Advice? Re: Freeview 7.1.1 won't start on Mac: segmentation fault - Freesurfer

1 Mar 2022


      External Email - Use Caution
Dear Freesurfer experts,
I am writing to request technical assistance with freeview. I use freesurfer and freeview in my current research, where they are very valuable tools. However, upon upgrading my macbook's OS to macOS Monterey, Version 12.2.1, I now am unable to open freeview; it quits immediately upon starting. The error message indicates a segmentation fault, and in fact my error (and the error message) appears to be exactly the same as the one encountered by Alex White in this thread: https://secure-web.cisco.com/1IXdnFyTKmN2mh6oaF1iVQ3_Ho1Z9szlPmaAOZrSIy7EZwF...
I have been in correspondence with Alex, and he mentioned that you were able to help him resolve the issue, but that it required you to send him a patched version of freeview (or freesurfer?). I have the identical problem on freeview 7.1.1 and 7.2.0, but if possible I would prefer to continue working with your latest version, 7.2.0.
Please do let me know if further information could help you understand this issue better. For the time being, I have copied the error message that prints to terminal and the full error report, both below.
Any help/advice is much appreciated.
Sincerely,
Sam Johnson
Postdoctoral Scholar
Yeatman Brain and Education Lab, Stanford University GSE
-----
# terminal error message:
(base) samjohns@DNab40bbcb 7.2.0 % freeview
/Applications/freesurfer/7.2.0/bin/freeview: line 2:  1968 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
# full crash report
-------------------------------------
Translated Report (Full Report Below)
-------------------------------------
Process:               freeview [1673]
Path:                  /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview
Identifier:            com.freesurfer.freeview
Version:               ???
Code Type:             X86-64 (Translated)
Parent Process:        Exited process [1672]
Responsible:           Terminal [1587]
User ID:               502
Date/Time:             2022-03-01 15:12:51.8713 -0800
OS Version:            macOS 12.2.1 (21D62)
Report Version:        12
Anonymous UUID:        DCA45306-7159-2569-6BDE-CF94BEE1E522
Time Awake Since Boot: 1200 seconds
System Integrity Protection: enabled
Crashed Thread:        0  Dispatch queue: com.apple.main-thread
Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x0000545845545f67
Exception Codes:       0x0000000000000001, 0x0000545845545f67
Exception Note:        EXC_CORPSE_NOTIFY
Termination Reason:    Namespace SIGNAL, Code 11 Segmentation fault: 11
Terminating Process:   exc handler [1673]
VM Region Info: 0x545845545f67 is not in any region.  Bytes after previous region: 92257060675432  Bytes before following region: 12815019253913
      REGION TYPE                    START - END         [ VSIZE] PRT/MAX SHRMOD  REGION DETAIL
      commpage (reserved)        1000000000-7000000000   [384.0G] ---/--- SM=NUL  ...(unallocated)
--->  GAP OF 0x5f9000000000 BYTES
      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-/rwx SM=PRV
Thread 0 Crashed::  Dispatch 0   freeview 1   QtWidgets 2   QtWidgets 3   QtWidgets 4   QtWidgets 5   QtCore 6   QtWidgets 7   QtWidgets 8   QtWidgets 9   QtCore 10  QtGui 11  QtGui 12  QtGui 13  libqcocoa.dylib 14  libqcocoa.dylib 15  libqcocoa.dylib 16  QtGui 17  QtWidgets 18  QtWidgets 19  QtWidgets 20  freeview 21  freeview 22  freeview 23  dyld

