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Advice? Re: Freeview 7.1.1 won't start on Mac: segmentation fault
by Sam Buck Johnson 01 Mar '22

01 Mar '22

External Email - Use Caution Dear Freesurfer experts, I am writing to request technical assistance with freeview. I use freesurfer and freeview in my current research, where they are very valuable tools. However, upon upgrading my macbook's OS to macOS Monterey, Version 12.2.1, I now am unable to open freeview; it quits immediately upon starting. The error message indicates a segmentation fault, and in fact my error (and the error message) appears to be exactly the same as the one encountered by Alex White in this thread: https://secure-web.cisco.com/1IXdnFyTKmN2mh6oaF1iVQ3_Ho1Z9szlPmaAOZrSIy7EZw… I have been in correspondence with Alex, and he mentioned that you were able to help him resolve the issue, but that it required you to send him a patched version of freeview (or freesurfer?). I have the identical problem on freeview 7.1.1 and 7.2.0, but if possible I would prefer to continue working with your latest version, 7.2.0. Please do let me know if further information could help you understand this issue better. For the time being, I have copied the error message that prints to terminal and the full error report, both below. Any help/advice is much appreciated. Sincerely, Sam Johnson Postdoctoral Scholar Yeatman Brain and Education Lab, Stanford University GSE ----- # terminal error message: (base) samjohns@DNab40bbcb 7.2.0 % freeview /Applications/freesurfer/7.2.0/bin/freeview: line 2: 1968 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" # full crash report ------------------------------------- Translated Report (Full Report Below) ------------------------------------- Process: freeview [1673] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Identifier: com.freesurfer.freeview Version: ??? Code Type: X86-64 (Translated) Parent Process: Exited process [1672] Responsible: Terminal [1587] User ID: 502 Date/Time: 2022-03-01 15:12:51.8713 -0800 OS Version: macOS 12.2.1 (21D62) Report Version: 12 Anonymous UUID: DCA45306-7159-2569-6BDE-CF94BEE1E522 Time Awake Since Boot: 1200 seconds System Integrity Protection: enabled Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x0000545845545f67 Exception Codes: 0x0000000000000001, 0x0000545845545f67 Exception Note: EXC_CORPSE_NOTIFY Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11 Terminating Process: exc handler [1673] VM Region Info: 0x545845545f67 is not in any region. Bytes after previous region: 92257060675432 Bytes before following region: 12815019253913 REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL commpage (reserved) 1000000000-7000000000 [384.0G] ---/--- SM=NUL ...(unallocated) ---> GAP OF 0x5f9000000000 BYTES MALLOC_NANO 600000000000-600008000000 [128.0M] rw-/rwx SM=PRV Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 freeview 0x104ec0ff8 0x104ce2000 + 1961976 1 QtWidgets 0x12046c6ed QWidget::event(QEvent*) + 1117 2 QtWidgets 0x12057dc45 QMainWindow::event(QEvent*) + 277 3 QtWidgets 0x12043070d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 4 QtWidgets 0x120431b12 QApplication::notify(QObject*, QEvent*) + 594 5 QtCore 0x12266e564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 6 QtWidgets 0x12048aa74 0x120420000 + 436852 7 QtWidgets 0x12043070d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 8 QtWidgets 0x120431b12 QApplication::notify(QObject*, QEvent*) + 594 9 QtCore 0x12266e564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 10 QtGui 0x1211e2a74 QGuiApplicationPrivate::processGeometryChangeEvent(QWindowSystemInterfacePrivate::GeometryChangeEvent*) + 516 11 QtGui 0x1211e3420 QGuiApplicationPrivate::processWindowScreenChangedEvent(QWindowSystemInterfacePrivate::WindowScreenChangedEvent*) + 736 12 QtGui 0x1211c1c33 bool QWindowSystemInterfacePrivate::handleWindowSystemEvent<QWindowSystemInterface::SynchronousDelivery>(QWindowSystemInterfacePrivate::WindowSystemEvent*) + 115 13 libqcocoa.dylib 0x121eb4c77 0x121e96000 + 126071 14 libqcocoa.dylib 0x121eae862 0x121e96000 + 100450 15 libqcocoa.dylib 0x121eae2eb 0x121e96000 + 99051 16 QtGui 