Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

Freeview problems
by Savoia, Alice (Stud. FPN) 17 Apr '24

17 Apr '24

External Email - Use Caution To whom it may concern, I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), but freeview shuts down immediately when I try to open any file. The license is in the correct place. Thank you for your help, Best regards.

3 8

Error using mris_transform in Freesurfer 7.4.1
by Noemí Hostalet 16 Apr '24

16 Apr '24

External Email - Use Caution Hi, I'm trying to run the following mris_transform command in Freesurfer version 7.4.1: mris_transform group1/z/Freesurfer/surf/lh.smoothwm group1/z/Freesurfer/mri/transforms/talairach.xfm group1/z/Freesurfer/surf/tal/lh.smoothwm.tal.asc But it's giving the following error: The transform does not have the valid src volume info. Either you specify it with --trx-src or make the transform to have the valid src info. In a previous version (Freesurfer 5.3) it ran without problems. Do you know what could be the problem? Thank you -- Noemí

2 1

Re: [Freesurfer] FreeSurfer Download and Install Error: Segmentation Fault
by fsbuild 15 Apr '24

15 Apr '24

External Email - Use Caution  If you setup the Freesurfer environment ... here using bash and not zsh ... hostname ~ bashThe default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://secure-web.cisco.com/1RXVOTUqK1IY787C_o3ARLPP6BLZ_gJwBTdWVVnMp01gcO… $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.4.1FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjectsMNI_DIR           /Applications/freesurfer/7.4.1/mni .... and point FS_LICENSE to your license.txt file, e.g., in your $HOME directory .... $ cd$ pwd/Users/myuserid$ ls license.txtlicense.txt$ export FS_LICENSE=license.txt$ head -1 license.txtyou(a)somewhere.com  <---- email you used to register .... then try running from the command line  ... $ freeview $SUBJECTS_DIR/bert/mri/T1.mgz Please keep in mind you will need to change SUBJECTS_DIR to some other path, e.g., $HOME/subjects $ mkdir -p $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects .... and put files there if you want to write /modify subject files and data since /Applications/freesurfer/7.4.1/subjects is read only by default (not intended to be used to write data). - R.On Apr 15, 2024, at 21:55, Angenelle Rosal <angenelle.rosal(a)mail.utoronto.ca> wrote:        External Email - Use Caution        Hello FreeSurfer Developers, I am currently using FreeSurfer 7.4.1 and I am attempting to upload the T1 image from subject “bert” using the terminal (I am using MacOS Ventura 13.5), as described in the demo video. However, freeview keeps quitting unexpectedly showing “2406 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MAC0S/freeview “$@” when I type in “freeview/Applications/freesurfer/7.4.1/subjects/bert/mri/T1.mgz”. When I manually open Freeview without the terminal and load such image using the “Load Volume” tab, it works fine. I’ve searched the archives list and it might be due to the location of my license. However, I believe my license is located in the correct file, as it is located in my Freesurfer file (/Applications/freesurfer/license.txt). And so, any advice to also solve this problem would be greatly appreciated! Thanks     _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

FreeSurfer Download and Install Error: Segmentation Fault
by Angenelle Rosal 15 Apr '24

15 Apr '24

External Email - Use Caution Hello FreeSurfer Developers, I am currently using FreeSurfer 7.4.1 and I am attempting to upload the T1 image from subject “bert” using the terminal (I am using MacOS Ventura 13.5), as described in the demo video. However, freeview keeps quitting unexpectedly showing “2406 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MAC0S/freeview “$@” when I type in “freeview/Applications/freesurfer/7.4.1/subjects/bert/mri/T1.mgz”. When I manually open Freeview without the terminal and load such image using the “Load Volume” tab, it works fine. I’ve searched the archives list and it might be due to the location of my license. However, I believe my license is located in the correct file, as it is located in my Freesurfer file (/Applications/freesurfer/license.txt). And so, any advice to also solve this problem would be greatly appreciated! Thanks

