Freesurfer

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30066 discussions

Re: [Freesurfer] freeview quit unexpectedly on Mac OS M1
by fsbuild 04 Jan '23

04 Jan '23

External Email - Use Caution Please try the following with the latest 7.3.2 release.  The release page is https://secure-web.cisco.com/19K4NxhUlkogZZJ6mlyOImaI2Y4zmXjc6dwibN… the link to the .pkg file is https://secure-web.cisco.com/1Wx2_5nhoR76Fau-VOEeMoQVIQIDXjamvDF-EF… 1) Install the 7.3.2 release listed above.  It will be installed as /Applications/freesurfer/7.3.2 2)  Open a new terminal window and run the bash shell as, $ arch -arm64 /bin/bash 3) Set FS_LICENSE to point to the license.txt file you downloaded after registering via the online form at https://secure-web.cisco.com/12TyPaJsjD6Q9mekQ3_jITFFbb2NrPRGCuk6aPL36fn1jh…  For example, it could be in your home directory as $HOME/license.txt.  It can be anywhere but you just have to set FS_LICENSE to its absolute path and test it can be read. $ ls $HOME/license.txt/Users/<your userid>/license.txt$ export FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEyou(a)youremail.something     <— email you used to register with 4) Setup the environment, $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.3.2-20220803-878457d --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.3.2FSFAST_HOME       /Applications/freesurfer/7.3.2/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.3.2/subjectsMNI_DIR           /Applications/freesurfer/7.3.2/mni 5) Try running freeview from the command line w/o any arguments to see if it opens an empty window, $ freeview 6)  If that worked, quit freeview and then run freeview from the command line again to open one of the provided volumes in the 7.3.2 release, $ freeview $SUBJECTS_DIR/bert/mri/brain.mgz 7) If that worked, then try running freeview from the command line on one of your own volume or surface files. - R.