0x1211ec1dc QWindowPrivate::create(bool, unsigned long long) + 140 17 QtWidgets 0x120459e31 QWidgetPrivate::create() + 1201 18 QtWidgets 0x120458b22 QWidget::create(unsigned long long, bool, bool) + 322 19 QtWidgets 0x12057e4d7 QMainWindow::setUnifiedTitleAndToolBarOnMac(bool) + 55 20 freeview 0x104eaf497 0x104ce2000 + 1889431 21 freeview 0x104ea950e 0x104ce2000 + 1864974 22 freeview 0x104de279a 0x104ce2000 + 1050522 23 dyld 0x2158184fe start + 462 Thread 1:: com.apple.rosetta.exceptionserver 0 runtime 0x7ff7ffc578e4 0x7ff7ffc53000 + 18660 1 runtime 0x7ff7ffc64928 0x7ff7ffc53000 + 71976 2 runtime 0x7ff7ffc660a4 0x7ff7ffc53000 + 77988 Thread 2: 0 runtime 0x7ff7ffc75814 0x7ff7ffc53000 + 141332 Thread 3: 0 runtime 0x7ff7ffc75814 0x7ff7ffc53000 + 141332 Thread 4:: Dispatch queue: com.apple.dock.fullscreen 0 dyld 0x215824e0c dyld4::Loader::LoaderRef::loader(dyld4::RuntimeState const&) const + 68 1 dyld 0x21582cdb1 dyld4::PrebuiltLoader::dependent(dyld4::RuntimeState const&, unsigned int, dyld4::Loader::DependentKind*) const + 95 2 dyld 0x215828a1e dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 532 3 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 4 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 5 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 6 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 7 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 8 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 9 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 10 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 11 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 12 dyld 0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 593 13 dyld 0x215837b4c dyld4::APIs::dlsym(void*, char const*) + 656 14 SkyLight 0x7ff811fbf581 __loginframework_vtable_block_invoke + 605 15 libdispatch.dylib 0x7ff80ccd8cc9 _dispatch_client_callout + 8 16 libdispatch.dylib 0x7ff80ccd9ec1 _dispatch_once_callout + 20 17 SkyLight 0x7ff811fc0de5 SLSCopyCurrentSessionPropertiesInternalBridge + 366 18 SkyLight 0x7ff811e6a097 SLSessionCopyCurrentDictionary + 12 19 AppKit 0x7ff80f9e04ee -[NSDockConnection _makeConnectionIfNeededWithRetryInterval:onDemand:] + 47 20 AppKit 0x7ff8101b9720 __35-[NSDockConnection startConnection]_block_invoke.37 + 45 21 libdispatch.dylib 0x7ff80ccd7ad8 _dispatch_call_block_and_release + 12 22 libdispatch.dylib 0x7ff80ccd8cc9 _dispatch_client_callout + 8 23 libdispatch.dylib 0x7ff80ccdecee _dispatch_lane_serial_drain + 696 24 libdispatch.dylib 0x7ff80ccdf7c8 _dispatch_lane_invoke + 366 25 libdispatch.dylib 0x7ff80cce97e1 _dispatch_workloop_worker_thread + 758 26 libsystem_pthread.dylib 0x7ff80ce8f074 _pthread_wqthread + 326 27 libsystem_pthread.dylib 0x7ff80ce8dffb start_wqthread + 15 Thread 5: 0 runtime 0x7ff7ffc75814 0x7ff7ffc53000 + 141332 Thread 6: 0 runtime 0x7ff7ffc75814 0x7ff7ffc53000 + 141332 Thread 7: 0 runtime 0x7ff7ffc75814 0x7ff7ffc53000 + 141332 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000545845545f5f rbx: 0x000000031e5aac00 rcx: 0x0000000000010000 rdx: 0x000000012046c6dd rdi: 0x00007ff815d4f000 rsi: 0x000000031e5a9c78 rbp: 0x000000031e5a9730 rsp: 0x000000031e5a9720 r8: 0x0000000000000000 r9: 0x0000000000000000 r10: 0x00000001220129e0 r11: 0x00007ff80f8c8bb9 r12: 0x00007ff175745090 r13: 0x000000031e5aac00 r14: 0x000000031e5a9c78 r15: 0x000000031e5a9c78 rip: 0x0000000104ec0ff8 rfl: 0x0000000000000203 tmp0: 0x0000000115a9c01c tmp1: 0x000000012046c6ed tmp2: 0x0000000120a3c1e8 Binary Images: 0x104ce2000 - 0x106349fff com.freesurfer.freeview (*) <35cc1656-e7ff-32a5-8ec9-9faf896f9915> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview 0x120420000 - 0x12085efff org.qt-project.QtWidgets (5.12) <ef671b84-7965-3c74-89df-09c3fa9096ca> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtWidgets.framework/Versions/5/QtWidgets 0x122484000 - 0x1229b9fff org.qt-project.QtCore (5.12) <ae294ca9-b3ec-3f0e-b67a-509a13c0c913> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/5/QtCore 0x1211ac000 - 0x1215f8fff org.qt-project.QtGui (5.12) <9cc34b01-ae4a-3ff2-ac1b-de08b8fbbbae> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtGui.framework/Versions/5/QtGui 