Freesurfer

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Setup Error with Freesurfer
by Aqeel Mohamed 10 Aug '23

10 Aug '23

External Email - Use Caution Hello, I am a new Freesurfer user and am currently struggling to run the freeview software on my MacBook Pro Ventura 13.5 OSX. I was following the step-by-step guide video on the Freesurfer wiki, but when it came to opening the 'bert' file, freeview would immediately crash (details of the report below). I unfortunately am a bit inexperienced with computers so I am unsure what the report means so would greatly appreciate any insight you can provide! I am also struggling to create a .license folder via terminal for my license key. I had hunted through the archives of the mailing list and managed to find a pico command but it is not letting me save the folder so would appreciate some help with this too! Apologies for such trivial questions - greatly appreciate any help you can provide! Aqeel ------------------------------------- Translated Report (Full Report Below) ------------------------------------- Process: freeview [6692] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Identifier: org.martinos.freeview Version: 7.3.2 (100) Code Type: X86-64 (Native) Parent Process: launchd [1] User ID: 501 Date/Time: 2023-08-10 16:58:22.6826 +0100 OS Version: macOS 13.5 (22G74) Report Version: 12 Bridge OS Version: 7.6 (20P6072) Anonymous UUID: 351902B9-A93B-A115-7A29-3096368C2B60 Sleep/Wake UUID: 446876E4-13F0-48EE-AD0E-42B66F9D7A3B Time Awake Since Boot: 8200 seconds Time Since Wake: 6630 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 0x0000000000000000 Exception Codes: 0x0000000000000001, 0x0000000000000000 Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11 Terminating Process: exc handler [6692] VM Region Info: 0 is not in any region. Bytes before following region: 4559671296 REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL UNUSED SPACE AT START ---> __TEXT 10fc71000-11133d000 [ 22.8M] r-x/r-x SM=COW ...acOS/freeview Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 QtGui 0x120a6a98c QPen::QPen() + 44 1 QtGui 0x120a29a3c QPainterState::QPainterState() + 60 2 QtGui 0x1209fb991 QRasterPaintEngine::createState(QPainterState*) const + 49 3 QtGui 0x120a1b77e QPainter::begin(QPaintDevice*) + 318 4 QtWidgets 0x121659345 QToolButton::paintEvent(QPaintEvent*) + 69 5 QtWidgets 0x12147b3fe QWidget::event(QEvent*) + 1262 6 QtWidgets 0x12165abc4 QToolButton::event(QEvent*) + 228 7 QtWidgets 0x12142b0b7 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247 8 QtWidgets 0x12142bffc QApplication::notify(QObject*, QEvent*) + 508 9 QtCore 0x1225631da QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170 10 QtWidgets 0x12146d6bd QWidgetPrivate::drawWidget(QPaintDevice*, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 3981 11 QtWidgets 0x1214752ef QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 1007 12 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 13 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 14 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 15 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 16 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 17 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 18 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 19 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 20 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 21 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 22 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 23 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 24 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 25 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 26 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 27 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 28 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 29 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 30 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 31 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 32 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 33 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 34 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 35 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 36 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 37 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 38 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 39 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 40 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 41 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 42 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 43 QtWidgets 0x1214751aa QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 682 44 QtWidgets 0x12146d7f8 QWidgetPrivate::drawWidget(QPaintDevice*, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 4296 45 QtWidgets 0x1214752ef QWidgetPrivate::paintSiblingsRecursive(QPaintDevice*, QList<QObject*> const&, int, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 1007 46 QtWidgets 0x12146d7f8 QWidgetPrivate::drawWidget(QPaintDevice*, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 4296 47 QtWidgets 0x12148d63e QWidgetRepaintManager::paintAndFlush() + 4654 48 QtWidgets 0x12148da9f QWidgetRepaintManager::sync() + 255 49 QtWidgets 0x12147b625 QWidget::event(QEvent*) + 1813 50 QtWidgets 0x1215ba5a4 QMainWindow::event(QEvent*) + 276 51 QtWidgets 0x12142b0b7 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247 52 QtWidgets 0x12142bffc QApplication::notify(QObject*, QEvent*) + 508 53 QtCore 0x1225631da QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170 54 QtCore 0x12256442c QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 1468 55 libqcocoa.dylib 0x121a3521b 0x121a1e000 + 94747 56 libqcocoa.dylib 0x121a3592b 0x121a1e000 + 96555 57 CoreFoundation 0x7ff8133a1f2a __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 58 CoreFoundation 0x7ff8133a1ecc __CFRunLoopDoSource0 + 157 59 CoreFoundation 0x7ff8133a1ca5 __CFRunLoopDoSources0 + 217 60 CoreFoundation 0x7ff8133a092f __CFRunLoopRun + 916 61 CoreFoundation 0x7ff81339ff31 CFRunLoopRunSpecific + 560 62 HIToolbox 0x7ff81ce20f3d RunCurrentEventLoopInMode + 292 63 HIToolbox 0x7ff81ce20d4e ReceiveNextEventCommon + 657 64 HIToolbox 0x7ff81ce20aa8 _BlockUntilNextEventMatchingListInModeWithFilter + 64 65 AppKit 0x7ff81643c25c _DPSNextEvent + 858 66 AppKit 0x7ff81643b106 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1214 67 AppKit 0x7ff81642d788 -[NSApplication run] + 586 68 libqcocoa.dylib 0x121a34833 0x121a1e000 + 92211 69 QtCore 0x12256c526 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 486 70 QtCore 0x1225637d5 QCoreApplication::exec() + 133 71 freeview 0x10fd89328 0x10fc71000 + 1147688 72 dyld 0x7ff812f6c41f start + 1903 Thread 1: 0 libsystem_pthread.dylib 0x7ff8132c1bb0 start_wqthread + 0 Thread 2: 0 libsystem_pthread.dylib 0x7ff8132c1bb0 start_wqthread + 0 Thread 3:: QThread 0 libsystem_kernel.dylib 0x7ff81328e2ae poll + 10 1 QtCore 0x1226e771e qt_safe_poll(pollfd*, unsigned int, timespec const*) + 94 2 QtCore 0x1226e8ff8 QEventDispatcherUNIX::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 792 3 QtCore 0x12256c526 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 486 4 QtCore 0x1226660ca QThread::exec() + 282 5 QtCore 0x1226ed093 