in the qMRMLSceneModel.

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libModuleDescriptionParser.dylib 0x0000000104c96e02 ModuleDescription::GetParameterDefaultValue(std::string const&) const + 66
1 libMRMLCLI.dylib 0x0000000104c7b7e3 vtkMRMLCommandLineModuleNode::SetParameterAsString(char const, std::string const&) + 67
2 libqSlicerBaseQTCLI.dylib 0x000000010028bf8c qSlicerCLIModuleUIHelper::setCommandLineModuleParameter(vtkMRMLCommandLineModuleNode, QString const&, QVariant const&) + 1356
3 QtCore 0x000000010aa952ae QMetaObject::activate(QObject, QMetaObject const, int, void) + 2030
4 libqSlicerBaseQTCLI.dylib 0x0000000100294679 qSlicerCLIModuleUIHelper::valueChanged(QString const&, QVariant const&) + 57
5 libqSlicerBaseQTCLI.dylib 0x000000010028ca47 qSlicerCLIModuleUIHelper::onValueChanged() + 183
6 libqSlicerBaseQTCLI.dylib 0x00000001002945f4 qSlicerCLIModuleUIHelper::qt_static_metacall(QObject*, QMetaObject::Call, int, void) + 36
7 QtCore 0x000000010aa952ae QMetaObject::activate(QObject, QMetaObject const, int, void) + 2030
8 QtCore 0x000000010aa952ae QMetaObject::activate(QObject, QMetaObject const, int, void*) + 2030
9 libqMRMLWidgets.dylib 0x000000010064b9a8 qMRMLNodeComboBox::currentNodeIDChanged(QString const&) + 56
10 libqMRMLWidgets.dylib 0x00000001005e473c qMRMLNodeComboBox::emitCurrentNodeChanged() + 172
11 libqMRMLWidgets.dylib 0x000000010064b6c5 qMRMLNodeComboBox::qt_static_metacall(QObject, QMetaObject::Call, int, void) + 837
12 QtCore 0x000000010aa952ae QMetaObject::activate(QObject, QMetaObject const, int, void) + 2030
13 QtGui 0x000000010a0097b8 QComboBoxPrivate::_q_emitCurrentIndexChanged(QModelIndex const&) + 136
14 QtGui 0x000000010a00e558 QComboBoxPrivate::setCurrentIndex(QModelIndex const&) + 744
15 QtGui 0x000000010a00d09e QComboBox::setCurrentIndex(int) + 94
16 libqMRMLWidgets.dylib 0x00000001005e50e4 qMRMLNodeComboBox::setCurrentNodeID(QString const&) + 1044
17 libqMRMLWidgets.dylib 0x00000001005e3eb3 qMRMLNodeComboBox::setCurrentNode(vtkMRMLNode) + 67
18 libqMRMLWidgets.dylib 0x00000001005e477c qMRMLNodeComboBox::emitCurrentNodeChanged() + 236
19 libqMRMLWidgets.dylib 0x000000010064b6c5 qMRMLNodeComboBox::qt_static_metacall(QObject, QMetaObject::Call, int, void) + 837
20 QtCore 0x000000010aa952ae QMetaObject::activate(QObject, QMetaObject const, int, void) + 2030
21 QtGui 0x000000010a0097b8 QComboBoxPrivate::_q_emitCurrentIndexChanged(QModelIndex const&) + 136
22 QtGui 0x000000010a00e558 QComboBoxPrivate::setCurrentIndex(QModelIndex const&) + 744
23 QtGui 0x000000010a00d276 QComboBoxPrivate::_q_rowsRemoved(QModelIndex const&, int, int) + 374
24 QtGui 0x000000010a012d3b QComboBox::qt_static_metacall(QObject*, QMetaObject::Call, int, void) + 827
25 QtCore 0x000000010aa952ae QMetaObject::activate(QObject, QMetaObject const, int, void) + 2030
26 QtCore 0x000000010aadd02f QAbstractItemModel::rowsRemoved(QModelIndex const&, int, int) + 63
27 QtCore 0x000000010aa76164 QAbstractItemModel::endRemoveRows() + 84
28 QtGui 0x000000010a1bcd35 QSortFilterProxyModelPrivate::remove_proxy_interval(QVector<int>&, QVector<int>&, int, int, QModelIndex const&, Qt::Orientation, bool) + 261
29 QtGui 0x000000010a1bcb82 QSortFilterProxyModelPrivate::remove_source_items(QVector<int>&, QVector<int>&, QVector<int> const&, QModelIndex const&, Qt::Orientation, bool) + 338
30 QtGui 0x000000010a1be863 QSortFilterProxyModelPrivate::source_items_about_to_be_removed(QModelIndex const&, int, int, Qt::Orientation) + 451
31 QtGui 0x000000010a1c34f3 QSortFilterProxyModel::qt_static_metacall(QObject*, QMetaObject::Call, int, void) + 771
32 QtCore 0x000000010aa952ae QMetaObject::activate(QObject, QMetaObject const, int, void) + 2030
33 QtCore 0x000000010aadcfdf QAbstractItemModel::rowsAboutToBeRemoved(QModelIndex const&, int, int) + 63
34 QtCore 0x000000010aa760e9 QAbstractItemModel::beginRemoveRows(QModelIndex const&, int, int) + 105
35 QtGui 0x000000010a1cc431 QStandardItem::removeRows(int, int) + 177
36 libqMRMLWidgets.dylib 0x00000001005f7b57 qMRMLSceneModel::updateScene() + 2055
37 libvtkCommon-6.3.1.dylib 0x000000010d5148a1 vtkCallbackCommand::Execute(vtkObject, unsigned long, void) + 33
38 libvtkCommon-6.3.1.dylib 0x000000010d61019e vtkSubjectHelper::InvokeEvent(unsigned long, void, vtkObject) + 1134
39 libMRMLCore.dylib 0x0000000104de5c21 vtkMRMLScene::EndState(unsigned long) + 625
40 libqSlicerApp.dylib 0x000000010008ec08 qSlicerAppMainWindow::qt_metacall(QMetaObject::Call, int, void) + 56
41 QtCore 0x000000010aa954d3 QMetaObject::activate(QObject, QMetaObject const, int, void**) + 2579
42 QtGui 0x0000000109ca6887 QAction::activate(QAction::ActionEvent) + 151
43 QtGui 0x0000000109c5c1f4 -[QCocoaMenuLoader qtDispatcherToQAction:] + 68
44 libsystem_trace.dylib 0x00007fff8843a07a _os_activity_initiate + 75
45 com.apple.AppKit 0x00007fff923a351d -[NSApplication sendAction:to:from:] + 460
46 com.apple.AppKit 0x00007fff923a32b7 -[NSMenuItem _corePerformAction] + 336
47 com.apple.AppKit 0x00007fff923a3017 -[NSCarbonMenuImpl performActionWithHighlightingForItemAtIndex:] + 114
48 libsystem_trace.dylib 0x00007fff8843a07a _os_activity_initiate + 75
49 com.apple.AppKit 0x00007fff923a1f05 -[NSMenu performKeyEquivalent:] + 357
50 com.apple.AppKit 0x00007fff923a10aa -[NSApplication _handleKeyEquivalent:] + 920
51 com.apple.AppKit 0x00007fff922b950f -[NSApplication sendEvent:] + 4274
52 QtGui 0x0000000109c5c662 -[QNSApplication sendEvent:] + 82
53 com.apple.AppKit 0x00007fff921ec03a -[NSApplication run] + 796
54 QtGui 0x0000000109c651a2 QEventDispatcherMac::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 994
55 QtCore 0x000000010aa7c157 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 487
56 QtCore 0x000000010aa7f1de QCoreApplication::exec() + 206
57 0x0000000100037646 main + 7158
58 0x0000000100035a44 start + 52