1 0

freeview quit unexpectedly on Mac OS M1
by Philipp Klar 04 Jan '23

04 Jan '23

External Email - Use Caution Hello FreeSurfer Developers, I am trying to run freesurfer which works fine up to a certain point. For example, starting freesurfer and loading a template works fine. But when I try loading a surface, freesurfer suddenly crashes after loading around 50% of the file. Hence, freesurfer starts fine, I can play around with it (a bit), but when loading certain files (the files are fine), the same error below comes up over and over again. ERROR: freeview quit unexpectedly. (see below for the full error.) 1) FreeSurfer version: 7.1.1 (the same problem occurs with the newest version 2) Platform: Macbook M1 Ventura 13.1 (22C65) 3) XQuartz 2.8.4 4) I ran export FREESURFER_HOME=/Applications/freesurfer/7.1.1 source $FREESURFER_HOME/SetUpFreeSurfer.sh 5) The lisence.txt is copied into /Applications/freesurfer/7.1.1 Thank you for any advice, Philipp ------------------------------------- Translated Report (Full Report Below) ------------------------------------- Process: freeview [1003] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Identifier: com.freesurfer.freeview Version: ??? Code Type: X86-64 (Translated) Parent Process: launchd [1] User ID: 501 Date/Time: 2023-01-04 06:40:59.8418 +0100 OS Version: macOS 13.1 (22C65) Report Version: 12 Anonymous UUID: 6C794FA2-0A28-9E00-8C0F-C5F42E1E1D41 Time Awake Since Boot: 200 seconds System Integrity Protection: enabled Crashed Thread: 19 ThreadIOWorker Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x00007f8c8bff0e60 Exception Codes: 0x0000000000000001, 0x00007f8c8bff0e60 Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11 Terminating Process: exc handler [1003] VM Region Info: 0x7f8c8bff0e60 is not in any region. Bytes after previous region: 141495905 Bytes before following region: 15790496 REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL MALLOC_TINY 7f8c83800000-7f8c83900000 [ 1024K] rw-/rwx SM=PRV ---> GAP OF 0x9600000 BYTES MALLOC_LARGE 7f8c8cf00000-7f8c94f00000 [128.0M] rw-/rwx SM=PRV Thread 0:: Dispatch queue: com.apple.main-thread 0 <translation info unavailable> 0x11512ea40 ??? 1 <translation info unavailable> 0x11512f3c8 ??? 2 libsystem_malloc.dylib 0x7ff8004dd2d9 nanov2_allocate_outlined + 246 3 libsystem_malloc.dylib 0x7ff8004dd8e1 nanov2_malloc_zero_on_alloc + 521 4 libc++abi.dylib 0x7ff80062c95a operator new(unsigned long) + 26 5 QtGui 0x11eb09154 QBrush::init(QColor const&, Qt::BrushStyle) + 276 6 QtGui 0x11eb0992d QBrush::QBrush(Qt::GlobalColor, Qt::BrushStyle) + 45 7 QtGui 0x11ea84557 0x11e934000 + 1377623 8 QtGui 0x11ea7b1ea 0x11e934000 + 1339882 9 QtGui 0x11ea7bbf9 0x11e934000 + 1342457 10 QtGui 0x11ea7b39c 0x11e934000 + 1340316 11 QtGui 0x11eaaadea 0x11e934000 + 1535466 12 QtGui 0x11eaae5db QTextDocumentFragment::fromHtml(QString const&, QTextDocument const*) + 107 13 QtGui 0x11eaa8411 QTextCursor::insertHtml(QString const&) + 257 14 QtWidgets 0x11dda7787 0x11dba7000 + 2099079 15 QtWidgets 0x11dd7f0a3 QTextEdit::append(QString const&) + 83 16 freeview 0x1027533da 0x1025dc000 + 1536986 17 freeview 0x102753bd7 0x1025dc000 + 1539031 18 QtCore 0x11fe278cc QMetaObject::activate(QObject*, int, int, void**) + 3132 19 QtCore 0x11fe2f432 QTimer::timerEvent(QTimerEvent*) + 98 20 QtCore 0x11fe1fcf6 QObject::event(QEvent*) + 102 