Freesurfer April 2021

freesurfer@nmr.mgh.harvard.edu

104 participants
144 discussions

Postdoc Position at the Buffalo Neuroimaging Analysis Center
by Michael Dwyer 13 Apr '21

13 Apr '21

External Email - Use Caution Dear all, The Buffalo Neuroimaging Analysis Center (BNAC), an interdisciplinary organization that is part of the Department of Neurology of The State University of New York at Buffalo (http://secure-web.cisco.com/15d0nEH6vnvRtzz4rIsQT20HCiBgIHP2i3Sb709ItZJSzog…) is looking for a post-doctoral fellow to be part of upcoming studies combining novel PET tracers with other imaging modalities to understand the pathology and progression of multiple sclerosis and other neurological diseases and disorders. Ideal start date is June 2021. The research program will be conducted at the University at Buffalo, Buffalo, NY, under the supervision of Professor Robert Zivadinov and Associate Professors Michael Dwyer and Ferdinand Schweser. The candidate will be part of ongoing and new collaborations and be able to work in a stimulating and inspiring environment. The fellow is expected to work closely with the team to plan and apply state-of-the-art PET approaches and fusion with MRI and other modalities. In addition, he/she will have the opportunity to develop new skills, analyze datasets, apply for grants, and develop a strong network of collaborations. The BNAC team includes neurologists, computer scientists, MR physicists, and many others working to uncover new ways to use neuroimaging to extend the boundaries of our current knowledge about neurological diseases and disorders like multiple sclerosis, Alzheimer’s disease, Parkinson’s disease and stroke among others. The BNAC is equipped with multiple 3T MRIs with active research agreements, a 9.4T Bruker MRI with CryoProbe and a prototype microPET insert, and a dedicated PET/CT research scanner. Requirements: • Ph.D. in neuroimaging, computer science, biomedical engineering, neuropsychology, physics, statistics, or a related field • Experience in statistical techniques, programming, and scripting • Substantial experience with PET imaging acquisition and analysis • Good record of scientific publications Additional preferred qualifications: • Experience with structural MRI, DTI, and/or fMRI • Clinical or research experience with aging and/or neurodegenerative disorders • Pre-clinical experience with MRI, CT, and/or PET image analysis To apply please contact Devon Oship at doship(a)bnac.net. -- Michael G. Dwyer, Ph.D. Associate Professor of Neurology and Biomedical Informatics Director, Neuroinfomatics Development and IT Units Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdwyer(a)bnac.net (716) 859-7065

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Re: [Freesurfer] Freeview will not run
by fsbuild 13 Apr '21

13 Apr '21

External Email - Use Caution Hello Aaron, The crash report lists issues with running the Qt package and that you are running zsh.   You could try running freeview under “bash” in the terminal window (which was the default in older versions of MacOS - it may tell you how to set that as your default shell). In a new terminal window you could try running, $ bash Check that the X windows distribution for MacOS is installed with,$ which Xquartz/opt/X11/bin/Xquartz If you don’t see that, then install Xquartz from https://secure-web.cisco.com/17-xR4PJeGXKy7MXV6eO9Mq8lIqfRBMTziNE… then try the “which” command again to find Xquartz. Then setup the freesurfer environment, $ export FREESURFER_HOME=/Applications/freesurfer/7.1.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.1.1 FSFAST_HOME       /Applications/freesurfer/7.1.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.1.1/subjects MNI_DIR           /Applications/freesurfer/7.1.1/mni $ which freeview /Applications/freesurfer/7.1.1/bin/freeview$ freeview …. empty freeview window should come up …. You can also run it form the terminal in the same double clicking on the icon in the Finder would do - which should also work, $ open -a /Applications/freesurfer/7.1.1/Freeview.app If you did not use the pkg installer to install freesurfer 7.1.1 (which needs admin privileges), then you could try the installer from, https://secure-web.cisco.com/1zOWcX0vk_HcCYLk0GOYUnNnAjoxNPWBoiPfrB5b6-q-5Y… - R. On Apr 13, 2021, at 01:08, Aaron Switzer <arswitze(a)ucalgary.ca> wrote:        External Email - Use Caution                External Email - Use Caution        Dear FreeSurfer experts,I am having troubles running Freeview on Mac OSX 10.15.7. I have Freesurfer 7.1.1. When I enter ‘freeview’ into terminal or double click the Freeview.app in FREESURFER_HOME, it crashes and I get the following error: aaronswitzer@Aarons-MacBook-Pro-2 ~ % freeview/Applications/freesurfer/7.1.1/bin/freeview: line 2:  2037 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“ (full error report below)I’ve gone through the suggestions given in the mail archive for a similar problem posted on June 14, 2020, to no avail. I have the most up to date X11 (v2.8.1),  FREESURFER_HOME is properly configured, I’ve tried uninstalling and reinstalling freesurfer, I’ve tried deleting edu.harvard.mgh.nmr.plist, and I tried building the freeview.zip file from GitHub.. Is there anything else I can try?Thank you for your help,Aaron

