Freesurfer November 2022

freesurfer@nmr.mgh.harvard.edu

80 participants
119 discussions

dcmunpack
by Jang, Woo Ju Albert W.,PhD 08 Nov '22

08 Nov '22

Hi, I need to unpack dcm files to my local workstation via dcmunpack command. Is it possible to install this command on my local workstation? Best, Albert

2 1

change in mask size
by priya padma 08 Nov '22

08 Nov '22

External Email - Use Caution Dear Team, I tried using freesurfer for skull stripping and I got results all of size 256X256X256 but the original data size is different, it's 512X512X537. Is there any way to bring back the original size in freesurfer? Any help would be appreciated. Thank you -- Best Regards Padma Priya *AI Developer * *PhenoMx, Inc.* *priya(a)phenomx.ai <priya(a)phenomx.ai> | (+82)10-5405-2685*

3 2

Question regarding General Linear Model analysis with Freesurfer
by Lyna Mariam El Haffaf 08 Nov '22

08 Nov '22

External Email - Use Caution Hi! I hope you are doing well! I am working on a paper where we used Freesurfer for whole brain analysis in intergroup comparison (g2v1). The objective of the analysis is to see if there is an association between neuropsychiatric symptoms and brain regions at different stages of Alzheimer's disease (Alzheimer, Mild cognitive impairment and cognitively normal participants). For this objective, a whole-brain analysis was performed using general linear model (GLM) analysis with FreeSurfer mri_glmfit for each neuropsychiatric symptoms of interest to assess their effect on brain’s cortical volume, thickness and area, between the groups (AD vs MCI, CN vs MCI, CN vs AD). We performed a Monte-Carlo correction on the results obtained. I was wondering if it was possible to add another correction for multiple group comparison in addition to the Monte-Carlo correction? Also, is it possible to add covariates by creating additional models using the GLM analysis with Freesurfer mri_glmfit? Thank you in advance! Lyna El Haffaf Graduate student in neuropsychology Université de Montréal

2 1

Re: [Freesurfer] Segmentation Fault (Ventura)
by fsbuild 07 Nov '22

07 Nov '22

External Email - Use Caution Hello Joann, If I read correctly, you are doing a remote mount of a shared network drive to your Mac to store/read/write the subject files but running the recon-all using your Mac processors. You might want to check the directory for the last subject processed to see if there are log files with any more info.  A segmentation fault can happen for various reasons, but we might be able to tell something if you can get a hold of the core dump file. There could be differences w.r.t  how Ventura maintains a connection to and interacts with a remote file system compared to Monterey, e.g., timeouts, authentication, file caching, etc .  If recon-all was proceeding normally and then no longer could see or access the remote file system when it needed to read or write a file, then the recon-all would fail.  But I would expect to see some message w.r.t file not found, permission denied and not just a segfault message. We have have not done any testing with MacOS Ventura and we don’t generally test on MacOS using remotely mounted file systems.  Many Mac users I know always stay one operating system release behind the latest version of MacOS.  They are only now upgrading from BigSur to Monterey since Ventura was officially released last month.   If I have test the latest release I try to wait until the first .1 release is out as the initial .0 releases are often the most buggy (for Ventura that would mean waiting for 13.1). - R. On Nov 7, 2022, at 17:27, Joann Stewart <stewart.joann3(a)yahoo.com> wrote:        External Email - Use Caution        Hello, I am attempting to analyze some structural morphometry data. I am having issues with the recon-all command that I am using. I am attempting to run this command on a shared network folder through my institution. Here is the exact command I am using : recon-all -subject 1306_A -i 1306/T1w/T1w_MPR.nii.gz -T2 1306/T2w/T2w_SPC.nii.gz -T2pial -all -qcache   On the server, when I run this command, it continues until I get to the segmentation portion. I have the full output of this command attached to the email in a word document titled “Recon-all output on server”. Attached I also have a copy of the recon-all.log file. There is another member in my lab who was able to use this command successfully with the same files and exact same code. He was using the same server that I was on, and we have exactly the same permissions on the server. The only difference is that I have updated my mac to Ventura and he has not yet updated his mac (he is using macOS Monterey 12.6).  We tried moving my files onto my desktop to see if the recon-all worked there as compared to the server. I simply moved the T1w & T2w NIfTI files onto my desktop from the server. When I run recon all sourcing from the NIfTI files on my desktop rather than the server, it works fine without error.  Therefore, we are wondering if it is an issue with the new Ventura update in conjunction with shared network folders. Do you have any suggestions or ideas based on the information I have provided? FreeSurfer version: freesurfer-darwin-macOS-7.3.2-20220804-6354275Platform: MacOS Ventura 13.0 Let me know if there is any more information that you need.  Thank you!<Recon-all output on server.docx><recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Segmentation Fault (Ventura)
by Joann Stewart 07 Nov '22