0x121e96000 - 0x121ffcfff libqcocoa.dylib (*) <14bc2336-68e6-3ace-b3a9-f21152a64785> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/platforms/libqcocoa.dylib 0x215813000 - 0x21587efff dyld (*) <7de33963-bbc5-3996-ba6e-f1d562c17c95> /usr/lib/dyld 0x7ff7ffc53000 - 0x7ff7ffc82fff runtime (*) <faca02c7-0a4c-3629-a746-55ddcfee9116> /usr/libexec/rosetta/runtime 0x7ff811d55000 - 0x7ff8120eafff com.apple.SkyLight (1.600.0) <eab4373e-52ca-38d7-963a-9f5bd71824e9> /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight 0x7ff80ccd6000 - 0x7ff80cd1cfff libdispatch.dylib (*) <67d92c93-aa68-34c2-964b-23e8a8d32098> /usr/lib/system/libdispatch.dylib 0x7ff80f86e000 - 0x7ff8106fffff com.apple.AppKit (6.9) <9d3ab204-4858-3120-b002-5c38b02edec4> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit 0x7ff80ce8c000 - 0x7ff80ce97fff libsystem_pthread.dylib (*) <ee564342-d8f2-396d-b642-40092cf34d82> /usr/lib/system/libsystem_pthread.dylib 0x0 - 0xffffffffffffffff ??? (*) <00000000-0000-0000-0000-000000000000> ??? External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 0 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=964.1M resident=0K(0%) swapped_out_or_unallocated=964.1M(100%) Writable regions: Total=1.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.2G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 256K 2 Activity Tracing 256K 1 CG backing stores 5056K 8 ColorSync 228K 25 CoreGraphics 8K 2 CoreUI image data 152K 1 Foundation 16K 1 Kernel Alloc Once 8K 1 MALLOC 216.2M 34 MALLOC guard page 192K 9 MALLOC_MEDIUM (reserved) 240.0M 2 reserved VM address space (unallocated) MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) Rosetta Arena 4096K 2 Rosetta Generic 736K 181 Rosetta IndirectBranch 512K 1 Rosetta JIT 128.0M 1 Rosetta Return Stack 100K 10 Rosetta Thread Context 100K 10 STACK GUARD 20K 5 Stack 11.1M 7 Stack Guard 56.0M 2 VM_ALLOCATE 8280K 29 VM_ALLOCATE (reserved) 4K 1 reserved VM address space (unallocated) __DATA 262.5M 320 __DATA_CONST 12.2M 173 __DATA_DIRTY 539K 99 __FONT_DATA 4K 1 __LINKEDIT 704.8M 29 __OBJC_RO 81.8M 1 __OBJC_RW 3136K 2 __TEXT 259.3M 332 __UNICODE 588K 1 dyld private memory 1024K 1 mapped file 5.1G 429 shared memory 848K 22 unshared pmap 5504K 3 =========== ======= ======= TOTAL 7.4G 1749 TOTAL, minus reserved VM space 6.8G 1749 ----------- Full Report ----------- {"app_name":"freeview","timestamp":"2022-03-01 15:12:52.00 -0800","app_version":"","slice_uuid":"35cc1656-e7ff-32a5-8ec9-9faf896f9915","build_version":"","platform":1,"bundleID":"com.freesurfer.freeview","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.2.1 (21D62)","incident_id":"78ED639A-5BDF-48BF-88B6-8A9AE3997115","name":"freeview"} { "uptime" : 1200, "procLaunch" : "2022-03-01 15:12:51.6463 -0800", "procRole" : "Background", "version" : 2, "userID" : 502, "deployVersion" : 210, "modelCode" : "MacBookPro17,1", "procStartAbsTime" : 30601251608, "coalitionID" : 1327, "osVersion" : { "train" : "macOS 12.2.1", "build" : "21D62", "releaseType" : "User" }, "captureTime" : "2022-03-01 15:12:51.8713 -0800", "incident" : "78ED639A-5BDF-48BF-88B6-8A9AE3997115", "bug_type" : "309", "pid" : 1673, "procExitAbsTime" : 30606634548, "translated" : true, "cpuType" : "X86-64", "procName" : "freeview", "procPath" : "\/Applications\/freesurfer\/*\/Freeview.app\/Contents\/MacOS\/freeview", "bundleInfo" : {"CFBundleIdentifier":"com.freesurfer.freeview"}, "storeInfo" : {"deviceIdentifierForVendor":"61B48C8D-0860-568E-953B-3DE776CD3C66","thirdParty":true}, "parentProc" : "Exited process", "parentPid" : 1672, "coalitionName" : "com.apple.Terminal", "crashReporterKey" : "DCA45306-7159-2569-6BDE-CF94BEE1E522", "responsiblePid" : 1587, "responsibleProc" : "Terminal", "sip" : "enabled", "vmRegionInfo" : "0x545845545f67 is not in any region. 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Bytes after previous region: 92257060675432 Bytes before following region: 12815019253913\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ", "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0}, "faultingThread" : 0, "threads" : 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Thunderbolt Bus: MacBook Pro, Apple Inc.