21 QtWidgets 0x11dbb770d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 22 QtWidgets 0x11dbb8b12 QApplication::notify(QObject*, QEvent*) + 594 23 QtCore 0x11fdf6564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 24 QtCore 0x11fe4fb7f QTimerInfoList::activateTimers() + 991 25 libqcocoa.dylib 0x11f652472 0x11f61e000 + 214130 26 CoreFoundation 0x7ff80074bee1 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 27 CoreFoundation 0x7ff80074be90 __CFRunLoopDoSource0 + 157 28 CoreFoundation 0x7ff80074bc5e __CFRunLoopDoSources0 + 212 29 CoreFoundation 0x7ff80074a8b8 __CFRunLoopRun + 943 30 CoreFoundation 0x7ff800749e8f CFRunLoopRunSpecific + 560 31 HIToolbox 0x7ff80a5d3766 RunCurrentEventLoopInMode + 292 32 HIToolbox 0x7ff80a5d3576 ReceiveNextEventCommon + 679 33 HIToolbox 0x7ff80a5d32b3 _BlockUntilNextEventMatchingListInModeWithFilter + 70 34 AppKit 0x7ff8037d0f33 _DPSNextEvent + 909 35 AppKit 0x7ff8037cfdb4 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1219 36 AppKit 0x7ff8037c23f7 -[NSApplication run] + 586 37 libqcocoa.dylib 0x11f653223 0x11f61e000 + 217635 38 QtCore 0x11fdf1b7f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 431 39 QtCore 0x11fdf6b72 QCoreApplication::exec() + 130 40 freeview 0x1026d42e6 0x1025dc000 + 1016550 41 dyld 0x213414310 start + 2432 Thread 1:: com.apple.rosetta.exceptionserver 0 runtime 0x7ff7ffc1e614 0x7ff7ffc1a000 + 17940 1 runtime 0x7ff7ffc2a530 0x7ff7ffc1a000 + 66864 2 runtime 0x7ff7ffc2bf30 0x7ff7ffc1a000 + 73520 Thread 2: 0 runtime 0x7ff7ffc3c87c 0x7ff7ffc1a000 + 141436 Thread 3:: QThread 0 ??? 0x7ff88f9a69a8 ??? 1 libsystem_kernel.dylib 0x7ff8006392d6 poll + 10 2 QtCore 0x11fe4c8d0 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 608 3 QtCore 0x11fe4e0c7 QEventDispatcherUNIX::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 903 4 QtCore 0x11fdf1b7f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 431 5 QtCore 0x11fc2d37c QThread::exec() + 140 6 QtCore 0x11fc2e2f3 0x11fc0c000 + 140019 7 libsystem_pthread.dylib 0x7ff800671259 _pthread_start + 125 8 libsystem_pthread.dylib 0x7ff80066cc7b thread_start + 15 Thread 4: 0 runtime 0x7ff7ffc3c87c 0x7ff7ffc1a000 + 141436 Thread 5: 0 runtime 0x7ff7ffc3c87c 0x7ff7ffc1a000 + 141436 Thread 6:: com.apple.NSEventThread 0 ??? 0x7ff88f9a69a8 ??? 1 libsystem_kernel.dylib 0x7ff8006325c2 mach_msg2_trap + 10 2 libsystem_kernel.dylib 0x7ff800640604 mach_msg2_internal + 82 3 libsystem_kernel.dylib 0x7ff800639635 mach_msg_overwrite + 723 4 libsystem_kernel.dylib 0x7ff8006328a8 mach_msg + 19 5 CoreFoundation 0x7ff80074c01b __CFRunLoopServiceMachPort + 145 6 CoreFoundation 0x7ff80074aa74 __CFRunLoopRun + 1387 7 CoreFoundation 0x7ff800749e8f CFRunLoopRunSpecific + 560 8 AppKit 0x7ff803931299 _NSEventThread + 132 9 libsystem_pthread.dylib 0x7ff800671259 _pthread_start + 125 10 libsystem_pthread.dylib 0x7ff80066cc7b thread_start + 15 Thread 7: 0 runtime 0x7ff7ffc3c87c 0x7ff7ffc1a000 + 141436 Thread 8: 0 runtime 0x7ff7ffc3c87c 0x7ff7ffc1a000 + 141436 Thread 9: 0 runtime 0x7ff7ffc3c87c 0x7ff7ffc1a000 + 141436 Thread 10: 0 ??? 0x7ff88f9a69a8 ??? 