07 Nov '22

External Email - Use Caution Hello, I am attempting to analyze some structural morphometry data. I am having issues with the recon-all command that I am using. I am attempting to run this command on a shared network folder through my institution. Here is the exact command I am using : recon-all -subject 1306_A -i 1306/T1w/T1w_MPR.nii.gz -T2 1306/T2w/T2w_SPC.nii.gz -T2pial -all -qcache On the server, when I run this command, it continues until I get to the segmentation portion. I have the full output of this command attached to the email in a word document titled “Recon-all output on server”. Attached I also have a copy of the recon-all.log file. There is another member in my lab who was able to use this command successfully with the same files and exact same code. He was using the same server that I was on, and we have exactly the same permissions on the server. The only difference is that I have updated my mac to Ventura and he has not yet updated his mac (he is using macOS Monterey 12.6). We tried moving my files onto my desktop to see if the recon-all worked there as compared to the server. I simply moved the T1w & T2w NIfTI files onto my desktop from the server. When I run recon all sourcing from the NIfTI files on my desktop rather than the server, it works fine without error. Therefore, we are wondering if it is an issue with the new Ventura update in conjunction with shared network folders. Do you have any suggestions or ideas based on the information I have provided? - FreeSurfer version: freesurfer-darwin-macOS-7.3.2-20220804-6354275 - Platform: MacOS Ventura 13.0 Let me know if there is any more information that you need. Thank you!