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Re: [Freesurfer] SAMSEG "lesion" (Illegal instruction) ~ running VM_67
by Cerri, Stefano 28 Feb '22

28 Feb '22

Hi Randy, Your run_samseg syntax is correct and yes, the "lesion" version of SAMSEG requires Tensorflow. The "illegal instruction" error is most probably related to an incompatible version of Tensorflow with your CPU instruction set. You should be able to replicate the error by typing: 1. fspython 1. import tensorflow Would you be able to run SAMSEG lesion on another host machine (possibly a relatively new one) and let us know if the error persists? Best, Stefano Dear R, Yes, I have tried to run "samseg_run" from the command line (I've repeated my syntax below).? I have looked both under the directory where the command ran that produced the ?Illegal instruction? error.? No crash file (a logfile?) or a "core" file were written.? I also looked?/var/crash but that folder was empty too. As I mentioned, I'm a LINUX novice.? I'm even more of a novice with regard to Python. However, I did take a quick at the code looking for any mention of tensorflow, and have copied the python script text as it exists below.? I have highlighted the only mention of tensorflow below.? Does this look like you expect it? Has tensorflow actually been incorporated into the VM??? Note that I have been able to successfully run Samseg without the --lesion flag and the process works just fine (about 20min runtime, aseg looks just fine in Freeview) Again, thanks for any guidance you can provide. -Randy xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx #!/usr/bin/env python import osimport sysimport jsonimport scipy.ioimport freesurfer as fsimport freesurfer.samseg as samseg # ------ Parse Command Line Arguments ------ parser = fs.utils.ArgumentParser() default_threads = int(os.environ.get('OMP_NUM_THREADS', 1)) # requiredparser.add_argument('-o', '--output', metavar='DIR', dest='outputDirectory', help='Output directory.', required=True)parser.add_argument('-i', '--input', nargs='+', action='extend', metavar='FILE', dest='inputFileNames', help='Input image(s).', required=True)# optional processing optionsparser.add_argument('-m', '--mode', nargs='+', help='Output basenames for the input image mode.')parser.add_argument('--threads', type=int, default=default_threads, help='Number of threads to use. Defaults to current OMP_NUM_THREADS or 1.')parser.add_argument('--reg-only', action='store_true', default=False, help='Only perform initial affine registration.')parser.add_argument('-r', '--reg', metavar='FILE', help='Skip initial affine registration and read transform from file.')parser.add_argument('--init-reg', metavar='FILE', help='Initial affine registration.')parser.add_argument('-a', '--atlas', metavar='DIR', help='Point to an alternative atlas directory.')parser.add_argument('--gmm', metav ar='FILE', help='Point to an alternative GMM file.')parser.add_argument('--ignore-unknown', action='store_true', help='Ignore final priors corresponding to unknown class.')parser.add_argument('--options', metavar='FILE', help='Override advanced options via a json file.')parser.add_argument('--pallidum-separate', action='store_true', default=False, help='Move pallidum outside of global white matter class. Use this flag when T2/flair is used.')# optional lesion optionsparser.add_argument('--lesion', action='store_true', default=False, help='Enable lesion segmentation (requires tensorflow).')parser.add_argument('--threshold', type=float, default=0.3, help='Lesion threshold for final segmentation. Lesion segmentation must be enabled.')parser.add_argument('--samples', type=int, default=50, help='Number of samples for lesion segmentation. Lesion segmentation must be enabled.')parser.add_argument('--burnin', type=int, default=50, help='Number of burn-in samples for lesion segmentation. Les ion segmentation must be enabled.')parser.ad! d_argume nt('--lesion-pseudo-samples', nargs=2, type=float, default=[500, 500], help='Lesion pseudo samples mean and variance.')parser.add_argument('--lesion-rho', type=float, default=50, help='Lesion ratio.')parser.add_argument('--lesion-mask-structure', default='Cortex', help='Intensity mask brain structure. Lesion segmentation must be enabled.')parser.add_argument('--lesion-mask-pattern', type=int, nargs='+', help='Lesion mask list (set value for each input volume): -1 below lesion mask structure mean, +1 above, 0 no mask. Lesion segmentation must be enabled.')# optional debugging optionsparser.add_argument('--history', action='store_true', default=False, help='Save history.')parser.add_argument('--save-posteriors', nargs='*', help='Save posterior volumes to the "posteriors" subdirectory.')parser.add_argument('--save-probabilities', action='store_true', help='Save final modal class probabilities to "probabilities" subdirectory.')parser.add_argument('--showfigs', action='store_true', defaul t=False, help='Show figures during run.')parser.add_argument('--save-mesh', action='store_true', help='Save the final mesh in template space.')parser.add_argument('--save-warp', action='store_true', help='Save the image->template warp field.')parser.add_argument('--movie', action='store_true', default=False, help='Show history as arrow key controlled time sequence.') args = parser.parse_args() # ------ Initial Setup ------ # Make sure freesurfer has been sourcedif not fs.fshome():? ? fs.fatal('FREESURFER_HOME must be set') # Start the process timertimer = fs.utils.Timer() # Create the output folderos.makedirs(args.outputDirectory, exist_ok=True) # Specify the maximum number of threads the GEMS code will usesamseg.setGlobalDefaultNumberOfThreads(args.threads) # Remove previous cost logcostfile = os.path.join(args.outputDirectory, 'cost.txt')if os.path.exists( costfile ):? ? os.remove( costfile )? # Get the atlas directoryatlasDir = os.environ.get('SAMSEG_DATA_DIR')if args.atlas:? ? atlasDir = args.atlasif not atlasDir:? ? # Altas defaults? ? if args.lesion:? ? ? ? defaultAtlas = '20Subjects_smoothing2_down2_smoothingForAffine2_lesion'? ? else:? ? ? ? defaultAtlas = '20Subjects_smoothing2_down2_smoothingForAffine2'? ? atlasDir = os.path.join(fs.fshome(), 'average', 'samseg', defaultAtlas) # Setup the visualization toolvisualizer = samseg.initVisualizer(args.showfigs, args.movie) # ------ Prepare Samseg Parameters ------ # Load user options from a JSON fileuserModelSpecifications = {}userOptimizationOptions = {}if args.options:? ? with open(args.options) as f:? ? ? ? userOptions = json.load(f)? ? if userOptions.get('modelSpecifications') is not None:?? ? ? ? userModelSpecifications = userOptions.get('modelSpecifications')? ? if userOptions.get('optimizationOptions') is not None:?? ? ? ? userOptimizationOptions = userOptions.get('optimizationOptions') # Check if --save-posteriors was specified without any structure search stringif args.save_posteriors is not None and len(args.save_posteriors) == 0:? ? savePosteriors = Trueelse:? ? savePosteriors = args.save_posteriors # ------ Run Samseg ------ samseg_kwargs = dict(? ? imageFileNames=args.inputFileNames,? ? atlasDir=atlasDir,? ? savePath=args.outputDirectory,? ? userModelSpecifications=userModelSpecifications,? ? userOptimizationOptions=userOptimizationOptions,? ? targetIntensity=110,? ? targetSearchStrings=[ 'Cerebral-White-Matter' ],? ? visualizer=visualizer,? ? saveHistory=args.history,? ? saveMesh=args.save_mesh,? ? savePosteriors=savePosteriors,? ? saveWarp=args.save_warp,? ? modeNames=args.mode,? ? pallidumAsWM=(not args.pallidum_separate),? ? saveModelProbabilities=args.save_probabilities,? ? gmmFileName=args.gmm,? ? ignoreUnknownPriors=args.ignore_unknown,) if args.lesion: ? ? # If lesion mask pattern is not specified, assume inputs are T1-contrast? ? lesion_mask_pattern = args.lesion_mask_pattern? ? if lesion_mask_pattern is None:? ? ? ? lesion_mask_pattern = [0] * len(args.inputFileNames)? ? ? ? print('Defaulting lesion mask pattern to %s' % str(lesion_mask_pattern)) ? ? # Delay import until here so that tensorflow doesn't get loaded unless needed? ? from freesurfer.samseg.SamsegLesion import SamsegLesion? ? samseg = SamsegLesion(**samseg_kwargs,? ? ? ? numberOfPseudoSamplesMean=args.lesion_pseudo_samples[0],? ? ? ? numberOfPseudoSamplesVariance=args.lesion_pseudo_samples[1],? ? ? ? rho=args.lesion_rho,? ? ? ? intensityMaskingSearchString=args.lesion_mask_structure,? ? ? ? intensityMaskingPattern=lesion_mask_pattern,? ? ? ? numberOfBurnInSteps=args.burnin,? ? ? ? numberOfSamplingSteps=args.samples,? ? ? ? threshold=args.threshold? ? ) else:? ? samseg = samseg.Samseg(**samseg_kwargs) _, _, _, optimizationSummary = samseg.segment(? ? costfile=costfile,? ? timer=timer,? ? transformFile=args.reg,? ? initTransformFile=args.init_reg,? ? reg_only=args.reg_only) # Save a summary of the optimization processwith open(costfile, 'a') as file:? ? for multiResolutionLevel, item in enumerate(optimizationSummary):? ? ? ? file.write('atlasRegistrationLevel%d %d %f\n' % (multiResolutionLevel, item['numberOfIterations'], item['perVoxelCost'])) timer.mark('run_samseg complete') xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx PS. Repeating the syntax from below. run_samseg --input /home/developer/subjects_new/o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T30-acc_orig__S689126_I1001975.nii /home/developer/subjects_new/rT1_o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T2-FLAIR__S689135_I1001984.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/developer/subjects_new/Lesion-test/ -----Original Message----- From: fsbuild <fsbuild(a)contbay.com> To: freesurfer(a)nmr.mgh.harvard.edu Cc: daedalus39(a)aol.com Sent: Thu, Feb 24, 2022 5:15 pm Subject: Re: [Freesurfer] SAMSEG "lesion" (Illegal instruction) ~ running VM_67 Hello Randy, I think the expectation is for users to run ?samseg? from the command line. ?(The samseg script is a front-end you run with command line options, e.g., ?help, which calls samseg_run that in turn runs the samseg python scripts in the freesurfer python distribution which includes the tensorflow code). I can?t speak to the validity of the command + options causing the crash, but I would look too see if a ?core? file was written in the directory where the command ran that produced the ?Illegal instruction? error and subsequent crash. ?The core file might also be under /var/crash. ?If you have the core file you could name it something unique and try uploading it to?https://secure-web.cisco.com/1_8ugcIT497YTUyY1vRRMjZbWfONaiAbR1P1Zg9-6zN… someone to look at. - R. On Feb 24, 2022, at 11:58, daedalus39(a)aol.com wrote: ????????External Email - Use Caution???????? Following up on yesterday's email: I looked up the help text for SAMSEG on the VM (?run_samseg ?help?).??The flag for --lesion indicates that Tensorflow is required.???? --lesion??????? Enable lesion segmentation (requires tensorflow).?I'm not sure is tensorflow is installed in VM_67, but "which tensorflow" returned nothing.? While my question only reported the ?core dump? and a request to check the syntax, I did ask if the ?lesion? flag was implemented in the VM.?? If it's not installed in VM_67, would you be able to offer some guidance as to where the safest download site is and some suggestions as to how to install it? Sincerely, -Randy -----Original Message----- From: daedalus39(a)aol.com To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Sent: Wed, Feb 23, 2022 1:19 pm Subject: SAMSEG "lesion" (Illegal instruction) ~ running VM_67 Dear Experts, I am trying to test SAMSEG "lesion" on VM_67 and after I entered: run_samseg --input /home/developer/subjects_new/o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T30-acc_orig__S689126_I1001975.nii /home/developer/subjects_new/rT1_o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T2-FLAIR__S689135_I1001984.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/developer/subjects_new/Lesion-test/ ...I got the following error Illegal instruction (core dumped) Is there anything glaringly wrong in my instruction/input phrase? Is SAMSEG "lesion" implemented in the new VM?? I was able to test the "basic" SAMSEG with a single T1 earlier this morning (it ran just fine) Thanks in advance for any help. -Randy_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1ajCHs20Ntg5vd9AD9I6GP72nyffMyNANWVvUGOngP_c0a…