queue: com.apple.main-thread 0x104ec0ff8 0x104ce2000 + 1961976 0x12046c6ed QWidget::event(QEvent*) + 1117 0x12057dc45 QMainWindow::event(QEvent*) + 277 0x12043070d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 0x120431b12 QApplication::notify(QObject*, QEvent*) + 594 0x12266e564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 0x12048aa74 0x120420000 + 436852 0x12043070d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 0x120431b12 QApplication::notify(QObject*, QEvent*) + 594 0x12266e564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 0x1211e2a74 QGuiApplicationPrivate::processGeometryChangeEvent(QWindowSystemInterfacePrivate::GeometryChangeEvent*) + 516 0x1211e3420 QGuiApplicationPrivate::processWindowScreenChangedEvent(QWindowSystemInterfacePrivate::WindowScreenChangedEvent*) + 736 0x1211c1c33 bool QWindowSystemInterfacePrivate::handleWindowSystemEventQWindowSystemInterface::SynchronousDelivery(QWindowSystemInterfacePrivate::WindowSystemEvent*) + 115 0x121eb4c77 0x121e96000 + 126071 0x121eae862 0x121e96000 + 100450 0x121eae2eb 0x121e96000 + 99051 0x1211ec1dc QWindowPrivate::create(bool, unsigned long long) + 140 0x120459e31 QWidgetPrivate::create() + 1201 0x120458b22 QWidget::create(unsigned long long, bool, bool) + 322 0x12057e4d7 QMainWindow::setUnifiedTitleAndToolBarOnMac(bool) + 55 0x104eaf497 0x104ce2000 + 1889431 0x104ea950e 0x104ce2000 + 1864974 0x104de279a 0x104ce2000 + 1050522 0x2158184fe start + 462
Thread 1:: com.apple.rosetta.exceptionserver
0   runtime                       	    0x7ff7ffc578e4 0x7ff7ffc53000 + 18660
1   runtime                       	    0x7ff7ffc64928 0x7ff7ffc53000 + 71976
2   runtime                       	    0x7ff7ffc660a4 0x7ff7ffc53000 + 77988
Thread 2:
0   runtime                       	    0x7ff7ffc75814 0x7ff7ffc53000 + 141332
Thread 3:
0   runtime                       	    0x7ff7ffc75814 0x7ff7ffc53000 + 141332
Thread 4::  Dispatch queue: com.apple.dock.fullscreen
0   dyld                          	       0x215824e0c dyld4::Loader::LoaderRef::loader(dyld4::RuntimeState const&) const + 68
1   dyld                          	       0x21582cdb1 dyld4::PrebuiltLoader::dependent(dyld4::RuntimeState const&, unsigned int, dyld4::Loader::DependentKind*) const + 95
2   dyld                          	       0x215828a1e dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 532
3   dyld                          	       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593
4   dyld                          	       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593
5   dyld                          	       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593
6   dyld                          	       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593
7   dyld                          	       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593
8   dyld                          	       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593
9   dyld                          	       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593
10  dyld                          	       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593
11  dyld                          	       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593
12  dyld                          	       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593
13  dyld                          	       0x215837b4c dyld4::APIs::dlsym(void*, char const*) + 656
14  SkyLight                      	    0x7ff811fbf581 __loginframework_vtable_block_invoke + 605
15  libdispatch.dylib             	    0x7ff80ccd8cc9 _dispatch_client_callout + 8
16  libdispatch.dylib             	    0x7ff80ccd9ec1 _dispatch_once_callout + 20
17  SkyLight                      	    0x7ff811fc0de5 SLSCopyCurrentSessionPropertiesInternalBridge + 366