1 0

Freeview keeps crushing on my mac
by Addison, Reuben 04 Nov '22

04 Nov '22

Translated Report (Full Report Below) ------------------------------------- Process: freeview [1595] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Identifier: com.freesurfer.freeview Version: ??? Code Type: X86-64 (Translated) Parent Process: launchd [1] User ID: 501 Date/Time: 2022-11-04 20:43:35.2335 -0400 OS Version: macOS 13.0 (22A380) Report Version: 12 Anonymous UUID: B1BCEA6F-A26D-F89C-B3D0-C46913EB13B2 Sleep/Wake UUID: 6E122B95-20E1-4C26-84B6-155F53AD714F Time Awake Since Boot: 930 seconds Time Since Wake: 316 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 [1595] VM Region Info: 0 is not in any region. Bytes before following region: 4333604864 REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL UNUSED SPACE AT START ---> __TEXT 1024d9000-103b41000 [ 22.4M] r-x/rwx SM=COW ...acOS/freeview Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 QtCore 0x11fc59a51 QThreadStorageData::get() const + 49 1 QtGui 0x11ea2d9fc QFontPrivate::engineForScript(int) const + 92 2 QtGui 0x11ea4a368 QFontMetrics::horizontalAdvance(QChar) const + 104 3 QtWidgets 0x11dd681d9 QProgressBar::sizeHint() const + 137 4 QtWidgets 0x11dbfbc89 QWidgetItemV2::updateCacheIfNecessary() const + 41 5 QtWidgets 0x11dbfc1e3 QWidgetItemV2::maximumSize() const + 67 6 QtWidgets 0x11dbebf11 0x11dbcb000 + 134929 7 QtWidgets 0x11dbed53b non-virtual thunk to QBoxLayout::sizeHint() const + 27 8 QtWidgets 0x11dbf8877 QLayout::totalSizeHint() const + 119 9 QtWidgets 0x11dc17235 QWidget::sizeHint() const + 37 10 QtWidgets 0x11dcbf103 QFrame::sizeHint() const + 67 11 QtWidgets 0x11dbfbc89 QWidgetItemV2::updateCacheIfNecessary() const + 41 12 QtWidgets 0x11dbfc1e3 QWidgetItemV2::maximumSize() const + 67 13 QtWidgets 0x11dbebf11 0x11dbcb000 + 134929 14 QtWidgets 0x11dbed53b non-virtual thunk to QBoxLayout::sizeHint() const + 27 15 QtWidgets 0x11dbf8877 QLayout::totalSizeHint() const + 119 16 QtWidgets 0x11dbf81e5 QLayout::activate() + 277 17 QtWidgets 0x11dc16f77 QWidgetPrivate::setVisible(bool) + 471 18 freeview 0x10253f10d 0x1024d9000 + 418061 19 QtCore 0x11fe43f81 QObject::event(QEvent*) + 753 20 QtWidgets 0x11dc1856a QWidget::event(QEvent*) + 4826 21 QtWidgets 0x11dbdb70d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 22 QtWidgets 0x11dbdcb12 QApplication::notify(QObject*, QEvent*) + 594 23 QtCore 0x11fe1a564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 24 QtCore 0x11fe1b79e QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 878 25 libqcocoa.dylib 0x11f677d39 0x11f642000 + 220473 26 libqcocoa.dylib 0x11f6784a8 0x11f642000 + 222376 27 CoreFoundation 0x7ff80f80def1 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 28 CoreFoundation 0x7ff80f80dea0 __CFRunLoopDoSource0 + 157 29 CoreFoundation 0x7ff80f80dc6e __CFRunLoopDoSources0 + 212 30 CoreFoundation 0x7ff80f80c8c8 __CFRunLoopRun + 943 31 CoreFoundation 0x7ff80f80be9f CFRunLoopRunSpecific + 560 32 HIToolbox 0x7ff819633bd6 RunCurrentEventLoopInMode + 292 33 HIToolbox 0x7ff8196339e6 ReceiveNextEventCommon + 679 34 HIToolbox 0x7ff819633723 _BlockUntilNextEventMatchingListInModeWithFilter + 70 35 AppKit 0x7ff812869b37 _DPSNextEvent + 909 36 AppKit 0x7ff8128689b8 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1219 37 AppKit 0x7ff81285aff3 -[NSApplication run] + 586 38 libqcocoa.dylib 0x11f677223 0x11f642000 + 217635 39 QtCore 0x11fe15b7f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 431 40 QtCore 0x11fe1ab72 QCoreApplication::exec() + 130 41 freeview 0x1025d97dd 0x1024d9000 + 1050589 42 dyld 0x213136310 start + 2432 Thread 1:: com.apple.rosetta.exceptionserver 0 runtime 0x7ff7ffc00750 0x7ff7ffbfc000 + 18256 1 runtime 0x7ff7ffc0c66c 0x7ff7ffbfc000 + 67180 2 runtime 0x7ff7ffc0e06c 0x7ff7ffbfc000 + 73836 Thread 2: 0 runtime 0x7ff7ffc1e87c 0x7ff7ffbfc000 + 141436 Thread 3: 0 runtime 0x7ff7ffc1e87c 0x7ff7ffbfc000 + 141436 Thread 4: 0 runtime 0x7ff7ffc1e87c 0x7ff7ffbfc000 + 141436 Thread 5:: QThread 0 ??? 0x7ff89e9ba9a8 ??? 1 libsystem_kernel.dylib 0x7ff80f6fb3ba poll + 10 2 QtCore 0x11fe708d0 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 608 3 QtCore 0x11fe720c7 QEventDispatcherUNIX::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 903 4 QtCore 0x11fe15b7f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 431 5 QtCore 0x11fc5137c QThread::exec() + 140 6 QtCore 0x11fc522f3 0x11fc30000 + 140019 7 libsystem_pthread.dylib 0x7ff80f733259 _pthread_start + 125 8 libsystem_pthread.dylib 0x7ff80f72ec7b thread_start + 15 Thread 6: 0 runtime 0x7ff7ffc1e87c 0x7ff7ffbfc000 + 141436 Thread 7:: com.apple.NSEventThread 0 ??? 0x7ff89e9ba9a8 ??? 1 libsystem_kernel.dylib 0x7ff80f6f46a2 mach_msg2_trap + 10 2 libsystem_kernel.dylib 0x7ff80f70267d mach_msg2_internal + 82 3 libsystem_kernel.dylib 0x7ff80f6fb71a mach_msg_overwrite + 723 4 libsystem_kernel.dylib 0x7ff80f6f4989 mach_msg + 19 5 CoreFoundation 0x7ff80f80e02b __CFRunLoopServiceMachPort + 145 6 CoreFoundation 0x7ff80f80ca84 __CFRunLoopRun + 1387 7 CoreFoundation 0x7ff80f80be9f CFRunLoopRunSpecific + 560 8 AppKit 0x7ff8129c9696 _NSEventThread + 132 9 libsystem_pthread.dylib 0x7ff80f733259 _pthread_start + 125 10 libsystem_pthread.dylib 0x7ff80f72ec7b thread_start + 15 Thread 8: 0 runtime 0x7ff7ffc1e87c 0x7ff7ffbfc000 + 141436 Thread 9: 0 runtime 0x7ff7ffc1e87c 0x7ff7ffbfc000 + 141436 Thread 10: 0 runtime 0x7ff7ffc1e87c 0x7ff7ffbfc000 + 141436 Thread 11:: ThreadIOWorker 0 libsystem_malloc.dylib 0x7ff80f585e2b free + 0 1 QtCore 0x11fcace69 QHashData::free_helper(void (*)(QHashData::Node*)) + 73 2 QtCore 0x11fef20fb 0x11fc30000 + 2892027 3 QtCore 0x11fef217e 0x11fc30000 + 2892158 4 QtCore 0x11fee18ce 0x11fc30000 + 2824398 5 QtCore 0x11fee5eda 0x11fc30000 + 2842330 6 libsystem_c.dylib 0x7ff80f629ccf __cxa_finalize_ranges + 409 7 libsystem_c.dylib 0x7ff80f629ae9 exit + 35 8 freeview 0x10375087c 0x1024d9000 + 19363964 9 freeview 0x1037d94f8 0x1024d9000 + 19924216 10 freeview 0x10254df2c 0x1024d9000 + 479020 11 freeview 0x10254e5bd 0x1024d9000 + 480701 12 freeview 0x102575cc5 0x1024d9000 + 642245 13 freeview 0x1026600af 0x1024d9000 + 1601711 14 QtCore 0x11fc522f3 0x11fc30000 + 140019 15 libsystem_pthread.dylib 0x7ff80f733259 _pthread_start + 125 16 libsystem_pthread.dylib 0x7ff80f72ec7b thread_start + 15 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x000060000115cb80 rbx: 0x00006000025f5650 rcx: 0x00000000000001fa rdx: 0x000000011ffd3310 rdi: 0x0000000000000107 rsi: 0x000000011fc53110 rbp: 0x00000003196fca00 rsp: 0x00000003196fc9c0 r8: 0x0000000000000400 r9: 0x00000000000003ff r10: 0x0000000000001d60 r11: 0x00006000009f6824 r12: 0x0000000000000003 r13: 