Freesurfer December 2022

freesurfer@nmr.mgh.harvard.edu

75 participants
92 discussions

create a mgz with one value
by Aaron Tanenbaum 15 Dec '22

15 Dec '22

External Email - Use Caution Hello, I am trying to generate a mgz with identical header and dimensions as another mgz file. However I would like all voxels to be set to one value. What is the best way to do this? Thank you

3 2

SynthSR and SynthSeg
by Yoonho Hwang 15 Dec '22

15 Dec '22

External Email - Use Caution Dear FS developers, Hi, I'm Yoonho. I know that new features, such as SynthSeg, SynthStrip, segment_subfields (beta version), etc, based on deep learning have been added after the FreeSurfer 7.3.2. Here I have questions (I read papers related to SynthSR, SynthSeg, SynthStrip, segment_subfields). *1. Can I use the SynthSR functions o**nly by FreeSurfer development (dev) version (https://secure-web.cisco.com/1ps3QL5XW2qOOptSgD9TqOIsWnQJlFGcz9nxZ59lvSiCbI… <https://secure-web.cisco.com/1ps3QL5XW2qOOptSgD9TqOIsWnQJlFGcz9nxZ59lvSiCbI…>)**?* *2. When T1WI data are processed with recon-all, are SynthSR and SynthSeg functions included in the "recon-all" process pipeline? If not, are SynthSR and SynthSeg processed separately?* *3. Is the recon-all process included in SynthSeg and SynthStrip by default?* *4. When I process T1WI data with Freesurfer dev version, is it installed based on the new version in HPC per version update for freesurfer?* *5. I think using SynthSR and SynthSeg functions can solve the Harmonization issue (data acquired from other manufacturers (Siemens, GE, Philips), protocols (FSPGR, MPRAGE, etc), and other sites). What do you think about that?* *6. In lh.w-g.pct.stats file, I know that "Mean" means GWC (gray/white matter contrast), which is (100/0.5)*[(white matter intensity - gray matter intensity)/(white matter intensity + gray matter intensity)], as far as I know, I want to know in detail whether the 0.5 term should be omitted and 100 is to appear as a percentage.* Thank you for reading my long question Please let me know if there is anything you don't understand. Looking forward to your feedback. Thank you very much. Sincerely, Yoonho --

2 1

High Resolution Freesurfer Error
by Brooklyn Wright 15 Dec '22

15 Dec '22

External Email - Use Caution Hi there 🙂 I am running into repeat difficulty with reconstructing ultra-high resolution T1w .nii images (0.25mm^3 voxel size). These have been submitted to rigorous preprocessing steps and I use hires flags and expert preferences however all of my attempts' output has some part of the brain missing as if it got two-thirds of the way through and then gave up. Have you got any suggestions on how to tackle this? Kindest, Brooklyn.

2 1

CSF mask generation
by priya padma 15 Dec '22

15 Dec '22

External Email - Use Caution Dear Team, I have tried creating binary CSF mask from # CSF: # - 4: Left-Lateral-Ventricle # - 14: 3rd-Ventricle # - 43: Right-Lateral-Ventricle but I would like to know whether is it possible for us to get outer CSF similar to fastsurfer. Any help would be highly appreciated. Thank you. -- Best Regards Padma Priya *AI Developer * *PhenoMx, Inc.* *priya(a)phenomx.ai <priya(a)phenomx.ai> | (+82)10-5405-2685*

2 1

Re: [Freesurfer] Creating and analyzing combined ROIs, combining different FreeSurfer versions
by Trolle, Carl 15 Dec '22