1 libsystem_kernel.dylib 0x7ff80063511a __psynch_cvwait + 10 2 libsystem_pthread.dylib 0x7ff8006717e1 _pthread_cond_wait + 1243 3 freeview 0x103983fed 0x1025dc000 + 20611053 4 freeview 0x1039770ea 0x1025dc000 + 20558058 5 freeview 0x1039740b8 0x1025dc000 + 20545720 6 freeview 0x1039768b5 0x1025dc000 + 20555957 7 freeview 0x10395fcac 0x1025dc000 + 20462764 8 freeview 0x103982d91 0x1025dc000 + 20606353 9 libsystem_pthread.dylib 0x7ff800671259 _pthread_start + 125 10 libsystem_pthread.dylib 0x7ff80066cc7b thread_start + 15 Thread 11: 0 ??? 0x7ff88f9a69a8 ??? 1 libsystem_kernel.dylib 0x7ff80063511a __psynch_cvwait + 10 2 libsystem_pthread.dylib 0x7ff8006717e1 _pthread_cond_wait + 1243 3 freeview 0x103983fed 0x1025dc000 + 20611053 4 freeview 0x1039770ea 0x1025dc000 + 20558058 5 freeview 0x1039740b8 0x1025dc000 + 20545720 6 freeview 0x1039768b5 0x1025dc000 + 20555957 7 freeview 0x10395fcac 0x1025dc000 + 20462764 8 freeview 0x103982d91 0x1025dc000 + 20606353 9 libsystem_pthread.dylib 0x7ff800671259 _pthread_start + 125 10 libsystem_pthread.dylib 0x7ff80066cc7b thread_start + 15 Thread 12: 0 ??? 0x7ff88f9a69a8 ??? 1 libsystem_kernel.dylib 0x7ff80063511a __psynch_cvwait + 10 2 libsystem_pthread.dylib 0x7ff8006717e1 _pthread_cond_wait + 1243 3 freeview 0x103983fed 0x1025dc000 + 20611053 4 freeview 0x1039770ea 0x1025dc000 + 20558058 5 freeview 0x1039740b8 0x1025dc000 + 20545720 6 freeview 0x1039768b5 0x1025dc000 + 20555957 7 freeview 0x10395fcac 0x1025dc000 + 20462764 8 freeview 0x103982d91 0x1025dc000 + 20606353 9 libsystem_pthread.dylib 0x7ff800671259 _pthread_start + 125 10 libsystem_pthread.dylib 0x7ff80066cc7b thread_start + 15 Thread 13: 0 ??? 0x7ff88f9a69a8 ??? 1 libsystem_kernel.dylib 0x7ff80063511a __psynch_cvwait + 10 2 libsystem_pthread.dylib 0x7ff8006717e1 _pthread_cond_wait + 1243 3 freeview 0x103983fed 0x1025dc000 + 20611053 4 freeview 0x1039770ea 0x1025dc000 + 20558058 5 freeview 0x1039740b8 0x1025dc000 + 20545720 6 freeview 0x1039768b5 0x1025dc000 + 20555957 7 freeview 0x10395fcac 0x1025dc000 + 20462764 8 freeview 0x103982d91 0x1025dc000 + 20606353 9 libsystem_pthread.dylib 0x7ff800671259 _pthread_start + 125 10 libsystem_pthread.dylib 0x7ff80066cc7b thread_start + 15 Thread 14: 0 ??? 0x7ff88f9a69a8 ??? 1 libsystem_kernel.dylib 0x7ff80063511a __psynch_cvwait + 10 2 libsystem_pthread.dylib 0x7ff8006717e1 _pthread_cond_wait + 1243 3 freeview 0x103983fed 0x1025dc000 + 20611053 4 freeview 0x1039770ea 0x1025dc000 + 20558058 5 freeview 0x1039740b8 0x1025dc000 + 20545720 6 freeview 0x1039768b5 0x1025dc000 + 20555957 7 freeview 0x10395fcac 0x1025dc000 + 20462764 8 freeview 0x103982d91 0x1025dc000 + 20606353 9 libsystem_pthread.dylib 0x7ff800671259 _pthread_start + 125 10 libsystem_pthread.dylib 0x7ff80066cc7b thread_start + 15 Thread 15: 0 ??? 0x7ff88f9a69a8 ??? 1 libsystem_kernel.dylib 0x7ff80063511a __psynch_cvwait + 10 2 libsystem_pthread.dylib 0x7ff8006717e1 _pthread_cond_wait + 1243 3 freeview 0x103983fed 0x1025dc000 + 20611053 4 freeview 0x1039770ea 0x1025dc000 + 20558058 5 freeview 0x1039740b8 0x1025dc000 + 20545720 6 freeview 0x1039768b5 0x1025dc000 + 20555957 7 freeview 0x10395fcac 0x1025dc000 + 20462764 8 freeview 0x103982d91 0x1025dc000 + 20606353 9 libsystem_pthread.dylib 0x7ff800671259 _pthread_start + 125 10 libsystem_pthread.dylib 0x7ff80066cc7b thread_start + 15 Thread 16: 0 ??? 0x7ff88f9a69a8 ??? 