Freesurfer October 2021

freesurfer@nmr.mgh.harvard.edu

81 participants
113 discussions

developer password
by Eli Bulger 29 Oct '21

29 Oct '21

External Email - Use Caution Hello, I am hoping to use Freesurfer on Windows 10. I have tried to use VirtualBox, but it requires a developer password. I have seen many emails on this mailing list where the password is provided through email. Is it possible to have a copy sent to this email? Thank you, _______________________ Eli Bulger Ph.D. Student, Biomedical Engineering Carnegie Mellon University

1 0

Postdoctoral Position – Pediatric Neuroimage Analysis and Deep Learning
by Gang Li 28 Oct '21

28 Oct '21

External Email - Use Caution A postdoctoral research associate position is available in the Department of Radiology and Biomedical Research Imaging Center at the University of North Carolina at Chapel Hill (UNC-Chapel Hill). Our current research focuses on the development of advanced image processing and deep learning techniques for pediatric neuroimaging data for better understanding the dynamic development of brain structure, function and connectivity in health and disease during the prenatal and early postnatal stages. The successful candidate will support our efforts in advancing pediatric neuroimaging analysis technologies (e.g., reconstruction, parcellation, registration, prediction, modeling, harmonization, etc.). We are seeking highly motivated individuals who have extensive research experience in medical image analysis and deep learning and demonstrated academic excellence, including publications in first-class journals or conferences. The candidate should have a Ph.D. (or equivalent) in Computer Science, Applied Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, Neuroscience, or related fields. Good command of programming tools including Python, C++, Linux, and scripting are necessary to carry out the research work in this group. The successful candidate will be part of a diverse group including neuroscientists, radiologists, psychologists, physicists, biostatistician, and computer scientists, and will build upon the group's extensive foundation on neuroimaging analysis (https://secure-web.cisco.com/13Nk5BnjS6JPAxxwIm0Lhc3q1raGx4_OpDQ-XY13280OPg…) The University of North Carolina at Chapel Hill is an equal opportunity and affirmative action employer. We strongly encourage applications from diverse backgrounds. Interested candidates should email a cover letter and a resume to Dr. Gang Li (gang_li(a)med.unc.edu)

1 0

Local GI MRI_segstats error
by COLLEEN PLETCHER 28 Oct '21

28 Oct '21

External Email - Use Caution Hello, I am trying to run mri_segstats for local GI indices. I am getting a file not found error for /tmp/mri_segstats.tmp.sub-1007_ses_01/.lh.176.ctab I did not get an error message when running the recon-all -localGI command and I am using freesurfer version 7.1.1. Any advice would be appreciated! Thanks, Colleen

2 4

Re: [Freesurfer] freeview segmentation fault: 11 on MacOS 10.15.7
by fsbuild 28 Oct '21

28 Oct '21

External Email - Use Caution Hello Emmanuel, You could try the suggestions in this post from last month, https://secure-web.cisco.com/1H6jl_CDKnKsqkQWb-ixQ370LPSa0jmM_IIgqtrwqvBfOr… It’s not formatted too well through the mail list archive, so I will try and send it to your private email separately. - R. On Oct 28, 2021, at 10:36, Emmanuel Guizar Rosales <emmanuel.guizarrosales(a)gmail.com> wrote:        External Email - Use Caution        Dear Freesurfer Team,I installed Freesurfer freesurfer-darwin-macOS-7.1.1-20200811-8b40551 and tried to view surface files in freeview. However, if I try to open surface files in freeview, it crashes.Note: I can open the Freeview.app, but as soon as I try to load a surface file, it crashes. If I try to start freeview from the terminal after runningexport FREESURFER_HOME=path/to/freesurfersource $FREESURFER_HOME/SetUpFreeSurfer.shfreeviewthe app won’t even start and return the following error in the terminal:/Applications/freesurfer/7..1.1/bin/freeview: line 2:  1202 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"Attached you will find the full problem report:Every help would be much appreciated!Best wishes,Emmanuel*

1 0

freeview segmentation fault: 11 on MacOS 10.15.7
by Emmanuel Guizar Rosales 28 Oct '21