0x1224f7000 + 2056339 6 libsystem_pthread.dylib 0x7ff8132c61d3 _pthread_start + 125 7 libsystem_pthread.dylib 0x7ff8132c1bd3 thread_start + 15 Thread 4:: Thread (pooled) 0 libsystem_kernel.dylib 0x7ff81328a0fe __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x7ff8132c6758 _pthread_cond_wait + 1242 2 QtCore 0x1226f704c 0x1224f7000 + 2097228 3 QtCore 0x1226f6d4e 0x1224f7000 + 2096462 4 QtCore 0x1226f6c9e QWaitCondition::wait(QMutex*, QDeadlineTimer) + 94 5 QtCore 0x1226f14f5 0x1224f7000 + 2073845 6 QtCore 0x1226ed093 0x1224f7000 + 2056339 7 libsystem_pthread.dylib 0x7ff8132c61d3 _pthread_start + 125 8 libsystem_pthread.dylib 0x7ff8132c1bd3 thread_start + 15 Thread 5:: Thread (pooled) 0 libsystem_kernel.dylib 0x7ff81328a0fe __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x7ff8132c6758 _pthread_cond_wait + 1242 2 QtCore 0x1226f704c 0x1224f7000 + 2097228 3 QtCore 0x1226f6d4e 0x1224f7000 + 2096462 4 QtCore 0x1226f6c9e QWaitCondition::wait(QMutex*, QDeadlineTimer) + 94 5 QtCore 0x1226f14f5 0x1224f7000 + 2073845 6 QtCore 0x1226ed093 0x1224f7000 + 2056339 7 libsystem_pthread.dylib 0x7ff8132c61d3 _pthread_start + 125 8 libsystem_pthread.dylib 0x7ff8132c1bd3 thread_start + 15 Thread 6:: Thread (pooled) 0 libsystem_kernel.dylib 0x7ff81328a0fe __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x7ff8132c6758 _pthread_cond_wait + 1242 2 QtCore 0x1226f704c 0x1224f7000 + 2097228 3 QtCore 0x1226f6d4e 0x1224f7000 + 2096462 4 QtCore 0x1226f6c9e QWaitCondition::wait(QMutex*, QDeadlineTimer) + 94 5 QtCore 0x1226f14f5 0x1224f7000 + 2073845 6 QtCore 0x1226ed093 0x1224f7000 + 2056339 7 libsystem_pthread.dylib 0x7ff8132c61d3 _pthread_start + 125 8 libsystem_pthread.dylib 0x7ff8132c1bd3 thread_start + 15 Thread 7:: Thread (pooled) 0 libsystem_kernel.dylib 0x7ff81328a0fe __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x7ff8132c6758 _pthread_cond_wait + 1242 2 QtCore 0x1226f704c 0x1224f7000 + 2097228 3 QtCore 0x1226f6d4e 0x1224f7000 + 2096462 4 QtCore 0x1226f6c9e QWaitCondition::wait(QMutex*, QDeadlineTimer) + 94 5 QtCore 0x1226f14f5 0x1224f7000 + 2073845 6 QtCore 0x1226ed093 0x1224f7000 + 2056339 7 libsystem_pthread.dylib 0x7ff8132c61d3 _pthread_start + 125 8 libsystem_pthread.dylib 0x7ff8132c1bd3 thread_start + 15 Thread 8:: Thread (pooled) 0 libsystem_kernel.dylib 0x7ff81328a0fe __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x7ff8132c6758 _pthread_cond_wait + 1242 2 QtCore 0x1226f704c 0x1224f7000 + 2097228 3 QtCore 0x1226f6d4e 0x1224f7000 + 2096462 4 QtCore 0x1226f6c9e QWaitCondition::wait(QMutex*, QDeadlineTimer) + 94 5 QtCore 0x1226f14f5 0x1224f7000 + 2073845 6 QtCore 0x1226ed093 0x1224f7000 + 2056339 7 libsystem_pthread.dylib 0x7ff8132c61d3 _pthread_start + 125 8 libsystem_pthread.dylib 0x7ff8132c1bd3 thread_start + 15 Thread 9:: Thread (pooled) 0 libsystem_kernel.dylib 0x7ff81328a0fe __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x7ff8132c6758 _pthread_cond_wait + 1242 2 QtCore 0x1226f704c 0x1224f7000 + 2097228 3 QtCore 0x1226f6d4e 0x1224f7000 + 2096462 4 QtCore 0x1226f6c9e QWaitCondition::wait(QMutex*, QDeadlineTimer) + 94 5 QtCore 0x1226f14f5 0x1224f7000 + 2073845 6 QtCore 0x1226ed093 0x1224f7000 + 2056339 7 libsystem_pthread.dylib 0x7ff8132c61d3 _pthread_start + 125 8 libsystem_pthread.dylib 0x7ff8132c1bd3 thread_start + 15 Thread 10:: Thread (pooled) 0 libsystem_kernel.dylib 0x7ff81328a0fe __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x7ff8132c6758 _pthread_cond_wait + 1242 2 QtCore 0x1226f704c 0x1224f7000 + 2097228 3 QtCore 0x1226f6d4e 0x1224f7000 + 2096462 4 QtCore 0x1226f6c9e QWaitCondition::wait(QMutex*, QDeadlineTimer) + 94 5 QtCore 0x1226f14f5 0x1224f7000 + 2073845 6 QtCore 0x1226ed093 0x1224f7000 + 2056339 7 libsystem_pthread.dylib 0x7ff8132c61d3 _pthread_start + 125 8 libsystem_pthread.dylib 0x7ff8132c1bd3 thread_start + 15 Thread 11:: Thread (pooled) 0 libsystem_kernel.dylib 0x7ff81328a0fe __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x7ff8132c6758 _pthread_cond_wait + 1242 2 QtCore 0x1226f704c 0x1224f7000 + 2097228 3 QtCore 0x1226f6d4e 0x1224f7000 + 2096462 4 QtCore 0x1226f6c9e QWaitCondition::wait(QMutex*, QDeadlineTimer) + 94 5 QtCore 0x1226f14f5 0x1224f7000 + 2073845 6 QtCore 0x1226ed093 0x1224f7000 + 2056339 7 libsystem_pthread.dylib 0x7ff8132c61d3 _pthread_start + 125 8 libsystem_pthread.dylib 0x7ff8132c1bd3 thread_start + 15 Thread 12:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x7ff8132875c2 mach_msg2_trap + 10 1 libsystem_kernel.dylib 0x7ff81329573d mach_msg2_internal + 78 2 libsystem_kernel.dylib 0x7ff81328e5f4 mach_msg_overwrite + 692 3 libsystem_kernel.dylib 0x7ff8132878aa mach_msg + 19 4 CoreFoundation 0x7ff8133a206f __CFRunLoopServiceMachPort + 145 5 CoreFoundation 0x7ff8133a0af0 __CFRunLoopRun + 1365 6 CoreFoundation 0x7ff81339ff31 CFRunLoopRunSpecific + 560 7 AppKit 0x7ff81659c3f5 _NSEventThread + 132 8 libsystem_pthread.dylib 0x7ff8132c61d3 _pthread_start + 125 9 libsystem_pthread.dylib 0x7ff8132c1bd3 thread_start + 15 Thread 13: 0 libsystem_pthread.dylib 0x7ff8132c1bb0 start_wqthread + 0 Thread 14: 0 libsystem_pthread.dylib 0x7ff8132c1bb0 start_wqthread + 0 Thread 15: 0 libsystem_pthread.dylib 0x7ff8132c1bb0 start_wqthread + 0 Thread 16:: ThreadIOWorker 0 QtGui 0x120b0ffe1 0x120872000 + 2744289 1 QtGui 0x120b04874 QFontDatabasePrivate::clearFamilies() + 228 2 QtGui 0x120b100f6 0x120872000 + 2744566 3 libsystem_c.dylib 0x7ff813197ba1 __cxa_finalize_ranges + 409 4 libsystem_c.dylib 0x7ff8131979bb exit + 35 5 freeview 0x110f0ccfc 0x10fc71000 + 19512572 6 freeview 0x110f96b18 0x10fc71000 + 20077336 7 freeview 0x10fcf3154 0x10fc71000 + 532820 8 freeview 0x10fcf37a8 0x10fc71000 + 534440 9 freeview 0x10fd1a1fb 0x10fc71000 + 692731 10 freeview 0x10fe119ca 0x10fc71000 + 1706442 11 QtCore 0x1226ed093 0x1224f7000 + 2056339 12 libsystem_pthread.dylib 0x7ff8132c61d3 _pthread_start + 125 13 libsystem_pthread.dylib 0x7ff8132c1bd3 thread_start + 15 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x00007f84d43b3240 rcx: 0x0000000000000000 rdx: 0x00007f84d43b3200 rdi: 0x00007f84d43b3240 rsi: 0x000060000124cbe0 rbp: 0x00007ff7b0288400 rsp: 0x00007ff7b02883d0 r8: 0x0000000000007873 r9: 0x5566931f84878c43 r10: 0x0000000000003f01 r11: 0x00007f84d4000000 r12: 0x00006000035320e0 r13: 0x0000600001f407e0 r14: 0x0000000000000000 r15: 0x00007ff7b0288560 rip: 0x0000000120a6a98c rfl: 0x0000000000010202 cr2: 0x0000000000000000 Logical CPU: 0 Error Code: 0x00000006 (no mapping for user data write) Trap Number: 14 Thread 0 instruction stream: 11 43 08 4c 89 f7 4c 89-ee e8 66 6b f1 ff 44 89 .C.L..L...fk..D. 63 18 44 89 7b 1c 8b 45-d4 89 43 20 48 83 c4 18 c.D.{..E..C H... 5b 41 5c 41 5d 41 5e 41-5f 5d c3 66 0f 1f 84 00 [A\A]A^A_].f.... 00 00 00 00 55 48 89 e5-41 57 41 56 41 54 53 48 ....UH..AWAVATSH 83 ec 10 48 89 fb 8a 05-80 d4 4f 00 8a 05 62 d4 ...H......O...b. 4f 00 84 c0 74 1b 48 8b-05 4f d4 4f 00 48 89 03 O...t.H..O.O.H.. [f0]83 00 01 48 83 c4 10-5b 41 5c 41 5e 41 5f 5d ....H...[A\A^A_] <== c3 48 8d 3d 3c d4 4f 00-e8 47 c0 44 00 85 c0 74 .H.=<.O..G.D...t d5 4c 8d 75 d8 4c 89 f7-be 02 00 00 00 ba 01 00 .L.u.L.......... 00 00 e8 5d 60 f1 ff bf-58 00 00 00 e8 c9 bf 44 ...]`...X......D 00 49 89 c7 c7 00 01 00-00 00 4c 8d 60 10 4c 89 .I........L.`.L. e7 e8 7e 59 f1 ff 0f 57-c0 41 0f 11 47 38 41 0f ..~Y...W.A..G8A. 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1 0