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Re: [Freesurfer] Annotation File ROIs to Volume
by Jacoby, John 28 Feb '22

28 Feb '22

Ah yep sorry, I see it. Thank you! Best, John

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Fwd: Gcut error: gcutted brain is much smaller than the mask.
by Begüm Cerrahoğlu 28 Feb '22

28 Feb '22

External Email - Use Caution Dear developers, I am trying to clean up the extra dura left after skullstripping. Watershed parameter does not prove to be much helpful and when I try gcut I get the error below. In the archives I came across this exact problem before, https://secure-web.cisco.com/1JREA1RCtgfPRaolYsneD7S5EwcqlaqoCEQHN3rqgzcSwx… However, there was not an end solution available in the archived email exchange. I am not interested in cerebellum and am okay with cutting the cerebellum out of the brain mask as long as it does not interfere with being able to distinctly separate cortex from cerebellum in the following steps. From skullstripping tutorials, I have read that one should not start erasing cerebellum from the brainmask directly and was wondering if you could let me know why? In sum, are there important reasons to keep the cerebellum despite only being interested in analyzing the cortex? If not, could you please let me know what could be the reason for gcut's failure and if there is anyway to disable failure detection so I can see if the gcutted brain is usable? >> " rm -f brainmask.gcuts.mgz >> mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz >> brainmask.gcuts.mgz >> >> INFO: Care must be taken to thoroughly inspect your data >> when using mri_gcut. In particular, inspect the edges of >> gm and cerebellum for over-aggressive cutting. >> Add -segmentation brainmask.gcuts.mgz to the tkmedit >> command string to view the voxels which gcut has removed. >> >> reading mask... >> white mean: 107.529232 >> threshold set to: 107.529232*0.400000=43.011693 >> calculating weights... >> doing mincut... >> now doing maxflow, be patient... >> g-cut done! >> post-processing... >> post-processing done! >> masking... >> ** Gcutted brain is much smaller than the mask! >> ** Using the mask as the output instead! >> >> cp brainmask.auto.mgz brainmask.mgz " 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0. 2) Platform: Linux Mint 20.2 Thank you greatly for your time and efforts. Kindest regards, Begum Cerrahoglu