15 Dec '22

Thank you for the reply, 1. Once each participant's aparc has been broken and we've created the desired new label for each participant, should we create this, the desired label, for fsaverage and follow the remaining steps of the ROI-tutorial (e.g resample with mris_label2label using fsaverage as the srcsubject)? Sorry didn't quite understand this part. 3. We can't seem to get mris_register and mri_ca_label working with FS711 or 720, it's running fine with 732 and the dev-version (attaching a simple montage to show the output we're getting; we've tried to force FreeSurfer to use a manually designated central sulcus to move the pre and post central gyri "forward"). I think there was a mention that mris_register wasn't running as intended prior to 732<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg73308.html>. Thank you for the clarification! Kind regards, Carl Message: 7 Date: Mon, 12 Dec 2022 10:34:15 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Creating and analyzing combined ROIs, combining different FreeSurfer versions To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <8e7e390b-bbef-00cd-29c6-bda799bfd81e(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" On 12/2/2022 12:35 PM, Trolle, Carl wrote: > Dear FreeSurfer team, > > 1. We're trying to focus our cortical analysis following suggestions > here > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23939.html.?… > FS ROI tutorial page?mentions that labels should be drawn or > registered on the fsaverage template; could we then break the > fsaverage aparc_annot atlas and combine the fsaverage labels of > interest into our new label or should we break each individual > subjects aparc_annot atlas and then create the combined ROI from > the subject specific labels? I'm assuming that we either way will > have to resample the combined label to each subject using > mri_label2label? > You should break each subject aparc and then combine. > > 1. > > > 2. When running the mri_glmfit-sim analysis later on, the thread > above mentions not using the --cache option. Can we use "--mczsim > 3 pos" instead for a one-sided test? > Yes > > 3. We've had some success in correcting incorrect parcellations using > the mris_register and mri_ca_label functions. As we had some > issues with mris_register in 7.1.1, we used the developer version > for these steps, but 7.1.1 when re-running recon-all as this is > the version we used for our study. Is it ok to combine versions > like this? > probably ok in this case, but what is the problem? > > 3. > > > Thank you for your time! > > Kind regards, > > Carl Trolle > Research fellow > Spaulding Neuroimaging Lab > > > Platform:?linux-centos7_x86_64-7.1.1-20200723-8b40551 > FreeSurfer version: 7.1.1 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu

2 1

Freeview quit unexpectedly
by Addison, Reuben 14 Dec '22

14 Dec '22

I am trying to use freeview to load a volume. I am using freesurfer 7.3.2 on the new M1 mac pro with ios ventura. Please view below the error report I am getting. Is there any work around it? I have tried different volumes but same issues Translated Report (Full Report Below) ------------------------------------- Process: freeview [2225] 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: 2022-12-14 22:18:58.4199 +0000 OS Version: macOS 13.0.1 (22A400) Report Version: 12 Anonymous UUID: 4DD80B35-B000-767B-D8E0-4CF3002E053F Sleep/Wake UUID: 305334BF-BD70-4E02-B20F-D4316B1A93BB Time Awake Since Boot: 16000 seconds Time Since Wake: 10255 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 0x000036da55ddc150 Exception Codes: 0x0000000000000001, 0x000036da55ddc150 Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11 Terminating Process: exc handler [2225] VM Region Info: 0x36da55ddc150 is not in any region. Bytes after previous region: 59830335029585 Bytes before following region: 45241744899760 REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL commpage (reserved) 1000000000-7000000000 [384.0G] ---/--- SM=NUL ...(unallocated) ---> GAP OF 0x5f9000000000 BYTES MALLOC_NANO 600000000000-600008000000 [128.0M] rw-/rwx SM=PRV Kernel Triage: VM - pmap_enter retried due to resource shortage VM - pmap_enter retried due to resource shortage VM - pmap_enter retried due to resource shortage Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libobjc.A.dylib 0x7ff80d3b0959 objc_storeWeak + 188 1 AppKit 0x7ff810895aaa -[NSWindow setDelegate:] + 199 2 libqcocoa.dylib 0x11d003d31 0x11cfe1000 + 142641 3 libqcocoa.dylib 0x11cffd672 0x11cfe1000 + 116338 4 libqcocoa.dylib 0x11cffd0fe 0x11cfe1000 + 114942 5 QtGui 0x11d622eb7 QWindowPrivate::create(bool, unsigned long long) + 151 6 QtWidgets 0x11c26d771 QWidgetPrivate::create() + 1185 7 QtWidgets 0x11c26c414 QWidget::create(unsigned long long, bool, bool) + 324 8 QtWidgets 0x11c27f81d QWidgetPrivate::setVisible(bool) + 189 9 freeview 0x100a60ded 0x1009f7000 + 433645 10 QtCore 0x11ece1b9f QObject::event(QEvent*) + 943 11 QtWidgets 0x11c280e9a QWidget::event(QEvent*) + 4698 12 QtWidgets 0x11c2459ea QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266 13 QtWidgets 0x11c246e11 QApplication::notify(QObject*, QEvent*) + 497 14 QtCore 0x11ecb6a34 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 15 QtCore 0x11ecb7d79 QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 809 16 libqcocoa.dylib 0x11d01b259 0x11cfe1000 + 238169 17 libqcocoa.dylib 0x11d01b9c8 0x11cfe1000 + 240072 18 CoreFoundation 0x7ff80d7f1ef1 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 19 CoreFoundation 0x7ff80d7f1ea0 __CFRunLoopDoSource0 + 157 20 CoreFoundation 0x7ff80d7f1c6e __CFRunLoopDoSources0 + 212 21 CoreFoundation 0x7ff80d7f08c8 __CFRunLoopRun + 943 22 CoreFoundation 0x7ff80d7efe9f CFRunLoopRunSpecific + 560 23 HIToolbox 0x7ff817617bd6 RunCurrentEventLoopInMode + 292 24 HIToolbox 0x7ff8176179e6 ReceiveNextEventCommon + 679 25 HIToolbox 0x7ff817617723 _BlockUntilNextEventMatchingListInModeWithFilter + 70 26 AppKit 0x7ff81084db37 _DPSNextEvent + 909 27 AppKit 0x7ff81084c9b8 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1219 28 AppKit 0x7ff81083eff3 -[NSApplication run] + 586 29 libqcocoa.dylib 0x11d01a62f 0x11cfe1000 + 235055 30 QtCore 0x11ecb2acf QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 431 31 QtCore 0x11ecb7042 QCoreApplication::exec() + 130 32 freeview 0x100afccb7 0x1009f7000 + 1072311 33 dyld 0x21190a310 start + 2432 Thread 1:: com.apple.rosetta.exceptionserver 0 runtime 0x7ff7fff18750 0x7ff7fff14000 + 18256 1 runtime 0x7ff7fff2466c 0x7ff7fff14000 + 67180 2 runtime 0x7ff7fff2606c 0x7ff7fff14000 + 73836 Thread 2:: QThread 0 ??? 0x7ff89c99e9a8 ??? 1 libsystem_kernel.dylib 0x7ff80d6df3ba poll + 10 2 QtCore 0x11ed19220 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 608 3 QtCore 0x11ed1aa21 QEventDispatcherUNIX::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 849 4 QtCore 0x11ecb2acf QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 431 5 QtCore 0x11eadf603 QThread::exec() + 131 6 QtCore 0x11eae0619 0x11eabe000 + 140825 7 libsystem_pthread.dylib 0x7ff80d717259 _pthread_start + 125 8 libsystem_pthread.dylib 0x7ff80d712c7b thread_start + 15 Thread 3:: com.apple.NSEventThread 0 ??? 