DSI Studio crashes on rat atlas

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Kamil Lipiński

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Aug 4, 2021, 5:46:57 AMAug 4
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Dear Dr. Yeh,

I am trying to get ROIs from atlas, but the software is crashing few seconds after I click Atlas with option WHS_SD_RAT selected. Do you have any suggestions why it goes wrong? I would be very grateful for any help.

Best Regards,
Kamil Lipinski

Attached crash details:

Process:               dsi_studio [1858]
Path:                  /Applications/dsi_studio.app/Contents/MacOS/dsi_studio
Identifier:            frank.dsi-studio
Version:               0
Code Type:             X86-64 (Native)
Parent Process:        ??? [1]
Responsible:           dsi_studio [1858]
User ID:               501

Date/Time:             2021-08-04 11:40:47.369 +0200
OS Version:            macOS 11.5.1 (20G80)
Report Version:        12
Bridge OS Version:     5.5 (18P4759a)
Anonymous UUID:        885B0761-05AE-4734-CD8A-90E2373016BF


Time Awake Since Boot: 3600 seconds

System Integrity Protection: enabled

Crashed Thread:        8

Exception Type:        EXC_CRASH (SIGABRT)
Exception Codes:       0x0000000000000000, 0x0000000000000000
Exception Note:        EXC_CORPSE_NOTIFY

Application Specific Information:
abort() called
terminating with uncaught exception of type char const*

Thread 0:: Dispatch queue: com.apple.main-thread
0   libsystem_kernel.dylib         0x00007fff204bebb2 __semwait_signal + 10
1   libsystem_c.dylib             0x00007fff2043ec1a nanosleep + 196
2   libc++.1.dylib                 0x00007fff2049193a std::__1::this_thread::sleep_for(std::__1::chrono::duration<long long, std::__1::ratio<1l, 1000000000l> > const&) + 73
3   frank.dsi-studio               0x000000010fa479aa fib_data::run_normalization(bool, bool) + 1978
4   frank.dsi-studio               0x000000010fa4c232 fib_data::can_map_to_mni() + 34
5   frank.dsi-studio               0x000000010f876f44 tracking_window::on_addRegionFromAtlas_clicked() + 52
6   frank.dsi-studio               0x000000010fb3d08e tracking_window::qt_metacall(QMetaObject::Call, int, void**) + 62
7   org.qt-project.QtCore         0x0000000110ba4bfd QMetaObject::activate(QObject*, int, int, void**) + 1773
8   org.qt-project.QtWidgets       0x000000010ff9abef 0x10fea0000 + 1027055
9   org.qt-project.QtWidgets       0x000000010ff9aa8c 0x10fea0000 + 1026700
10  org.qt-project.QtWidgets       0x000000010ff9bbbf QAbstractButton::mouseReleaseEvent(QMouseEvent*) + 271
11  org.qt-project.QtWidgets       0x000000010feec5fd QWidget::event(QEvent*) + 445
12  org.qt-project.QtWidgets       0x000000010feb08ed QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
13  org.qt-project.QtWidgets       0x000000010feb3748 QApplication::notify(QObject*, QEvent*) + 7336
14  org.qt-project.QtCore         0x0000000110b73ef4 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
15  org.qt-project.QtWidgets       0x000000010feb1210 QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer<QWidget>&, bool, bool) + 896
16  org.qt-project.QtWidgets       0x000000010ff0baae 0x10fea0000 + 441006
17  org.qt-project.QtWidgets       0x000000010ff0a795 0x10fea0000 + 436117
18  org.qt-project.QtWidgets       0x000000010feb08ed QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
19  org.qt-project.QtWidgets       0x000000010feb1cf2 QApplication::notify(QObject*, QEvent*) + 594
20  org.qt-project.QtCore         0x0000000110b73ef4 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
21  org.qt-project.QtGui           0x000000011047627c QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*) + 3404
22  org.qt-project.QtGui           0x0000000110476602 QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*) + 4306
23  org.qt-project.QtGui           0x000000011045d5ab QWindowSystemInterface::sendWindowSystemEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 219
24  libqcocoa.dylib               0x0000000112f879d0 0x112f57000 + 199120
25  libqcocoa.dylib               0x0000000112f88130 0x112f57000 + 201008
26  com.apple.CoreFoundation       0x00007fff205ea94c __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
27  com.apple.CoreFoundation       0x00007fff205ea8b4 __CFRunLoopDoSource0 + 180
28  com.apple.CoreFoundation       0x00007fff205ea634 __CFRunLoopDoSources0 + 242
29  com.apple.CoreFoundation       0x00007fff205e905c __CFRunLoopRun + 893
30  com.apple.CoreFoundation       0x00007fff205e861c CFRunLoopRunSpecific + 563
31  com.apple.HIToolbox           0x00007fff2882da83 RunCurrentEventLoopInMode + 292
32  com.apple.HIToolbox           0x00007fff2882d6b6 ReceiveNextEventCommon + 284
33  com.apple.HIToolbox           0x00007fff2882d583 _BlockUntilNextEventMatchingListInModeWithFilter + 70
34  com.apple.AppKit               0x00007fff22def502 _DPSNextEvent + 864
35  com.apple.AppKit               0x00007fff22dedcd5 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1364
36  com.apple.AppKit               0x00007fff22de0049 -[NSApplication run] + 586
37  libqcocoa.dylib               0x0000000112f870ab 0x112f57000 + 196779
38  org.qt-project.QtCore         0x0000000110b6f55f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 431
39  org.qt-project.QtCore         0x0000000110b74502 QCoreApplication::exec() + 130
40  frank.dsi-studio               0x000000010f768d7f main + 1407
41  libdyld.dylib                 0x00007fff2050cf3d start + 1