0x0000000000000000 r14: 0x0000000000000000 r15: 0x0000000000000002 rip: <unavailable> rfl: 0x0000000000000203 tmp0: 0x000000011fc59a3a tmp1: 0x000000011fc59a3a tmp2: 0x000000012025bbd4 Binary Images: 0x11fc30000 - 0x120165fff org.qt-project.QtCore (5.12) <ae294ca9-b3ec-3f0e-b67a-509a13c0c913> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/5/QtCore 0x11e958000 - 0x11eda4fff org.qt-project.QtGui (5.12) <9cc34b01-ae4a-3ff2-ac1b-de08b8fbbbae> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtGui.framework/Versions/5/QtGui 0x11dbcb000 - 0x11e009fff org.qt-project.QtWidgets (5.12) <ef671b84-7965-3c74-89df-09c3fa9096ca> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtWidgets.framework/Versions/5/QtWidgets 0x1024d9000 - 0x103b40fff com.freesurfer.freeview (*) <35cc1656-e7ff-32a5-8ec9-9faf896f9915> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview 0x11f642000 - 0x11f7a8fff libqcocoa.dylib (*) <14bc2336-68e6-3ace-b3a9-f21152a64785> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/platforms/libqcocoa.dylib 0x7ff80f78f000 - 0x7ff80fc26fff com.apple.CoreFoundation (6.9) <bca7763f-086a-3837-b278-2f8046e4e885> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation 0x7ff819604000 - 0x7ff8198fbff2 com.apple.HIToolbox (2.1.1) <ff73b93b-3c5b-3f73-948f-0a35a80f7fad> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox 0x7ff81282b000 - 0x7ff81382fff6 com.apple.AppKit (6.9) <817d572e-eb8c-3999-b7a0-68e1c4b47266> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit 0x213130000 - 0x2131c7fff dyld (*) <0f050705-2258-3d40-b7bc-f3b35a44bbea> /usr/lib/dyld 0x7ff7ffbfc000 - 0x7ff7ffc2bfff runtime (*) <6f797d84-b330-3656-9a0d-7b3dbd3f8a07> /usr/libexec/rosetta/runtime 0x0 - 0xffffffffffffffff ??? (*) <00000000-0000-0000-0000-000000000000> ??? 0x7ff80f6f3000 - 0x7ff80f72cff7 libsystem_kernel.dylib (*) <0c2fd2c9-777c-3355-b70f-7b1b6e9d1b0b> /usr/lib/system/libsystem_kernel.dylib 0x7ff80f72d000 - 0x7ff80f738ff7 libsystem_pthread.dylib (*) <13b5e252-77d1-31e1-888d-1c5f4426ea87> /usr/lib/system/libsystem_pthread.dylib 0x7ff80f584000 - 0x7ff80f5b0ff7 libsystem_malloc.dylib (*) <d95d8c17-9f95-3076-a449-fbc4d1e9ad57> /usr/lib/system/libsystem_malloc.dylib 0x7ff80f5fb000 - 0x7ff80f683fff libsystem_c.dylib (*) <5efaf10b-2ec1-32ed-b077-80125e552c8d> /usr/lib/system/libsystem_c.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 0 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=469.3M resident=0K(0%) swapped_out_or_unallocated=469.3M(100%) Writable regions: Total=2.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.2G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 1280K 10 Activity Tracing 256K 1 CG backing stores 4032K 4 CG image 208K 21 ColorSync 256K 29 CoreAnimation 68.3M 33 CoreGraphics 12K 2 CoreImage 44K 11 CoreUI image data 3740K 26 Foundation 16K 1 Kernel Alloc Once 8K 1 MALLOC 491.9M 76 MALLOC guard page 192K 8 MALLOC_MEDIUM (reserved) 920.0M 8 reserved VM address space (unallocated) MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) Rosetta Arena 4096K 2 Rosetta Generic 1516K 376 Rosetta IndirectBranch 1024K 1 Rosetta JIT 128.0M 1 Rosetta Return Stack 200K 20 Rosetta Thread Context 200K 20 STACK GUARD 28K 7 Stack 13.1M 11 Stack Guard 56.0M 4 VM_ALLOCATE 2200K 44 VM_ALLOCATE (reserved) 4K 1 reserved VM address space (unallocated) __CTF 756 1 __DATA 