1 0

I've tried what to do. But, still freeview doesn't work
by 이준하 14 Apr '24

14 Apr '24

External Email - Use Caution I've put in my license.txt file in the freesurfer file but, freeview doesn't work 'Freesurfer quits unexpectedly' Below there is the reason of the quit. ------------------------------------- Translated Report (Full Report Below) ------------------------------------- Process: freeview [71133] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Identifier: org.martinos.freeview Version: 7.3.2 (100) Code Type: X86-64 (Translated) Parent Process: launchd [1] User ID: 501 Date/Time: 2024-04-14 01:16:02.7236 +0900 OS Version: macOS 14.4.1 (23E224) Report Version: 12 Anonymous UUID: FC5C035F-28AB-6F06-73F3-E7191C14B2D7 Sleep/Wake UUID: E0A8B706-B7C5-4F83-AEE3-9FB1B80DF90F Time Awake Since Boot: 60000 seconds Time Since Wake: 15301 seconds System Integrity Protection: enabled Notes: PC register does not match crashing frame (0x0 vs 0x100EA3B98) Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x5367756265442f7b -> 0x0000756265442f7b (possible pointer authentication failure) Exception Codes: 0x0000000000000001, 0x5367756265442f7b Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11 Terminating Process: exc handler [71133] VM Region Info: 0x756265442f7b is not in any region. Bytes after previous region: 23511813074812 Bytes before following region: 11219858346117 REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL MALLOC_NANO 600000000000-600020000000 [512.0M] rw-/rwx SM=PRV ---> GAP OF 0x1f9698f00000 BYTES MALLOC_TINY 7f96b8f00000-7f96b9000000 [ 1024K] rw-/rwx SM=PRV Error Formulating Crash Report: PC register does not match crashing frame (0x0 vs 0x100EA3B98) Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 freeview 0x100ea3b98 0x100cb0000 + 2046872 1 QtWidgets 0x11d14a413 QWidget::event(QEvent*) + 1283 2 QtWidgets 0x11d2895a4 QMainWindow::event(QEvent*) + 276 3 QtWidgets 0x11d0fa0b7 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247 4 QtWidgets 0x11d0faffc QApplication::notify(QObject*, QEvent*) + 508 5 QtCore 0x11dfbc1da QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170 6 QtWidgets 0x11d161de4 0x11d0ee000 + 474596 7 QtWidgets 0x11d15fd5a 0x11d0ee000 + 466266 8 QtWidgets 0x11d0fa0b7 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247 9 QtWidgets 0x11d0faffc QApplication::notify(QObject*, QEvent*) + 508 10 QtCore 0x11dfbc1da QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170 11 QtGui 0x11eef482d QGuiApplicationPrivate::processGeometryChangeEvent(QWindowSystemInterfacePrivate::GeometryChangeEvent*) + 493 12 QtGui 0x11eef5036 QGuiApplicationPrivate::processWindowScreenChangedEvent(QWindowSystemInterfacePrivate::WindowScreenChangedEvent*) + 470 13 QtGui 0x11ef4d29c 0x11ee6c000 + 922268 14 libqcocoa.dylib 0x11c866a50 0x11c81d000 + 301648 15 libqcocoa.dylib 0x11c85f8c9 0x11c81d000 + 272585 16 libqcocoa.dylib 0x11c85f37c 0x11c81d000 + 271228 17 QtGui 0x11ef3e93e QWindowPrivate::create(bool, unsigned long long) + 206 18 QtWidgets 0x11d138d9d QWidgetPrivate::create() + 1037 19 QtWidgets 0x11d136881 QWidget::create(unsigned long long, bool, bool) + 321 20 QtWidgets 0x11d1388e7 QWidgetPrivate::createWinId() + 103 21 QtWidgets 0x11d1388e7 QWidgetPrivate::createWinId() + 103 22 QtWidgets 0x11d1388e7 QWidgetPrivate::createWinId() + 103 23 QtWidgets 0x11d1388e7 QWidgetPrivate::createWinId() + 103 24 QtWidgets 0x11d1388e7 QWidgetPrivate::createWinId() + 103 25 QtWidgets 0x11d1388e7 QWidgetPrivate::createWinId() + 103 26 QtWidgets 0x11d139631 QWidget::winId() const + 65 27 freeview 0x100fab964 0x100cb0000 + 3127652 28 freeview 0x100fab88f 0x100cb0000 + 3127439 29 freeview 0x100d3b59f 0x100cb0000 + 570783 30 freeview 0x100e236cc 0x100cb0000 + 1521356 31 freeview 0x100e263e5 0x100cb0000 + 1532901 32 freeview 0x100e97a1a 0x100cb0000 + 1997338 33 freeview 0x100e8efa3 0x100cb0000 + 1961891 34 freeview 0x100dc82e5 0x100cb0000 + 1147621 35 dyld 0x2119d1366 start + 1942 Thread 1:: com.apple.rosetta.exceptionserver 0 runtime 0x7ff7fff6e494 0x7ff7fff6a000 + 17556 Thread 2: 0 runtime 0x7ff7fff8c94c 0x7ff7fff6a000 + 141644 Thread 3: 0 runtime 0x7ff7fff8c94c 0x7ff7fff6a000 + 141644 Thread 4: 0 runtime 0x7ff7fff8c94c 0x7ff7fff6a000 + 141644 Thread 5: 0 runtime 0x7ff7fff8c94c 0x7ff7fff6a000 + 141644 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x5367756265442f73 rbx: 0x0000000316760cd0 rcx: 0x000000011d14a403 rdx: 0x000000011d14b178 rdi: 0x00007ffc9ccd7698 rsi: 0x000000031675f5f8 rbp: 0x000000031675f290 rsp: 0x000000031675f280 r8: 0x0000000000000841 r9: 0x0000000000000000 r10: 0x000000011c8c74a8 r11: 0x00007ff81b0573cf r12: 0x00007f96d8f46680 r13: 0x0000000316760cd0 r14: 0x000000031675f5f8 r15: 0x000000031675f5f8 rip: <unavailable> rfl: 0x0000000000000217 tmp0: 0x0000000111b6c154 tmp1: 0x000000011d14a413 tmp2: 0x000000011d77b594 Binary