Thread 1:: com.apple.NSEventThread
0   libsystem_kernel.dylib         0x00007fff204bc2ba mach_msg_trap + 10
1   libsystem_kernel.dylib         0x00007fff204bc62c mach_msg + 60
2   com.apple.CoreFoundation       0x00007fff205eab2f __CFRunLoopServiceMachPort + 316
3   com.apple.CoreFoundation       0x00007fff205e920f __CFRunLoopRun + 1328
4   com.apple.CoreFoundation       0x00007fff205e861c CFRunLoopRunSpecific + 563
5   com.apple.AppKit               0x00007fff22f755ca _NSEventThread + 124
6   libsystem_pthread.dylib       0x00007fff204f18fc _pthread_start + 224
7   libsystem_pthread.dylib       0x00007fff204ed443 thread_start + 15

Thread 2:
0   libsystem_pthread.dylib       0x00007fff204ed420 start_wqthread + 0

Thread 3:
0   libsystem_pthread.dylib       0x00007fff204ed420 start_wqthread + 0

Thread 4:
0   libsystem_pthread.dylib       0x00007fff204ed420 start_wqthread + 0

Thread 5:
0   libsystem_pthread.dylib       0x00007fff204ed420 start_wqthread + 0

Thread 6:
0   libsystem_pthread.dylib       0x00007fff204ed420 start_wqthread + 0

Thread 7:
0   libsystem_pthread.dylib       0x00007fff204ed420 start_wqthread + 0

Thread 8 Crashed:
0   libsystem_kernel.dylib         0x00007fff204c292e __pthread_kill + 10
1   libsystem_pthread.dylib       0x00007fff204f15bd pthread_kill + 263
2   libsystem_c.dylib             0x00007fff20446406 abort + 125
3   libc++abi.dylib               0x00007fff204b4ef2 abort_message + 241
4   libc++abi.dylib               0x00007fff204a65fd demangling_terminate_handler() + 266
5   libobjc.A.dylib               0x00007fff2039f595 _objc_terminate() + 104
6   libc++abi.dylib               0x00007fff204b4307 std::__terminate(void (*)()) + 8
7   libc++abi.dylib               0x00007fff204b6beb __cxxabiv1::failed_throw(__cxxabiv1::__cxa_exception*) + 27
8   libc++abi.dylib               0x00007fff204b6bb2 __cxa_throw + 116
9   frank.dsi-studio               0x000000010f81eb7d 0x10f759000 + 809853
10  frank.dsi-studio               0x000000010fa4aa91 0x10f759000 + 3086993
11  frank.dsi-studio               0x000000010fa51a2d 0x10f759000 + 3115565
12  libsystem_pthread.dylib       0x00007fff204f18fc _pthread_start + 224
13  libsystem_pthread.dylib       0x00007fff204ed443 thread_start + 15