Pass code to open the virtual box image
by Roshan Cherian 09 Aug '23

09 Aug '23

External Email - Use Caution Hi, I kindly request you to share the pass code to open the virtual box image Regards, Roshan John

1 0

converting preprocessed surface functional data to volume
by wangzhiwei3233 09 Aug '23

09 Aug '23

External Email - Use Caution Dear Freesurfer experts, I am going to do convert the preprocessed surface functional data to volume in fsaverage space so that I can used the processed data in SPM for further analysis, saying, beta series analysis. Because the trial nubmer is not same for each subject in my experiment, I think freesurfer can not deal with this condition (please tell me if I am wrong). I tried mri_surf2vol, it worked. But it is time consuming. It takes around 5 minutes per 10 volumes. In addition, the result volume is too big (67MB/ volume for 256*256*256 matrix, 1mm resolution). The code is as follows: mri_surf2vol --o ${Dir_Subj_fMRI}/$isub/bold/${irun}/Ribbon/${iVolume} --subject fsaverage --so ${SUBJECTS_DIR}/fsaverage/surf/lh.white ${Dir_Subj_fMRI}/$isub/bold/${irun}/LH/${iVolume} --so ${SUBJECTS_DIR}/fsaverage/surf/rh.white ${Dir_Subj_fMRI}/$isub/bold/${irun}/RH/${iVolume} Are there better ways to accomplish my goal? Best, Zhiwei

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Re: [Freesurfer] Use freeview to visualize white and pial surface
by fsbuild 09 Aug '23