28 Oct '21

External Email - Use Caution Dear Freesurfer Team, I installed Freesurfer freesurfer-darwin-macOS-7.1.1-20200811-8b40551 and tried to view surface files in freeview. However, if I try to open surface files in freeview, it crashes. Note: I can open the Freeview.app, but as soon as I try to load a surface file, it crashes. If I try to start freeview from the terminal after running export FREESURFER_HOME=path/to/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh freeview the app won’t even start and return the following error in the terminal: /Applications/freesurfer/7.1.1/bin/freeview: line 2: 1202 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" Attached you will find the full problem report: Every help would be much appreciated! Best wishes, Emmanuel ****PROBLEM REPORT**** Process: freeview [1202] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Identifier: com.freesurfer.freeview Version: 0 Code Type: X86-64 (Native) Parent Process: ??? [1201] Responsible: Terminal [630] User ID: 501 Date/Time: 2021-10-28 16:33:37.270 +0200 OS Version: Mac OS X 10.15.7 (19H1419) Report Version: 12 Bridge OS Version: 3.0 (14Y908) Anonymous UUID: F9BF3DDE-6823-A14A-B2C1-7126A1F33CD6 Time Awake Since Boot: 1500 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 0x000000006149584e Exception Note: EXC_CORPSE_NOTIFY Termination Signal: Segmentation fault: 11 Termination Reason: Namespace SIGNAL, Code 0xb Terminating Process: exc handler [1202] VM Regions Near 0x6149584e: --> __TEXT 000000010cd9f000-000000010e398000 [ 22.0M] r-x/rwx SM=COW /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Application Specific Information: dyld: in dlsym() Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 com.freesurfer.freeview 0x000000010cf67df8 0x10cd9f000 + 1871352 1 org.qt-project.QtWidgets 0x000000011d84c6ed QWidget::event(QEvent*) + 1117 2 org.qt-project.QtWidgets 0x000000011d95dc45 QMainWindow::event(QEvent*) + 277 3 org.qt-project.QtWidgets 0x000000011d81070d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 4 org.qt-project.QtWidgets 0x000000011d811b12 QApplication::notify(QObject*, QEvent*) + 594 5 org.qt-project.QtCore 0x000000011e4e5564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 6 org.qt-project.QtWidgets 0x000000011d86aa74 0x11d800000 + 436852 7 org.qt-project.QtWidgets 0x000000011d81070d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 8 org.qt-project.QtWidgets 0x000000011d811b12 QApplication::notify(QObject*, QEvent*) + 594 9 org.qt-project.QtCore 0x000000011e4e5564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 10 org.qt-project.QtGui 0x000000011dddea74 QGuiApplicationPrivate::processGeometryChangeEvent(QWindowSystemInterfacePrivate::GeometryChangeEvent*) + 516 11 org.qt-project.QtGui 0x000000011dddf420 QGuiApplicationPrivate::processWindowScreenChangedEvent(QWindowSystemInterfacePrivate::WindowScreenChangedEvent*) + 736 12 org.qt-project.QtGui 0x000000011ddbdc33 bool QWindowSystemInterfacePrivate::handleWindowSystemEvent<QWindowSystemInterface::SynchronousDelivery>(QWindowSystemInterfacePrivate::WindowSystemEvent*) + 115 13 libqcocoa.dylib 0x0000000120d6ac77 0x120d4c000 + 126071 14 libqcocoa.dylib 0x0000000120d64862 0x120d4c000 + 100450 15 libqcocoa.dylib 0x0000000120d642eb 0x120d4c000 + 99051 16 org.qt-project.QtGui 0x000000011dde81dc QWindowPrivate::create(bool, unsigned long long) + 140 17 org.qt-project.QtWidgets 0x000000011d839e31 QWidgetPrivate::create() + 1201 18 org.qt-project.QtWidgets 0x000000011d838b22 QWidget::create(unsigned long long, bool, bool) + 322 19 org.qt-project.QtWidgets 0x000000011d95e4d7 QMainWindow::setUnifiedTitleAndToolBarOnMac(bool) + 55 20 com.freesurfer.freeview 0x000000010cf58037 0x10cd9f000 + 1806391 21 com.freesurfer.freeview 0x000000010cf5224e 0x10cd9f000 + 1782350 22 com.freesurfer.freeview 0x000000010ce972a3 0x10cd9f000 + 1016483 23 libdyld.dylib 0x00007fff73c4dcc9 start + 1 Thread 1: 0 libsystem_pthread.dylib 0x00007fff73e4db68 start_wqthread + 0 Thread 2: 0 libsystem_pthread.dylib 0x00007fff73e4db68 