The following script does NOT reproduce the crash on its own, but the following steps will:

• start slicer
• paste the script
• select the volumes as input and output
• apply
• close scene -> crash

slicer.util.selectModule('MedianImageFilter')

slicer.util.delayDisplay('Enter filter')

import SampleData
from SampleData import SampleDataLogic
sampleDatalogic = SampleDataLogic()

fixed = sampleDatalogic.downloadMRBrainTumor1()

outputVolume = slicer.vtkMRMLScalarVolumeNode()
slicer.mrmlScene.AddNode(outputVolume)

parameters = {
'fixedVolume' : fixed,
'outputVolume' : outputVolume,
}
cmdLineNode = slicer.cli.runSync(slicer.modules.medianimagefilter, parameters=parameters)

I have not been able to reproduce this with a debug build.

But I confirmed the crash still occurs with the current nightly build on mac using the following steps:

• download MRHead
• enter median filter module
• select head as input, create new output
• run the module (all fine to this point)
• close the scene -> Crash

The stack trace is identical in both 4.5.0-1 and the nightly (the one posted in note 13800 above)

I was able to reproduce this with the latest windows nightly (on a windows 7 machine). The stack trace looks like it is the same issue. I don't have an up to date windows debug build but I've pinged Andras to see if he can replicate the issue.