0x7ff89c99e9a8 ??? 1 libsystem_kernel.dylib 0x7ff80d6d86a2 mach_msg2_trap + 10 2 libsystem_kernel.dylib 0x7ff80d6e667d mach_msg2_internal + 82 3 libsystem_kernel.dylib 0x7ff80d6df71a mach_msg_overwrite + 723 4 libsystem_kernel.dylib 0x7ff80d6d8989 mach_msg + 19 5 CoreFoundation 0x7ff80d7f202b __CFRunLoopServiceMachPort + 145 6 CoreFoundation 0x7ff80d7f0a84 __CFRunLoopRun + 1387 7 CoreFoundation 0x7ff80d7efe9f CFRunLoopRunSpecific + 560 8 AppKit 0x7ff8109ad696 _NSEventThread + 132 9 libsystem_pthread.dylib 0x7ff80d717259 _pthread_start + 125 10 libsystem_pthread.dylib 0x7ff80d712c7b thread_start + 15 Thread 4: 0 runtime 0x7ff7fff3687c 0x7ff7fff14000 + 141436 Thread 5: 0 runtime 0x7ff7fff3687c 0x7ff7fff14000 + 141436 Thread 6: 0 runtime 0x7ff7fff3687c 0x7ff7fff14000 + 141436 Thread 7: 0 runtime 0x7ff7fff3687c 0x7ff7fff14000 + 141436 Thread 8: 0 runtime 0x7ff7fff3687c 0x7ff7fff14000 + 141436 Thread 9: 0 runtime 0x7ff7fff3687c 0x7ff7fff14000 + 141436 Thread 10: 0 runtime 0x7ff7fff3687c 0x7ff7fff14000 + 141436 Thread 11:: ThreadIOWorker 0 <translation info unavailable> 0x113899864 ??? 1 <translation info unavailable> 0x1137603d8 ??? 2 dyld 0x211913e7c dyld4::Reaper::markDependentOfInUseImages() + 56 3 dyld 0x211913edd dyld4::Reaper::garbageCollect() + 75 4 dyld 0x21191438a dyld4::RuntimeState::garbageCollectInner() + 232 5 dyld 0x211913c48 dyld4::RuntimeState::decDlRefCount(dyld4::Loader const*) + 208 6 dyld 0x21193ba90 dyld4::APIs::dlclose(void*) + 208 7 QtCore 0x11ecb0d25 0x11eabe000 + 2043173 8 QtCore 0x11ecab5a0 0x11eabe000 + 2020768 9 QtCore 0x11eca4d96 0x11eabe000 + 1994134 10 QtCore 0x11eca506e 0x11eabe000 + 1994862 11 QtCore 0x11ece0f2c QObject::~QObject() + 2140 12 QtCore 0x11eca63ae QFactoryLoader::~QFactoryLoader() + 94 13 QtCore 0x11eca681e QFactoryLoader::~QFactoryLoader() + 14 14 QtGui 0x11d6891a6 0x11d5dc000 + 709030 15 libsystem_c.dylib 0x7ff80d60dccf __cxa_finalize_ranges + 409 16 libsystem_c.dylib 0x7ff80d60dae9 exit + 35 17 freeview 0x101c8ab3c 0x1009f7000 + 19479356 18 freeview 0x101d11118 0x1009f7000 + 20029720 19 freeview 0x100a70dac 0x1009f7000 + 499116 20 freeview 0x100a71438 0x1009f7000 + 500792 21 freeview 0x100a98cde 0x1009f7000 + 662750 22 freeview 0x100b850ea 0x1009f7000 + 1630442 23 QtCore 0x11eae0619 0x11eabe000 + 140825 24 libsystem_pthread.dylib 0x7ff80d717259 _pthread_start + 125 25 libsystem_pthread.dylib 0x7ff80d712c7b thread_start + 15 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x0000000000000000 rcx: 0x0000000000000103 rdx: 0x0000600001c7c150 rdi: 0x000036da55ddc150 rsi: 0x00007ffffffffff8 rbp: 0x00000003163eeb30 rsp: 0x00000003163eead0 r8: 0x00007f7d740db540 r9: 0x00000000000001ff r10: 0x00007ff850d6f658 r11: 0x00007ff81081ff94 r12: 0x0000000000000000 r13: 0x00007ff850d53880 r14: 0x00007f7d740db5f0 r15: 0x00007ff850d545c0 rip: <unavailable> rfl: 0x0000000000000202 tmp0: 0x0000000000000000 tmp1: 0x00007ff80d3b091b tmp2: 0x00007ff89c9b1224 Binary Images: 0x7ff80d3a4000 - 0x7ff80d3dffe0 libobjc.A.dylib (*) <2ae3c5f8-a564-3b7e-8f07-3e0df7e1e885> /usr/lib/libobjc.A.dylib 0x7ff81080f000 - 0x7ff811813ff6 com.apple.AppKit (6.9) <817d572e-eb8c-3999-b7a0-68e1c4b47266> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit 0x11cfe1000 - 0x11d14ffff libqcocoa.dylib (*) <d4ab240b-4535-3aec-b72b-5ffc4750e4e5> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/platforms/libqcocoa.dylib 0x11d5dc000 - 0x11dac5fff org.qt-project.QtGui (5.15) <cbcec35a-ee54-354f-9c2b-188ac6b2790d> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtGui.framework/Versions/5/QtGui 0x11c235000 - 0x11c67bfff org.qt-project.QtWidgets (5.15) <b432d666-dcab-320a-8496-78a67f554c0e> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtWidgets.framework/Versions/5/QtWidgets 0x1009f7000 - 0x10209efff com.freesurfer.freeview (*) <2d93be07-b47e-3b61-92dc-947be65a61af> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview 0x11eabe000 - 0x11f02efff org.qt-project.QtCore (5.15) <c723812a-f7a5-3001-98d5-e60e8daa6ffb> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/5/QtCore 0x7ff80d773000 - 0x7ff80dc0afff com.apple.CoreFoundation (6.9) <bca7763f-086a-3837-b278-2f8046e4e885> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation 0x7ff8175e8000 - 0x7ff8178dfff2 com.apple.HIToolbox (2.1.1) <ff73b93b-3c5b-3f73-948f-0a35a80f7fad> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox 0x211904000 - 0x21199bfff dyld (*) <28fd2071-57f3-3873-87bf-e4f674a82de6> /usr/lib/dyld 0x7ff7fff14000 - 0x7ff7fff43fff runtime (*) <6f797d84-b330-3656-9a0d-7b3dbd3f8a07> /usr/libexec/rosetta/runtime 0x0 - 0xffffffffffffffff ??? (*) <00000000-0000-0000-0000-000000000000> ??? 