start_wqthread + 0 Thread 3: 0 libsystem_pthread.dylib 0x00007fff73e4db68 start_wqthread + 0 Thread 4: 0 libsystem_pthread.dylib 0x00007fff73e4db68 start_wqthread + 0 Thread 5: 0 libsystem_pthread.dylib 0x00007fff73e4db68 start_wqthread + 0 Thread 6:: Dispatch queue: com.apple.dock.fullscreen 0 dyld 0x0000000126431c68 ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 204 1 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 2 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 3 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 4 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 5 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 6 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 7 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 8 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 9 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 10 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 11 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 12 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 13 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 14 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 15 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 16 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 17 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 18 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 19 dyld 0x0000000126431d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 20 dyld 0x0000000126431e5a ImageLoader::findExportedSymbolInImageOrDependentImages(char const*, ImageLoader::LinkContext const&, ImageLoader const**) const + 88 21 dyld 0x000000012642f54f dlsym_internal + 401 22 libdyld.dylib 0x00007fff73c39a09 dlsym + 195 23 com.apple.SkyLight 0x00007fff68ff9f21 __loginframework_vtable_block_invoke + 97 24 libdispatch.dylib 0x00007fff73bf4658 _dispatch_client_callout + 8 25 libdispatch.dylib 0x00007fff73bf57de _dispatch_once_callout + 20 26 com.apple.SkyLight 0x00007fff68ffba55 SLSCopyCurrentSessionPropertiesInternalBridge + 366 27 com.apple.SkyLight 0x00007fff68ee0ed3 SLSessionCopyCurrentDictionary + 12 28 com.apple.AppKit 0x00007fff36e1dd3a -[NSDockConnection _makeConnectionIfNeededWithRetryInterval:onDemand:] + 47 29 com.apple.AppKit 0x00007fff36e1dcff __35-[NSDockConnection startConnection]_block_invoke.41 + 45 30 libdispatch.dylib 0x00007fff73bf36c4 _dispatch_call_block_and_release + 12 31 libdispatch.dylib 0x00007fff73bf4658 _dispatch_client_callout + 8 32 libdispatch.dylib 0x00007fff73bf9c44 _dispatch_lane_serial_drain + 597 33 libdispatch.dylib 0x00007fff73bfa5d6 _dispatch_lane_invoke + 363 34 libdispatch.dylib 0x00007fff73c03c09 _dispatch_workloop_worker_thread + 596 35 libsystem_pthread.dylib 0x00007fff73e4ea3d _pthread_wqthread + 290 36 libsystem_pthread.dylib 0x00007fff73e4db77 start_wqthread + 15 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000061495846 rbx: 0x00007ffee2e5e998 rcx: 0x0000000000010000 rdx: 0x000000011d84c6dd rdi: 0x00000001264c7ac8 rsi: 0x00007ffee2e5da38 rbp: 0x00007ffee2e5d4f0 rsp: 0x00007ffee2e5d4e0 r8: 0x0000000000000000 r9: 0x00000000fffffe00 r10: 0x00000001264bca38 r11: 0x000000011e4e55b0 r12: 0x00007fdcbb6f6060 r13: 0x00007ffee2e5e998 r14: 0x00007ffee2e5da38 r15: 0x00007ffee2e5da38 rip: 0x000000010cf67df8 rfl: 0x0000000000010207 cr2: 0x000000006149584e Logical CPU: 2 Error Code: 0x00000004 (no mapping for user data read) Trap Number: 14 Binary Images: 0x10cd9f000 - 0x10e397ff7 +com.freesurfer.freeview (0) <5D2F3B3B-4E77-33B0-BCD0-96FC46B58202> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview 0x11d800000 - 0x11dc3eff7 +org.qt-project.QtWidgets (5.12 - 5.12.7) <EF671B84-7965-3C74-89DF-09C3FA9096CA> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtWidgets.framework/Versions/5/QtWidgets 0x11dda8000 - 0x11e1f4fe7 +org.qt-project.QtGui (5.12 - 5.12.7) <9CC34B01-AE4A-3FF2-AC1B-DE08B8FBBBAE> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtGui.framework/Versions/5/QtGui 0x11e2fb000 - 0x11e830ff7 +org.qt-project.QtCore (5.12 - 