Thread 8 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x000070000f8dc000  rcx: 0x000070000f8dafa8  rdx: 0x0000000000000000
  rdi: 0x000000000001e967  rsi: 0x0000000000000006  rbp: 0x000070000f8dafd0  rsp: 0x000070000f8dafa8
   r8: 0x000070000f8dae70   r9: 0x0000000000000000  r10: 0x0000000000000000  r11: 0x0000000000000246
  r12: 0x000000000001e967  r13: 0x0000003000000008  r14: 0x0000000000000006  r15: 0x0000000000000016
  rip: 0x00007fff204c292e  rfl: 0x0000000000000246  cr2: 0x00007fff87213db8
  
Logical CPU:     0
Error Code:      0x02000148
Trap Number:     133

Thread 8 instruction stream not available.

Thread 8 last branch register state not available.


Binary Images:
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    0x7fff20f6f000 -     0x7fff20fbcfff  com.apple.Lexicon-framework (1.0 - 86.2) <0E57E9C3-00A8-307E-B2DE-98720083D3E2> /System/Library/PrivateFrameworks/Lexicon.framework/Versions/A/Lexicon
    0x7fff20fbd000 -     0x7fff2102bfff  libSparse.dylib (106) <70D44B7A-1D2B-39F1-B606-6423E640D950> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparse.dylib
    0x7fff2102c000 -     0x7fff210a9fff  com.apple.SystemConfiguration (1.20 - 1.20) <C0C8BDF4-5049-33E3-B9BE-38045B039A47> /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
    0x7fff210aa000 -     0x7fff210defff  libCRFSuite.dylib (50) <0CBFE708-F55B-3B66-A06A-8BCB9355F169> /usr/lib/libCRFSuite.dylib
    0x7fff210df000 -     0x7fff21317fff  libmecabra.dylib (929.10) <083F04E5-49A8-397C-8014-7DAD0C55C568> /usr/lib/libmecabra.dylib
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    0x7fff41345000 -     0x7fff41363fff  libCGInterfaces.dylib (544.4) <D5D0AD69-E651-3BE2-B87A-4A035DCD9DBF> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib
    0x7fff438f2000 -     0x7fff43b65fff  com.apple.RawCamera.bundle (9.10.0 - 1450.3) <B52BB328-7FEE-304D-AFE1-532021A21ED6> /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
    0x7fff46438000 -     0x7fff46443fff  libGPUSupportMercury.dylib (18.5.9) <118D2300-226D-337B-9F75-B5A8880E9293> /System/Library/PrivateFrameworks/GPUSupport.framework/Versions/A/Libraries/libGPUSupportMercury.dylib
    0x7fff5cfff000 -     0x7fff5d000fff  libLatin2Converter.dylib (90) <9FE15271-EE88-374A-883E-303D6BEEE281> /System/Library/CoreServices/Encodings/libLatin2Converter.dylib
    0x7fff5ddba000 -     0x7fff5e249fff  com.apple.driver.AppleIntelKBLGraphicsMTLDriver (16.5.2 - 16.0.5) <B6C0830D-0992-3489-BFF5-6D8C5027D4F0> /System/Library/Extensions/AppleIntelKBLGraphicsMTLDriver.bundle/Contents/MacOS/AppleIntelKBLGraphicsMTLDriver
    0x7fff5e24a000 -     0x7fff5ecadfff  libSC.dylib (4.6.20) <C4EEC78B-6BC3-3324-9053-0A68F3F78FD4> /System/Library/Extensions/AMDShared.bundle/Contents/PlugIns/libSC.dylib
    0x7fff5efe2000 -     0x7fff5ffc9fff  com.apple.driver.AppleIntelKBLGraphicsGLDriver (16.5.2 - 16.0.5) <8241D321-1B03-3B34-9A76-D341BF7D70F2> /System/Library/Extensions/AppleIntelKBLGraphicsGLDriver.bundle/Contents/MacOS/AppleIntelKBLGraphicsGLDriver
