Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

TRACULA intensity normalization
by Silvia De Francesco 24 Apr '23

24 Apr '23

External Email - Use Caution Dear developers, Does TRACULA perform an intensity normalization of the DWI image, as recon-all do for the T1? Thanks, Silvia

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Re: [Freesurfer] free view crash report
by fsbuild 24 Apr '23

24 Apr '23

External Email - Use Caution If you are using a second monitor, then disconnect it so you are only using the primary laptop screen/monitor.   There have been issues displaying images properly when using multiple monitors with MacOS. If you have not tried running freeview directly from the command line, then please try the following. Open a new terminal window and run the bash shell, $ bash … prompt will change ... $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh … output with variable settings … Then see if freeview opens an empty window, $ freeview If that works, then quit freeview and try to display one of the existing volumes in the distribution, $ freeview $FREESURFER_HOME/subjects/bert/mri/brain.mgz If that works, then quit freeview and try to display your own surface/volume files. - R. On 4/20/23 12:24, Suman Nag (hulosom(a)gmail.com) wrote:         External Email - Use Caution         hi, i have downloaded 7.3.2 version on my macbook pro ,os 13.1. When i am trying to load volume from subjec > bert > T1.mgz or other .nii volume freeview crashing unexpectedly. below the error log,,please kindly  help.God bless.

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Re: [Freesurfer] freesurfer 5.3 license on ubuntu 22
by fsbuild 24 Apr '23

24 Apr '23

External Email - Use Caution The 5.3 release dates back to ~10 years ago when CentOS4 was current.  Because of changes to the crypt libraries since then (Ubuntu 22, CentOS8), it is no longer possible to decode a license for older versions of freesurfer on newer iterations of linux OS's.  Your alternative is to use Ubuntu 22 to host a container or VM, e.g., in VirtualBox, to run the version of the old OS you previously ran the 5.3 release under.  You can obtain copies of end of life'd OS iso images from the respective linux vendors web site - under OS archives or some similar title - in order to create a VM/container to run the old OS. - R. On Apr 23, 2023, at 21:59, Hadas, Itay <ihadas(a)health.ucsd.edu> wrote:        External Email - Use Caution        Hi,I am looking for workaround to run freesurfer 5.3 on ubuntu 22 - I get the ERROR: Invalid FreeSurfer license key found in license file $FREESURFER_HOME/license.txtother versions works fine.Thanks,Itay _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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freesurfer 5.3 license on ubuntu 22
by Hadas, Itay 23 Apr '23

23 Apr '23

External Email - Use Caution Hi, I am looking for workaround to run freesurfer 5.3 on ubuntu 22 - I get the ERROR: Invalid FreeSurfer license key found in license file $FREESURFER_HOME/license.txt other versions works fine. Thanks, Itay

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Re: [Freesurfer] Hippocampal/amygdala subfields hemisphere error
by Hemond, Christopher 20 Apr '23

20 Apr '23

External Email - Use Caution Dear Juan, Thank you for the reply. In the base/tmp directory there is one folder, "hippoSF_T1_long.v22_right" and an empty text file "filled.edits.txt". I don't see any directory pointing to the left hemisphere. In the right hemisphere directory, there are the following files: T1resampled_0.mgz T1resampled_1.mgz T1resampled_2.mgz asegModBinDilated.mgz asegModBinDilatedResampled.mgz asegModCHA_tp_0.mgz asegModCHA_tp_1.mgz asegModCHA_tp_2.mgz asegMod_tp_0.mgz asegMod_tp_1.mgz asegMod_tp_2.mgz asegRotated_tp_1.mgz asegRotated_tp_2.mgz asmr1.mgz asmr2.mgz asmr3.mgz compressionLookupTable.txt discreteLabelsMergedBodyHeadNoMLorGCDGResampledT1_tp_1.mgz discreteLabelsMergedBodyHeadNoMLorGCDG_tp_1.mgz discreteLabelsMergedBodyHeadResampledT1_tp_1.mgz discreteLabelsMergedBodyHead_tp_1.mgz discreteLabelsMergedBodyHead_tp_2.mgz discreteLabelsResampledT1_tp_1.mgz discreteLabelsWholeBodyHeadResampledT1_tp_1.mgz discreteLabelsWholeBodyHead_tp_1.mgz discreteLabelsWholeBodyHead_tp_2.mgz discreteLabels_all_tp_1.mgz discreteLabels_all_tp_2.mgz discreteLabels_tp_1.mgz discreteLabels_tp_2.mgz hippoAmygBinaryMask.mgz hippoAmygBinaryMask_autoCropped.mgz hippoAmygBinaryMask_autoCropped_opened.mgz hippoAmygBinaryMask_tp_1.mgz hippoAmygBinaryMask_tp_1_autoCropped.mgz hippoAmygBinaryMask_tp_2.mgz hippoAmygBinaryMask_tp_2_autoCropped.mgz hippoMask.mgz hippoMaskDilated.mgz hippoMaskResampled.mgz hippoMaskResampledDilated.mgz imageDump.mgz imageDump_rigidly_coregistered.mgz image_tp_1.mgz image_tp_2.mgz kk2.mgz rigidToAffineBase.lta tp_1_to_base.lta tp_2_to_base.lta trash.lta volumesAmygdala_tp_1.txt volumesAmygdala_tp_2.txt volumesHippo_tp_1.txt volumesHippo_tp_2.txt warpedMeshNoAffine_tp_1.txt.gz warpedMeshNoAffine_tp_2.txt.gz warpedMesh_tp_1.txt.gz warpedMesh_tp_2.txt.gz warpedOriginalMeshBase.txt.gz warpedOriginalMeshTP1.txt.gz warpedOriginalMeshTP2.txt.gz Hope this helps to potentially make some headway? Thanks very much again in advance. Best regards, Chris The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, transmission, re-transmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer.