1 libsystem_kernel.dylib 0x7ff80063511a __psynch_cvwait + 10 2 libsystem_pthread.dylib 0x7ff8006717e1 _pthread_cond_wait + 1243 3 freeview 0x103983fed 0x1025dc000 + 20611053 4 freeview 0x1039770ea 0x1025dc000 + 20558058 5 freeview 0x1039740b8 0x1025dc000 + 20545720 6 freeview 0x1039768b5 0x1025dc000 + 20555957 7 freeview 0x10395fcac 0x1025dc000 + 20462764 8 freeview 0x103982d91 0x1025dc000 + 20606353 9 libsystem_pthread.dylib 0x7ff800671259 _pthread_start + 125 10 libsystem_pthread.dylib 0x7ff80066cc7b thread_start + 15 Thread 17: 0 ??? 0x7ff88f9a69a8 ??? 1 libsystem_kernel.dylib 0x7ff80063511a __psynch_cvwait + 10 2 libsystem_pthread.dylib 0x7ff8006717e1 _pthread_cond_wait + 1243 3 freeview 0x103983fed 0x1025dc000 + 20611053 4 freeview 0x1039770ea 0x1025dc000 + 20558058 5 freeview 0x1039740b8 0x1025dc000 + 20545720 6 freeview 0x1039768b5 0x1025dc000 + 20555957 7 freeview 0x10395fcac 0x1025dc000 + 20462764 8 freeview 0x103982d91 0x1025dc000 + 20606353 9 libsystem_pthread.dylib 0x7ff800671259 _pthread_start + 125 10 libsystem_pthread.dylib 0x7ff80066cc7b thread_start + 15 Thread 18: 0 ??? 0x7ff88f9a69a8 ??? 1 libsystem_kernel.dylib 0x7ff80063511a __psynch_cvwait + 10 2 libsystem_pthread.dylib 0x7ff8006717e1 _pthread_cond_wait + 1243 3 freeview 0x103983fed 0x1025dc000 + 20611053 4 freeview 0x1039770ea 0x1025dc000 + 20558058 5 freeview 0x1039740b8 0x1025dc000 + 20545720 6 freeview 0x1039768b5 0x1025dc000 + 20555957 7 freeview 0x10395fcac 0x1025dc000 + 20462764 8 freeview 0x103982d91 0x1025dc000 + 20606353 9 libsystem_pthread.dylib 0x7ff800671259 _pthread_start + 125 10 libsystem_pthread.dylib 0x7ff80066cc7b thread_start + 15 Thread 19 Crashed:: ThreadIOWorker 0 freeview 0x1038ad864 0x1025dc000 + 19732580 1 freeview 0x1038a8f73 0x1025dc000 + 19713907 2 freeview 0x102645047 0x1025dc000 + 430151 3 freeview 0x1026ae6e4 0x1025dc000 + 861924 4 freeview 0x1027550fe 0x1025dc000 + 1544446 5 QtCore 0x11fc2e2f3 0x11fc0c000 + 140019 6 libsystem_pthread.dylib 0x7ff800671259 _pthread_start + 125 7 libsystem_pthread.dylib 0x7ff80066cc7b thread_start + 15 Thread 19 crashed with X86 Thread State (64-bit): rax: 0x000000000f0f0e60 rbx: 0x0000000000000000 rcx: 0x00007f8cc61c0000 rdx: 0x0000000000000004 rdi: 0x000000000030302e rsi: 0x00007f8c7cf00000 rbp: 0x0000000319d7de20 rsp: 0x0000000319d7d5b0 r8: 0x0000000000000000 r9: 0xffffffff00000000 r10: 0x00007ff843cdd9a0 r11: 0x00007ff843cde650 r12: 0x000060000371ae68 r13: 0x00007f8d3dd74000 r14: 0x0000000103cf47b0 r15: 0x0000000000000009 rip: <unavailable> rfl: 0x0000000000000283 tmp0: 0x00007f8cc61c0000 tmp1: 0x00007f8c8cf00000 tmp2: 0x0000000114b07218 Binary Images: 0x0 - 0xffffffffffffffff ??? (*) <00000000-0000-0000-0000-000000000000> ??? 0x7ff8004c2000 - 0x7ff8004eefff libsystem_malloc.dylib (*) <f609f029-bcd0-3a54-b48a-99b3ce8378ce> /usr/lib/system/libsystem_malloc.dylib 0x7ff80061b000 - 0x7ff800630ff7 libc++abi.dylib (*) <1fa4a590-f60c-3813-a408-a407fbcd0e89> /usr/lib/libc++abi.dylib 0x11e934000 - 0x11ed80fff org.qt-project.QtGui (5.12) <9cc34b01-ae4a-3ff2-ac1b-de08b8fbbbae> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtGui.framework/Versions/5/QtGui 0x11dba7000 - 0x11dfe5fff org.qt-project.QtWidgets (5.12) <ef671b84-7965-3c74-89df-09c3fa9096ca> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtWidgets.framework/Versions/5/QtWidgets 0x1025dc000 - 0x103bd4fff com.freesurfer.freeview (*) <5d2f3b3b-4e77-33b0-bcd0-96fc46b58202> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview 0x11fc0c000 - 0x120141fff org.qt-project.QtCore (5.12) <ae294ca9-b3ec-3f0e-b67a-509a13c0c913> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/5/QtCore 0x11f61e000 - 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0x7ff800676ff7 libsystem_pthread.dylib (*) <5920e36f-53ec-33f0-b675-8ae48b58418c> /usr/lib/system/libsystem_pthread.