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How to make a planar cut in Freeview 7.1.1
by Brandon Ingram 27 Feb '22

27 Feb '22

External Email - Use Caution Hi all, I have been trying to create a flat patch of occipital cortex using the following tutorial (https://secure-web.cisco.com/18Kww5tnkyQOlM1ft0T_n7raXdSOUfLM9sJBa4TZ-zMjq2…) I have tried following the instructions in Freeview and am able to create a cut down the calcarine sulcus, but cannot find the “cut plane” button described. I was wondering whether this is implemented in Freeview, or whether this tool is only available in tksurfer? Freesurfer Version: 7.1.1 OS: Mac OS, Monterey 12.2.1 Many thanks! Brandon

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Re: [Freesurfer] SAMSEG "lesion" (Illegal instruction) ~ running VM_67
by fsbuild 26 Feb '22

26 Feb '22

External Email - Use Caution Hello Randy, I think the expectation is for users to run “samseg” from the command line.  (The samseg script is a front-end you run with command line options, e.g., —help, which calls samseg_run that in turn runs the samseg python scripts in the freesurfer python distribution which includes the tensorflow code). I can’t speak to the validity of the command + options causing the crash, but I would look too see if a “core” file was written in the directory where the command ran that produced the “Illegal instruction” error and subsequent crash.  The core file might also be under /var/crash.  If you have the core file you could name it something unique and try uploading it to https://secure-web.cisco.com/13zdjoSMY5sCPpxW673b6aDxUESbBUC7j-BF_P… someone to look at. - R. On Feb 24, 2022, at 11:58, daedalus39(a)aol.com wrote:        External Email - Use Caution        Following up on yesterday's email:I looked up the help text for SAMSEG on the VM (“run_samseg –help”).  The flag for --lesion indicates that Tensorflow is required.     --lesion        Enable lesion segmentation (requires tensorflow). I'm not sure is tensorflow is installed in VM_67, but "which tensorflow" returned nothing.  While my question only reported the “core dump” and a request to check the syntax, I did ask if the “lesion” flag was implemented in the VM.  If it's not installed in VM_67, would you be able to offer some guidance as to where the safest download site is and some suggestions as to how to install it?Sincerely,-Randy-----Original Message-----From: daedalus39(a)aol.comTo: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>Sent: Wed, Feb 23, 2022 1:19 pmSubject: SAMSEG "lesion" (Illegal instruction) ~ running VM_67Dear Experts,I am trying to test SAMSEG "lesion" on VM_67 and after I entered:run_samseg --input /home/developer/subjects_new/o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T30-acc_orig__S689126_I1001975.nii /home/developer/subjects_new/rT1_o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T2-FLAIR__S689135_I1001984.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/developer/subjects_new/Lesion-test/...I got the following errorIllegal instruction (core dumped)Is there anything glaringly wrong in my instruction/input phrase?Is SAMSEG "lesion" implemented in the new VM?  I was able to test the "basic" SAMSEG with a single T1 earlier this morning (it ran just fine)Thanks in advance for any help.-Randy_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Using mri_transform with output of bbregister
by Tisdall, Dylan 25 Feb '22

25 Feb '22

External Email - Use Caution Hi all, Thanks again for all the help so far with getting my data registered and surfaces extracted. I have one further issue that I'm hoping to get help with. I've used bbregister to align my T2 scan with the surfaces from my T1 scan. However, the output is resampled down to 1mm iso and a 256^3 volume; I'd like to keep the native 0.8 mm resolution and FOV if possible (acknowledging, of course, there's actually some blurring in the interpolation, but just for the sake of nominal consistency). I tried to work around this by applying the .lta output by bbregister to my T2 scan (with the goal of eventually using the --out-like flag to specify the sampling resolution, but not doing that yet): mri_transform T2_SPACE.nii.gz T2_SPACE_transform.lta T2_SPACE_warped.nii.gz However, when I load the resulting output volume (T2_SPACE_warped.nii.gz) in freeview, it has swapped axes. Strangely, this isn't the case with the output volume generated by bbregister... it's well-aligned with the surfaces. Similarly, if I load the T2_SPACE.nii.gz into freeview, and apply T2_SPACE_transform.lta as part of the load command, the volume is well-aligned. So what's different about how mri_transform applies that .lta file, compared to bbregister and freeview? Is there a way to just get bbregister to resample my T2 scan with the original resolution and FOV, so I can avoid applying mri_transform altogether? I don't see an --out-like option for bbregister, but is there a different flag? Thanks again, Dylan

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Neverending mris_fix_topology
by Peled, Noam 25 Feb '22