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Freeview will not run
by Aaron Switzer 13 Apr '21

13 Apr '21

External Email - Use Caution Dear FreeSurfer experts, I am having troubles running Freeview on Mac OSX 10.15.7. I have Freesurfer 7.1.1. When I enter ‘freeview’ into terminal or double click the Freeview.app in FREESURFER_HOME, it crashes and I get the following error: aaronswitzer@Aarons-MacBook-Pro-2 ~ % freeview /Applications/freesurfer/7.1.1/bin/freeview: line 2: 2037 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“ (full error report below) I’ve gone through the suggestions given in the mail archive for a similar problem posted on June 14, 2020, to no avail. I have the most up to date X11 (v2.8.1), FREESURFER_HOME is properly configured, I’ve tried uninstalling and reinstalling freesurfer, I’ve tried deleting edu.harvard.mgh.nmr.plist, and I tried building the freeview.zip file from GitHub. Is there anything else I can try? Thank you for your help, Aaron Process: freeview [2117] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Identifier: com.freesurfer.freeview Version: 0 Code Type: X86-64 (Native) Parent Process: zsh [2089] Responsible: Terminal [385] User ID: 501 Date/Time: 2021-04-12 22:56:19.290 -0600 OS Version: Mac OS X 10.15.7 (19H524) Report Version: 12 Bridge OS Version: 3.0 (14Y908) Anonymous UUID: C4040AA1-B39A-9CDF-C9B1-A6690AB8C713 Time Awake Since Boot: 1800 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 0x0000000000000029 Exception Note: EXC_CORPSE_NOTIFY Termination Signal: Segmentation fault: 11 Termination Reason: Namespace SIGNAL, Code 0xb Terminating Process: exc handler [2117] VM Regions Near 0x29: --> __TEXT 0000000106f2a000-0000000108552000 [ 22.2M] 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 0x00000001070fb114 0x106f2a000 + 1904916 1 org.qt-project.QtWidgets 0x0000000117a056ed QWidget::event(QEvent*) + 1117 2 org.qt-project.QtWidgets 0x0000000117b16c45 QMainWindow::event(QEvent*) + 277 3 org.qt-project.QtWidgets 0x00000001179c970d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 4 org.qt-project.QtWidgets 0x00000001179cab12 QApplication::notify(QObject*, QEvent*) + 594 5 org.qt-project.QtCore 0x000000011869d564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 6 org.qt-project.QtWidgets 0x0000000117a23a74 0x1179b9000 + 436852 7 org.qt-project.QtWidgets 0x00000001179c970d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 8 org.qt-project.QtWidgets 0x00000001179cab12 QApplication::notify(QObject*, QEvent*) + 594 9 org.qt-project.QtCore 0x000000011869d564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 10 org.qt-project.QtGui 0x0000000117f94a74 QGuiApplicationPrivate::processGeometryChangeEvent(QWindowSystemInterfacePrivate::GeometryChangeEvent*) + 516 11 org.qt-project.QtGui 0x0000000117f95420 QGuiApplicationPrivate::processWindowScreenChangedEvent(QWindowSystemInterfacePrivate::WindowScreenChangedEvent*) + 736 12 org.qt-project.QtGui 0x0000000117f73c33 bool QWindowSystemInterfacePrivate::handleWindowSystemEvent<QWindowSystemInterface::SynchronousDelivery>(QWindowSystemInterfacePrivate::WindowSystemEvent*) + 