Images: 0x2119cb000 - 0x211a5bfff dyld (*) <899f1e34-b624-3162-8003-04daa6829461> /usr/lib/dyld 0x11c3da000 - 0x11c3e6fff libobjc-trampolines.dylib (*) <3d9756e6-f86a-324d-bfd7-dc2d59c27956> /usr/lib/libobjc-trampolines.dylib 0x11c64e000 - 0x11c655fff libqmacjp2.dylib (*) <41234a69-0606-3f7d-ac82-499b68e7ca40> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqmacjp2.dylib 0x11c636000 - 0x11c63dfff libqtga.dylib (*) <4f81c0d1-a27e-3ad1-848f-f6d98b196553> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqtga.dylib 0x11c591000 - 0x11c598fff libqicns.dylib (*) <cf2b53cc-5f03-3dcf-b1dc-d5b19cc7b39e> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqicns.dylib 0x12416c000 - 0x1241d7fff libqtiff.dylib (*) <a588fa3d-680f-33b2-b1b3-02a035bd7cad> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqtiff.dylib 0x123e00000 - 0x123e6ffff libqjpeg.dylib (*) <fb2e4cb6-67fd-3b9d-94d9-d0f3053fc895> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqjpeg.dylib 0x11c576000 - 0x11c57dfff libqmacheif.dylib (*) <e76b1e74-e944-34d2-8d84-5cf2834a81d0> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqmacheif.dylib 0x11c559000 - 0x11c560fff libqico.dylib (*) <794fb25c-3196-3e6b-aef6-714be0814505> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqico.dylib 0x123f1a000 - 0x123fa9fff libqwebp.dylib (*) <eca0ac78-e7ba-3a03-aeca-2be5c17b3900> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqwebp.dylib 0x11c541000 - 0x11c548fff libqwbmp.dylib (*) <01c3f1c0-9acd-317c-947e-a49f4e3d27fc> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqwbmp.dylib 0x11c4da000 - 0x11c4e1fff libqgif.dylib (*) <bcc35720-04d0-304a-a77b-a1037536d0c7> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqgif.dylib 0x11c5ba000 - 0x11c5e1fff libqmacstyle.dylib (*) <5d5fd017-f4d1-3b54-9845-648d0af93171> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/styles/libqmacstyle.dylib 0x11c81d000 - 0x11c8b8fff libqcocoa.dylib (*) <ea4d92c7-1e56-3035-973a-cc1b9e855893> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/platforms/libqcocoa.dylib 0x11d0ee000 - 0x11d59dfff org.qt-project.QtWidgets (6.4) <0c19fe5b-8080-3277-b0d7-db86b1abfa73> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtWidgets.framework/Versions/A/QtWidgets 0x11ee6c000 - 0x11f537fff org.qt-project.QtGui (6.4) <9c994073-fbbb-32e0-8f98-4ba06dd0b45c> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtGui.framework/Versions/A/QtGui 0x11df50000 - 0x11e447fff org.qt-project.QtCore (6.4) <e2b9aa6f-b72b-3985-846f-c337ba7fbfbe> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/A/QtCore 0x11c684000 - 0x11c707fff org.qt-project.QtDBus (6.4) <ce1dbd3c-3df5-3b52-a631-8c079db6bbe9> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtDBus.framework/Versions/A/QtDBus 0x7ff7fff6a000 - 0x7ff7fff99fff runtime (*) <cac146cd-fadd-39a0-8bd7-30c2e15d10cf> /usr/libexec/rosetta/runtime 0x11ba9a000 - 0x11baedfff libRosettaRuntime (*) <8a85f070-3849-3b55-adde-143cc5902f92> /Library/Apple/*/libRosettaRuntime 0x100cb0000 - 0x10237bfff org.martinos.freeview (7.3.2) <9f2f99e0-7cdf-3b5d-a8c3-7152207d0e6a> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview 0x0 - 0xffffffffffffffff ??? (*) <00000000-0000-0000-0000-000000000000> ??? 0x7ff81affe000 - 0x7ff81c42bff5 com.apple.AppKit (6.9) <4905ef83-f061-3c82-bc30-70a4def63eee> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit 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=549.7M resident=0K(0%) swapped_out_or_unallocated=549.7M(100%) Writable regions: Total=1.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.3G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Activity Tracing 256K 1 ColorSync 224K 25 CoreGraphics 8K 2 CoreServices 192K 1 Foundation 16K 1 Kernel Alloc Once 8K 1 MALLOC 955.2M 34 MALLOC guard page 192K 12 Rosetta Arena 4096K 2 Rosetta Generic 1256K 311 Rosetta IndirectBranch 512K 1 Rosetta JIT 128.0M 1 Rosetta Return Stack 100K 10 Rosetta Thread Context 100K 10 STACK GUARD 16K 4 Stack 10.1M 5 Stack Guard 56.0M 1 VM_ALLOCATE 308K 20 VM_ALLOCATE (reserved) 4K 1 reserved VM address space (unallocated) __CTF 824 1 __DATA 264.2M 393 __DATA_CONST 19.7M 227 __DATA_DIRTY 815K 115 __FONT_DATA 2352 1 __LINKEDIT 180.3M 24 __OBJC_RO 71.7M 1 __OBJC_RW 2193K 2 __TEXT 369.4M 411 dyld private memory 260K 2 mapped file 138.6M 76 shared memory 800K 13 =========== ======= ======= TOTAL 2.2G 1709 TOTAL, minus reserved VM space 2.2G 1709 ----------- Full Report ----------- {"app_name":"freeview","timestamp":"2024-04-14 01:16:03.00 +0900","app_version":"7.3.2","slice_uuid":"9f2f99e0-7cdf-3b5d-a8c3-7152207d0e6a","build_version":"100","platform":1,"bundleID":"org.martinos.freeview","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.4.1 (23E224)","roots_installed":0,"name":"freeview","incident_id":"A88C9838-73BC-48E8-A67A-D9798E15943E"} { "uptime" : 60000, "procRole" : "Foreground", "version" : 