ModuleDescriptionParser.dll!000007feba968c51() Unknown
MRMLCLI.dll!000007fef5042bcd() Unknown
MRMLCLI.dll!000007fef50459de() Unknown
qSlicerBaseQTCLI.dll!000007fee154100e() Unknown
qSlicerBaseQTCLI.dll!000007fee1543313() Unknown
QTCORE4.dll!00000000550fc871() Unknown
qSlicerBaseQTCLI.dll!000007fee154689b() Unknown
qSlicerBaseQTCLI.dll!000007fee1540bf6() Unknown
QTCORE4.dll!00000000550fc871() Unknown
QTCORE4.dll!00000000550fc871() Unknown
qMRMLWidgets.dll!000007feb8d610da() Unknown
qMRMLWidgets.dll!000007feb8d156b3() Unknown
qMRMLWidgets.dll!000007feb8d60e6f() Unknown
QTCORE4.dll!00000000550fc871() Unknown
QTGUI4.dll!00000000646cd10c() Unknown
QTGUI4.dll!00000000646d37c5() Unknown
QTGUI4.dll!00000000646d35f2() Unknown
qMRMLWidgets.dll!000007feb8d1706c() Unknown
qMRMLWidgets.dll!000007feb8d16f6a() Unknown
qMRMLWidgets.dll!000007feb8d15660() Unknown
qMRMLWidgets.dll!000007feb8d60e6f() Unknown
QTCORE4.dll!00000000550fc871() Unknown
QTGUI4.dll!00000000646cd10c() Unknown
QTGUI4.dll!00000000646d37c5() Unknown
QTGUI4.dll!00000000646d35f2() Unknown
QTGUI4.dll!00000000646cd91b() Unknown
QTCORE4.dll!00000000550fc871() Unknown
QTCORE4.dll!00000000551415f0() Unknown
QTCORE4.dll!00000000550e5a8b() Unknown
QTGUI4.dll!00000000648582a2() Unknown
QTGUI4.dll!00000000648591d7() Unknown
QTGUI4.dll!00000000648534d2() Unknown
QTCORE4.dll!00000000550fc871() Unknown
QTCORE4.dll!0000000055141490() Unknown
QTCORE4.dll!00000000550e241d() Unknown
QTGUI4.dll!00000000648618a8() Unknown
QTGUI4.dll!00000000648614d6() Unknown
qMRMLWidgets.dll!000007feb8d2827b() Unknown
vtkCommon-6.3.dll!000007febd3cd804() Unknown
vtkCommon-6.3.dll!000007febd47ddab() Unknown
MRMLCore.dll!000007febeceffa0() Unknown
qSlicerApp.dll!000007fee17b51f1() Unknown
QTCORE4.dll!00000000550fc965() Unknown
QTGUI4.dll!000000006437a2b0() Unknown
QTGUI4.dll!000000006437be6a() Unknown
QTGUI4.dll!0000000064392f26() Unknown
QTGUI4.dll!0000000064392bc0() Unknown
qSlicerBaseQTGUI.dll!000007febef676ae() Unknown
QTCORE4.dll!00000000550ede1c() Unknown
QTGUI4.dll!00000000643bfb03() Unknown
QTGUI4.dll!00000000643c0fd8() Unknown
QTGUI4.dll!0000000064391797() Unknown
qSlicerBaseQTGUI.dll!000007febef676ae() Unknown
QTCORE4.dll!00000000550ede1c() Unknown
QTGUI4.dll!000000006440ce05() Unknown
QTGUI4.dll!000000006440de58() Unknown
QTGUI4.dll!00000000643f9c3f() Unknown
[External Code]
QTCORE4.dll!0000000055112c13() Unknown
QTGUI4.dll!00000000643f2205() Unknown
QTCORE4.dll!00000000550ead9c() Unknown
QTCORE4.dll!00000000550ed360() Unknown
SlicerApp-real.exe!000000013fce2177() Unknown
SlicerApp-real.exe!000000013fce2d8e() Unknown
SlicerApp-real.exe!000000013fce3715() Unknown
[External Code]

Committed a change that will probably fix the issue in rev 24930

Tested on windows with the nightly build 2016-02-17 and no crash.

Thanks Andras!

Just tested on 2016-02-23 (linux mint lmde) -- median filt/close -- and no crash as well. Thanks!

Thanks for testing!