115 13 libqcocoa.dylib 0x000000011b76ac77 0x11b74c000 + 126071 14 libqcocoa.dylib 0x000000011b764862 0x11b74c000 + 100450 15 libqcocoa.dylib 0x000000011b7642eb 0x11b74c000 + 99051 16 org.qt-project.QtGui 0x0000000117f9e1dc QWindowPrivate::create(bool, unsigned long long) + 140 17 org.qt-project.QtWidgets 0x00000001179f2e31 QWidgetPrivate::create() + 1201 18 org.qt-project.QtWidgets 0x00000001179f1b22 QWidget::create(unsigned long long, bool, bool) + 322 19 org.qt-project.QtWidgets 0x0000000117b174d7 QMainWindow::setUnifiedTitleAndToolBarOnMac(bool) + 55 20 com.freesurfer.freeview 0x00000001070e9857 0x106f2a000 + 1833047 21 com.freesurfer.freeview 0x00000001070e38fe 0x106f2a000 + 1808638 22 com.freesurfer.freeview 0x00000001070247ea 0x106f2a000 + 1026026 23 libdyld.dylib 0x00007fff6b7b3cc9 start + 1 Thread 1: 0 libsystem_pthread.dylib 0x00007fff6b9b3b68 start_wqthread + 0 Thread 2:: Dispatch queue: com.apple.dock.fullscreen 0 dyld 0x0000000120e0089a ImageLoader::trieWalk(unsigned char const*, unsigned char const*, char const*) + 194 1 dyld 0x0000000120e0a400 ImageLoaderMachOCompressed::findShallowExportedSymbol(char const*, ImageLoader const**) const + 112 2 dyld 0x0000000120e04075 ImageLoaderMachO::findExportedSymbol(char const*, bool, char const*, ImageLoader const**) const + 37 3 dyld 0x0000000120dfcb1a ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 254 4 dyld 0x0000000120dfcbbe ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 5 dyld 0x0000000120dfcbbe ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 6 dyld 0x0000000120dfcbbe ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 7 dyld 0x0000000120dfcbbe ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 8 dyld 0x0000000120dfcbbe ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 9 dyld 0x0000000120dfccda ImageLoader::findExportedSymbolInImageOrDependentImages(char const*, ImageLoader::LinkContext const&, ImageLoader const**) const + 88 10 dyld 0x0000000120dfa3c3 dlsym_internal + 401 11 libdyld.dylib 0x00007fff6b79fa09 dlsym + 195 12 com.apple.SkyLight 0x00007fff60b70124 __loginframework_vtable_block_invoke + 564 13 libdispatch.dylib 0x00007fff6b75a658 _dispatch_client_callout + 8 14 libdispatch.dylib 0x00007fff6b75b7de _dispatch_once_callout + 20 15 com.apple.SkyLight 0x00007fff60b71a85 SLSCopyCurrentSessionPropertiesInternalBridge + 366 16 com.apple.SkyLight 0x00007fff60a56ee3 SLSessionCopyCurrentDictionary + 12 17 com.apple.AppKit 0x00007fff2ea9670a -[NSDockConnection _makeConnectionIfNeededWithRetryInterval:onDemand:] + 47 18 com.apple.AppKit 0x00007fff2ea966cf __35-[NSDockConnection startConnection]_block_invoke.41 + 45 19 libdispatch.dylib 0x00007fff6b7596c4 _dispatch_call_block_and_release + 12 20 libdispatch.dylib 0x00007fff6b75a658 _dispatch_client_callout + 8 21 libdispatch.dylib 0x00007fff6b75fc44 _dispatch_lane_serial_drain + 597 22 libdispatch.dylib 0x00007fff6b7605d6 _dispatch_lane_invoke + 363 23 libdispatch.dylib 0x00007fff6b769c09 _dispatch_workloop_worker_thread + 596 24 libsystem_pthread.dylib 0x00007fff6b9b4a3d _pthread_wqthread + 290 25 libsystem_pthread.dylib 0x00007fff6b9b3b77 start_wqthread + 15 Thread 3: 0 libsystem_pthread.dylib 0x00007fff6b9b3b68 start_wqthread + 0 Thread 4: 0 libsystem_pthread.dylib 0x00007fff6b9b3b68 start_wqthread + 0 Thread 5: 0 libsystem_pthread.dylib 0x00007fff6b9b3b68 start_wqthread + 0 Thread 6: 0 libsystem_pthread.dylib 0x00007fff6b9b3b68 start_wqthread + 0 Thread 7: 0 libsystem_pthread.dylib 0x00007fff6b9b3b68 start_wqthread + 0 Thread 8: 0 libsystem_pthread.dylib 0x00007fff6b9b3b68 start_wqthread + 0 Thread 9: 0 libsystem_pthread.dylib 0x00007fff6b9b3b68 start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000108562738 rbx: 0x00007ffee8cd3698 rcx: 0x0000000000010000 rdx: 0x0000000117a056dd rdi: 0x0000000000000001 rsi: 0x00007ffee8cd2708 rbp: 0x00007ffee8cd21c0 rsp: 0x00007ffee8cd21b0 r8: 0x0000000000000000 r9: 0x0000000000000100 r10: 0x0000000120e86a98 r11: 0x000000011869d5b0 r12: 0x00007f907677bf30 r13: 0x00007ffee8cd3698 r14: 0x00007ffee8cd2708 r15: 0x00007ffee8cd2708 rip: 0x00000001070fb114 rfl: 0x0000000000010207 cr2: 0x0000000000000029 Logical CPU: 4 Error Code: 0x00000004 (no mapping for user data read) Trap Number: 14 Binary Images: 0x106f2a000 - 0x108551fff +com.freesurfer.freeview (0) <2C3FDDEC-DEC1-3036-B993-7A638DA1BECD> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview 0x1179b9000 - 0x117df7ff7 +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 0x117f5e000 - 0x1183aafe7 +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 0x1184b3000 - 0x1189e8ff7 +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 0x118b8a000 - 0x118bb3ff7 +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 0x11b74c000 - 0x11b8b2fff +libqcocoa.dylib (0) <14BC2336-68E6-3ACE-B3A9-F21152A64785> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/platforms/libqcocoa.dylib 0x11b8ff000 - 0x11b95dfff +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 0x11de1a000 - 0x11de3ffff +libqmacstyle.dylib (0) <05CC7ADD-D833-3744-93D6-D859235085A3> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/styles/libqmacstyle.dylib 0x11de50000 - 0x11de56ff3 +libqgif.dylib (0) <B67892CC-B844-3404-B289-B572937D144D> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqgif.dylib 0x11de5a000 - 0x11de61ffb +libqicns.dylib (0) <2904A297-57DA-3089-953A-B4AC2E539486> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqicns.dylib 0x11de66000 - 0x11de6bff3 +libqico.dylib (0) <55050416-63A6-3F0F-B0C3-C067186CB93A> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqico.dylib 0x11de70000 - 0x11ded3ffb +libqjpeg.dylib (0) <9928EF62-0B3A-3994-89B3-456715992C07> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqjpeg.dylib 0x11ded9000 - 0x11dedeff7 +libqmacheif.dylib (0) <82101836-3A14-3102-B49C-06B07F7D3263> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqmacheif.dylib 0x11dee3000 - 0x11dee8ffb +libqmacjp2.dylib (0) <A05D9F8D-0076-391B-A805-67F106C11EE7> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqmacjp2.dylib 0x11deed000 - 0x11def1ffb +libqtga.dylib (0) <94EB07B0-6C36-30F0-AB07-A2535214DB5E> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqtga.dylib 0x11def5000 - 0x11df5aff3 +libqtiff.dylib (0) <BDF2E544-2CA2-377E-92CA-79DAF65E47E4> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqtiff.dylib 0x11df62000 - 0x11df65ff3 +libqwbmp.dylib (0) <2CD47DD7-A3AD-3997-B0A3-5E3AE772971B> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqwbmp.dylib 0x11df69000 - 0x11dffdff7 +libqwebp.dylib (0) <8A9124AF-CA0F-3982-B325-B4DAEB7FB374> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqwebp.dylib 0x11e006000 - 0x11e009047 libobjc-trampolines.dylib (787.1) <88F9B648-C455-36F8-BBB9-7D1A9F57D073> /usr/lib/libobjc-trampolines.dylib 0x120dea000 - 0x120e7bf47 dyld (750.6) <326C6480-04F4-3164-A363-53079A148E2F> /usr/lib/dyld 0x7fff2473b000 - 0x7fff24988ff8 com.apple.RawCamera.bundle (9.02.0 - 1350.29) <59F81722-039E-33F5-A20E-936E997575A3> /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera 0x7fff2498b000 - 0x7fff24ab9ff8 com.apple.AMDMTLBronzeDriver (3.10.19 - 3.1.0) <508182CB-F4B3-3C29-9C0B-E90B8C4A49D2> /System/Library/Extensions/AMDMTLBronzeDriver.bundle/Contents/MacOS/AMDMTLBronzeDriver 0x7fff2b452000 - 0x7fff2b851ff3 com.apple.driver.AppleIntelSKLGraphicsMTLDriver (14.7.12 - 14.0.7) <5E89BA00-08EA-35C5-A594-035799EB59A1> /System/Library/Extensions/AppleIntelSKLGraphicsMTLDriver.bundle/Contents/MacOS/AppleIntelSKLGraphicsMTLDriver 0x7fff2cee3000 - 0x7fff2cee7ffb com.apple.agl (3.3.3 - AGL-3.3.3) <84E67213-B55E-3118-A916-3EE3A501E52E> /System/Library/Frameworks/AGL.framework/Versions/A/AGL 0x7fff2d2d0000 - 0x7fff2d2d0fff com.apple.Accelerate (1.11 - Accelerate 1.11) <4F9977AE-DBDB-3A16-A536-AC1F9938DCDD> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate 0x7fff2d2d1000 - 0x7fff2d2e7fef 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 0x7fff2d2e8000 - 0x7fff2d93efff 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 0x7fff2d93f000 - 0x7fff2dba6ff7 libBLAS.dylib (1303.60.1) <C6C2D42F-7456-3DBF-8BE2-9AA06EFC78FD> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 0x7fff2dba7000 - 0x7fff2e07afef libBNNS.dylib (144.100.2) <99C61C48-B14C-3DA6-8C31-6BF72DA0A3A9> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBNNS.dylib 0x7fff2e07b000 - 0x7fff2e416fff libLAPACK.dylib (1303.60.1) 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libsystem_info.dylib (538) <8A321605-5480-330B-AF9E-64E65DE61747> /usr/lib/system/libsystem_info.dylib 0x7fff6b8f4000 - 0x7fff6b920ff7 libsystem_kernel.dylib (6153.141.16) <05E98124-C845-374E-A323-8D6CFB60926F> /usr/lib/system/libsystem_kernel.dylib 0x7fff6b921000 - 0x7fff6b968fff libsystem_m.dylib (3178) <00F331F1-0D09-39B3-8736-1FE90E64E903> /usr/lib/system/libsystem_m.dylib 0x7fff6b969000 - 0x7fff6b990fff libsystem_malloc.dylib (283.100.6) <8549294E-4C53-36EB-99F3-584A7393D8D5> /usr/lib/system/libsystem_malloc.dylib 0x7fff6b991000 - 0x7fff6b99effb libsystem_networkextension.dylib (1095.140.2) <F06C65C5-2CBE-313C-96E1-A09240F9FE57> /usr/lib/system/libsystem_networkextension.dylib 0x7fff6b99f000 - 0x7fff6b9a8ff7 