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Freesurfer archive password
by Даниил Кирдяшкин 20 Apr '23

20 Apr '23

External Email - Use Caution Hello, Could you please provide the password required to open the archive containing the freesurfer ubuntu virtual machine. Thanks in advance. Best regards, Dan

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free view crash report
by Suman Nag 20 Apr '23

20 Apr '23

External Email - Use Caution hi, i have downloaded 7.3.2 version on my macbook pro ,os 13.1. When i am trying to load volume from subjec > bert > T1.mgz or other .nii volume freeview crashing unexpectedly. below the error log,,please kindly help.God bless. ------------------------------------- Translated Report (Full Report Below) ------------------------------------- Process: freeview [72775] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Identifier: com.freesurfer.freeview Version: ??? Code Type: X86-64 (Native) Parent Process: launchd [1] User ID: 501 Date/Time: 2023-04-20 20:23:40.7252 +0400 OS Version: macOS 13.3.1 (22E261) Report Version: 12 Bridge OS Version: 7.4 (20P4252) Anonymous UUID: A303602D-BEFC-606B-8FB1-A45BB90A0D8A Sleep/Wake UUID: D99A417E-B2FD-4DB8-AA1A-9BACB6DEC3CF Time Awake Since Boot: 120000 seconds Time Since Wake: 7385 seconds System Integrity Protection: enabled Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: UNKNOWN_0xD at 0x0000000000000000 Exception Codes: 0x000000000000000d, 0x0000000000000000 Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11 Terminating Process: exc handler [72775] VM Region Info: 0 is not in any region. Bytes before following region: 4414844928 REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL UNUSED SPACE AT START ---> __TEXT 107253000-1088fb000 [ 22.7M] r-x/r-x SM=COW ...acOS/freeview Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 QtGui 0x11926b4be QPen::QPen() + 46 1 QtGui 0x11923b9a5 QPainterState::QPainterState() + 69 2 QtGui 0x119211e91 QRasterPaintEngine::createState(QPainterState*) const + 49 3 QtGui 0x11922b4bd QPainter::begin(QPaintDevice*) + 253 4 QtGui 0x11922b3b7 QPainter::QPainter(QPaintDevice*) + 247 5 QtWidgets 0x1184100b7 QWidgetPrivate::drawWidget(QPaintDevice*, QRegion const&, QPoint const&, QFlags<QWidgetPrivate::DrawWidgetFlag>, QPainter*, QWidgetRepaintManager*) + 2967 6 QtWidgets 0x1183f1f0c 0x1183d4000 + 122636 7 QtWidgets 0x1183f2112 0x1183d4000 + 123154 8 QtWidgets 0x11841f2ad QWidget::event(QEvent*) + 1645 9 QtWidgets 0x118532a35 QMainWindow::event(QEvent*) + 277 10 QtWidgets 0x1183e49ea QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266 11 QtWidgets 0x1183e5e11 QApplication::notify(QObject*, QEvent*) + 497 12 QtCore 0x119daca34 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 13 QtCore 0x119dadd79 QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 809 14 libqcocoa.dylib 0x118137259 0x1180fd000 + 238169 15 libqcocoa.dylib 0x1181379c8 0x1180fd000 + 240072 16 CoreFoundation 0x7ff81a0e906a __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 17 CoreFoundation 0x7ff81a0e900c __CFRunLoopDoSource0 + 157 18 CoreFoundation 0x7ff81a0e8de5 __CFRunLoopDoSources0 + 217 19 CoreFoundation 0x7ff81a0e7a6f __CFRunLoopRun + 916 20 CoreFoundation 0x7ff81a0e7071 CFRunLoopRunSpecific + 560 21 HIToolbox 0x7ff823b4ffcd RunCurrentEventLoopInMode + 292 22 HIToolbox 0x7ff823b4fc14 ReceiveNextEventCommon + 199 23 HIToolbox 0x7ff823b4fb38 _BlockUntilNextEventMatchingListInModeWithFilter + 64 24 AppKit 