5.12.7) <AE294CA9-B3EC-3F0E-B67A-509A13C0C913> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/5/QtCore 0x120d4c000 - 0x120eb2fff +libqcocoa.dylib (0) <14BC2336-68E6-3ACE-B3A9-F21152A64785> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/platforms/libqcocoa.dylib 0x120eff000 - 0x120f5dfff +org.qt-project.QtDBus (5.12 - 5.12.7) <3D9A10D9-CB4E-3A1B-8664-BD25993D5FF3> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtDBus.framework/Versions/5/QtDBus 0x120f76000 - 0x120f9fff7 +org.qt-project.QtPrintSupport (5.12 - 5.12.7) <9AB0608C-8F2E-3FC1-B144-04ECEC6FA634> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtPrintSupport.framework/Versions/5/QtPrintSupport 0x1235bd000 - 0x1235e2fff +libqmacstyle.dylib (0) <05CC7ADD-D833-3744-93D6-D859235085A3> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/styles/libqmacstyle.dylib 0x1235f3000 - 0x1235f9ff3 +libqgif.dylib (0) <B67892CC-B844-3404-B289-B572937D144D> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqgif.dylib 0x1235fd000 - 0x123604ffb +libqicns.dylib (0) <2904A297-57DA-3089-953A-B4AC2E539486> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqicns.dylib 0x123609000 - 0x12360eff3 +libqico.dylib (0) <55050416-63A6-3F0F-B0C3-C067186CB93A> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqico.dylib 0x123613000 - 0x123676ffb +libqjpeg.dylib (0) <9928EF62-0B3A-3994-89B3-456715992C07> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqjpeg.dylib 0x12367c000 - 0x123681ff7 +libqmacheif.dylib (0) <82101836-3A14-3102-B49C-06B07F7D3263> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqmacheif.dylib 0x123686000 - 0x12368bffb +libqmacjp2.dylib (0) <A05D9F8D-0076-391B-A805-67F106C11EE7> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqmacjp2.dylib 0x123690000 - 0x123694ffb +libqtga.dylib (0) <94EB07B0-6C36-30F0-AB07-A2535214DB5E> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqtga.dylib 0x123698000 - 0x1236fdff3 +libqtiff.dylib (0) <BDF2E544-2CA2-377E-92CA-79DAF65E47E4> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqtiff.dylib 0x123705000 - 0x123708ff3 +libqwbmp.dylib (0) <2CD47DD7-A3AD-3997-B0A3-5E3AE772971B> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqwbmp.dylib 0x12370c000 - 0x1237a0ff7 +libqwebp.dylib (0) <8A9124AF-CA0F-3982-B325-B4DAEB7FB374> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqwebp.dylib 0x1237a9000 - 0x1237ac047 libobjc-trampolines.dylib (787.1) <88F9B648-C455-36F8-BBB9-7D1A9F57D073> /usr/lib/libobjc-trampolines.dylib 0x12641f000 - 0x1264b1267 dyld (750.7) <0191F040-B591-3082-B8D9-498DC11D3BB5> /usr/lib/dyld 0x7fff2cac2000 - 0x7fff2cd0fff8 com.apple.RawCamera.bundle (9.02.0 - 1350.30) <5337D338-FB27-3B70-91C8-096357BEFAC2> /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera 0x7fff323d0000 - 0x7fff327cfff1 com.apple.driver.AppleIntelKBLGraphicsMTLDriver (14.7.18 - 14.0.7) <139EC6F8-4675-3EFE-ABCE-7139B9A25035> /System/Library/Extensions/AppleIntelKBLGraphicsMTLDriver.bundle/Contents/MacOS/AppleIntelKBLGraphicsMTLDriver 0x7fff3526a000 - 0x7fff3526effb com.apple.agl (3.3.3 - AGL-3.3.3) <CDC14585-934E-32C4-B454-436898CE6DC7> /System/Library/Frameworks/AGL.framework/Versions/A/AGL 0x7fff35657000 - 0x7fff35657fff com.apple.Accelerate (1.11 - Accelerate 1.11) <4F9977AE-DBDB-3A16-A536-AC1F9938DCDD> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate 0x7fff35658000 - 0x7fff3566efef libCGInterfaces.dylib (524.2.1) <8FD09D09-BB19-36C5-ADE9-4F22DA235AEE> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib 0x7fff3566f000 - 0x7fff35cc5fff com.apple.vImage (8.1 - 524.2.1) <EA6F5FF2-7A1B-35D5-A5A3-D2B3386ECB75> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage 0x7fff35cc6000 - 0x7fff35f2dff7 libBLAS.dylib (1303.60.1) <C6C2D42F-7456-3DBF-8BE2-9AA06EFC78FD> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 0x7fff35f2e000 - 0x7fff36401fef libBNNS.dylib (144.100.2) <99C61C48-B14C-3DA6-8C31-6BF72DA0A3A9> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBNNS.dylib 0x7fff36402000 - 0x7fff3679dfff libLAPACK.dylib (1303.60.1) <5E3E3867-50C3-3E6A-9A2E-007CE77A4641> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib 0x7fff3679e000 - 0x7fff367b3fec libLinearAlgebra.dylib (1303.60.1) <3D433800-0099-33E0-8C81-15F83247B2C9> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLinearAlgebra.dylib 0x7fff367b4000 - 0x7fff367b9ff3 libQuadrature.dylib (7) <371F36A7-B12F-363E-8955-F24F7C2048F6> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libQuadrature.dylib 0x7fff367ba000 - 0x7fff3682afff libSparse.dylib (103) <B8A10D0C-4577-343D-B310-A3E81265D107> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparse.dylib 0x7fff3682b000 - 0x7fff3683dfef libSparseBLAS.dylib (1303.60.1) <B147FEF6-A0DB-3830-BF06-45BEC58DB576> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparseBLAS.dylib 0x7fff3683e000 - 0x7fff36a15fd7 libvDSP.dylib (735.140.1) <D63DC0A5-B8B4-3562-A574-E73BC3B57407> 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0x7fff6a462ff3 com.apple.TCC (1.0 - 1) <520B2095-42EF-3837-99D3-393CA377ADBA> /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC 0x7fff6a987000 - 0x7fff6aa4dff0 com.apple.TextureIO (3.10.9 - 3.10.9) <EEDAB753-329A-396A-8119-5BEDF7DB5A56> /System/Library/PrivateFrameworks/TextureIO.framework/Versions/A/TextureIO 0x7fff6ac1d000 - 0x7fff6ae75ff0 com.apple.UIFoundation (1.0 - 662) <EC55B9E5-7E62-380A-9AB1-FC7BEF663653> /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation 0x7fff6bb12000 - 0x7fff6bb32ffc com.apple.UserManagement (1.0 - 1) <9F00880E-6EA6-3684-B208-455E14EC07C8> /System/Library/PrivateFrameworks/UserManagement.framework/Versions/A/UserManagement 0x7fff6cb6f000 - 0x7fff6cb70fff com.apple.WatchdogClient.framework (1.0 - 67.120.2) <FFA17DA1-F6DD-34D3-A708-1F73C8BA7EA7> /System/Library/PrivateFrameworks/WatchdogClient.framework/Versions/A/WatchdogClient 0x7fff6d7a0000 - 0x7fff6d7a3ffa com.apple.dt.XCTTargetBootstrap (1.0 - 16091) <D459D628-58C5-39A6-B7E8-B691CBEECEC1> /System/Library/PrivateFrameworks/XCTTargetBootstrap.framework/Versions/A/XCTTargetBootstrap 0x7fff6d81d000 - 0x7fff6d82bff5 com.apple.audio.caulk (1.0 - 32.3) <06D695EA-E2BC-31E4-9816-9C12542BA744> /System/Library/PrivateFrameworks/caulk.framework/Versions/A/caulk 0x7fff6db6d000 - 0x7fff6db6fff3 com.apple.loginsupport (1.0 - 1) <540BB904-0A51-3B37-A436-969D24CD28AC> /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport 0x7fff6db70000 - 0x7fff6db83ffd com.apple.login (3.0 - 3.0) <4483035E-7BEB-3CEB-AC1B-A765FBC12678> /System/Library/PrivateFrameworks/login.framework/Versions/A/login 0x7fff70653000 - 0x7fff70686ffa libAudioToolboxUtility.dylib (1104.100) <BF879AA5-26B5-3F7F-9721-E97194BBFA43> /usr/lib/libAudioToolboxUtility.dylib 0x7fff7068d000 - 0x7fff706c1fff libCRFSuite.dylib (48) <5E5DE3CB-30DD-34DC-AEF8-FE8536A85E96> /usr/lib/libCRFSuite.dylib 0x7fff706c4000 - 0x7fff706cefff libChineseTokenizer.dylib (34) <7F0DA183-1796-315A-B44A-2C234C7C50BE> /usr/lib/libChineseTokenizer.dylib 0x7fff7075a000 - 0x7fff7075cff7 libDiagnosticMessagesClient.dylib (112) <C94F3B7B-1854-38EB-9778-834501C53B3F> /usr/lib/libDiagnosticMessagesClient.dylib 0x7fff707a2000 - 0x7fff70959ffb libFosl_dynamic.dylib (100.4) <737573B2-190A-3BA1-8220-807AD0A2CE5E> /usr/lib/libFosl_dynamic.dylib 0x7fff70980000 - 0x7fff70986ff3 libIOReport.dylib (54) <75D177C4-BAD7-3285-B8E1-3019F49B3178> /usr/lib/libIOReport.dylib 0x7fff70a68000 - 0x7fff70a6ffff libMatch.1.dylib (36) <5C6F3971-9D9E-3630-BDB6-60BFC5A665E0> /usr/lib/libMatch.1.dylib 0x7fff70a9e000 - 0x7fff70abeff7 libMobileGestalt.dylib (826.140.5) <2BE94E6A-FA61-312F-84A1-F764D71B7E39> /usr/lib/libMobileGestalt.dylib 0x7fff70c30000 - 0x7fff70c31fff libSystem.B.dylib (1281.100.1) <B6B1DAD9-40C3-39BE-89D3-1F8C9692A7A3> /usr/lib/libSystem.B.dylib 0x7fff70cbe000 - 0x7fff70cbffff libThaiTokenizer.dylib (3) <4F4ADE99-0D09-3223-B7C0-C407AB6DE8DC> 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- 0x7fff720a9ff1 libmecabra.dylib (883.11) <E31DE74D-1B88-377F-ACD3-D789D29C3AE7> /usr/lib/libmecabra.dylib 0x7fff72416000 - 0x7fff72445fff libncurses.5.4.dylib (57) <995DFEEA-40F3-377F-B73D-D02AC59D591F> /usr/lib/libncurses.5.4.dylib 