09 Aug '23

External Email - Use Caution  I could be wrong, but maybe that error is a function of what code path is being executed, the order of operations to render the graphics, etc.  It may not be as straightforward as either all images are going to work or none are going to work. I would try to test on a known/supported system.  If you still get the same errors, then that would help us reproduce it on the systems we have. - R. On Aug 8, 2023, at 22:42, DS <zkypis(a)126.com> wrote:        External Email - Use Caution        Hi expert,Thanks for discussing it. I really appreciate it. That's very helpful. I have forwarded this message to admin, so that he will install it. But, I have another question. Before I visualize these images, I previously successfully loaded lh.white and lh.pial from another subject. If our system is not compatible with Freeview, why can I show these images from other subjects? Technically, under the current system, Freeview would not have worked with any images. Do you have any thoughts? Thank you so much.PS. I agree with your suggestions. We recently moved from RHEL 8 to RHEL 9, we have discarded RHEL 8. So, I guess that's why I met these issues.At 2023-08-09 10:21:46, "fsbuild" <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Thank you for posting that output.  It shows you are running RHEL or Red Hat Enterprise Linux 9.1 (or the officially supported release downstream from CentOS9).  That explains why your version of mesa packages is rev 22.So your best option is to try installing the 7.4.1 CentOS8 Stream installer, https://secure-web.cisco.com/142cnesLA-45N-BegLaDTx7pgSNN6b…, e.g., via,$ sudo yum install ./freesurfer-CentOS8-7.4.1-1.x86_64.rpmAfter a successful install,  you would set FREESURFER_HOME to /usr/local/freesurfer/7.4.1-1 and then source the freesurfer setup script under that directory.While it may install just fine, there is no guarantee everything is going to work correctly with the newer versions of system libraries in RHEL 9.  We have not tested on and currently do not officially support freesurfer running on RHEL 9/CentOS9 Stream.If you continue to have issues, you might want to inquire to your system administrators if a RHEL 8 or Ubuntu 22 machine is available to run freesurfer on.  Barring that, you could create and run a VM (virtual machine) or container to host one of the linux OS’s we have installers for under that download link (https://secure-web.cisco.com/1X9AQaZtJeadUY-H3cja_TNqCr6QrBvjw4KkCn4svX1XWG… The supported OS's are CentOS 8, 7 and Ubuntu 22, 20, 18.  You could host that VM or container on top of Red Hat Enterprise Linux 9.1 or most any other OS.RHEL has its own built in virtualization software called “qemu”.  You system, administrators may already have qemu setup and working on your RHEL 9.1 machine.  If so, you could ask them to setup qemu to run RHEL 8 and then install freesurfer-CentOS8-7.4.1-1.x86_64.rpm in that VM.Please note that it is easier to run Freeview in a VM compared to a container in order to view images.- R.On Aug 8, 2023, at 20:38, DS <zkypis(a)126.com> wrote:        External Email - Use Caution        Hi expert,Thanks for your reply. I have contacted our admin to fix the installer issue, as our admin installed this FreeSurfer. But, at the same time, I try to get the version of our system by running "cat /etc/os-release", i.e.NAME="Red Hat Enterprise Linux"VERSION="9.1 (Plow)"ID="rhel"ID_LIKE="fedora"VERSION_ID="9.1"PLATFORM_ID="platform:el9"PRETTY_NAME="Red Hat Enterprise Linux 9.1 (Plow)"ANSI_COLOR="0;31"LOGO="fedora-logo-icon"CPE_NAME="cpe:/o:redhat:enterprise_linux:9::baseos"HOME_URL="https://secure-web.cisco.com/1ovUBbgYTLCz1nbzkl9474qBgKoMJVy6A6BR-gSZxobrLQ…"DOCUMENTATION_URL="https://secure-web.cisco.com/1YHt_3Kl_WACiMrQZPigOxi-y-JpM1LXc_Y3FoRtkAm3yx…"BUG_REPORT_URL="https://secure-web.cisco.com/15PdMKi4XHIUQ2p4okhnqW4F7Bc7TAi1USdeSlxfZ7p9h8…"REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 9"REDHAT_BUGZILLA_PRODUCT_VERSION=9.1REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"REDHAT_SUPPORT_PRODUCT_VERSION="9.1"Once I have any updates, I will let you know. Thanks.At 2023-08-09 02:58:47, "fsbuild" <fsbuild(a)contbay.com> wrote:        External Email - Use Caution         The output in your previous email lists an error from a mesa version 22 header file found on your system under mesa-22.0.3/src/mesa/vbo.  Mesa 22 implements the OpenGL 4.6 API which may not work reliably with some graphics card drivers.It might help to know what OS release you are running by sending along the output from,$ cat /etc/os-releaseYou could try setting a minimal environment and ensure LD_LIBRARY_PATH is not in use before setting up the freesurfer environment, e.g.,$ export PATH=/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin$ unset LD_LIBRARY_PATH.... then setup the freesurfer environment ...$ export FREESURFER_HOME=/your/path/to/freesurfer/install$ source $FREESURFER_HOME/SetUpFreeSurfer.shIf you have not already done so, I would also try downloading and running (with sudo)  the freesurfer 7.4.1 .rpm or .deb file installer that matches your system via the links under, https://secure-web.cisco.com/19mV_2omzOOMClnHd5VkjlNUycKu9VqctfxoKta5Q498bJ…; The installer might find a conflict with what's installed on your system (and refuse to proceed), or alternately change/add versions of some packages including mesa.  If the install succeeds, then the path to FREESURFER_HOME you can try will be /usr/local/freesurfer followed by ../7.4.1 or ./7.4..1-1 depending upon your linux system.- R.On 8/8/23 11:22, DS (zkypis(a)126.com) wrote:        External Email - Use Caution        I tried to load one surface first, and there is no problem. But, after I load the second surface, the GUI was suddenly closed, and reported the same error. ../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion `used_next <= save->vertex_store->buffer_in_ram_size' failed.I thought this might be a RAM issue, but I tried to load larger surface files, and then they can be loaded smoothly. That's why I am confused about it. Do you have any thoughts? Thanks..At 2023-08-08 22:28:44, "Wang, Ruopeng" <RWANG4(a)mgh.harvard.edu> wrote:        External Email - Use Caution        I don’t think this is the case since you can load 1 surface without problem. What if you load one surface from the command-line, then load the other one from the GUI?On Aug 8, 2023, at 9:45 AM, DS <zkypis(a)126.com> wrote:        External Email - Use Caution        Hi expert,Thanks for your feedback. I am also using 7.4.1. I remember we previously had an issue with loading libGLU when we use 7.3.2. So, we installed 7.4.1 to fix this issue. And now I am using 7.4.1. Do you think there might be something with other parts of this tool?Thank you so much.At 2023-08-08 21:27:34, "Wang, Ruopeng" <RWANG4(a)mgh.harvard.edu> wrote:        External Email - Use Caution        What version of freesurfer are you using? I tried with 7.4.1 and the latest dev build, both can load these 2 files together without problem.On Aug 7, 2023, at 8:11 PM, DS <zkypis(a)126.com> wrote:        External Email - Use Caution        Hi expert,Thanks for your tips. Here is the output after typing "mris_info lh.white"SURFACE INFO ======================================== type        : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACEnum vertices: 159999num faces   : 319994num strips  : 0surface area: 98524.6vg.valid: 1AvgFaceArea      0.307895AvgVtxArea       0.615783AvgVtxDist       