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=471.1M resident=0K(0%) swapped_out_or_unallocated=471.1M(100%) Writable regions: Total=5.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.5G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 384K 3 Activity Tracing 256K 1 CG backing stores 4032K 4 CG image 344K 37 ColorSync 248K 29 CoreAnimation 70.4M 29 CoreGraphics 20K 3 CoreImage 32K 8 CoreUI image data 4352K 32 Foundation 16K 1 Kernel Alloc Once 8K 1 MALLOC 4.2G 176 MALLOC guard page 192K 8 MALLOC_MEDIUM (reserved) 808.0M 8 reserved VM address space (unallocated) OpenGL GLSL 256K 3 Rosetta Arena 4096K 2 Rosetta Generic 1328K 329 Rosetta IndirectBranch 1024K 1 Rosetta JIT 128.0M 1 Rosetta Return Stack 360K 36 Rosetta Thread Context 360K 36 STACK GUARD 24K 6 Stack 84.6M 19 Stack Guard 56.1M 13 VM_ALLOCATE 2884K 127 VM_ALLOCATE (reserved) 4K 1 reserved VM address space (unallocated) __CTF 756 1 __DATA 261.8M 368 __DATA_CONST 14.9M 207 __DATA_DIRTY 672K 110 __FONT_DATA 2352 1 __GLSLBUILTINS 5174K 1 __LINKEDIT 171.5M 28 __OBJC_RO 65.4M 1 __OBJC_RW 1985K 2 __TEXT 299.6M 385 dyld private memory 256K 1 mapped file 4.3G 1320 shared memory 820K 19 unshared pmap 14.5M 10 =========== ======= ======= TOTAL 10.5G 3368 TOTAL, minus reserved VM space 9.7G 3368 ----------- Full Report ----------- {"app_name":"freeview","timestamp":"2023-01-04 06:41:02.00 +0100","app_version":"","slice_uuid":"5d2f3b3b-4e77-33b0-bcd0-96fc46b58202","build_version":"","platform":1,"bundleID":"com.freesurfer.freeview","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.1 (22C65)","roots_installed":0,"name":"freeview","incident_id":"8902A204-8AA5-4F8D-BDC9-5A41503728E1"} { "uptime" : 200, "procRole" : "Foreground", "version" : 2, "userID" : 501, "deployVersion" : 210, "modelCode" : "MacBookPro18,1", "coalitionID" : 991, "osVersion" : { "train" : "macOS 13.1", "build" : "22C65", "releaseType" : "User" }, "captureTime" : "2023-01-04 06:40:59.8418 +0100", "incident" : "8902A204-8AA5-4F8D-BDC9-5A41503728E1", "pid" : 1003, "translated" : true, "cpuType" : "X86-64", "roots_installed" : 0, "bug_type" : "309", "procLaunch" : "2023-01-04 06:40:19.1409 +0100", "procStartAbsTime" : 3915140085, "procExitAbsTime" : 4891545476, "procName" : "freeview", "procPath" : "\/Applications\/freesurfer\/*\/Freeview.app\/Contents\/MacOS\/freeview", "bundleInfo" : {"CFBundleIdentifier":"com.freesurfer.freeview"}, "storeInfo" : {"deviceIdentifierForVendor":"ECA7D20D-3527-5929-84D2-7552905EA9D5","thirdParty":true}, "parentProc" : "launchd", "parentPid" : 1, "coalitionName" : "com.freesurfer.freeview", "crashReporterKey" : "6C794FA2-0A28-9E00-8C0F-C5F42E1E1D41", "throttleTimeout" : 2147483647, "sip" : "enabled", "vmRegionInfo" : "0x7f8c8bff0e60 is not in any region. 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02:35:52 version 20.10.965.9.8.7.129 FWID 01-b0e84a9b Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports Network Service: Wi-Fi, AirPort, en0 USB Device: USB31Bus USB Device: USB31Bus USB Device: USB31Bus Thunderbolt Bus: MacBook Pro, Apple Inc. Thunderbolt Bus: MacBook Pro, Apple Inc. Thunderbolt Bus: MacBook Pro, Apple Inc.