libsystem_notify.dylib (241.100.2) <FA22F928-D91B-3AA5-96BB-3186AC0FB264> /usr/lib/system/libsystem_notify.dylib 0x7fff6b9a9000 - 0x7fff6b9b1fef libsystem_platform.dylib (220.100.1) <009A7C1F-313A-318E-B9F2-30F4C06FEA5C> /usr/lib/system/libsystem_platform.dylib 0x7fff6b9b2000 - 0x7fff6b9bcfff libsystem_pthread.dylib (416.100.3) <62CB1A98-0B8F-31E7-A02B-A1139927F61D> /usr/lib/system/libsystem_pthread.dylib 0x7fff6b9bd000 - 0x7fff6b9c1ff3 libsystem_sandbox.dylib (1217.141.2) <051C4018-4345-3034-AC98-6DE42FB8273B> /usr/lib/system/libsystem_sandbox.dylib 0x7fff6b9c2000 - 0x7fff6b9c4fff libsystem_secinit.dylib (62.100.2) <F80872AA-E1FD-3D7E-8729-467656EC6561> /usr/lib/system/libsystem_secinit.dylib 0x7fff6b9c5000 - 0x7fff6b9ccffb libsystem_symptoms.dylib (1238.120.2) <702D0910-5C34-3D43-9631-8BD215DE4FE1> /usr/lib/system/libsystem_symptoms.dylib 0x7fff6b9cd000 - 0x7fff6b9e3ff2 libsystem_trace.dylib (1147.120.1) <BC141783-66D9-3137-A783-211B38E49ADB> /usr/lib/system/libsystem_trace.dylib 0x7fff6b9e5000 - 0x7fff6b9eaff7 libunwind.dylib (35.4) <42B7B509-BAFE-365B-893A-72414C92F5BF> /usr/lib/system/libunwind.dylib 0x7fff6b9eb000 - 0x7fff6ba20ffe libxpc.dylib (1738.140.2) <54EEF402-42C7-3995-BADE-93C48EFC4452> /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: 2228 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=619.7M resident=0K(0%) swapped_out_or_unallocated=619.7M(100%) Writable regions: Total=359.3M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=359.3M(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 128K 1 Activity Tracing 256K 1 CG backing stores 1600K 4 CoreImage 32K 4 CoreUI image data 188K 2 Dispatch continuations 16.0M 1 Foundation 4K 1 Kernel Alloc Once 8K 1 MALLOC 86.5M 43 MALLOC guard page 32K 7 STACK GUARD 56.0M 10 Stack 12.6M 10 VM_ALLOCATE 68K 8 __DATA 268.5M 306 __DATA_CONST 20K 1 __FONT_DATA 4K 1 __LINKEDIT 393.0M 22 __OBJC_RO 32.3M 1 __OBJC_RW 1908K 2 __TEXT 226.8M 301 __UNICODE 564K 1 mapped file 55.9M 17 shared memory 656K 19 =========== ======= ======= TOTAL 1.1G 764 Model: MacBookPro13,3, BootROM 429.80.1.0.0, 4 processors, Quad-Core Intel Core i7, 2.6 GHz, 16 GB, SMC 2.38f12 Graphics: kHW_IntelHDGraphics530Item, Intel HD Graphics 530, spdisplays_builtin Graphics: kHW_AMDRadeonPro450Item, AMD Radeon Pro 450, spdisplays_pcie_device, 2 GB Memory Module: BANK 0/DIMM0, 8 GB, LPDDR3, 2133 MHz, 0x802C, 0x4D5435324C31473332443450472D30393320 Memory Module: BANK 1/DIMM0, 8 GB, LPDDR3, 2133 MHz, 0x802C, 0x4D5435324C31473332443450472D30393320 AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x15A), Broadcom BCM43xx 1.0 (7.77.111.1 AirPortDriverBrcmNIC-1615.3) Bluetooth: Version 7.0.6f8, 3 services, 27 devices, 1 incoming serial ports Network Service: Wi-Fi, AirPort, en0 Network Service: Thunderbolt Bridge, Ethernet, bridge0 USB Device: USB 3.0 Bus USB Device: Keyboard Hub USB Device: Apple Keyboard USB Device: Mobile Drive USB Device: Apple T1 Controller Thunderbolt Bus: MacBook Pro, Apple Inc., 41.2 Thunderbolt Device: Macintosh, Apple Inc. Thunderbolt Bus: MacBook Pro, Apple Inc., 41.2