0.858784StdVtxDist       0.223460ctr                     : (-34.5623, -3.52124, 27.1753)original vertex space   : surfaceRASvertex locs             : surfaceRASVolume Geometry (vg)volume geometry:extent  : (384, 384, 384)voxel   : ( 0.5000,  0.5000,  0.5000)x_(ras) : (-1.0000, -0..0000,  0..0000)y_(ras) : ( 0.0000, -0.0000, -1.0000)z_(ras) : ( 0.0000,  1.0000,  0.0000)c_(ras) : (-2.4468,  9.5993, -9..7705)file    : /project/bbl-bgd/zhisha/yanyang_zhang_7t/S59_VASO/20230308_S59_T01/fs_segmentation/fs_output/mri/wm.mgzVolume Geometry vox2ras-0.50000   0.00000   0.00000   93.55320;-0.00000  -0.00000   0.50000  -86.40073; 0.00000  -0.50000   0.00000   86.22952; 0.00000   0.00000   0.00000   1.00000;Volume Geometry vox2ras-tkr-0.50000   0.00000   0.00000   96.00000; 0.00000   0.00000   0.50000  -96.00000; 0.00000  -0.50000   0.00000   96.00000; 0.00000   0.00000   0.00000   1.00000;cmd[0]: ProgramName: mris_remove_intersection  ProgramArguments: mris_remove_intersection ..../surf/lh.orig ../surf/lh.orig  ProgramVersion: 7.4.0  TimeStamp: 2023/07/26-08:06:34-GMT  BuildTime: May 10 2023 00:12:43  BuildStamp: freesurfer-linux-centos7_x86_64-7.4.0-20230510-e558e6e  User: zhisha  Machine: linc1  Platform: Linux  PlatformVersion: 3.10.0-1160.76.1.el7.x86_64  CompilerName: GCC  CompilerVersion: 4.8.5mris_infocreationtime 2023/08/07-23:56:25-GMTsysname  Linuxhostname reslnvhpc0281machine  x86_64surfacefile lh.whitehemicode    0talairach_flag  0rescale     0.000000nvertices   159999nfaces      319994total_area  98524.593750group_avg_vtxarea_loaded 0avgfacearea  0.307895avgvtxarea  0..615783avgvtxdist  0.858784stdvtxdist  0.223460vtx0xyz   -10.953291 -78.142456 0.268743num_intersecting_faces 255If I type "mris_info lh.pial", the output is SURFACE INFO ======================================== type        : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACEnum vertices: 159999num faces   : 319994num strips  : 0surface area: 119400vg.valid: 1AvgFaceArea      0.373132AvgVtxArea       0.746256AvgVtxDist       0.975444StdVtxDist       0.419796ctr                     : (-34.8974, -3.52912, 26.0063)original vertex space   : surfaceRASvertex locs             : surfaceRASVolume Geometry (vg)volume geometry:extent  : (384, 384, 384)voxel   : ( 0.5000,  0.5000,  0.5000)x_(ras) : (-1.0000, -0.0000,  0..0000)y_(ras) : ( 0.0000, -0.0000, -1.0000)z_(ras) : ( 0.0000,  1.0000,  0.0000)c_(ras) : (-2.4468,  9.5993, -9..7705)file    : /project/bbl-bgd/zhisha/yanyang_zhang_7t/S59_VASO/20230308_S59_T01/fs_segmentation/fs_output/mri/wm.mgzVolume Geometry vox2ras-0.50000   0.00000   0.00000   93.55320;-0.00000  -0.00000   0.50000  -86.40073; 0.00000  -0.50000   0.00000   86.22952; 0.00000   0.00000   0.00000   1.00000;Volume Geometry vox2ras-tkr-0.50000   0.00000   0.00000   96.00000; 0.00000   0.00000   0.50000  -96.00000; 0.00000  -0.50000   0.00000   96.00000; 0.00000   0.00000   0.00000   1.00000;cmd[0]: ProgramName: mris_remove_intersection  ProgramArguments: mris_remove_intersection .../surf/lh.orig ../surf/lh.orig  ProgramVersion: 7.4.0  TimeStamp: 2023/07/26-08:06:34-GMT  BuildTime: May 10 2023 00:12:43  BuildStamp: freesurfer-linux-centos7_x86_64-7.4.0-20230510-e558e6e  User: zhisha  Machine: linc1  Platform: Linux  PlatformVersion: 3.10.0-1160..76.1.el7.x86_64  CompilerName: GCC  CompilerVersion: 4.8.5mris_infocreationtime 2023/08/08-00:01:31-GMTsysname  Linuxhostname reslnvhpc0281machine  x86_64surfacefile lh.pialhemicode    0talairach_flag  0rescale     0.000000nvertices   159999nfaces      319994total_area  119400.148438group_avg_vtxarea_loaded 0avgfacearea  0.373132avgvtxarea  0.746256avgvtxdist  0.975444stdvtxdist  0.419796vtx0xyz   -10.917007 -79.515175 0.469994num_intersecting_faces 261But, I only load lh.white or lh.pial, freeview can show it. If I load both at the same time, it does not work. Anyway, I uploaded both files to google drive, here is the link (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1xbUwsICRfi1E7lDL9hEEwJW8TX1HxMHXZNTvO…) Hopefully, these images could more info to solve the problem. Thank you so much for your help.Best,CainAt 2023-08-08 04:44:41, "Fischl, Bruce R.,PHD" <BFISCHL(a)mgh.harvard.edu> wrote:        External Email - Use Caution        Hmm, can you try running mris_info lh.white mris_info lh.pial and see if those work? What if you just bring up the pial and not the white? Maybe you can put those files in a dropbox and one of us (Ruopeng?) can take a look? From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DSSent: Monday, August 7, 2023 4:00 PMTo: Freesurfer support list <freesurfer@nmr.mgh..harvard.edu>Subject: Re: [Freesurfer] Use freeview to visualize white and pial surface         External Email - Use Caution        Hi expert,I do not think it's related to RAM. When I try to load some images larger than the image that it fails to load, it also works. So, I guess it might be related to other issues. PS. the current free RAM is 6GB. Best,Cain  At 2023-08-08 03:49:29, "Fischl, Bruce R.,PHD" <BFISCHL(a)mgh.harvard.edu> wrote:        External Email - Use Caution        Maybe you are at the edge of how much ram you have in that machine? How much free memory do you have? From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DSSent: Monday, August 7, 2023 3:48 PMTo: Freesurfer support list <freesurfer@nmr.mgh..harvard.edu>Subject: Re: [Freesurfer] Use freeview to visualize white and pial surface         External Email - Use Caution        Hi expert,Thanks for your reply. I used the following command line.freeview -f \lh.white:edgecolor=blue \lh.pial:edgecolor=red I also tried to load these images by clicking the icons on the interface of Freeview. But, both approaches do not work. The first image it loads just flashed, and then it's closed when it started to load the second image. But, I tried some images from another subject, then it works.Best,Cain  At 2023-08-08 03:13:52, "Fischl, Bruce R.,PHD" <BFISCHL(a)mgh.harvard.edu> wrote:        External Email - Use Caution        What is your freeview command line/ From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DSSent: Monday, August 7, 2023 2:51 PMTo: freesurfer@nmr.mgh.harvard.eduSubject: [Freesurfer] Use freeview to visualize white and pial surface         External Email - Use Caution        I have a question about freeview. Recently, when I loaded lh.pial and lh.white at the same time, the freeview was suddenly aborted and reported the following error. ../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion `used_next <= save->vertex_store->buffer_in_ram_size' failed. But, if I load lh.pial or lh.white separately, I found it’s working. I guess there might be inconsistent parameters between the two files, because when I check another subject, both files can be visualized very well. Do you have any thoughts about this issue? Thank you so much for any suggestions. PS. Previously I posted this question with the images that I use to troubleshoot the problem. But, I received an email saying that "this message need approval from moderator, because the files are larger than expected". However, I never receive any update/reply from the moderator so far. Best,Cain_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZtTzHVi07t3guHFWU4KEEb7iZ_TSNGKJmu8x_… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1mqOnvMY04s6NDHJ3oU95i_lFUMHr2FQSIyY3RDzc4kfiV… Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Use freeview to visualize white and pial surface
by fsbuild 08 Aug '23