18  SkyLight                      	    0x7ff811e6a097 SLSessionCopyCurrentDictionary + 12
19  AppKit                        	    0x7ff80f9e04ee -[NSDockConnection _makeConnectionIfNeededWithRetryInterval:onDemand:] + 47
20  AppKit                        	    0x7ff8101b9720 __35-[NSDockConnection startConnection]_block_invoke.37 + 45
21  libdispatch.dylib             	    0x7ff80ccd7ad8 _dispatch_call_block_and_release + 12
22  libdispatch.dylib             	    0x7ff80ccd8cc9 _dispatch_client_callout + 8
23  libdispatch.dylib             	    0x7ff80ccdecee _dispatch_lane_serial_drain + 696
24  libdispatch.dylib             	    0x7ff80ccdf7c8 _dispatch_lane_invoke + 366
25  libdispatch.dylib             	    0x7ff80cce97e1 _dispatch_workloop_worker_thread + 758
26  libsystem_pthread.dylib       	    0x7ff80ce8f074 _pthread_wqthread + 326
27  libsystem_pthread.dylib       	    0x7ff80ce8dffb start_wqthread + 15
Thread 5:
0   runtime                       	    0x7ff7ffc75814 0x7ff7ffc53000 + 141332
Thread 6:
0   runtime                       	    0x7ff7ffc75814 0x7ff7ffc53000 + 141332
Thread 7:
0   runtime                       	    0x7ff7ffc75814 0x7ff7ffc53000 + 141332
Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000545845545f5f  rbx: 0x000000031e5aac00  rcx: 0x0000000000010000  rdx: 0x000000012046c6dd
  rdi: 0x00007ff815d4f000  rsi: 0x000000031e5a9c78  rbp: 0x000000031e5a9730  rsp: 0x000000031e5a9720
   r8: 0x0000000000000000   r9: 0x0000000000000000  r10: 0x00000001220129e0  r11: 0x00007ff80f8c8bb9
  r12: 0x00007ff175745090  r13: 0x000000031e5aac00  r14: 0x000000031e5a9c78  r15: 0x000000031e5a9c78
  rip: 0x0000000104ec0ff8  rfl: 0x0000000000000203
 tmp0: 0x0000000115a9c01c tmp1: 0x000000012046c6ed tmp2: 0x0000000120a3c1e8
Binary Images:
       0x104ce2000 -        0x106349fff com.freesurfer.freeview (*) <35cc1656-e7ff-32a5-8ec9-9faf896f9915> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview
       0x120420000 -        0x12085efff org.qt-project.QtWidgets (5.12) <ef671b84-7965-3c74-89df-09c3fa9096ca> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtWidgets.framework/Versions/5/QtWidgets
       0x122484000 -        0x1229b9fff org.qt-project.QtCore (5.12) <ae294ca9-b3ec-3f0e-b67a-509a13c0c913> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/5/QtCore
       0x1211ac000 -        0x1215f8fff org.qt-project.QtGui (5.12) <9cc34b01-ae4a-3ff2-ac1b-de08b8fbbbae> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtGui.framework/Versions/5/QtGui
       0x121e96000 -        0x121ffcfff libqcocoa.dylib (*) <14bc2336-68e6-3ace-b3a9-f21152a64785> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/platforms/libqcocoa.dylib
       0x215813000 -        0x21587efff dyld (*) <7de33963-bbc5-3996-ba6e-f1d562c17c95> /usr/lib/dyld
    0x7ff7ffc53000 -     0x7ff7ffc82fff runtime (*) <faca02c7-0a4c-3629-a746-55ddcfee9116> /usr/libexec/rosetta/runtime
    0x7ff811d55000 -     0x7ff8120eafff com.apple.SkyLight (1.600.0) <eab4373e-52ca-38d7-963a-9f5bd71824e9> /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight
    0x7ff80ccd6000 -     0x7ff80cd1cfff libdispatch.dylib (*) <67d92c93-aa68-34c2-964b-23e8a8d32098> /usr/lib/system/libdispatch.dylib
    0x7ff80f86e000 -     0x7ff8106fffff com.apple.AppKit (6.9) <9d3ab204-4858-3120-b002-5c38b02edec4> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
    0x7ff80ce8c000 -     0x7ff80ce97fff libsystem_pthread.dylib (*) <ee564342-d8f2-396d-b642-40092cf34d82> /usr/lib/system/libsystem_pthread.dylib
               0x0 - 0xffffffffffffffff ??? (*) <00000000-0000-0000-0000-000000000000> ???