2, "userID" : 501, "deployVersion" : 210, "modelCode" : "MacBookPro17,1", "coalitionID" : 7319, "osVersion" : { "train" : "macOS 14.4.1", "build" : "23E224", "releaseType" : "User" }, "captureTime" : "2024-04-14 01:16:02.7236 +0900", "codeSigningMonitor" : 1, "incident" : "A88C9838-73BC-48E8-A67A-D9798E15943E", "pid" : 71133, "translated" : true, "cpuType" : "X86-64", "roots_installed" : 0, "bug_type" : "309", "procLaunch" : "2024-04-14 01:16:01.9699 +0900", "procStartAbsTime" : 1445178590551, "procExitAbsTime" : 1445196413129, "procName" : "freeview", "procPath" : "\/Applications\/freesurfer\/*\/Freeview.app\/Contents\/MacOS\/freeview", "bundleInfo" : {"CFBundleShortVersionString":"7.3.2","CFBundleVersion":"100","CFBundleIdentifier":"org.martinos.freeview"}, "storeInfo" : {"deviceIdentifierForVendor":"CD01D798-2AF2-590F-BF8D-A141D73D599B","thirdParty":true}, "parentProc" : "launchd", "parentPid" : 1, "coalitionName" : "org.martinos.freeview", "crashReporterKey" : "FC5C035F-28AB-6F06-73F3-E7191C14B2D7", "lowPowerMode" : 1, "codeSigningID" : "", "codeSigningTeamID" : "", "codeSigningValidationCategory" : 0, "codeSigningTrustLevel" : 4294967295, "wakeTime" : 15301, "sleepWakeUUID" : "E0A8B706-B7C5-4F83-AEE3-9FB1B80DF90F", "sip" : "enabled", "vmRegionInfo" : "0x756265442f7b is not in any region. Bytes after previous region: 23511813074812 Bytes before following region: 11219858346117\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV \n---> GAP OF 0x1f9698f00000 BYTES\n MALLOC_TINY 7f96b8f00000-7f96b9000000 [ 1024K] rw-\/rwx SM=PRV ", "exception" : {"codes":"0x0000000000000001, 0x5367756265442f7b","rawCodes":[1,6009901293215428475],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x5367756265442f7b -> 0x0000756265442f7b (possible pointer authentication failure)"}, "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"exc handler","byPid":71133}, "vmregioninfo" : "0x756265442f7b is not in any region. Bytes after previous region: 23511813074812 Bytes before following region: 11219858346117\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV \n---> GAP OF 0x1f9698f00000 BYTES\n MALLOC_TINY 7f96b8f00000-7f96b9000000 [ 1024K] 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" : [{"triggered":true,"id":913800,"threadState":{"flavor":"x86_THREAD_STATE","rbp":{"value":13261730448},"r12":{"value":140285861717632},"rosetta":{"tmp2":{"value":4789351828},"tmp1":{"value":4782859283},"tmp0":{"value":4592157012}},"rbx":{"value":13261737168},"r8":{"value":2113},"r15":{"value":13261731320},"r10":{"value":4773934248},"rdx":{"value":4782862712,"symbolLocation":4712,"symbol":"QWidget::event(QEvent*)"},"rdi":{"value":140722939197080},"r9":{"value":0},"r13":{"value":13261737168},"rflags":{"value":535},"rax":{"value":6009901293215428467},"rsp":{"value":13261730432},"r11":{"value":140703581959119,"symbolLocation":0,"symbol":"-[NSView window]"},"rcx":{"value":4782859267,"symbolLocation":1267,"symbol":"QWidget::event(QEvent*)"},"r14":{"value":13261731320},"rsi":{"value":13261731320}},"queue":"com.apple.main-thread","frames":[{"imageOffset":2046872,"imageIndex":20},{"imageOffset":377875,"symbol":"QWidget::event(QEvent*)","symbolLocation":1283,"imageIndex":14},{"imageOffset":1684900,"symbol":"QMainWindow::event(QEvent*)","symbolLocation":276,"imageIndex":14},{"imageOffset":49335,"symbol":"QApplicationPrivate::notify_helper(QObject*, QEvent*)","symbolLocation":247,"imageIndex":14},{"imageOffset":53244,"symbol":"QApplication::notify(QObject*, QEvent*)","symbolLocation":508,"imageIndex":14},{"imageOffset":442842,"symbol":"QCoreApplication::notifyInternal2(QObject*, QEvent*)","symbolLocation":170,"imageIndex":16},{"imageOffset":474596,"imageIndex":14},{"imageOffset":466266,"imageIndex":14},{"imageOffset":49335,"symbol":"QApplicationPrivate::notify_helper(QObject*, 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"experimentId" : "66105e203b960674f9490906", "deploymentId" : 400000001 } ] }, "reportNotes" : [ "PC register does not match crashing frame (0x0 vs 0x100EA3B98)" ] } Model: MacBookPro17,1, BootROM 10151.101.3, proc 8:4:4 processors, 8 GB, SMC Graphics: Apple M1, Apple M1, Built-In Display: Color LCD, 2560 x 1600 Retina, Main, MirrorOff, Online Display: C32JG5x, 2560 x 1440 (QHD/WQHD - Wide Quad High Definition), MirrorOff, Online Memory Module: LPDDR4, Hynix AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x4378), wl0: Jan 13 2024 03:06:59 version 18.20.440.9.7.8.167 FWID 01-7be24857 AirPort: Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports Network Service: Wi-Fi, AirPort, en0 USB Device: USB31Bus USB Device: USB3.0 Hub USB Device: USB2.0 Hub USB Device: USB Keyboard USB Device: USB 2.0 Hub USB Device: USB 10/100 LAN USB Device: USB Optical Mouse USB Device: USB31Bus Thunderbolt Bus: MacBook Pro, Apple Inc. Thunderbolt Bus: MacBook Pro, Apple Inc.