0x7fff72575000 - 0x7fff729f1ff5 libnetwork.dylib (1880.120.4) <BA294A54-F309-398D-B308-F97032AFF555> /usr/lib/libnetwork.dylib 0x7fff72a92000 - 0x7fff72ac5fde libobjc.A.dylib (787.1) <6DF81160-5E7F-3E31-AA1E-C875E3B98AF6> /usr/lib/libobjc.A.dylib 0x7fff72ad8000 - 0x7fff72adcfff libpam.2.dylib (25.100.1) <0502F395-8EE6-3D2A-9239-06FD5622E19E> /usr/lib/libpam.2.dylib 0x7fff72adf000 - 0x7fff72b15fff libpcap.A.dylib (89.120.2) <86DAA475-805A-3E01-86C5-6CAE4D1D9BC6> /usr/lib/libpcap.A.dylib 0x7fff72b99000 - 0x7fff72bb1fff libresolv.9.dylib (67.40.1) <C57EDFEF-D36A-310B-8D14-8C68A625B1E8> /usr/lib/libresolv.9.dylib 0x7fff72bb3000 - 0x7fff72bf7ff7 libsandbox.1.dylib (1217.141.6) <1B5B5733-BAD1-3FB6-BA75-2AC4FDCCE7CE> /usr/lib/libsandbox.1.dylib 0x7fff72c0b000 - 0x7fff72c0cff7 libspindump.dylib (281.3) <AE8C1AE9-5CBC-332F-BBE8-370A2A19FED6> /usr/lib/libspindump.dylib 0x7fff72c0d000 - 0x7fff72df7ff7 libsqlite3.dylib (308.6) <33057143-AB4E-348B-9650-98BC48866F34> /usr/lib/libsqlite3.dylib 0x7fff73048000 - 0x7fff7304bffb libutil.dylib (57) <F01467F6-23A7-37EE-A170-33CE1577B41D> /usr/lib/libutil.dylib 0x7fff7304c000 - 0x7fff73059ff7 libxar.1.dylib (425.2) <EE964412-9E25-30B3-BCC0-CCEFBCC8094B> /usr/lib/libxar.1.dylib 0x7fff7305f000 - 0x7fff73141fff libxml2.2.dylib (33.9) <B72D22CE-3429-3217-A8DD-5C9D2077C980> /usr/lib/libxml2.2.dylib 0x7fff73145000 - 0x7fff7316dfff libxslt.1.dylib (16.12) <42938E5F-5FE9-3265-8D10-1D1115BC5402> /usr/lib/libxslt.1.dylib 0x7fff7316e000 - 0x7fff73180ff3 libz.1.dylib (76) <793D9643-CD83-3AAC-8B96-88D548FAB620> /usr/lib/libz.1.dylib 0x7fff73a2f000 - 0x7fff73a34ff3 libcache.dylib (83) <AF488D13-9E89-35E0-B078-BE37CC5B8586> /usr/lib/system/libcache.dylib 0x7fff73a35000 - 0x7fff73a40fff libcommonCrypto.dylib (60165.120.1) <C7912BE5-993E-3581-B2A0-6AABDC8C5562> /usr/lib/system/libcommonCrypto.dylib 0x7fff73a41000 - 0x7fff73a48fff libcompiler_rt.dylib (101.2) <49B8F644-5705-3F16-BBE0-6FFF9B17C36E> /usr/lib/system/libcompiler_rt.dylib 0x7fff73a49000 - 0x7fff73a52ff7 libcopyfile.dylib (166.40.1) <3C481225-21E7-370A-A30E-0CCFDD64A92C> /usr/lib/system/libcopyfile.dylib 0x7fff73a53000 - 0x7fff73ae5fdb libcorecrypto.dylib (866.140.2) <E9AAA2A6-D0D4-328A-BEA2-4DC5E513BA30> /usr/lib/system/libcorecrypto.dylib 0x7fff73bf2000 - 0x7fff73c32ff0 libdispatch.dylib (1173.100.2) <CD9C059C-91D9-30E8-8926-5B9CD0D5D4F5> /usr/lib/system/libdispatch.dylib 0x7fff73c33000 - 0x7fff73c69fff libdyld.dylib (750.7) <AB99C9EE-7127-3451-89AB-339F8F2CEE61> /usr/lib/system/libdyld.dylib 0x7fff73c6a000 - 0x7fff73c6affb libkeymgr.dylib (30) <DB3337BE-01CA-3425-BD0C-87774FC0CDC0> /usr/lib/system/libkeymgr.dylib 0x7fff73c6b000 - 0x7fff73c77ff3 libkxld.dylib (6153.141.40.1) <7C1BE75F-51A9-3717-BB4D-FD3A3388E060> /usr/lib/system/libkxld.dylib 0x7fff73c78000 - 0x7fff73c78ff7 liblaunch.dylib (1738.140.3) <E2CFD17D-F36C-3734-8F37-16798799EF9E> /usr/lib/system/liblaunch.dylib 0x7fff73c79000 - 0x7fff73c7eff7 libmacho.dylib (959.0.1) <AA613A9C-961A-3B67-B696-4622FA59FC4E> /usr/lib/system/libmacho.dylib 0x7fff73c7f000 - 0x7fff73c81ff3 libquarantine.dylib (110.40.3) <F234E51D-FD0B-3EE4-B679-AE3EE9C536C3> /usr/lib/system/libquarantine.dylib 0x7fff73c82000 - 0x7fff73c83ff7 libremovefile.dylib (48) <7C7EFC79-BD24-33EF-B073-06AED234593E> /usr/lib/system/libremovefile.dylib 0x7fff73c84000 - 0x7fff73c9bff3 libsystem_asl.dylib (377.60.2) <1563EE02-0657-3B78-99BE-A947C24122EF> /usr/lib/system/libsystem_asl.dylib 0x7fff73c9c000 - 0x7fff73c9cff7 libsystem_blocks.dylib (74) <0D53847E-AF5F-3ACF-B51F-A15DEA4DEC58> /usr/lib/system/libsystem_blocks.dylib 0x7fff73c9d000 - 0x7fff73d24fff libsystem_c.dylib (1353.100.4) <BCD3F031-4A3F-32CF-AB9A-D6EE7A7499D4> /usr/lib/system/libsystem_c.dylib 0x7fff73d25000 - 0x7fff73d28ffb libsystem_configuration.dylib (1061.141.2) <393137B7-3631-3450-B6F4-95EECD3ADDFF> /usr/lib/system/libsystem_configuration.dylib 0x7fff73d29000 - 0x7fff73d2cfff libsystem_coreservices.dylib (114.1) <72857ADA-AA97-398B-B089-F50B2E89064B> /usr/lib/system/libsystem_coreservices.dylib 