25 Feb '22

Dear group, I'm trying to run recon-all (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551) on my Martinos' desktop. I killed it after waiting quite a of time for the mris_fix_topology to be completed: Waiting for PID 225967 of (225964 225967) to complete... What can I do to be able to process this subject? I attached the recon-all log. You can also find all the logs here: /autofs/space/mmvtclin_001/thibault/1/users/npeled/subjects/UN07/scripts Thanks! Noam

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PetSurfer: subcortical volume-based analysis
by Jennifer Bramen 25 Feb '22

25 Feb '22

External Email - Use Caution Dear Freesurfer Developers I am doing an ROI--based amyloid PET scan analysis. I have completed all of the steps from the PetSurfer wiki. I now have the preprocessed, averaged, resampled, smoothed PET data in MNI305 space which is constrained to the subcortical gray matter mask. How do I extract mean intensity within all of the subcortical ROI? Thank you! Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069

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NeuroImage: Reports: Call for papers for Special Issue on Replication findings in neuroimaging studies
by YAN Chao-Gan 25 Feb '22

25 Feb '22

External Email - Use Caution Replication is essential for progress in science. There are several reasons why findings may not replicate, including sampling variability, limited statistical power, cultural/population influences, and improvements in data acquisition and analysis methods. Replication studies are our best attempt at confirming or questioning the reliability of important findings. Replication studies also provide a crucial mechanism for reaching consensus about empirical support for or against a theory. Unfortunately, replication studies are difficult to publish, because many journals judge them as “lacking novelty.” For these reasons, we have created a special issue that highlights replication studies. We invite submissions that seek to replicate published neuroimaging studies, regardless of whether the initial results are confirmed. The primary criteria for acceptance are methodological and statistical rigor -- not conceptual novelty. Novel results are also welcomed, but authors must clearly state which analyses are replications and which are novel. Researchers may use their own collected data, original data from the to-be-replicated study, or publicly available data. We hope that this special issue will help highlight the importance of rigorous replication studies for ensuring progress in neuroimaging. *Submission instructions* The Neuroimage: Reports submission system is open for submissions to our Special Issue from *01 Oct 2021*. When submitting your manuscript please select the article type “*VSI: Replication*”. Please submit your manuscript before *01 Mar 2022.* All submissions deemed suitable to be sent for peer review will be reviewed by at least two independent reviewers. Once your manuscript is accepted, it will go into production, and will be simultaneously published in the current regular issue and pulled into the online Special Issue. Articles from this Special Issue will appear in different regular issues of the journal, though they will be clearly marked and branded as Special Issue articles. Please see an example here: https://secure-web.cisco.com/1CJkKxcFEBPguyPfb5m0Yr2MoiAzErZw3HYZKhuEAMSHET… Please ensure you read the Guide for Authors before writing your manuscript. The Guide for Authors and link to submit your manuscript is available on the Journal’s homepage at: https://secure-web.cisco.com/1VSgggrvcDPky-89wNR6lcPY0XqXuCfOZAX-r7Wa1HcuPp… Inquiries, including questions about appropriate topics, may be sent electronically to Dr. Yan Chao-Gan (ycg.yan(a)gmail.com) Best, Chao-Gan -- Chao-Gan YAN, Ph.D. Professor, Principal Investigator Director, International Big-Data Center for Depression Research Director, Magnetic Resonance Imaging Research Center Institute of Psychology, Chinese Academy of Sciences 16 Lincui Road, Chaoyang District, Beijing 100101, China - Initiator <http://secure-web.cisco.com/1sqIAAZ4sZdTTXMKfxT5Aar2JR-7UiWQN4aQSU7ygjFTldr…>DPABI <http://secure-web.cisco.com/1oInECTabhfK3d2rurp29HORgmXMA7sq2SIDskuFNuKnDgO…> <http://secure-web.cisco.com/1sqIAAZ4sZdTTXMKfxT5Aar2JR-7UiWQN4aQSU7ygjFTldr…>, DPABISurf, <http://secure-web.cisco.com/1XPTEW4lBFtrlvcsygGbgiVdlAQ26ae4_S7nefApkjEds0k…>DPARSF <http://secure-web.cisco.com/1sqIAAZ4sZdTTXMKfxT5Aar2JR-7UiWQN4aQSU7ygjFTldr…>, and The R-fMRI Network <http://secure-web.cisco.com/1TCtydiq5Yh8xn1WXFHq0xSYHUMfBiOaJiSlkzkVhdXs_ms…> ( RFMRI.ORG <http://secure-web.cisco.com/1Y_OweFD7n8m7sSc_adhdgF-QyZ2_4q16Hw2t4tYSmw0HA2…>) http://secure-web.cisco.com/1p7GiR8RwAPykrvrU-kv5cEmnIMwRR95RSJmBn47-AcsD64… http://secure-web.cisco.com/1wC4UpbExTFsWuXE3IWRwjCjcBW1uPj-8MrNX4mlQzLH_o7…

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