How are you opening the freeview GUI? Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lykke Silfwerbrand lykke.silfwerbrand@neuro.uu.se Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Thursday, February 14, 2019 at 1:47 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unexpected termination of freeviewer
External Email - Use Caution Hi, Yes, I am sure that I set the FREESURFER_HOME and sourced SetUpSurfer.sh I haven’t made any changes. Also, I can open the freeview GUI, it only crashes when I try to load something. I have no problem running recon all on the two machines either (two similar macbook pros, that get the same errors) Lykke
14 feb. 2019 kl. 19:27 skrev Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu>: Hi, you were able to use freeview before without it crashing – have you made any changes to the distribution since then? Are you sure that you’ve set FREESURFER_HOME and sourced the FS environment before calling freeview? Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Lykke Silfwerbrand <lykke.silfwerbrand@neuro.uu.semailto:lykke.silfwerbrand@neuro.uu.se> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, February 14, 2019 at 10:59 AM To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Unexpected termination of freeviewer
External Email - Use Caution Hi, I used freeviewer a few weeks ago without any problems, but now that I want to continue my analysis it terminates as a try to load a volume or a surface. (same computer, same setting) I have tried the “sudo -E fs_update” and to disable SIP, freeviewer still terminates the same way with the same error message, see below.
Any help is much appreciated! Lykke PhD candidate Neuro Science Uppsala University
Process: Freeview [1713] Path: /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview Identifier: com.yourcompany.Freeview Version: ??? Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: Freeview [1713] User ID: 271794372
Date/Time: 2019-02-14 16:48:18.395 +0100 OS Version: Mac OS X 10.14.3 (18D109) Report Version: 12 Bridge OS Version: 3.0 (14Y674) Anonymous UUID: A7073C18-5895-3A14-4551-409200FFED72
Time Awake Since Boot: 2500 seconds
System Integrity Protection: disabled
Crashed Thread: 9
Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000 Exception Note: EXC_CORPSE_NOTIFY
Termination Reason: DYLD, [0x4] Symbol missing
Dyld Error Message: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib
Thread 0:: Dispatch queue: com.apple.main-thread 0 libobjc.A.dylib 0x00007fff6605e681 search_method_list(method_list_t const*, objc_selector*) + 78 1 libobjc.A.dylib 0x00007fff6605e614 getMethodNoSuper_nolock(objc_class*, objc_selector*) + 98 2 libobjc.A.dylib 0x00007fff66060a73 lookUpImpOrForward + 328 3 libobjc.A.dylib 0x00007fff66060494 _objc_msgSend_uncached + 68 4 com.apple.AppKit 0x00007fff3747e426 -[NSView(NSInternal) _allocAuxiliary] + 227 5 com.apple.AppKit 0x00007fff374b241c -[NSView initWithFrame:] + 36 6 com.apple.AppKit 0x00007fff374bd14f -[NSNextStepFrame initWithFrame:styleMask:owner:] + 74 7 com.apple.AppKit 0x00007fff374bb709 -[NSWindow _commonInitFrame:styleMask:backing:defer:] + 610 8 com.apple.AppKit 0x00007fff374baf5e -[NSWindow _initContent:styleMask:backing:defer:contentView:] + 1202 9 com.apple.AppKit 0x00007fff374baaa6 -[NSWindow initWithContentRect:styleMask:backing:defer:] + 45 10 QtGui 0x0000000120ba003f QMacInputContext::reset() + 30319 11 QtGui 0x0000000120b9fedc QMacInputContext::reset() + 29964 12 QtGui 0x0000000120b9289a QWidgetPrivate::setWindowLevel() + 810 13 QtGui 0x0000000120b8ffb1 QWidgetPrivate::createWindow_sys() + 145 14 QtGui 0x0000000120b900bf qt_mac_window_for(QWidget const*) + 159 15 QtGui 0x0000000120b923b1 QWidgetPrivate::setModal_sys() + 145 16 QtGui 0x0000000120c4b698 QWidget::create(long, bool, bool) + 360 17 QtGui 0x0000000120c4c909 QWidget::setVisible(bool) + 121 18 com.yourcompany.Freeview 0x000000010fe7241c FloatingStatusBar::ShowProgress() + 60 19 com.yourcompany.Freeview 0x000000010fe26aab FloatingStatusBar::qt_metacall(QMetaObject::Call, int, void**) + 251 20 QtCore 0x00000001208ede99 QObject::event(QEvent*) + 1081 21 QtGui 0x0000000120c4d83e QWidget::event(QEvent*) + 78 22 QtGui 0x0000000120bf315d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 189 23 QtGui 0x0000000120bf918d QApplication::notify(QObject*, QEvent*) + 349 24 QtCore 0x00000001207f34dc