08 Aug '23

External Email - Use Caution Thank you for posting that output.  It shows you are running RHEL or Red Hat Enterprise Linux 9.1 (or the officially supported release downstream from CentOS9).  That explains why your version of mesa packages is rev 22. So your best option is to try installing the 7.4.1 CentOS8 Stream installer, https://secure-web.cisco.com/13Yh2Zpq9lfBw2Tx4PthJHddojpo9K…, e.g., via, $ sudo yum install ./freesurfer-CentOS8-7.4.1-1.x86_64.rpm After a successful install,  you would set FREESURFER_HOME to /usr/local/freesurfer/7.4.1-1 and then source the freesurfer setup script under that directory. While it may install just fine, there is no guarantee everything is going to work correctly with the newer versions of system libraries in RHEL 9.  We have not tested on and currently do not officially support freesurfer running on RHEL 9/CentOS9 Stream. If you continue to have issues, you might want to inquire to your system administrators if a RHEL 8 or Ubuntu 22 machine is available to run freesurfer on.  Barring that, you could create and run a VM (virtual machine) or container to host one of the linux OS’s we have installers for under that download link (https://secure-web.cisco.com/1NdQZ9ARlP_lmvayOFl13KH1foHnEmo3DsGCA8LmwoJi1b… The supported OS's are CentOS 8, 7 and Ubuntu 22, 20, 18.  You could host that VM or container on top of Red Hat Enterprise Linux 9.1 or most any other OS. RHEL has its own built in virtualization software called “qemu”.  You system, administrators may already have qemu setup and working on your RHEL 9.1 machine.  If so, you could ask them to setup qemu to run RHEL 8 and then install freesurfer-CentOS8-7.4.1-1.x86_64.rpm in that VM. Please note that it is easier to run Freeview in a VM compared to a container in order to view images. - R. On Aug 8, 2023, at 20:38, DS <zkypis@126..com> wrote:        External Email - Use Caution        Hi expert,Thanks for your reply. I have contacted our admin to fix the installer issue, as our admin installed this FreeSurfer. But, at the same time, I try to get the version of our system by running "cat /etc/os-release", i.e.NAME="Red Hat Enterprise Linux"VERSION="9.1 (Plow)"ID="rhel"ID_LIKE="fedora"VERSION_ID="9.1"PLATFORM_ID="platform:el9"PRETTY_NAME="Red Hat Enterprise Linux 9.1 (Plow)"ANSI_COLOR="0;31"LOGO="fedora-logo-icon"CPE_NAME="cpe:/o:redhat:enterprise_linux:9::baseos"HOME_URL="https://secure-web.cisco.com/1XApM7qkseMu45J2kbm9Wvmirf5GLxoeehLie2RNWvR3Cq…"DOCUMENTATION_URL="https://secure-web.cisco.com/1KVP29f2nVxu6VGypY0-4fnWlTeue0RkLc6RYfAmeCs1rW…"BUG_REPORT_URL="https://secure-web.cisco.com/1F1bSssRfJjrdP0pSKPbHm6DQ0qWFXYpO2E6CYe7cDWR93…"REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 9"REDHAT_BUGZILLA_PRODUCT_VERSION=9.1REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"REDHAT_SUPPORT_PRODUCT_VERSION="9.1"Once I have any updates, I will let you know. Thanks.At 2023-08-09 02:58:47, "fsbuild" <fsbuild(a)contbay.com> wrote:        External Email - Use Caution         The output in your previous email lists an error from a mesa version 22 header file found on your system under mesa-22.0.3/src/mesa/vbo.  Mesa 22 implements the OpenGL 4.6 API which may not work reliably with some graphics card drivers.It might help to know what OS release you are running by sending along the output from,$ cat /etc/os-releaseYou could try setting a minimal environment and ensure LD_LIBRARY_PATH is not in use before setting up the freesurfer environment, e.g.,$ export PATH=/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin$ unset LD_LIBRARY_PATH.... then setup the freesurfer environment ...$ export FREESURFER_HOME=/your/path/to/freesurfer/install$ source $FREESURFER_HOME/SetUpFreeSurfer.shIf you have not already done so, I would also try downloading and running (with sudo)  the freesurfer 7.4.1 .rpm or .deb file installer that matches your system via the links under, https://secure-web.cisco.com/1KvVO99vt2vqP8xjrRb_LuYRd6FaW2M1gKknTTiTsMBq_p…; The installer might find a conflict with what's installed on your system (and refuse to proceed), or alternately change/add versions of some packages including mesa.  If the install succeeds, then the path to FREESURFER_HOME you can try will be /usr/local/freesurfer followed by ../7.4.1 or ./7.4.1-1 depending upon your linux system.- R.On 8/8/23 11:22, DS (zkypis(a)126.com) wrote:        External Email - Use Caution        I tried to load one surface first, and there is no problem. But, after I load the second surface, the GUI was suddenly closed, and reported the same error. ../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion `used_next <= save->vertex_store->buffer_in_ram_size' failed.I thought this might be a RAM issue, but I tried to load larger surface files, and then they can be loaded smoothly. That's why I am confused about it. Do you have any thoughts? Thanks.At 2023-08-08 22:28:44, "Wang, Ruopeng" <RWANG4(a)mgh.harvard.edu> wrote:        External Email - Use Caution        I don’t think this is the case since you can load 1 surface without problem. What if you load one surface from the command-line, then load the other one from the GUI?On Aug 8, 2023, at 9:45 AM, DS <zkypis(a)126.com> wrote:        External Email - Use Caution        Hi expert,Thanks for your feedback. I am also using 7.4.1. I remember we previously had an issue with loading libGLU when we use 7.3.2. So, we installed 7.4.1 to fix this issue. And now I am using 7.4.1. Do you think there might be something with other parts of this tool?Thank you so much.At 2023-08-08 21:27:34, "Wang, Ruopeng" <RWANG4(a)mgh.harvard.edu> wrote:        External Email - Use Caution        What version of freesurfer are you using? I tried with 7.4.1 and the latest dev build, both can load these 2 files together without problem.On Aug 7, 2023, at 8:11 PM, DS <zkypis(a)126.com> wrote:        External Email - Use Caution        Hi expert,Thanks for your tips. Here is the output after typing "mris_info lh.white"SURFACE INFO ======================================== type        : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACEnum vertices: 159999num faces   : 319994num strips  : 0surface area: 98524.6vg.valid: 1AvgFaceArea      0.307895AvgVtxArea       0.615783AvgVtxDist       0.858784StdVtxDist       0.223460ctr                     : (-34.5623, -3.52124, 27.1753)original vertex space   : surfaceRASvertex locs             : surfaceRASVolume Geometry (vg)volume geometry:extent  : (384, 384, 384)voxel   : ( 0.5000,  0.5000,  0.5000)x_(ras) : (-1.0000, -0.0000,  0..0000)y_(ras) : ( 0.0000, -0.0000, -1.0000)z_(ras) : ( 0.0000,  1.0000,  0.0000)c_(ras) : (-2.4468,  9.5993, -9...7705)file    : /project/bbl-bgd/zhisha/yanyang_zhang_7t/S59_VASO/20230308_S59_T01/fs_segmentation/fs_output/mri/wm.mgzVolume Geometry vox2ras-0.50000   0.00000   0.00000   93.55320;-0.00000  -0.00000   0.50000  -86.40073; 0.00000  -0.50000   0.00000   86.22952; 0.00000   0.00000   0.00000   1.00000;Volume Geometry vox2ras-tkr-0.50000   0.00000   0.00000   96.00000; 0.00000   0.00000   0.50000  -96.00000; 0..00000  -0.50000   0.00000   96.00000; 0.00000   0.00000   0.00000   1.00000;cmd[0]: ProgramName: mris_remove_intersection  ProgramArguments: mris_remove_intersection .../surf/lh.orig ../surf/lh.orig  ProgramVersion: 7.4.0  TimeStamp: 2023/07/26-08:06:34-GMT  BuildTime: May 10 2023 00:12:43  BuildStamp: freesurfer-linux-centos7_x86_64-7.4.0-20230510-e558e6e  User: zhisha  Machine: linc1  Platform: Linux  PlatformVersion: 3.10.0-1160.76.1.el7.x86_64  CompilerName: GCC  CompilerVersion: 4.8.5mris_infocreationtime 2023/08/07-23:56:25-GMTsysname  Linuxhostname reslnvhpc0281machine  x86_64surfacefile lh.whitehemicode    0talairach_flag  0rescale     0.000000nvertices   159999nfaces      319994total_area  98524.593750group_avg_vtxarea_loaded 0avgfacearea  0.307895avgvtxarea  0.615783avgvtxdist  0.858784stdvtxdist  0.223460vtx0xyz   -10.953291 -78.142456 0.268743num_intersecting_faces 255If I type "mris_info lh.pial", the output is SURFACE INFO ======================================== type        : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACEnum vertices: 159999num faces   : 319994num strips  : 0surface area: 119400vg.valid: 1AvgFaceArea      0.373132AvgVtxArea       0.746256AvgVtxDist       0.975444StdVtxDist       0.419796ctr                     : (-34.8974, -3.52912, 26.0063)original vertex space   : surfaceRASvertex locs             : surfaceRASVolume Geometry (vg)volume geometry:extent  : (384, 384, 384)voxel   : ( 0.5000,  0.5000,  0.5000)x_(ras) : (-1.0000, -0.0000,  0..0000)y_(ras) : ( 0.0000, -0.0000, -1.0000)z_(ras) : ( 0.0000,  1.0000,  0.0000)c_(ras) : (-2.4468,  9.5993, -9..7705)file    : /project/bbl-bgd/zhisha/yanyang_zhang_7t/S59_VASO/20230308_S59_T01/fs_segmentation/fs_output/mri/wm.mgzVolume Geometry vox2ras-0.50000   0.00000   0.00000   93.55320;-0.00000  -0.00000   0.50000  -86.40073; 0.00000  -0.50000   0.00000   86.22952; 0.00000   0.00000   0.00000   1.00000;Volume Geometry vox2ras-tkr-0.50000   0.00000   0.00000   96.00000; 0.00000   0.00000   0.50000  -96.00000; 0.00000  -0.50000   0.00000   96.00000; 0.00000   0.00000   0.00000   1.00000;cmd[0]: ProgramName: mris_remove_intersection  ProgramArguments: mris_remove_intersection .../surf/lh.orig ../surf/lh.orig  ProgramVersion: 7.4.0  TimeStamp: 2023/07/26-08:06:34-GMT  BuildTime: May 10 2023 00:12:43  BuildStamp: freesurfer-linux-centos7_x86_64-7.4.0-20230510-e558e6e  User: zhisha  Machine: linc1  Platform: Linux  PlatformVersion: 3.10.0-1160.76.1.el7.x86_64  CompilerName: GCC  CompilerVersion: 4.8.5mris_infocreationtime 2023/08/08-00:01:31-GMTsysname  Linuxhostname reslnvhpc0281machine  x86_64surfacefile lh.pialhemicode    0talairach_flag  0rescale     0.000000nvertices   159999nfaces      319994total_area  119400.148438group_avg_vtxarea_loaded 0avgfacearea  0.373132avgvtxarea  0.746256avgvtxdist  0.975444stdvtxdist  0.419796vtx0xyz   -10.917007 -79.515175 0.469994num_intersecting_faces 261But, I only load lh.white or lh.pial, freeview can show it. If I load both at the same time, it does not work. Anyway, I uploaded both files to google drive, here is the link (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1YJDMrREh7o4JA6Md6MGLS1QpFDcBHmCMZhhhg…) Hopefully, these images could more info to solve the problem. Thank you so much for your help.Best,CainAt 2023-08-08 04:44:41, "Fischl, Bruce R.,PHD" <BFISCHL(a)mgh.harvard.edu> wrote:        External Email - Use Caution        Hmm, can you try running mris_info lh.white mris_info lh.pial and see if those work? What if you just bring up the pial and not the white? Maybe you can put those files in a dropbox and one of us (Ruopeng?) can take a look? From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DSSent: Monday, August 7, 2023 4:00 PMTo: Freesurfer support list <freesurfer@nmr.mgh..harvard.edu>Subject: Re: [Freesurfer] Use freeview to visualize white and pial surface         External Email - Use Caution        Hi expert,I do not think it's related to RAM. When I try to load some images larger than the image that it fails to load, it also works. So, I guess it might be related to other issues. PS. the current free RAM is 6GB. Best,Cain  At 2023-08-08 03:49:29, "Fischl, Bruce R.,PHD" <BFISCHL(a)mgh.harvard.edu> wrote:        External Email - Use Caution        Maybe you are at the edge of how much ram you have in that machine? How much free memory do you have? From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DSSent: Monday, August 7, 2023 3:48 PMTo: Freesurfer support list <freesurfer@nmr.mgh..harvard.edu>Subject: Re: [Freesurfer] Use freeview to visualize white and pial surface         External Email - Use Caution        Hi expert,Thanks for your reply. I used the following command line.freeview -f \lh.white:edgecolor=blue \lh.pial:edgecolor=red I also tried to load these images by clicking the icons on the interface of Freeview. But, both approaches do not work. The first image it loads just flashed, and then it's closed when it started to load the second image. But, I tried some images from another subject, then it works.Best,Cain  At 2023-08-08 03:13:52, "Fischl, Bruce R.,PHD" <BFISCHL(a)mgh.harvard.edu> wrote:        External Email - Use Caution        What is your freeview command line/ From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DSSent: Monday, August 7, 2023 2:51 PMTo: freesurfer@nmr.mgh.harvard.eduSubject: [Freesurfer] Use freeview to visualize white and pial surface         External Email - Use Caution        I have a question about freeview. Recently, when I loaded lh..pial and lh.white at the same time, the freeview was suddenly aborted and reported the following error. ../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion `used_next <= save->vertex_store->buffer_in_ram_size' failed. But, if I load lh.pial or lh.white separately, I found it’s working. I guess there might be inconsistent parameters between the two files, because when I check another subject, both files can be visualized very well. Do you have any thoughts about this issue? Thank you so much for any suggestions. PS. Previously I posted this question with the images that I use to troubleshoot the problem. But, I received an email saying that "this message need approval from moderator, because the files are larger than expected". However, I never receive any update/reply from the moderator so far. Best,Cain_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1P9lntWFAFvmtA1FQBqoPJyQayhrDwcvIT0L87… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1bMw5vAv0qgyrz82-kyOVAhA1bUaljoC_GwYWe16027eIJ… Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Use freeview to visualize white and pial surface
by fsbuild 08 Aug '23