2 1

Re: [Freesurfer] freesurfer doesn't work
by fsbuild 14 Apr '24

14 Apr '24

External Email - Use Caution  If you have not already done so, please make sure your license.txt file has been setup in the shell for the freesurfer commands to read. Go to the URL below, fill out the form, and wait for license.txt to be emailed to the address you provided. https://secure-web.cisco.com/1S0vdVHQI48_A4EBWTDRa1pv58cpXoGqSkuGFlQee0x1XY… Download license.txt file,e.g. into your Downloads folder.   Then in bash or zsh you can do,$ cd $HOME… download license.txt from email into Downloads folder ...$ mv Downloads/license.txt .$ export FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEyou(a)somewhere.com   <—— email you used to registerYou can add the export command above into your shell init file so FS_LICENSE will be set when you launch a new terminal window. - R. On Apr 13, 2024, at 13:08, 이준하 <dlwnsgk1105(a)naver.com> wrote:        External Email - Use Caution        I can't open freesurfer and I don't know why. It says 'Freesurfer quit unexpectedly'

2 2

freesurfer doesn't work
by 이준하 13 Apr '24

13 Apr '24

External Email - Use Caution I can't open freesurfer and I don't know why. It says 'Freesurfer quit unexpectedly' Below there is the reason of the quit. ------------------------------------- Translated Report (Full Report Below) ------------------------------------- Process: freeview [71133] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Identifier: org.martinos.freeview Version: 7.3.2 (100) Code Type: X86-64 (Translated) Parent Process: launchd [1] User ID: 501 Date/Time: 2024-04-14 01:16:02.7236 +0900 OS Version: macOS 14.4.1 (23E224) Report Version: 12 Anonymous UUID: FC5C035F-28AB-6F06-73F3-E7191C14B2D7 Sleep/Wake UUID: E0A8B706-B7C5-4F83-AEE3-9FB1B80DF90F Time Awake Since Boot: 60000 seconds Time Since Wake: 15301 seconds System Integrity Protection: enabled Notes: PC register does not match crashing frame (0x0 vs 0x100EA3B98) Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x5367756265442f7b -> 0x0000756265442f7b (possible pointer authentication failure) Exception Codes: 0x0000000000000001, 0x5367756265442f7b Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11 Terminating Process: exc handler [71133] VM Region Info: 0x756265442f7b is not in any region. Bytes after previous region: 23511813074812 Bytes before following region: 11219858346117 REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL MALLOC_NANO 600000000000-600020000000 [512.0M] rw-/rwx SM=PRV ---> GAP OF 0x1f9698f00000 BYTES MALLOC_TINY 7f96b8f00000-7f96b9000000 [ 1024K] rw-/rwx SM=PRV Error Formulating Crash Report: PC register does not match crashing frame (0x0 vs 0x100EA3B98) Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 freeview 0x100ea3b98 0x100cb0000 + 2046872 1 QtWidgets 0x11d14a413 QWidget::event(QEvent*) + 1283 2 QtWidgets 0x11d2895a4 QMainWindow::event(QEvent*) + 276 3 QtWidgets 0x11d0fa0b7 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247 4 QtWidgets 0x11d0faffc QApplication::notify(QObject*, QEvent*) + 508 5 QtCore 0x11dfbc1da QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170 6 QtWidgets 0x11d161de4 0x11d0ee000 + 474596 7 QtWidgets 0x11d15fd5a 0x11d0ee000 + 466266 8 QtWidgets 0x11d0fa0b7 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247 9 QtWidgets 0x11d0faffc QApplication::notify(QObject*, QEvent*) + 508 10 QtCore 0x11dfbc1da QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170 11 QtGui 0x11eef482d QGuiApplicationPrivate::processGeometryChangeEvent(QWindowSystemInterfacePrivate::GeometryChangeEvent*) + 493 12 QtGui 0x11eef5036 QGuiApplicationPrivate::processWindowScreenChangedEvent(QWindowSystemInterfacePrivate::WindowScreenChangedEvent*) + 470 13 QtGui 0x11ef4d29c 0x11ee6c000 + 922268 14 libqcocoa.dylib 0x11c866a50 0x11c81d000 + 301648 15 libqcocoa.dylib 0x11c85f8c9 0x11c81d000 + 272585 16 libqcocoa.dylib 0x11c85f37c 0x11c81d000 + 271228 17 QtGui 0x11ef3e93e QWindowPrivate::create(bool, unsigned long long) + 206 18 QtWidgets 0x11d138d9d