261.7M 367 __DATA_CONST 14.8M 207 __DATA_DIRTY 672K 110 __FONT_DATA 2352 1 __GLSLBUILTINS 5174K 1 __LINKEDIT 171.1M 28 __OBJC_RO 65.1M 1 __OBJC_RW 1980K 2 __TEXT 298.2M 381 dyld private memory 256K 1 mapped file 4.3G 1330 shared memory 816K 17 unshared pmap 13.8M 10 =========== ======= ======= TOTAL 7.1G 3176 TOTAL, minus reserved VM space 5.8G 3176 ----------- Full Report ----------- {"app_name":"freeview","timestamp":"2022-11-04 20:43:35.00 -0400","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 13.0 (22A380)","roots_installed":0,"name":"freeview","incident_id":"AA8E5DFB-2DCE-44EA-A098-850E5A5E320A"} { "uptime" : 930, "procRole" : "Foreground", "version" : 2, "userID" : 501, "deployVersion" : 210, "modelCode" : "MacBookPro18,2", "coalitionID" : 909, "osVersion" : { "train" : "macOS 13.0", "build" : "22A380", "releaseType" : "User" }, "captureTime" : "2022-11-04 20:43:35.2335 -0400", "incident" : "AA8E5DFB-2DCE-44EA-A098-850E5A5E320A", "pid" : 1595, "translated" : true, "cpuType" : "X86-64", "roots_installed" : 0, "bug_type" : "309", "procLaunch" : "2022-11-04 20:42:43.0274 -0400", "procStartAbsTime" : 21283681272, "procExitAbsTime" : 22536310181, "procName" : "freeview", "procPath" : "\/Applications\/freesurfer\/*\/Freeview.app\/Contents\/MacOS\/freeview", "bundleInfo" : {"CFBundleIdentifier":"com.freesurfer.freeview"}, "storeInfo" : {"deviceIdentifierForVendor":"9787528D-571D-5D22-ADD3-18E1DA75C5F1","thirdParty":true}, "parentProc" : "launchd", "parentPid" : 1, "coalitionName" : "com.freesurfer.freeview", "crashReporterKey" : "B1BCEA6F-A26D-F89C-B3D0-C46913EB13B2", "wakeTime" : 316, "sleepWakeUUID" : "6E122B95-20E1-4C26-84B6-155F53AD714F", "sip" : "enabled", "vmRegionInfo" : "0 is not in any region. Bytes before following region: 4333604864\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1024d9000-103b41000 [ 22.4M] r-x\/rwx SM=COW ...acOS\/freeview", "exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"}, "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"exc handler","byPid":1595}, "vmregioninfo" : "0 is not in any region. Bytes before following region: 4333604864\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1024d9000-103b41000 [ 22.4M] r-x\/rwx SM=COW ...acOS\/freeview", "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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"SIRI_UNDERSTANDING_MORPHUN" : "62ec7220c682040ba94e6a20" }, "deploymentId" : 240000468 } ], "experiments" : [ ] } } Model: MacBookPro18,2, BootROM 8419.41.10, proc 10:8:2 processors, 32 GB, SMC Graphics: Apple M1 Max, Apple M1 Max, Built-In Display: Color LCD, 3456 x 2234 Retina, Main, MirrorOff, Online Memory Module: LPDDR5, Samsung AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x4387), wl0: Sep 3 2022 02:35:52 version 20.10.965.9.8.7.129 FWID 01-b0e84a9b Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports Network Service: Wi-Fi, AirPort, en0 USB Device: USB31Bus USB Device: USB31Bus USB Device: USB31Bus Thunderbolt Bus: Laptop, Apple Inc. Thunderbolt Bus: Laptop, Apple Inc. Thunderbolt Bus: Laptop, Apple Inc. Reuben N. Addison Postdoctoral Fellow Brain Recovery Lab MGH Institute of Health Professions<https://www.mghihp.edu/> Charlestown Navy Yard | 36 1st Avenue, Boston MA 02129 p. 225-439-5354 | raddison(a)mghihp.edu<mailto:raddison@mghihp.edu>