0x7fff73d2d000 - 0x7fff73d35fff libsystem_darwin.dylib (1353.100.4) <19242BF1-BAF6-3DF0-AAD3-93E3E0870DBE> /usr/lib/system/libsystem_darwin.dylib 0x7fff73d36000 - 0x7fff73d3dfff libsystem_dnssd.dylib (1096.100.3) <EBB4C2C2-E031-3094-B40A-E67BF261D295> /usr/lib/system/libsystem_dnssd.dylib 0x7fff73d3e000 - 0x7fff73d3fffb libsystem_featureflags.dylib (17) <29FD922A-EC2C-3F25-BCCC-B58D716E60EC> /usr/lib/system/libsystem_featureflags.dylib 0x7fff73d40000 - 0x7fff73d8dff7 libsystem_info.dylib (538) <8A321605-5480-330B-AF9E-64E65DE61747> /usr/lib/system/libsystem_info.dylib 0x7fff73d8e000 - 0x7fff73dbaff7 libsystem_kernel.dylib (6153.141.40.1) <383B8E9D-B065-3F56-A3DA-B38564280249> /usr/lib/system/libsystem_kernel.dylib 0x7fff73dbb000 - 0x7fff73e02fff libsystem_m.dylib (3178) <00F331F1-0D09-39B3-8736-1FE90E64E903> /usr/lib/system/libsystem_m.dylib 0x7fff73e03000 - 0x7fff73e2afff libsystem_malloc.dylib (283.100.6) <8549294E-4C53-36EB-99F3-584A7393D8D5> /usr/lib/system/libsystem_malloc.dylib 0x7fff73e2b000 - 0x7fff73e38ffb libsystem_networkextension.dylib (1095.140.2) <F06C65C5-2CBE-313C-96E1-A09240F9FE57> /usr/lib/system/libsystem_networkextension.dylib 0x7fff73e39000 - 0x7fff73e42ff7 libsystem_notify.dylib (241.100.2) <FA22F928-D91B-3AA5-96BB-3186AC0FB264> /usr/lib/system/libsystem_notify.dylib 0x7fff73e43000 - 0x7fff73e4bfef libsystem_platform.dylib (220.100.1) <009A7C1F-313A-318E-B9F2-30F4C06FEA5C> /usr/lib/system/libsystem_platform.dylib 0x7fff73e4c000 - 0x7fff73e56fff libsystem_pthread.dylib (416.100.3) <62CB1A98-0B8F-31E7-A02B-A1139927F61D> /usr/lib/system/libsystem_pthread.dylib 0x7fff73e57000 - 0x7fff73e5bff3 libsystem_sandbox.dylib (1217.141.6) <ACACC5C9-CE29-394C-87AD-3AF5FDDA942E> /usr/lib/system/libsystem_sandbox.dylib 0x7fff73e5c000 - 0x7fff73e5efff libsystem_secinit.dylib (62.100.2) <F80872AA-E1FD-3D7E-8729-467656EC6561> /usr/lib/system/libsystem_secinit.dylib 0x7fff73e5f000 - 0x7fff73e66ffb libsystem_symptoms.dylib (1238.120.2) <702D0910-5C34-3D43-9631-8BD215DE4FE1> /usr/lib/system/libsystem_symptoms.dylib 0x7fff73e67000 - 0x7fff73e7dff2 libsystem_trace.dylib (1147.120.1) <BC141783-66D9-3137-A783-211B38E49ADB> /usr/lib/system/libsystem_trace.dylib 0x7fff73e7f000 - 0x7fff73e84ff7 libunwind.dylib (35.4) <42B7B509-BAFE-365B-893A-72414C92F5BF> /usr/lib/system/libunwind.dylib 0x7fff73e85000 - 0x7fff73ebaffe libxpc.dylib (1738.140.3) <8DA7D88F-AE2F-3BCF-8426-8D041E57A9AA> /usr/lib/system/libxpc.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: 937 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=618.3M resident=0K(0%) swapped_out_or_unallocated=618.3M(100%) Writable regions: Total=313.8M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=313.8M(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 128K 1 Activity Tracing 256K 1 CG backing stores 1824K 4 CoreImage 32K 4 CoreUI image data 188K 2 Dispatch continuations 8192K 1 Foundation 4K 1 Kernel Alloc Once 8K 1 MALLOC 50.3M 34 MALLOC guard page 32K 8 STACK GUARD 56.0M 7 Stack 11.0M 7 VM_ALLOCATE 84K 12 __DATA 268.3M 304 __DATA_CONST 20K 1 __FONT_DATA 4K 1 __LINKEDIT 392.9M 22 __OBJC_RO 32.3M 1 __OBJC_RW 1904K 1 __TEXT 225.4M 299 __UNICODE 564K 1 mapped file 57.2M 17 shared memory 640K 15 =========== ======= ======= TOTAL 1.1G 745 Model: MacBookPro14,2, BootROM 429.140.8.0.0, 2 processors, Dual-Core Intel Core i7, 3.5 GHz, 16 GB, SMC 2.44f6 Graphics: kHW_IntelIrisGraphics650Item, Intel Iris Plus Graphics 650, spdisplays_builtin Memory Module: BANK 0/DIMM0, 8 GB, LPDDR3, 2133 MHz, 0x80CE, 0x4B3445424533303445422D45474347202020 Memory Module: BANK 1/DIMM0, 8 GB, LPDDR3, 2133 MHz, 0x80CE, 0x4B3445424533303445422D45474347202020 AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x171), Broadcom BCM43xx 1.0 (7.77.111.1 AirPortDriverBrcmNIC-1615.4) Bluetooth: Version 7.0.6f8, 3 services, 27 devices, 1 incoming serial ports Network Service: Wi-Fi, AirPort, en0 USB Device: USB 3.0 Bus USB Device: Apple T1 Controller Thunderbolt Bus: MacBook Pro, Apple Inc., 41.4 Thunderbolt Bus: MacBook Pro, Apple Inc., 41.4