External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by all processes on this machine:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=964.1M resident=0K(0%) swapped_out_or_unallocated=964.1M(100%)
Writable regions: Total=1.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.2G(100%)
VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Accelerate framework               256K        2 
Activity Tracing                   256K        1 
CG backing stores                 5056K        8 
ColorSync                          228K       25 
CoreGraphics                         8K        2 
CoreUI image data                  152K        1 
Foundation                          16K        1 
Kernel Alloc Once                    8K        1 
MALLOC                           216.2M       34 
MALLOC guard page                  192K        9 
MALLOC_MEDIUM (reserved)         240.0M        2         reserved VM address space (unallocated)
MALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)
Rosetta Arena                     4096K        2 
Rosetta Generic                    736K      181 
Rosetta IndirectBranch             512K        1 
Rosetta JIT                      128.0M        1 
Rosetta Return Stack               100K       10 
Rosetta Thread Context             100K       10 
STACK GUARD                         20K        5 
Stack                             11.1M        7 
Stack Guard                       56.0M        2 
VM_ALLOCATE                       8280K       29 
VM_ALLOCATE (reserved)               4K        1         reserved VM address space (unallocated)
__DATA                           262.5M      320 
__DATA_CONST                      12.2M      173 
__DATA_DIRTY                       539K       99 
__FONT_DATA                          4K        1 
__LINKEDIT                       704.8M       29 
__OBJC_RO                         81.8M        1 
__OBJC_RW                         3136K        2 
__TEXT                           259.3M      332 
__UNICODE                          588K        1 
dyld private memory               1024K        1 
mapped file                        5.1G      429 
shared memory                      848K       22 
unshared pmap                     5504K        3 
===========                     =======  ======= 
TOTAL                              7.4G     1749 
TOTAL, minus reserved VM space     6.8G     1749
-----------
Full Report
-----------
{"app_name":"freeview","timestamp":"2022-03-01 15:12:52.00 -0800","app_version":"","slice_uuid":"35cc1656-e7ff-32a5-8ec9-9faf896f9915","build_version":"","platform":1,"bundleID":"com.freesurfer.freeview","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.2.1 (21D62)","incident_id":"78ED639A-5BDF-48BF-88B6-8A9AE3997115","name":"freeview"}
{
  "uptime" : 1200,
  "procLaunch" : "2022-03-01 15:12:51.6463 -0800",
  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro17,1",
  "procStartAbsTime" : 30601251608,
  "coalitionID" : 1327,
  "osVersion" : {
    "train" : "macOS 12.2.1",
    "build" : "21D62",
    "releaseType" : "User"
  },
  "captureTime" : "2022-03-01 15:12:51.8713 -0800",
  "incident" : "78ED639A-5BDF-48BF-88B6-8A9AE3997115",
  "bug_type" : "309",
  "pid" : 1673,
  "procExitAbsTime" : 30606634548,
  "translated" : true,
  "cpuType" : "X86-64",
  "procName" : "freeview",
  "procPath" : "/Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview",
  "bundleInfo" : {"CFBundleIdentifier":"com.freesurfer.freeview"},
  "storeInfo" : {"deviceIdentifierForVendor":"61B48C8D-0860-568E-953B-3DE776CD3C66","thirdParty":true},
  "parentProc" : "Exited process",
  "parentPid" : 1672,
  "coalitionName" : "com.apple.Terminal",
  "crashReporterKey" : "DCA45306-7159-2569-6BDE-CF94BEE1E522",
  "responsiblePid" : 1587,
  "responsibleProc" : "Terminal",
  "sip" : "enabled",
  "vmRegionInfo" : "0x545845545f67 is not in any region.  Bytes after previous region: 92257060675432  Bytes before following region: 12815019253913\n      REGION TYPE                    START - END         [ VSIZE] PRT/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-/rwx SM=PRV  ",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x0000545845545f67","rawCodes":[1,92738097012583],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000545845545f67"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"exc handler","byPid":1673},
  "vmregioninfo" : "0x545845545f67 is not in any region.  Bytes after previous region: 92257060675432  Bytes before following region: 12815019253913\n      REGION TYPE                    START - END         [ VSIZE] PRT/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-/rwx SM=PRV  ",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : [{"triggered":true,"id":21764,"threadState":{"r13":{"value":13394160640},"rflags":{"value":515},"rax":{"value":92738097012575},"rosetta":{"tmp2":{"value":4842570216},"tmp1":{"value":4836476653},"tmp0":{"value":4658413596}},"r14":{"value":13394156664},"rsi":{"value":13394156664},"r8":{"value":0},"rdx":{"value":4836476637,"symbolLocation":1101,"symbol":"QWidget::event(QEvent*)"},"r10":{"value":4865468896},"r9":{"value":0},"r15":{"value":13394156664},"rbx":{"value":13394160640},"r11":{"value":140703389486009,"symbolLocation":0,"symbol":"-[NSView 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