0x7ff80d6d7000 - 0x7ff80d710ff7 libsystem_kernel.dylib (*) <0c2fd2c9-777c-3355-b70f-7b1b6e9d1b0b> /usr/lib/system/libsystem_kernel.dylib 0x7ff80d711000 - 0x7ff80d71cff7 libsystem_pthread.dylib (*) <13b5e252-77d1-31e1-888d-1c5f4426ea87> /usr/lib/system/libsystem_pthread.dylib 0x7ff80d5df000 - 0x7ff80d667fff 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=470.5M resident=0K(0%) swapped_out_or_unallocated=470.5M(100%) Writable regions: Total=1.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.9G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 1408K 11 Activity Tracing 256K 1 CG backing stores 4032K 4 CG image 196K 21 ColorSync 248K 29 CoreAnimation 196K 23 CoreGraphics 12K 2 CoreImage 44K 11 CoreUI image data 4244K 31 Foundation 16K 1 Kernel Alloc Once 8K 1 MALLOC 284.3M 55 MALLOC guard page 192K 8 MALLOC_MEDIUM (reserved) 832.0M 7 reserved VM address space (unallocated) MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) Rosetta Arena 4096K 2 Rosetta Generic 1392K 345 Rosetta IndirectBranch 1024K 1 Rosetta JIT 128.0M 1 Rosetta Return Stack 220K 22 Rosetta Thread Context 220K 22 STACK GUARD 28K 7 Stack 13.1M 11 Stack Guard 56.0M 4 VM_ALLOCATE 2088K 42 VM_ALLOCATE (reserved) 4K 1 reserved VM address space (unallocated) __CTF 756 1 __DATA 262.3M 365 __DATA_CONST 14.8M 207 __DATA_DIRTY 672K 110 __FONT_DATA 2352 1 __GLSLBUILTINS 5174K 1 __LINKEDIT 171.2M 26 __OBJC_RO 65.1M 1 __OBJC_RW 1980K 2 __TEXT 299.4M 379 dyld private memory 256K 1 mapped file 4.6G 1353 shared memory 824K 18 unshared pmap 13.9M 10 =========== ======= ======= TOTAL 7.0G 3139 TOTAL, minus reserved VM space 5.9G 3139 ----------- Full Report ----------- {"app_name":"freeview","timestamp":"2022-12-14 22:19:00.00 +0000","app_version":"","slice_uuid":"2d93be07-b47e-3b61-92dc-947be65a61af","build_version":"","platform":1,"bundleID":"com.freesurfer.freeview","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.0.1 (22A400)","roots_installed":0,"name":"freeview","incident_id":"FC47845E-9AF0-4621-94A7-ABA20D077434"} { "uptime" : 16000, "procRole" : "Foreground", "version" : 2, "userID" : 501, "deployVersion" : 210, "modelCode" : "MacBookPro18,2", "coalitionID" : 2267, "osVersion" : { "train" : "macOS 13.0.1", "build" : "22A400", "releaseType" : "User" }, "captureTime" : "2022-12-14 22:18:58.4199 +0000", "incident" : "FC47845E-9AF0-4621-94A7-ABA20D077434", "pid" : 2225, "translated" : true, "cpuType" : "X86-64", "roots_installed" : 0, "bug_type" : "309", "procLaunch" : "2022-12-14 22:17:28.5469 +0000", "procStartAbsTime" : 401273671314, "procExitAbsTime" : 403428436613, "procName" : "freeview", "procPath" : "\/Applications\/freesurfer\/*\/Freeview.app\/Contents\/MacOS\/freeview", "bundleInfo" : {"CFBundleIdentifier":"com.freesurfer.freeview"}, "storeInfo" : {"deviceIdentifierForVendor":"CB3EE7BE-82AB-55C3-AD55-17DCE77D8A12","thirdParty":true}, "parentProc" : "launchd", "parentPid" : 1, "coalitionName" : "com.freesurfer.freeview", "crashReporterKey" : "4DD80B35-B000-767B-D8E0-4CF3002E053F", "wakeTime" : 10255, "sleepWakeUUID" : "305334BF-BD70-4E02-B20F-D4316B1A93BB", "sip" : "enabled", "vmRegionInfo" : "0x36da55ddc150 is not in any region. Bytes after previous region: 59830335029585 Bytes before following region: 45241744899760\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ", "exception" : {"codes":"0x0000000000000001, 0x000036da55ddc150","rawCodes":[1,60311371366736],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000036da55ddc150"}, "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"exc handler","byPid":2225}, "ktriageinfo" : "VM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\n", "vmregioninfo" : "0x36da55ddc150 is not in any region. 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Thunderbolt Bus: Laptop, Apple Inc. Thunderbolt Bus: Laptop, Apple Inc.