1 0

Re: [Freesurfer] Help: Aparcstats and asegstats not working
by fsbuild 02 Jan '23

02 Jan '23

External Email - Use Caution SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: atleast 1 subject must be provided')?It does not look like you are running a python 2.X.  That may be because only python3 is installed by default. $ which python $ which python2 $ which python3 /bin/python3 … if you need to install python2, you can do it with ... $ sudo apt update$ sudo apt install python2 $ which python2/bin/python2$ python2 --version Python 2.7.18 One way or another you need “python” to report it is a 2.X version *after* you set FREESURFER_HOME and source the freesurfer setup script.  To force “python” to run as “python2” you can try using an alias, $ alias python=python2$ python --version Python 2.7.18 Similarly, if you needed python to run as python3 you could reset the alias to use =python3 instead. For the error,  print 'ERROR: subjects are not specified (use --subjects SUBJECTS)’I would check the subjects you are listing as argument can be found as directories under what SUBJECTS_DIR is currently set to. - R.

3 5

Requst password for Ubuntu 18.04.06 compressed image with the FreeSurfer 7.2.0
by Asger CD Pedersen 02 Jan '23

02 Jan '23

External Email - Use Caution Dear Freesurfer devolper I'm working on installing free surfer Ubuntu image. It would be lovely if it was possible to receive the password for the "Ubuntu 18.04.06 compressed image with the FreeSurfer 7.2.0" Regards -Asger

1 0

freesurfer 7.3.2 ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
by 李梦君 02 Jan '23

02 Jan '23

External Email - Use Caution Dear Freesurfer Experts I have installed the freesurfer 7.3.2, ERROR: mpr2mni305 failed has been reported in the recon-all -s T1(filename) -all, following is the recon-all.log. What should I do in to repair this problem Thanks!

