Freesurfer April 2024

freesurfer@nmr.mgh.harvard.edu

54 participants
64 discussions

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. 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" : 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1 0

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

1 0

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.

2 3

Surface vertex tkr-ras to native T1 RAS without volume files
by Dipterix Wang 11 Apr '24

11 Apr '24

External Email - Use Caution Dear FreeSurfer devs, I'm writing a program in JavaScript that converts FreeSurfer surface (mesh) files to other formats, which require the vertices to sit in scanner RAS coordinates. Right now I'm relying on the FreeSurfer *brain.finalsurf.mgz* or *T1.mgz* file to obtain the Torig (vox to tkr-ras) and Norig (vox to scanner ras) matrices, and using these matrices to calculate the rigid transform. This approach requires the users to upload the mgz volume files (but I only need the transforms). Today I found that each binary surface file (e.g. lh.pial) has a little footer that starts with uint32 sequence `2 0 20`, followed by the meta information such as xras, yras, zras, and cras. For example: valid = 1 # volume info valid filename = ../mri/filled-pretess127.mgz volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 cras = -1.000000000000000e+00 -1.700000000000000e+01 1.900000000000000e+01 \u0000\u0000\u0000\u0003\u0000\u0000\u0000\u0000\u0000\u0000\u0001 From what I understand, cras is the xyz of the volume center, which is the translation from mesh vertices xyz (in tkr-ras) to native scanner RAS. I wonder if I can rely on this information to calculate the transform from tkr-ras to scan-ras, if so, where are the rotation matrices? (Affine/rigid transform is a 4x4 matrix, if cras is the translation, where are the first 3x3 elements, are those always identity matrices?) Best, - Dipterix

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Re: [Freesurfer] WMH-SynthSeg - Torch module not found
by Corinne Alison Donnay 11 Apr '24

11 Apr '24

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 torch ModuleNotFoundError: 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.gz Arguments 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 UNet3D ModuleNotFoundError: No module named 'unet3d' [donnayca@cn4270 anat]$ fspython Python 3.8.13 (default, Apr 21 2022, 14:55:37) [GCC 8.3.1 20190311 (Red Hat 8.3.1-3)] on linux Type "help", "copyright", "credits" or "license" for more information. >>> exit() Thank you! Corinne From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Saturday, April 6, 2024 at 1:04 PM To: Freesurfer support list <freesurfer(a)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 Iglesias http://secure-web.cisco.com/1dHOeDzqKyQVK1dVoIBFTpN8aJzkFmLHSyp5Kt30eRmYaZV… From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Date: Friday, April 5, 2024 at 3:58 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] WMH-SynthSeg - Torch module not found Dear 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, /E PS: I just updated the wiki to include this information. -- Juan Eugenio Iglesias http://secure-web.cisco.com/1dHOeDzqKyQVK1dVoIBFTpN8aJzkFmLHSyp5Kt30eRmYaZV… From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Corinne Alison Donnay <corinne.donnay(a)linacre.ox.ac.uk> Date: Friday, April 5, 2024 at 12:43 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)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<https://secure-web.cisco.com/13uSpbM7Qfplsr0IlNG1yQzvDu3TL4ODjz8qdEUly_QzsK…>. 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: [cid:image001.png@01DA8B65.91CED520] Is there any way to fix this or figure out what is wrong? Thank you! Corinne

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PetSurfer: Can kinetic modeling be applied to PET data with single frame?
by WONG Wan Wa 11 Apr '24

11 Apr '24

External Email - Use Caution Hi experts, As stated in the subject, can kinetic modeling be applied to PET data with only one frame? Or we just stop at ROI analysis without kinetic modeling? Best, Angel

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Probabilistic segmentation neonates
by Hamza Kebiri 10 Apr '24

10 Apr '24

External Email - Use Caution Hello, Is there a FreeSurfer tool to output a probabilistic tissue segmentation (gray/white matter proportions) tailored for the newborns (especially in the thalamus) ? Thank you very much. All the best, Hamza Kebiri

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NextBrain Segmentation PyTorch-GPU Compatibility Error
by AmirHussein Abdolalizadeh 10 Apr '24

10 Apr '24

External Email - Use Caution Hi, I'm using NextBrain segmentation tool on our cluster which has NVIDIA H100 GPUs and I'm getting this error: NVIDIA H100 with CUDA capability sm_90 is not compatible with the current PyTorch installation. The current PyTorch install supports CUDA capabilities sm_37 sm_50 sm_60 sm_70 sm_75 sm_80 sm_86. If you want to use the NVIDIA H100 GPU with PyTorch, please check the instructions at https://secure-web.cisco.com/1dXRtbKFFWRnAd7DYiR89C9QyPNuu24f97dyifrR_gDGXs… Should I contact our cluster managers in this regard or is there a specific workaround that can overcome this issue? Best, Amir

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Several faculty jobs at University of Chicago in Aging + Alzheimer's and related dementias
by Adam Martersteck 09 Apr '24

09 Apr '24

External Email - Use Caution *Apologies for cross-posting* The University of Chicago's Department of Neurology is recruiting several faculty members at any rank to join the Healthy Aging & Alzheimer’s Research Care (HAARC) Center. We welcome candidates with research interests that align with our mission including topics and methods such as digital biomarkers, blood-based biomarkers, imaging biomarkers (MRI, PET), large-dataset curation, social determinants of health, assessment of cognition, memory, psychosocial wellbeing, functional outcomes, neuropathologic, nonpharmacologic interventions, and implementation science. We are looking for (1) a tenure track faculty (any rank, with or without tenure), (2) a non-tenure track faculty (any rank), (3) a behavioral neurologist, and (4) a full professor of neuroimmunology to direct a program in neuroinflammation. Clinical neuropsychologists, behavioral neurologists, and cognitive neuroscientists with an interest in contributing to a collaborative multidisciplinary research center are encouraged to apply. We especially welcome applicants from URM groups, which are African American, Latino, Native American, Pacific Islanders, women, and individuals with disabilities. For more information see our website: https://secure-web.cisco.com/10L7_lboSnfTgH5hrqe1sUZtGSywMbqb47r96NhJAp4tK2… Tenure track faculty position: https://secure-web.cisco.com/1OeZ6fDc9_LaXQp8riD9fIo6-CzZ7ojZNXgL4wc93ARP8I… Non-tenure track faculty position: http://secure-web.cisco.com/17J6yWYJ2zsoku90RYF2YU_thqO3lxxSRJXfK4HSbPzjCan… Behavioral neurologist: https://secure-web.cisco.com/1ZT7et8OCIVgBMktDPuQAx1nX2C27i0IwlduDjDBH2QFZf… Tenured full professor in neuroimmunology, with endowed chair: https://secure-web.cisco.com/1aGaEvfSfHQUMYR0p_DyIC-4_q2Xse9-YUKKvf1BxySfjo… -- *Adam Martersteck, PhD * *(he/him)**Assistant Professor of Neurology* | The University of Chicago, Healthy Aging & Alzheimer's Research Care (HAARC) Center *Address *| 850 East 58th Street | Chicago, IL 60637 *Phone *| 773-795-1683 *Email *| martersteck(a)uchicago.edu

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Freesurfer April 2024