    0x7fff6977b000 -     0x7fff6977ffff  libmetal_timestamp.dylib (31001.192.1) <6DF2DFF7-F8BE-3B77-8C85-0FE5E858F67E> /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/31001/Libraries/libmetal_timestamp.dylib
    0x7fff6bbc6000 -     0x7fff6bbccfff  libCoreFSCache.dylib (200.10) <D26083D4-A370-3C8D-A13E-32D69EBF73EF> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib
    0x7fff6bbcd000 -     0x7fff6bbd1fff  libCoreVMClient.dylib (200.10) <E582E0A3-2898-301C-9B5A-A17978ACFAA7> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
    0x7fff6bbd2000 -     0x7fff6bbe1fff  com.apple.opengl (18.5.9 - 18.5.9) <149F2F08-3FD7-3271-945C-238BDCAA3133> /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
    0x7fff6bbe2000 -     0x7fff6bbe4fff  libCVMSPluginSupport.dylib (18.5.9) <97DC9BD9-1BED-3D17-B499-3967775A011C> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
    0x7fff6bbe5000 -     0x7fff6bbedfff  libGFXShared.dylib (18.5.9) <7B502C01-1C03-3388-878B-A0A85223F3A5> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
    0x7fff6bbee000 -     0x7fff6bc21fff  libGLImage.dylib (18.5.9) <2CCBC785-6F45-33DE-B790-066AF4C69048> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
    0x7fff6bc22000 -     0x7fff6bc5efff  libGLU.dylib (18.5.9) <53602650-F093-334F-9D96-2B4FE2359E7A> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
    0x7fff6bc5f000 -     0x7fff6bdf2fff  libGLProgrammability.dylib (18.5.9) <A85B6455-FB77-3E5E-AD6C-27543EDC4415> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
    0x7fff6bdf3000 -     0x7fff6bdfdfff  libGL.dylib (18.5.9) <9E1A856D-D393-3FDC-ABDF-E29282A6B83E> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
    0x7fff6bdfe000 -     0x7fff6bf7bfff  GLEngine (18.5.9) <42EA70F3-CD0B-3C41-8A78-90AEE7CB0F96> /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine
    0x7fff6bf7c000 -     0x7fff6bfa4fff  GLRendererFloat (18.5.9) <4953ACAF-885A-310A-BFDF-777C9627CCDE> /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat
    0x7fff6d23d000 -     0x7fff6d295fff  com.apple.opencl (4.6 - 4.6) <5FD1A8D9-17B9-316B-8CA4-6BE553B936CE> /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
    0x7fff6e1df000 -     0x7fff6e22efff  ATIRadeonX6000SCLib.dylib (4.6.20) <75006034-8B36-37C0-93A2-769147EE3021> /System/Library/Extensions/AMDRadeonX6000GLDriver.bundle/Contents/MacOS/ATIRadeonX6000SCLib.dylib
    0x7fff6e33f000 -     0x7fff6e346fff  com.apple.agl (3.3.4 - AGL-3.3.3) <C7C621A8-A60D-3486-A4E6-74A1D696A369> /System/Library/Frameworks/AGL.framework/Versions/A/AGL
    0x7fff77a71000 -     0x7fff77a78fff  libRosetta.dylib (203.58) <A7FFAFB5-B0AB-312E-8EB6-FAF56D76FB7D> /usr/lib/libRosetta.dylib

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=775.1M resident=0K(0%) swapped_out_or_unallocated=775.1M(100%)
Writable regions: Total=731.2M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=731.2M(100%)
 