1 0

"Smooth display" in FreeView using command line
by Arman Avesta 04 Nov '22

04 Nov '22

External Email - Use Caution Hi Gang, Happy Friday! I'm using this little command to overlay two volumes (brainbox.mgz and target.nii.gz) in FreeView: freeview -v brainbox.mgz:opacity=0.75 target.nii.gz:colormap=heat:opacity=0.5 I want to show target.nii.gz contours as "Smooth display", which is a checkbox in FreeView as shown here: Is there a property in the "freeview" command (like :colormap or :opacity) that can do it (instead of checking that box in FreeView every time)? I randomly tried :display=smooth, but it didn't work :D Thank you for your help, Arman

2 1

Fw: TRACULA error- segmentation fault
by Shanika Jayakody 03 Nov '22

03 Nov '22

External Email - Use Caution Dear TRACULA team I got an error in pre processing that "Writing output files to /gs/gsfs0/users/helena_blumen_lab/TRACULA/30285/dlabel/syn/lh.cst_avg16_syn_bbr_* Writing spline volume to /gs/gsfs0/users/helena_blumen_lab/TRACULA/30285/dlabel/syn/lh.cst_avg16_syn_bbr_cpts_7.nii.gz Segmentation fault (core dumped) Linux cpu-769.cluster.local 4.18.0-305.19.1.el8_4.x86_64 #1 SMP Tue Sep 7 07:07:31 EDT 2021 x86_64 x86_64 x86_64 GNU/Linux" I checked Freesurfer mail and found it could happen when older version are used but I use 7.2 I have attached the configuration file. Thank you for any suggestions. This happened for another ID as well but for a different tract. I have been using similar configuration files and trac-prep finished without error for my other subjects Regards Oshadi

1 0

Longitudinal stream bug ?
by Lauri Tuominen 03 Nov '22

03 Nov '22

External Email - Use Caution Hi FreeSurfer Developers, I am trying to run a longitudinal analysis on Ubuntu 20.04.1 LTS, freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551, and Python 3.8.5. I use the following command: long_mris_slopes --qdec ../tables/long.all.table.dat \ --meas thickness \ --hemi lh \ --sd $SUBJECTS_DIR \ --do-spc --do-label \ --generic-time \ --fwhm 15 \ --qcache fsaverage \ --stack-spc ../group/lh.generictime.thickness-spc.stack.mgh \ --isec-labels lh.generictime.fsaverage.cortex.label Error message I get is this: mris_calc -o ./tmp-template_P08_lh_thickness_mfuld5s6/betam.mgh ./tmp-template_P08_lh_thickness_mfuld5s6/betam.mgh add ./tmp-template_P08_lh_thickness_mfuld5s6/beta0.mgh Saving result to './tmp-template_P08_lh_thickness_mfuld5s6/betam.mgh' (type = MGH ) [ ok ] Traceback (most recent call last): File "/mnt/scratch/software/freesurfer//python/scripts/long_mris_slopes", line 1005, in <module> if fwhm > 0: TypeError: '>' not supported between instances of 'str' and 'int' I tried to search for this error but did not see anything. Would anyone have any thoughts on how to fix this? Thanks in advance Lauri Tuominen?

1 1

Requesting Pass Code for FS_7_2_0_ubuntu_18_04_06.ova VirtualBox Image
by Preston Bowman 03 Nov '22

03 Nov '22

External Email - Use Caution Good morning, I would like to kindly request the pass code for the FS_7_2_0_ubuntu_18_04_06.ova VirtualBox Image. Thanks, Preston

1 0

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