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VM password
by r ll 14 Dec '22

14 Dec '22

External Email - Use Caution Hello! Could I request for password to unzip ova.7z file: FS_7_2_0_ubuntu_18_04_06.ova Thanks, Rebeca

1 0

ERROR: cannot find or read transforms/talairach.m3z
by ANWAR Rauf 14 Dec '22

14 Dec '22

External Email - Use Caution Hi I am creating the source model using the tutorial of Fieldtrip. The part of activity involves using freesurfer, I get the error after running the command recon-all -autorecon2 -subjid $SUBJECTNAME And the error is given as reading transform from transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z error: No such file or directory error: transforms/talairach.m3z: could not open transform I have looked online and mostly people get this error, when they limited RAM, however I have roughly 13 Gb of RAM at my disposal. Any help in this regard will be greatly appreciated. Thanks Rauf

2 1

Password
by Fabien Rech 14 Dec '22

14 Dec '22

External Email - Use Caution Hello I have downloaded the virtual machine FS_7_2_0_Ubuntu_18_04_06.ova.7z <https://secure-web.cisco.com/1qUPe-P47gvxAYMnwB4S_TKKGgEmZnkOOEb9TAZuYqD17f…> from your website. Could you please give me the password to open the archive ? Thank you by advance Best regards Fabien -- Cet e-mail a été vérifié par le logiciel antivirus d'Avast. http://secure-web.cisco.com/1uhdYvZXoI5XlpdwdUTXhO-iPuLM8A4VdaonwEvO6lEEJJo…

1 0

Re: [Freesurfer] High Resolution Freesurfer Error
by Glasser, Matt 13 Dec '22

13 Dec '22

External Email - Use Caution How about a picture of the problem? At least at one time, some of FreeSurfer was limited to 256^3 voxels and there is a maximum resolution that you can fit a human brain in with that. Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Brooklyn Wright <brooklyn.rose14(a)outlook.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, December 13, 2022 at 9:18 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] High Resolution Freesurfer Error External Email - Use Caution Hi there 🙂 I am running into repeat difficulty with reconstructing ultra-high resolution T1w .nii images (0.25mm^3 voxel size). These have been submitted to rigorous preprocessing steps and I use hires flags and expert preferences however all of my attempts' output has some part of the brain missing as if it got two-thirds of the way through and then gave up. Have you got any suggestions on how to tackle this? Kindest, Brooklyn. ________________________________ 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.

1 0

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