2 1

Password for virtual machine FS_7_2_0_ubuntu_18_04_06
by Riccardo Accetta 02 Jan '23

02 Jan '23

External Email - Use Caution Hi can I have the password for the virtual machine that I have downloaded ? Thanks Best Regards Riccardo Accetta

1 0

Re: [Freesurfer] Freeview crashes after installing the software
by fsbuild 02 Jan '23

02 Jan '23

External Email - Use Caution Please try the following with the latest 7.3.2 release if you are not already running 7.3.2.  The release page is https://secure-web.cisco.com/1zn1v_OOPT0MJ0XxXSk4mw5hbeQD4yegZ0PSsC… the link to the .pkg file is https://secure-web.cisco.com/17qSx4asejqc1SOr4BdhhxtQLAqSTPmbMEBpF2… 1) Install the 7.3.2 release listed above.  It will be installed as /Applications/freesurfer/7.3.2 2)  Open a new terminal window and run the bash shell as, $ arch -arm64 /bin/bash 3) Set FS_LICENSE to point to the license.txt file you downloaded after registering via the online form at https://secure-web.cisco.com/1hvYfe1hO7ZqQEnaogRQmpJSBSH4ZqL7YpQWNvh19EOSXJ…  For example, it could be in your home directory as $HOME/license.txt.  It can be anywhere but you just have to set FS_LICENSE to its absolute path and test it can be read. $ ls $HOME/license.txt/Users/<your userid>/license.txt$ export FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEyou(a)youremail.something     <— email you used to register with 4) Setup the environment, $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.3.2-20220803-878457d -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.3.2 FSFAST_HOME       /Applications/freesurfer/7.3.2/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.3.2/subjects MNI_DIR           /Applications/freesurfer/7.3.2/mni 5) Try running freeview from the command line w/o any arguments to see if it opens an empty window, $ freeview 6)  If that worked, quit freeview and then run freeview from the command line again to open one of the provided volumes in the 7.3.2 release, $ freeview $SUBJECTS_DIR/bert/mri/brain.mgz 7) If that worked, then try running freeview from the command line on one of your own volume or surface files. - R. On Dec 30, 2022, at 12:55, Seyedeh Nasim Adnani <sza0127(a)auburn.edu> wrote:        External Email - Use Caution        Hello, I have a MacBook Pro with Ventura 13.1 OS, 64 GB, SMC Apple M1 Max.I recently started installing the freesurfer software but unfortunately, a simple volume loading into the freeview crashes without displaying any image.I have tried installing various python versions (2,3) and modifying the PATH but nothing seems to help. Now, I wonder if the software is compatible with my mac. Is there any way I can make it work on my system? Many thanks in advance for your help. Best,Nasim Adnani,Sza0127@auburn.edu_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Password for FreeSurfer project
by Sangeen Khan 01 Jan '23

01 Jan '23

External Email - Use Caution Hi, I’m interested in the freesurfer project. Can I have the password to unzip the virtual machine FS_7_2_0_Ubuntu_18_04_06.ova.7z? Thanks Sangeen khan

1 0

Freeview crashes after installing the software
by Seyedeh Nasim Adnani 30 Dec '22

30 Dec '22

External Email - Use Caution Hello, I have a MacBook Pro with Ventura 13.1 OS, 64 GB, SMC Apple M1 Max. I recently started installing the freesurfer software but unfortunately, a simple volume loading into the freeview crashes without displaying any image. I have tried installing various python versions (2,3) and modifying the PATH but nothing seems to help. Now, I wonder if the software is compatible with my mac. Is there any way I can make it work on my system? Many thanks in advance for your help. Best, Nasim Adnani, Sza0127(a)auburn.edu

1 0

Help: Aparcstats and asegstats not working
by vittal korann 29 Dec '22

29 Dec '22

External Email - Use Caution Hi Freesurfer experts, I am trying to collate all morphological parameters like thickness, area, volume, etc. When I tried executing the command " asegstats2table --subjects Met001 met002 .... --hemi lh --meas area --tablefile Area_aseg_stats.txt ", it failed and I got the below error which is highlighted. File "/usr/local/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax File "/usr/local/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax File "/usr/local/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: atleast 1 subject must be provided')? File "/usr/local/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: atleast 1 subject must be provided')? I am using the Freesurfer version6 and ubuntu 20.04. A similar error was reported in the forum and I also tried the suggested solution by setting python2.7 as the default version. However, nothing has worked out for me. Any help would be highly appreaciated. Thanks, Vittal

1 0

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