QCoreApplication::notifyInternal(QObject*, QEvent*) + 124 25 QtCore 0x00000001208e10cb QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 731 26 com.apple.CoreFoundation 0x00007fff39f08395 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 27 com.apple.CoreFoundation 0x00007fff39f0833b __CFRunLoopDoSource0 + 108 28 com.apple.CoreFoundation 0x00007fff39eebdd1 __CFRunLoopDoSources0 + 195 29 com.apple.CoreFoundation 0x00007fff39eeb37a __CFRunLoopRun + 1219 30 com.apple.CoreFoundation 0x00007fff39eeac64 CFRunLoopRunSpecific + 463 31 com.apple.HIToolbox 0x00007fff39181ab5 RunCurrentEventLoopInMode + 293 32 com.apple.HIToolbox 0x00007fff391817eb ReceiveNextEventCommon + 618 33 com.apple.HIToolbox 0x00007fff39181568 _BlockUntilNextEventMatchingListInModeWithFilter + 64 34 com.apple.AppKit 0x00007fff3743c363 _DPSNextEvent + 997 35 com.apple.AppKit 0x00007fff3743b102 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1362 36 com.apple.AppKit 0x00007fff37435165 -[NSApplication run] + 699 37 QtGui 0x0000000120bae174 QDesktopWidget::resizeEvent(QResizeEvent*) + 12724 38 QtCore 0x00000001208dfa34 QEventLoop::processEvents(QFlagsQEventLoop::ProcessEventsFlag) + 68 39 QtCore 0x00000001208dfd54 QEventLoop::exec(QFlagsQEventLoop::ProcessEventsFlag) + 180 40 QtCore 0x00000001208e137c QCoreApplication::exec() + 188 41 com.yourcompany.Freeview 0x000000010ff03f58 main + 6232 42 com.yourcompany.Freeview 0x000000010fe24974 start + 52
Thread 1: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796
Thread 2: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796
Thread 3: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796
Thread 4: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796
Thread 5:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x00007fff6727617a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff672766d0 mach_msg + 60 2 com.apple.CoreFoundation 0x00007fff39eebfde __CFRunLoopServiceMachPort + 337 3 com.apple.CoreFoundation 0x00007fff39eeb52d __CFRunLoopRun + 1654 4 com.apple.CoreFoundation 0x00007fff39eeac64 CFRunLoopRunSpecific + 463 5 com.apple.AppKit 0x00007fff37444f89 _NSEventThread + 160 6 libsystem_pthread.dylib 0x00007fff67330305 _pthread_body + 126 7 libsystem_pthread.dylib 0x00007fff6733326f _pthread_start + 70 8 libsystem_pthread.dylib 0x00007fff6732f415 thread_start + 13
Thread 6: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796
Thread 7: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796
Thread 8:: CVDisplayLink 0 libsystem_kernel.dylib 0x00007fff672797de __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff67333593 _pthread_cond_wait + 724 2 com.apple.CoreVideo 0x00007fff3bd2be90 CVDisplayLink::runIOThread() + 722 3 libsystem_pthread.dylib 0x00007fff67330305 _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff6733326f _pthread_start + 70 5 libsystem_pthread.dylib 0x00007fff6732f415 thread_start + 13
Thread 9 Crashed: 0 dyld 0x0000000128c4e456 __abort_with_payload + 10 1 dyld 0x0000000128c4dc4d abort_with_payload_wrapper_internal + 82 2 dyld 0x0000000128c4dc7f abort_with_payload + 9 3 dyld 0x0000000128c0baea dyld::halt(char const*) + 343 4 dyld 0x0000000128c0bc17 dyld::fastBindLazySymbol(ImageLoader**, unsigned long) + 170 5 libdyld.dylib 0x00007fff67128c1a dyld_stub_binder + 282 6 ??? 0x00000001204dd018 0 + 4836937752 7 com.yourcompany.Freeview 0x000000010fead0df LayerMRI::LoadVolumeFromFile() + 399 8 com.yourcompany.Freeview 0x000000010ff79ea1 ThreadIOWorker::run() + 1361 9 QtCore 0x00000001208275b5 QThread::setPriority(QThread::Priority) + 469 10 libsystem_pthread.dylib 0x00007fff67330305 _pthread_body + 126 11 libsystem_pthread.dylib 0x00007fff6733326f _pthread_start + 70 12 libsystem_pthread.dylib 0x00007fff6732f415 thread_start + 13
Thread 9 crashed with X86 Thread State (64-bit): rax: 0x0000000002000209 rbx: 0x0000000000000000 rcx: 0x000070000787ea48 rdx: 0x000070000787eeb0 rdi: 0x0000000000000006 rsi: 0x0000000000000004 rbp: 0x000070000787ea90 rsp: 0x000070000787ea48 r8: 0x000070000787eab0 r9: 0x0000000000000000 r10: 0x0000000000000098 r11: 0x0000000000000246 r12: 0x0000000000000098 r13: 0x000070000787eeb0 r14: 0x0000000000000004 r15: 0x0000000000000006 rip: 0x0000000128c4e456 rfl: 0x0000000000000246 cr2: 0x000000012519c000
Logical CPU: 0 Error Code: 0x02000209 Trap Number: 133
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