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same ROI with different stats
by Wei Shao 28 Oct '21

28 Oct '21

External Email - Use Caution Hi, Freesurfer exports I'm wondering what is the difference in the stat folder when it comes to the same ROI. For example, I have found the entorhinal from 4 different stats files and the values are slightly different. lh.aparc.DKTatlas.stats entorhinal 665 393 1528 3.174 0.788 0.085 0.021 5 0.5 lh.aparc.pial.stats entorhinal 848 799 1906 3.159 0.787 0.199 0.068 16 3.1 lh.BA_exvivo.stats entorhinal_exvivo 570 346 1394 3.000 1.015 0.083 0.023 5 0.4 lh.BA_exvivo.thresh.stats entorhinal_exvivo 344 205 918 3.450 0.520 0.057 0.010 1 0.1 I‘m really appreciate it if you can provide me some instructions about these 4 Best, Wei

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Re: [Freesurfer] orig/001.mgz to brain.mgz transformation?
by Billah, Tashrif 28 Oct '21

28 Oct '21

Thank you Douglas, I enjoyed reading your referral. However, I did not get answer to any of my questions. Can you take a second look? Best, Tashrif Date: Wed, 27 Oct 2021 11:41:35 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] orig/001.mgz to brain.mgz transformation? To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <c72019a8-4724-f403-d309-0f5403fc21ed(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" On 10/27/2021 10:58 AM, Billah, Tashrif wrote: > Hi, > > 1. What is the name of the space of wmparc.mgz? I see that it is in > the same space of brain.mgz. > Yes > > 1. > > > 2. What transform file brings orig/001.mgz to brain.mgz? > See https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat > > Best, > Tashrif ------------------------------------------------------------- Tashrif Billah, MS Research Engineer Brigham and Women's Hospital Harvard Medical School tbillah(a)bwh.harvard.edu<mailto:tbillah@bwh.harvard.edu>

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Re: [Freesurfer] developer password
by fsbuild 27 Oct '21

27 Oct '21

External Email - Use Caution Sending the info to your email shortly. - R. On Oct 20, 2021, at 10:31, Joshua Ericson <josheric(a)hssdschools.org> wrote:        External Email - Use Caution        I am attempting to start Freesurfer - Ubuntu via VirtualBox on Windows 10, but it requests a login password for the "Developer" account, while installation guide assumes automatic login. Would you be able to provide a password please?Joshua Ericson Technology EducationBay Port High School_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

manual segmentation
by 刘卫 27 Oct '21

27 Oct '21

External Email - Use Caution Hello FreeSurfer Developers, I would like to ask, on free surfer, can I directly analyze the data that I run automatically? Do I need to perform manual segmentation again? Thanks!

2 1

orig/001.mgz to brain.mgz transformation?
by Billah, Tashrif 27 Oct '21

27 Oct '21

Hi, 1. What is the name of the space of wmparc.mgz? I see that it is in the same space of brain.mgz. 2. What transform file brings orig/001.mgz to brain.mgz? Best, Tashrif

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Freesurfer October 2021