08 Aug '23

External Email - Use Caution   The output in your previous email lists an error from a mesa version 22 header file found on your system under mesa-22.0.3/src/mesa/vbo.  Mesa 22 implements the OpenGL 4.6 API which may not work reliably with some graphics card drivers. It might help to know what OS release you are running by sending along the output from, $ cat /etc/os-release You could try setting a minimal environment and ensure LD_LIBRARY_PATH is not in use before setting up the freesurfer environment, e.g., $ export PATH=/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin $ unset LD_LIBRARY_PATH .... then setup the freesurfer environment ... $ export FREESURFER_HOME=/your/path/to/freesurfer/install $ source $FREESURFER_HOME/SetUpFreeSurfer.sh If you have not already done so, I would also try downloading and running (with sudo)  the freesurfer 7.4.1 .rpm or .deb file installer that matches your system via the links under, https://secure-web.cisco.com/10GLtxtMlgiuFybMD0cY_brZC5MXIy0CPYlNkhR4pAp0qW…; The installer might find a conflict with what's installed on your system (and refuse to proceed), or alternately change/add versions of some packages including mesa.  If the install succeeds, then the path to FREESURFER_HOME you can try will be /usr/local/freesurfer followed by ../7.4.1 or ./7.4.1-1 depending upon your linux system. - R. On 8/8/23 11:22, DS (zkypis(a)126.com) wrote:         External Email - Use Caution         I tried to load one surface first, and there is no problem. But, after I load the second surface, the GUI was suddenly closed, and reported the same error.  .../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion `used_next <= save->vertex_store->buffer_in_ram_size' failed. I thought this might be a RAM issue, but I tried to load larger surface files, and then they can be loaded smoothly. That's why I am confused about it. Do you have any thoughts? Thanks. At 2023-08-08 22:28:44, "Wang, Ruopeng" <RWANG4(a)mgh.harvard.edu> wrote:         External Email - Use Caution         I don’t think this is the case since you can load 1 surface without problem. What if you load one surface from the command-line, then load the other one from the GUI? On Aug 8, 2023, at 9:45 AM, DS <zkypis(a)126.com> wrote:         External Email - Use Caution         Hi expert, Thanks for your feedback. I am also using 7.4.1. I remember we previously had an issue with loading libGLU when we use 7.3.2. So, we installed 7.4.1 to fix this issue. And now I am using 7.4.1. Do you think there might be something with other parts of this tool? Thank you so much. At 2023-08-08 21:27:34, "Wang, Ruopeng" <RWANG4(a)mgh.harvard.edu> wrote:         External Email - Use Caution         What version of freesurfer are you using? I tried with 7.4.1 and the latest dev build, both can load these 2 files together without problem. On Aug 7, 2023, at 8:11 PM, DS <zkypis(a)126.com> wrote:         External Email - Use Caution         Hi expert, Thanks for your tips. Here is the output after typing "mris_info lh.white" SURFACE INFO ========================================  type        : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 159999 num faces   : 319994 num strips  : 0 surface area: 98524.6 vg.valid: 1 AvgFaceArea      0.307895 AvgVtxArea       0.615783 AvgVtxDist       0.858784 StdVtxDist       0.223460 ctr                     : (-34.5623, -3.52124, 27.1753) original vertex space   : surfaceRAS vertex locs             : surfaceRAS Volume Geometry (vg) volume geometry: extent  : (384, 384, 384) voxel   : ( 0.5000,  0.5000,  0.5000) x_(ras) : (-1.0000, -0.0000,  0.0000) y_(ras) : ( 0.0000, -0.0000, -1.0000) z_(ras) : ( 0.0000,  1.0000,  0.0000) c_(ras) : (-2.4468,  9.5993, -9.7705) file    : /project/bbl-bgd/zhisha/yanyang_zhang_7t/S59_VASO/20230308_S59_T01/fs_segmentation/fs_output/mri/wm.mgz Volume Geometry vox2ras -0.50000   0.00000   0.00000   93.55320; -0.00000  -0.00000   0.50000  -86.40073;  0.00000  -0.50000   0.00000   86.22952;  0.00000   0.00000   0.00000   1.00000; Volume Geometry vox2ras-tkr -0.50000   0.00000   0.00000   96.00000;  0.00000   0.00000   0.50000  -96.00000;  0.00000  -0.50000   0.00000   96.00000;  0.00000   0.00000   0.00000   1.00000; cmd[0]: ProgramName: mris_remove_intersection  ProgramArguments: mris_remove_intersection .../surf/lh.orig ../surf/lh.orig  ProgramVersion: 7.4.0  TimeStamp: 2023/07/26-08:06:34-GMT  BuildTime: May 10 2023 00:12:43  BuildStamp: freesurfer-linux-centos7_x86_64-7.4.0-20230510-e558e6e  User: zhisha  Machine: linc1  Platform: Linux  PlatformVersion: 3.10.0-1160.76.1.el7.x86_64  CompilerName: GCC  CompilerVersion: 4.8.5 mris_info creationtime 2023/08/07-23:56:25-GMT sysname  Linux hostname reslnvhpc0281 machine  x86_64 surfacefile lh.white hemicode    0 talairach_flag  0 rescale     0.000000 nvertices   159999 nfaces      319994 total_area  98524.593750 group_avg_vtxarea_loaded 0 avgfacearea  0.307895 avgvtxarea  0.615783 avgvtxdist  0.858784 stdvtxdist  0.223460 vtx0xyz   -10.953291 -78.142456 0.268743 num_intersecting_faces 255 If I type "mris_info lh.pial", the output is  SURFACE INFO ========================================  type        : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 159999 num faces   : 319994 num strips  : 0 surface area: 119400 vg.valid: 1 AvgFaceArea      0.373132 AvgVtxArea       0.746256 AvgVtxDist       0.975444 StdVtxDist       0.419796 ctr                     : (-34.8974, -3.52912, 26.0063) original vertex space   : surfaceRAS vertex locs             : surfaceRAS Volume Geometry (vg) volume geometry: extent  : (384, 384, 384) voxel   : ( 0.5000,  0.5000,  0.5000) x_(ras) : (-1.0000, -0.0000,  0.0000) y_(ras) : ( 0.0000, -0.0000, -1.0000) z_(ras) : ( 0.0000,  1.0000,  0.0000) c_(ras) : (-2.4468,  9.5993, -9.7705) file    : /project/bbl-bgd/zhisha/yanyang_zhang_7t/S59_VASO/20230308_S59_T01/fs_segmentation/fs_output/mri/wm.mgz Volume Geometry vox2ras -0.50000   0.00000   0.00000   93.55320; -0.00000  -0.00000   0.50000  -86.40073;  0.00000  -0.50000   0.00000   86.22952;  0.00000   0.00000   0.00000   1.00000; Volume Geometry vox2ras-tkr -0.50000   0.00000   0.00000   96.00000;  0.00000   0.00000   0.50000  -96.00000;  0.00000  -0.50000   0.00000   96.00000;  0.00000   0.00000   0.00000   1.00000; cmd[0]: ProgramName: mris_remove_intersection  ProgramArguments: mris_remove_intersection .../surf/lh.orig ../surf/lh.orig  ProgramVersion: 7.4.0  TimeStamp: 2023/07/26-08:06:34-GMT  BuildTime: May 10 2023 00:12:43  BuildStamp: freesurfer-linux-centos7_x86_64-7.4.0-20230510-e558e6e  User: zhisha  Machine: linc1  Platform: Linux  PlatformVersion: 3.10.0-1160.76.1.el7.x86_64  CompilerName: GCC  CompilerVersion: 4.8.5 mris_info creationtime 2023/08/08-00:01:31-GMT sysname  Linux hostname reslnvhpc0281 machine  x86_64 surfacefile lh.pial hemicode    0 talairach_flag  0 rescale     0.000000 nvertices   159999 nfaces      319994 total_area  119400.148438 group_avg_vtxarea_loaded 0 avgfacearea  0.373132 avgvtxarea  0.746256 avgvtxdist  0.975444 stdvtxdist  0.419796 vtx0xyz   -10.917007 -79.515175 0.469994 num_intersecting_faces 261 But, I only load lh.white or lh.pial, freeview can show it. If I load both at the same time, it does not work. Anyway, I uploaded both files to google drive, here is the link (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ISmWHEli28NnENV_byotaYOAH92Vv6ZabBjx2…) Hopefully, these images could more info to solve the problem. Thank you so much for your help. Best, Cain At 2023-08-08 04:44:41, "Fischl, Bruce R.,PHD" <BFISCHL(a)mgh.harvard.edu> wrote:         External Email - Use Caution         Hmm, can you try running   mris_info lh.white   mris_info lh.pial   and see if those work? What if you just bring up the pial and not the white? Maybe you can put those files in a dropbox and one of us (Ruopeng?) can take a look?   From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of DS Sent: Monday, August 7, 2023 4:00 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Use freeview to visualize white and pial surface           External Email - Use Caution         Hi expert, I do not think it's related to RAM. When I try to load some images larger than the image that it fails to load, it also works. So, I guess it might be related to other issues.  PS. the current free RAM is 6GB.   Best, Cain     At 2023-08-08 03:49:29, "Fischl, Bruce R.,PHD" <BFISCHL(a)mgh.harvard.edu> wrote:         External Email - Use Caution         Maybe you are at the edge of how much ram you have in that machine? How much free memory do you have?   From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DS Sent: Monday, August 7, 2023 3:48 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Use freeview to visualize white and pial surface           External Email - Use Caution         Hi expert, Thanks for your reply. I used the following command line. freeview -f \ lh.white:edgecolor=blue \ lh.pial:edgecolor=red   I also tried to load these images by clicking the icons on the interface of Freeview. But, both approaches do not work. The first image it loads just flashed, and then it's closed when it started to load the second image. But, I tried some images from another subject, then it works. Best, Cain     At 2023-08-08 03:13:52, "Fischl, Bruce R.,PHD" <BFISCHL(a)mgh.harvard.edu> wrote:         External Email - Use Caution         What is your freeview command line/   From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DS Sent: Monday, August 7, 2023 2:51 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Use freeview to visualize white and pial surface           External Email - Use Caution         I have a question about freeview. Recently, when I loaded lh.pial and lh.white at the same time, the freeview was suddenly aborted and reported the following error.   .../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion `used_next <= save->vertex_store->buffer_in_ram_size' failed.   But, if I load lh.pial or lh.white separately, I found it’s working.. I guess there might be inconsistent parameters between the two files, because when I check another subject, both files can be visualized very well.  Do you have any thoughts about this issue? Thank you so much for any suggestions.   PS. Previously I posted this question with the images that I use to troubleshoot the problem. But, I received an email saying that "this message need approval from moderator, because the files are larger than expected". However, I never receive any update/reply from the moderator so far.   Best, Cain _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1GO2CxTprXM0WjXwNu3z8MZSD_Kaq9fpHjRhGgnYQQ2kXb… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1GO2CxTprXM0WjXwNu3z8MZSD_Kaq9fpHjRhGgnYQQ2kXb… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1GO2CxTprXM0WjXwNu3z8MZSD_Kaq9fpHjRhGgnYQQ2kXb… Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