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Some func. error during recon-all process
by Horsng Junn 12 Apr '21

12 Apr '21

External Email - Use Caution Hi Yoonho, I'm not an expert but since your inquiry doesn't yet have a reply I thought I'd try to answer it as much as I can. 1. -whitesurf process is preceded over smooth2 and inflated2 in recon-all file, really it is not. why? It seems the second smooth -> inflate -> sphere process is run just to help with the spherical registration and thus the parcellation. I think -whitesurf must be run after that second smooth2 and inflate2 process because it depends on the parcellation result for some anatomical information to make sure the surface geometry is correct, but it still uses the original tessellation result as its basis as the second smoothing might hurt the resulting surface quality. 2. This error first started during -cortribbon process, also occurs in other processes such as -cortparc2, -cortparc3, -hyporelabel, -aparc2aseg, and -wmparc. But these process does not ask for a file called aseg as input if you check it on the homepage. Can you tell me how to fix it? In not just those places but many other places, FS uses some hard-coded input files to read in the segmentation results, transformation matrix, annotation info, etc. I think you just need to provide it with the required segmentation file. Best, Horsng

1 1

Use Hippocampal segmentation sub-nuclei on other brain softwares
by Borghi, G. (Gregorio) 12 Apr '21

12 Apr '21

External Email - Use Caution Dear All, I have been stuck on this issue for quite some time. What I am trying to do is running a segmentation on both amygdala and hippocampus, and then to look at the different activation of the segmented sub-fields of both structures during a social-emotional task. However, despite my efforts I have not been able to find a way for translating either the segmented output files to bring them in a format that can be used by R, FSL, or SPM. Is there anyone who might have an answer on how to do that? Or is there a function in freesurfer that provides the list of voxel coordinates per volume for each hippocampal and amygdala subfields? Kind regards, Gregorio Borghi

2 1

How to edit GM when WM is ok
by Caroline Chwiesko 09 Apr '21

09 Apr '21

External Email - Use Caution Hello Freesurfer experts, i am doing some editing after recon-all. I have the issue that one gyrus is not captured by the pial surface. There is no wm that is wrong and that i could correct. It looks like this gyrus has a weird angle so there is actually no WM visible. How can such an error be corrected? I am happy to send a couple images if needed. Thank you very much in advance for any help! Cheers Carolin

2 13

MRI RA Position at Ohio State
by Hayes, Scott M. 09 Apr '21

09 Apr '21

External Email - Use Caution Research Assistant Position The Buckeye Brain Aging Lab (B-BAL) Department of Psychology The Ohio State University Applications are being sought for a full-time research assistant position in the Buckeye Brain Aging Lab (B-BAL; thebbal.com<http://secure-web.cisco.com/1HjejvxI7VUxlECPLn2YyeI79In8qatKRagfSEjyO8G66zH…>) directed by Dr. Scott Hayes. The B-BAL studies the relationships among aging, physical activity, cognition and the brain [using Magnetic Resonance Imaging (MRI) metrics]. We also examine neural correlates of memory in healthy and clinical populations. The Research Assistant 1 assists in the general coordination and conduct of research in the B-BAL, including administration of neuropsychological tests and/or questionnaires to young and older adults; recruits, screens, and schedules human subjects, including coordination of subject appointments (cognitive, MRI, and physical fitness assessments), subject payments, and submission of IRB amendments; assists with participant recruitment efforts between the laboratory and community partners; assists with research lab purchases and maintains lab supplies; assists with cognitive, MRI, and physical fitness data collection, including obtaining informed consent, cognitive testing (computer and paper and pencil based testing), MRI data acquisition, and record keeping; assists with cognitive and MRI data processing and analyses, supervises undergraduate research assistants. Desired qualifications include: Bachelor's degree in psychology, neuroscience, computer science, engineering, or physics; programming experience in unix, python, matlab, as well as experience in neuroimaging data analyses; knowledge of software packages, such as FreeSurfer, FSL, AFNI, SPM, CONN, R. The position is available for one year with the possibility of extension for additional years based on satisfactory performance and availability of funds. If you are interested in being considered for the position, please apply online at https://secure-web.cisco.com/1sICga4tsxcHZeNaUj6ZIbnSVd8ouX635dTqvkezT0yVfL… Submit a cover letter, writing sample (research paper from course, poster presented at a conference), current CV and arrange to have two reference letters emailed to bbal(a)osu.edu<mailto:bbal@osu.edu> . If you have questions about the position or the lab, please email bbal(a)osu.edu<mailto:bbal@osu.edu> . To build a diverse workforce, The Ohio State University encourages applications from all individuals. Ohio State is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to age, race, color, religion, sex, sexual orientation, gender identity, national origin, disability status, or protected veteran status.

1 0

MCSRCH error using sample data (001.mgz and 002.mgz)
by Yoonho Hwang 09 Apr '21

09 Apr '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute cortical thickness and to analyze it between groups. So I perform "recon-all", but rather than using recon-all -all, some problems arise while performing each of the steps in it. These problems are as follwing. *sample-001.mgz and sample-002.mgz in /usr/local/freesurfer/**subjects/ are used. What is this problem happening? * *IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010* *Resulting transform:* * 1.09487 -0.03668 0.00057 -10.07315;* * 0.03682 1.10413 0.22705 -54.96997;* *-0.00899 -0.18307 0.95770 22.82867;* * 0.00000 0.00000 0.00000 1.00000;* 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 2) Platform: Ubuntu release 18.04.1 3) uname -a: Linux LABPC 5.4.0-70-generic #78~18.04.1-Ubuntu SMP Sat Mar 20 14:10:07 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank you very much. Sincerely, Yoonho -- *Hwang, Yoonho* *Medical Image Processing Laboratory (MIPL),* *Department of Biomedical Engineering, Yonsei University.* *#218 Sanhak-Kwan, 1, Yeonsedae-gil, Heungeop-myeon, Wonju,* *Gangwon-do, 26493, Republic of Korea.* *Office: +82-33-760-2499* *Email: ken.lmstar11(a)gmail.com <ken.lmstar11(a)gmail.com>*