                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Accelerate framework               384K        3 
Activity Tracing                   256K        1 
CG backing stores                 5472K       12 
CG image                           196K       23 
CoreAnimation                    249.2M       65 
CoreGraphics                        16K        3 
CoreUI image data                 3720K       41 
Foundation                          16K        1 
Kernel Alloc Once                    8K        1 
MALLOC                           327.9M      163 
MALLOC guard page                   32K        7 
MALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)
STACK GUARD                       56.0M        9 
Stack                             12.1M        9 
VM_ALLOCATE                        924K       39 
__DATA                            27.6M      345 
__DATA_CONST                      14.3M      181 
__DATA_DIRTY                       565K      103 
__FONT_DATA                          4K        1 
__GLSLBUILTINS                    5176K        1 
__LINKEDIT                       508.2M       30 
__OBJC_RO                         70.2M        1 
__OBJC_RW                         2496K        3 
__TEXT                           266.9M      340 
__UNICODE                          588K        1 
mapped file                       95.6M       42 
shared memory                      780K       18 
===========                     =======  ======= 
TOTAL                              2.0G     1444 
TOTAL, minus reserved VM space     1.6G     1444 

Model: MacBookPro16,1, BootROM 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0), 6 processors, 6-Core Intel Core i7, 2,6 GHz, 16 GB, SMC 
Graphics: kHW_IntelUHDGraphics630Item, Intel UHD Graphics 630, spdisplays_builtin
Graphics: kHW_AMDRadeonPro5300MItem, AMD Radeon Pro 5300M, spdisplays_pcie_device, 4 GB
Memory Module: BANK 0/ChannelA-DIMM0, 8 GB, DDR4, 2667 MHz, Micron, 8ATF1G64HZ-2G6E1
Memory Module: BANK 2/ChannelB-DIMM0, 8 GB, DDR4, 2667 MHz, Micron, 8ATF1G64HZ-2G6E1
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x7BF), wl0: Jul  7 2021 02:54:21 version 9.30.444.17.32.5.70 FWID 01-6551fb93
Bluetooth: Version 8.0.5d7, 3 services, 27 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en0
USB Device: 2-Port USB 3.1 Hub
USB Device: USB 3.1 Bus
USB Device: 3-Port USB 2.1 Hub
USB Device: Razer Ornata Chroma
USB Device: Corsair Gaming HARPOON RGB Mouse
USB Device: Apple T2 Bus
USB Device: Composite Device
USB Device: Touch Bar Backlight
USB Device: Touch Bar Display
USB Device: Apple Internal Keyboard / Trackpad
USB Device: Headset
USB Device: Ambient Light Sensor
USB Device: FaceTime HD Camera (Built-in)
USB Device: Apple T2 Controller
Thunderbolt Bus: MacBook Pro, Apple Inc., 63.5
Thunderbolt Bus: MacBook Pro, Apple Inc., 63.5

Frank Yeh

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Aug 25, 2021, 6:28:31 PMAug 25
to dsi-s...@googlegroups.com
Hi Kamil,

    Could you update DSI Studio and see if it works?

    If the problem persists, you may upload sample data, and I will check it out and fix the bug.

Best regards,
Frank

   

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Kamil Lipiński

unread,
Sep 6, 2021, 6:48:51 AMSep 6
to DSI Studio
Dear Dr. Yeh,

Thank you for your reply! I downloaded the latest version, it seems the problem has been solved, and DSI Studio works fine now. Additionally, I wondered if it is possible to perform segmentation based on structural study and then apply it to DWI (using DSI studio only)? What I am looking for is something like FSL provides - FLIRT Registration low res ->high res -> reference, and then FAST segmentation.

Best Regards,
Kamil Lipinski

Frank Yeh

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Sep 6, 2021, 9:44:30 AMSep 6
to dsi-s...@googlegroups.com
Thanks for the suggestion.
I am listing this on the to-do list and hopefully provide this function in the future.
Frank

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