2 1

Use freeview to visualize white and pial surface
by DS 08 Aug '23

08 Aug '23

External Email - Use Caution I have a question about freeview. Recently, when I loaded lh.pial and lh.white at the same time, the freeview was suddenly aborted and reported the following error. ../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion `used_next <= save->vertex_store->buffer_in_ram_size' failed. But, if I load lh.pial or lh.white separately, I found it’s working. I guess there might be inconsistent parameters between the two files, because when I check another subject, both files can be visualized very well. Do you have any thoughts about this issue? Thank you so much for any suggestions. PS. Previously I posted this question with the images that I use to troubleshoot the problem. But, I received an email saying that "this message need approval from moderator, because the files are larger than expected". However, I never receive any update/reply from the moderator so far. Best, Cain

3 10

followup question on computing merged volumes of both hemispheres
by inbal paran 08 Aug '23

08 Aug '23

External Email - Use Caution By hand/matlab - simply to sum the volumes in each hemisphere? e.g., Rt. Caudate+ Lt. Caudate? ----- You'll have to do it by hand or maybe in matlab; you can use fast_ldtable.m to load in the tables in matlab On 8/5/2023 4:54 AM, inbal paran wrote: External Email - Use Caution Hello FreeSurfer Developers, I need to compute the volume of specific bilateral cortical and subcortical ROIs. I already ran reacon-all on all of my subjects, and I extracted volumes of the ROIs per hemisphere of both the cortical and subcortical brain regions (aseg and aparc). How can I compute the merged volume of both hemispheres per each ROI? The freesurfer version I am using: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Thank you Inbal -- *Inbal Paran, M.PT <http://secure-web.cisco.com/1Z9QuT-veibLSEyJxGKDxTdAyAoxIqlB6JWuujOlYgppYXY…>.* Schwartz Movement analysis & Rehabilitation Laboratory, Physical Therapy Department, Recanati School for Community Health Professions. Faculty of Health Sciences at Ben-Gurion University of the Negev.

1 0

Re: [Freesurfer] Freesurfer version and Installation
by fsbuild 08 Aug '23

08 Aug '23

External Email - Use Caution  The mri_synthsr script in the 7.4.1 release from June 2023 offers 3 models - one version 1.0 model and two version 2.0 models (depending upon the arguments).  The default in the absence of any qualifying arguments is the general version 2 model. - R.           if args.v1:             print('Using version 1 model from July 2021')             path_model = os.path.join(os.environ.get('FREESURFER_HOME'), 'models', 'synthsr_v10_210712.h5')          elif args.lowfield:            print('Using model for low-field scans from January 2023 (version 2)')             path_model = os.path.join(os.environ.get('FREESURFER_HOME'), 'models', 'synthsr_lowfield_v20_230130.h5')          else:             print('Using general model from January 2023 (version 2)')             path_model = os.path.join(os.environ.get('FREESURFER_HOME'), 'models', 'synthsr_v20_230130.h5’) On Aug 8, 2023, at 04:52, hmarzban(a)student.ubc.ca wrote:        External Email - Use Caution        Hello,Thank you for your response.I have an additional question: I am utilizing Synthsr version 2.0. Is this particular version included in The 7.4.1 version of freeusrfer?RegardsHengamehFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of hmarzban@student.ubc.ca<hmarzban@student.ubc.ca>Sent: Monday, July 31, 2023 11:38:48 AMTo: freesurfer@nmr.mgh.harvard.eduSubject: [Freesurfer] Freesurfer version and Installation [CAUTION: Non-UBC Email]        External Email - Use Caution        Dear Freesurfer developers,Previously, I downloaded the freesurfer-linux-centos7_x86_64-dev-20230331-e304091 version and successfully analyzed some data using this version. Now, I find myself in the need to reinstall Freesurfer, but I am unable to locate the source file on your website.Could you kindly guide me to where I can find the mentioned version? Alternatively, if this specific version is no longer available, please advise me on which version I should download and install to achieve the same results as before.Thank you very much for your assistance.RegardsHengameh_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Freesurfer version and Installation
by hmarzban＠student.ubc.ca 08 Aug '23

08 Aug '23

External Email - Use Caution Dear Freesurfer developers, Previously, I downloaded the freesurfer-linux-centos7_x86_64-dev-20230331-e304091 version and successfully analyzed some data using this version. Now, I find myself in the need to reinstall Freesurfer, but I am unable to locate the source file on your website. Could you kindly guide me to where I can find the mentioned version? Alternatively, if this specific version is no longer available, please advise me on which version I should download and install to achieve the same results as before. Thank you very much for your assistance. Regards Hengameh

1 1

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