2 1

Assistant Professor Position in Cognitive Neurosciences of Language - University of Geneva Switzerland
by Narly Golestani 09 Apr '21

09 Apr '21

External Email - Use Caution Dear all, An Assistant Professor Position in Cognitive Neuroscience of Language is available at the University of Geneva, Switzerland. The position will be in the Psychology section of the Faculty of Psychology and Education Science https://secure-web.cisco.com/1Hn_XNE0p1RKSeisul8uuWPjqFsyEgiu5lMCeaHhECmbSV…, with access to Campus Biotech Facilities "https://secure-web.cisco.com/1T_pbFAMOQE6rzfyb3YUonEwo8892rX5KOMFJx0YbtN0GP…". This position is opened in the context of the NCCR (National Center of Research Competence) "Evolving Language" - http://secure-web.cisco.com/1EWS_y03OVjFu46pudQ4_4N5frGWZHwtV250Dr-BazQ5r_f…. The whole application process can be carried in English. It is required that the successful candidate acquire a working command of French within the first two years in the position. The application deadline is on May 19th, 2021 - please see https://secure-web.cisco.com/1CDMYP8n3cNlL1DfRxXDUt3T2Rps02kJ9kWAYpxlTVcYAo… for more information. We would be most thankful if you could distribute widely. Thanks in advance, and best wishes, Narly Golestani. ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Brain and Language Lab Prof. Narly GOLESTANI Department of Psychology Campus Biotech 9 Chemin des Mines, 1202 Genève +41 22 379 53 52 <https://secure-web.cisco.com/1dinoEmfX1o7ZFkPOcSggpavzSzXiCY2uRru-c5xw5IuM6…>http://secure-web.cisco.com/1y3jxPvURbRT3R3lkfnmhThYAOCwHy0AdTX2xoqOS-umHjg… https://secure-web.cisco.com/1UIgPKfsx4cUK4nmQkVjd2UWtKIAXemv5JGehU-Zt0LIHz… ----------------------------------------------------------------------------------------------------------------------------------------------------------------- <https://secure-web.cisco.com/1dinoEmfX1o7ZFkPOcSggpavzSzXiCY2uRru-c5xw5IuM6…>

1 0

Some func. error during recon-all process
by Yoonho Hwang 09 Apr '21

09 Apr '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute cortical thickness and to analyze it between groups. So I perform "recon-all", but rather than using recon-all -all, some problems arise while performing each of the steps in it. These problems are as follwing. 1. -whitesurf process is preceded over smooth2 and inflated2 in recon-all file, really it is not. why? 2. This error first started during -cortribbon process, also occurs in other processes such as -cortparc2, -cortparc3, -hyporelabel, -aparc2aseg, and -wmparc. But these process does not ask for a file called aseg as input if you check it on the homepage. Can you tell me how to fix it? error: mghRead(/media/hwang/Disk1/cp2ANZ/FREESURFER/mri/aseg.mgz, -1): could not open file error: cannot compute vol stats without /media/hwang/Disk1/cp2ANZ/FREESURFER/mri/aseg.mgz Command exited with non-zero status 1 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 2) Platform: Ubuntu release 18.04.1 3) uname -a: Linux LABPC 5.4.0-70-generic #78~18.04.1-Ubuntu SMP Sat Mar 20 14:10:07 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank you very much. Sincerely, Yoonho -- *Hwang, Yoonho* *Medical Image Processing Laboratory (MIPL),* *Department of Biomedical Engineering, Yonsei University.* *#218 Sanhak-Kwan, 1, Yeonsedae-gil, Heungeop-myeon, Wonju,* *Gangwon-do, 26493, Republic of Korea.* *Office: +82-33-760-2499* *Email: ken.lmstar11(a)gmail.com <ken.lmstar11(a)gmail.com>*

1 0

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Freesurfer April 2021