QWidgetPrivate::create() + 1037 19 QtWidgets 0x11d136881 QWidget::create(unsigned long long, bool, bool) + 321 20 QtWidgets 0x11d1388e7 QWidgetPrivate::createWinId() + 103 21 QtWidgets 0x11d1388e7 QWidgetPrivate::createWinId() + 103 22 QtWidgets 0x11d1388e7 QWidgetPrivate::createWinId() + 103 23 QtWidgets 0x11d1388e7 QWidgetPrivate::createWinId() + 103 24 QtWidgets 0x11d1388e7 QWidgetPrivate::createWinId() + 103 25 QtWidgets 0x11d1388e7 QWidgetPrivate::createWinId() + 103 26 QtWidgets 0x11d139631 QWidget::winId() const + 65 27 freeview 0x100fab964 0x100cb0000 + 3127652 28 freeview 0x100fab88f 0x100cb0000 + 3127439 29 freeview 0x100d3b59f 0x100cb0000 + 570783 30 freeview 0x100e236cc 0x100cb0000 + 1521356 31 freeview 0x100e263e5 0x100cb0000 + 1532901 32 freeview 0x100e97a1a 0x100cb0000 + 1997338 33 freeview 0x100e8efa3 0x100cb0000 + 1961891 34 freeview 0x100dc82e5 0x100cb0000 + 1147621 35 dyld 0x2119d1366 start + 1942 Thread 1:: com.apple.rosetta.exceptionserver 0 runtime 0x7ff7fff6e494 0x7ff7fff6a000 + 17556 Thread 2: 0 runtime 0x7ff7fff8c94c 0x7ff7fff6a000 + 141644 Thread 3: 0 runtime 0x7ff7fff8c94c 0x7ff7fff6a000 + 141644 Thread 4: 0 runtime 0x7ff7fff8c94c 0x7ff7fff6a000 + 141644 Thread 5: 0 runtime 0x7ff7fff8c94c 0x7ff7fff6a000 + 141644 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x5367756265442f73 rbx: 0x0000000316760cd0 rcx: 0x000000011d14a403 rdx: 0x000000011d14b178 rdi: 0x00007ffc9ccd7698 rsi: 0x000000031675f5f8 rbp: 0x000000031675f290 rsp: 0x000000031675f280 r8: 0x0000000000000841 r9: 0x0000000000000000 r10: 0x000000011c8c74a8 r11: 0x00007ff81b0573cf r12: 0x00007f96d8f46680 r13: 0x0000000316760cd0 r14: 0x000000031675f5f8 r15: 0x000000031675f5f8 rip: <unavailable> rfl: 0x0000000000000217 tmp0: 0x0000000111b6c154 tmp1: 0x000000011d14a413 tmp2: 0x000000011d77b594 Binary Images: 0x2119cb000 - 0x211a5bfff dyld (*) <899f1e34-b624-3162-8003-04daa6829461> /usr/lib/dyld 0x11c3da000 - 0x11c3e6fff libobjc-trampolines.dylib (*) <3d9756e6-f86a-324d-bfd7-dc2d59c27956> /usr/lib/libobjc-trampolines.dylib 0x11c64e000 - 0x11c655fff libqmacjp2.dylib (*) <41234a69-0606-3f7d-ac82-499b68e7ca40> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqmacjp2.dylib 0x11c636000 - 0x11c63dfff libqtga.dylib (*) <4f81c0d1-a27e-3ad1-848f-f6d98b196553> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqtga.dylib 0x11c591000 - 0x11c598fff libqicns.dylib (*) <cf2b53cc-5f03-3dcf-b1dc-d5b19cc7b39e> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqicns.dylib 0x12416c000 - 0x1241d7fff libqtiff.dylib (*) <a588fa3d-680f-33b2-b1b3-02a035bd7cad> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqtiff.dylib 0x123e00000 - 0x123e6ffff libqjpeg.dylib (*) <fb2e4cb6-67fd-3b9d-94d9-d0f3053fc895> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqjpeg.dylib 0x11c576000 - 0x11c57dfff libqmacheif.dylib (*) <e76b1e74-e944-34d2-8d84-5cf2834a81d0> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqmacheif.dylib 0x11c559000 - 0x11c560fff libqico.dylib (*) <794fb25c-3196-3e6b-aef6-714be0814505> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqico.dylib 0x123f1a000 - 0x123fa9fff libqwebp.dylib (*) <eca0ac78-e7ba-3a03-aeca-2be5c17b3900> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqwebp.dylib 0x11c541000 - 0x11c548fff libqwbmp.dylib (*) <01c3f1c0-9acd-317c-947e-a49f4e3d27fc> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqwbmp.dylib 0x11c4da000 - 0x11c4e1fff libqgif.dylib (*) <bcc35720-04d0-304a-a77b-a1037536d0c7> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqgif.dylib 0x11c5ba000 - 0x11c5e1fff libqmacstyle.dylib (*) <5d5fd017-f4d1-3b54-9845-648d0af93171> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/styles/libqmacstyle.dylib 0x11c81d000 - 0x11c8b8fff libqcocoa.dylib (*) <ea4d92c7-1e56-3035-973a-cc1b9e855893> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/platforms/libqcocoa.dylib 0x11d0ee000 - 0x11d59dfff org.qt-project.QtWidgets (6.4) <0c19fe5b-8080-3277-b0d7-db86b1abfa73> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtWidgets.framework/Versions/A/QtWidgets 0x11ee6c000 - 0x11f537fff org.qt-project.QtGui (6.4) <9c994073-fbbb-32e0-8f98-4ba06dd0b45c> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtGui.framework/Versions/A/QtGui 0x11df50000 - 0x11e447fff org.qt-project.QtCore (6.4) <e2b9aa6f-b72b-3985-846f-c337ba7fbfbe> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/A/QtCore 0x11c684000 - 0x11c707fff org.qt-project.QtDBus (6.4) <ce1dbd3c-3df5-3b52-a631-8c079db6bbe9> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtDBus.framework/Versions/A/QtDBus 0x7ff7fff6a000 - 0x7ff7fff99fff runtime (*) <cac146cd-fadd-39a0-8bd7-30c2e15d10cf> /usr/libexec/rosetta/runtime 0x11ba9a000 - 0x11baedfff libRosettaRuntime (*) <8a85f070-3849-3b55-adde-143cc5902f92> /Library/Apple/*/libRosettaRuntime 0x100cb0000 - 0x10237bfff org.martinos.freeview (7.3.2) <9f2f99e0-7cdf-3b5d-a8c3-7152207d0e6a> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview 0x0 - 0xffffffffffffffff ??? (*) <00000000-0000-0000-0000-000000000000> ??? 0x7ff81affe000 - 0x7ff81c42bff5 com.apple.AppKit (6.9) <4905ef83-f061-3c82-bc30-70a4def63eee> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit 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=549.7M resident=0K(0%) swapped_out_or_unallocated=549.7M(100%) Writable regions: Total=1.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.3G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Activity Tracing 256K 1 ColorSync 224K 25 CoreGraphics 8K 2 CoreServices 192K 1 Foundation 16K 1 Kernel Alloc Once 8K 1 MALLOC 955.2M 34 MALLOC guard page 192K 12 Rosetta Arena 4096K 2 Rosetta Generic 1256K 311 Rosetta IndirectBranch 512K 1 Rosetta JIT 128.0M 1 Rosetta Return Stack 100K 10 Rosetta Thread Context 100K 10 STACK GUARD 16K 4 Stack 10.1M 5 Stack Guard 56.0M 1 VM_ALLOCATE 308K 20 VM_ALLOCATE (reserved) 4K 1 reserved VM address space (unallocated) __CTF 824 1 __DATA 264.2M 393 __DATA_CONST 19.7M 227 __DATA_DIRTY 815K 115 __FONT_DATA 2352 1 __LINKEDIT 180.3M 24 __OBJC_RO 71.7M 1 __OBJC_RW 2193K 2 __TEXT 369.4M 411 dyld private memory 260K 2 mapped file 138.6M 76 shared memory 800K 13 =========== ======= ======= TOTAL 2.2G 1709 TOTAL, minus reserved VM space 2.2G 1709 ----------- Full Report ----------- {"app_name":"freeview","timestamp":"2024-04-14 01:16:03.00 +0900","app_version":"7.3.2","slice_uuid":"9f2f99e0-7cdf-3b5d-a8c3-7152207d0e6a","build_version":"100","platform":1,"bundleID":"org.martinos.freeview","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.4.1 (23E224)","roots_installed":0,"name":"freeview","incident_id":"A88C9838-73BC-48E8-A67A-D9798E15943E"} { "uptime" : 60000, "procRole" : "Foreground", "version" : 2, "userID" : 501, "deployVersion" : 210, "modelCode" : "MacBookPro17,1", "coalitionID" : 7319, "osVersion" : { "train" : "macOS 14.4.1", "build" : "23E224", "releaseType" : "User" }, "captureTime" : "2024-04-14 01:16:02.7236 +0900", "codeSigningMonitor" : 1, "incident" : "A88C9838-73BC-48E8-A67A-D9798E15943E", "pid" : 71133, "translated" : true, "cpuType" : "X86-64", "roots_installed" : 0, "bug_type" : "309", "procLaunch" : "2024-04-14 01:16:01.9699 +0900", "procStartAbsTime" : 1445178590551, "procExitAbsTime" : 1445196413129, "procName" : "freeview", "procPath" : "\/Applications\/freesurfer\/*\/Freeview.app\/Contents\/MacOS\/freeview", "bundleInfo" : {"CFBundleShortVersionString":"7.3.2","CFBundleVersion":"100","CFBundleIdentifier":"org.martinos.freeview"}, "storeInfo" : {"deviceIdentifierForVendor":"CD01D798-2AF2-590F-BF8D-A141D73D599B","thirdParty":true}, "parentProc" : "launchd", "parentPid" : 1, "coalitionName" : "org.martinos.freeview", "crashReporterKey" : "FC5C035F-28AB-6F06-73F3-E7191C14B2D7", "lowPowerMode" : 1, "codeSigningID" : "", "codeSigningTeamID" : "", "codeSigningValidationCategory" : 0, "codeSigningTrustLevel" : 4294967295, "wakeTime" : 15301, "sleepWakeUUID" : "E0A8B706-B7C5-4F83-AEE3-9FB1B80DF90F", "sip" : "enabled", "vmRegionInfo" : "0x756265442f7b is not in any region. 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Re: [Freesurfer] WMH-SynthSeg - Torch module not found
by fsbuild 12 Apr '24

12 Apr '24

External Email - Use Caution  The current nightly build dated April 12th available from under,https://secure-web.cisco.com/1eprQplECVjQEgFy-DNvfPnzwSjew2U260XYR6pj… should have all the modules as well. - R. On Apr 11, 2024, at 10:03, Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote:The  idea would be to source 7.4.1 and then run:fspython  [location_of_FS_dev]/python/packages/WMHSynthSeg/inference.py [arguments]Cheers,/Eugenio --Juan Eugenio Iglesiashttp://http://secure-web.cisco.com/1Bz_4nONhypuVg0at2yxM7j3iTzJ-6ae… <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Corinne Alison Donnay <corinne.donnay@linacre.ox.ac.uk>Date: Wednesday, April 10, 2024 at 8:39 AMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] WMH-SynthSeg - Torch module not found        External Email - Use Caution        Hi Eugenio,  Thanks for getting back to me – I had the newest version installed and still get the same error (pasted below). mri_WMHsynthseg --i flair_ax.nii.gz --o flair_ax_WML.nii.gz --threads -1 Arguments seem correct; loading Python packages...Traceback (most recent call last):  File "/usr/local/apps/freesurfer/dev-2024-04-19/python/packages/WMHSynthSeg/inference.py", line 284, in <module>    main()  File "/usr/local/apps/freesurfer/dev-2024-04-19/python/packages/WMHSynthSeg/inference.py", line 76, in main    import torchModuleNotFoundError: No module named 'torch' I also installed FreeSurfer 7.4.1. Would you be able to expand on what you mean by  “a way around this is installing FreeSurfer 7.4.1, and using its fspython to run the WMh-SynthSeg code”? I loaded FreeSurfer 7.4.1, and then changed the location of the model in inference.py and tried using FreeSurfer 7.4.1 fspython but now its missing the 'unet3d' module: [donnayca@cn4270 anat]$ module load freesurfer[-] Unloading freesurfer  7.4.1 on cn4270 [+] Loading freesurfer  7.4.1  on cn4270  [donnayca@cn4270 anat]$ fspython ../inference_cd.py --i flair_ax.nii.gz --o flair_ax_WML.nii.gzArguments seem correct; loading Python packages...Traceback (most recent call last):  File "../inference_cd.py", line 285, in <module>    main()  File "../inference_cd.py", line 79, in main    from unet3d.model import UNet3DModuleNotFoundError: No module named 'unet3d'[donnayca@cn4270 anat]$ fspythonPython 3.8.13 (default, Apr 21 2022, 14:55:37) [GCC 8.3.1 20190311 (Red Hat 8.3.1-3)] on linuxType "help", "copyright", "credits" or "license" for more information.>>> exit() Thank you!CorinneFrom: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Date: Saturday, April 6, 2024 at 1:04 PMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] WMH-SynthSeg - Torch module not found Wrong answer: apparently this has been fixed in the latest dev; maybe try that?Cheers,/Eugenio --Juan Eugenio Iglesiashttp://http://secure-web.cisco.com/1Bz_4nONhypuVg0at2yxM7j3iTzJ-6ae… <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu>Date: Friday, April 5, 2024 at 3:58 PMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] WMH-SynthSeg - Torch module not foundDear Corinne,A bunch of libraries are currently broken in the development version; apologies for this. A way around this is installing FreeSurfer 7.4.1, and using its fspython to run the WMh-SynthSeg code. Apologies for the inconvenience!Cheers,/EPS: I just updated the wiki to include this information. --Juan Eugenio Iglesiashttp://http://secure-web.cisco.com/1Bz_4nONhypuVg0at2yxM7j3iTzJ-6ae… <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Corinne Alison Donnay <corinne.donnay@linacre.ox.ac.uk>Date: Friday, April 5, 2024 at 12:43 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] WMH-SynthSeg - Torch module not found        External Email - Use Caution        Good Afternoon! I was working with my IT department to install the development version of FreeSurfer on our server so that I could use WMH-SynthSeg. IT installed development version 2024-04-14. After loading the freesurfer development module, and running source $FREESURFER_HOME/SetUpFreeSurfer.sh, I still get the following error: <image001.png> Is there any way to fix this or figure out what is wrong? Thank you!Corinne_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_synthmorph
by Antoine Royer 11 Apr '24

11 Apr '24

External Email - Use Caution Hi, I am developping a Nextflow DSL2 module through nf-core for registration using mri_synthmorph, through the dockerised version: https://secure-web.cisco.com/1F0tLsgl5mSp6FHNJceZtb0_zJW26GZiSS0O_W7cYXg5eO… Here is a couple of screenshots showing the ressource consumption of my computer and through Docker. I don't have any issue running it locally, but there seems to be an issue through my container which is set at 16 core at 24 GB. Does anyone have any insight on how to troubleshoot this? Thank you!

2 1

Re: [Freesurfer] Recon-all stuck at topology fix
by Bhole, Salil 11 Apr '24

11 Apr '24

External Email - Use Caution Hello, I have tried to process this MRI a few times now and it always seems to get stuck on the step I have pasted below here. I have tried to fix the defect myself by editing the voxels manually, but that has also not seemed to help. I've looked through the MRI and there are no obvious deformities/defects. Any help with the next steps would be much appreciated. Best, Salil 49 defects to be corrected 0 vertices coincident reading input surface /Applications/freesurfer/7.4.1/subjects/Ross_MRI_Neg_LITT/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -8.8808 (-4.4404) -vertex loglikelihood: -7.5174 (-3.7587) -normal dot loglikelihood: -3.4734 (-3.4734) -quad curv loglikelihood: -5.9156 (-2.9578) Total Loglikelihood : -25.7872 CORRECTING DEFECT 0 (vertices=116175, convex hull=11639, v0=288) ________________________________ From: Bhole, Salil Sent: Wednesday, April 10, 2024 5:59 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Recon-all stuck at topology fix Hello, I have tried to process this MRI a few times now and it always seems to get stuck on the step I have pasted below here. I have tried to fix the defect myself by editing the voxels manually, but that has also not seemed to help. I've looked through the MRI and there are no obvious deformities/defects. Any help with the next steps would be much appreciated. Best, Salil 49 defects to be corrected 0 vertices coincident reading input surface /Applications/freesurfer/7.4.1/subjects/Ross_MRI_Neg_LITT/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -8.8808 (-4.4404) -vertex loglikelihood: -7.5174 (-3.7587) -normal dot loglikelihood: -3.4734 (-3.4734) -quad curv loglikelihood: -5.9156 (-2.9578) Total Loglikelihood : -25.7872 CORRECTING DEFECT 0 (vertices=116175, convex hull=11639, v0=288) ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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