0x7ff81d1797a0 _DPSNextEvent + 858 25 AppKit 0x7ff81d17864a -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1214 26 AppKit 0x7ff81d16acb8 -[NSApplication run] + 586 27 libqcocoa.dylib 0x11813662f 0x1180fd000 + 235055 28 QtCore 0x119da8acf QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 431 29 QtCore 0x119dad042 QCoreApplication::exec() + 130 30 freeview 0x107358cb7 0x107253000 + 1072311 31 dyld 0x7ff819cb341f start + 1903 Thread 1: 0 libsystem_pthread.dylib 0x7ff81a008bb0 start_wqthread + 0 Thread 2: 0 libsystem_pthread.dylib 0x7ff81a008bb0 start_wqthread + 0 Thread 3:: QThread 0 libsystem_kernel.dylib 0x7ff819fd529e poll + 10 1 QtCore 0x119e0f220 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 608 2 QtCore 0x119e10a21 QEventDispatcherUNIX::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 849 3 QtCore 0x119da8acf QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 431 4 QtCore 0x119bd5603 QThread::exec() + 131 5 QtCore 0x119bd6619 0x119bb4000 + 140825 6 libsystem_pthread.dylib 0x7ff81a00d1d3 _pthread_start + 125 7 libsystem_pthread.dylib 0x7ff81a008bd3 thread_start + 15 Thread 4:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x7ff819fce5b2 mach_msg2_trap + 10 1 libsystem_kernel.dylib 0x7ff819fdc72d mach_msg2_internal + 78 2 libsystem_kernel.dylib 0x7ff819fd55e4 mach_msg_overwrite + 692 3 libsystem_kernel.dylib 0x7ff819fce89a mach_msg + 19 4 CoreFoundation 0x7ff81a0e91af __CFRunLoopServiceMachPort + 145 5 CoreFoundation 0x7ff81a0e7c30 __CFRunLoopRun + 1365 6 CoreFoundation 0x7ff81a0e7071 CFRunLoopRunSpecific + 560 7 AppKit 0x7ff81d2d9909 _NSEventThread + 132 8 libsystem_pthread.dylib 0x7ff81a00d1d3 _pthread_start + 125 9 libsystem_pthread.dylib 0x7ff81a008bd3 thread_start + 15 Thread 5: 0 libsystem_pthread.dylib 0x7ff81a008bb0 start_wqthread + 0 Thread 6: 0 libsystem_pthread.dylib 0x7ff81a008bb0 start_wqthread + 0 Thread 7: 0 libsystem_pthread.dylib 0x7ff81a008bb0 start_wqthread + 0 Thread 8:: ThreadIOWorker 0 dyld 0x7ff819cae506 _kernelrpc_mach_vm_deallocate_trap + 10 1 dyld 0x7ff819cb12e2 mach_vm_deallocate + 29 2 dyld 0x7ff819cdabee lsl::EphemeralAllocator::reset() + 280 3 dyld 0x7ff819cbe391 dyld4::RuntimeState::withCurrentProcessSnapshot(void (lsl::EphemeralAllocator&, dyld4::Atlas::ProcessSnapshot*) block_pointer) + 483 4 dyld 0x7ff819cbe4f8 dyld4::RuntimeState::notifyDebuggerUnload(std::__1::span<dyld4::Loader const*, 18446744073709551615ul> const&) + 94 5 dyld 0x7ff819cbdd38 dyld4::RuntimeState::notifyUnload(std::__1::span<dyld4::Loader const*, 18446744073709551615ul> const&) + 1186 6 dyld 0x7ff819cbd764 dyld4::RuntimeState::garbageCollectInner() + 444 7 dyld 0x7ff819cbd025 dyld4::RuntimeState::decDlRefCount(dyld4::Loader const*) + 205 8 dyld 0x7ff819ce662e dyld4::APIs::dlclose(void*) + 202 9 QtCore 0x119da6d25 0x119bb4000 + 2043173 10 QtCore 0x119da15a0 0x119bb4000 + 2020768 11 QtCore 0x119d9ad96 0x119bb4000 + 1994134 12 QtCore 0x119d9b06e 0x119bb4000 + 1994862 13 QtCore 0x119dd6f2c QObject::~QObject() + 2140 14 QtCore 0x119d9c3ae QFactoryLoader::~QFactoryLoader() + 94 15 QtCore 0x119d9c81e QFactoryLoader::~QFactoryLoader() + 14 16 QtGui 0x1190291a6 0x118f7c000 + 709030 17 libsystem_c.dylib 0x7ff819edeba1 __cxa_finalize_ranges + 409 18 libsystem_c.dylib 0x7ff819ede9bb exit + 35 19 freeview 0x1084e6b3c 0x107253000 + 19479356 20 freeview 0x10856d118 0x107253000 + 20029720 21 freeview 0x1072ccdac 0x107253000 + 499116 22 freeview 0x1072cd438 0x107253000 + 500792 23 freeview 0x1072f4cde 0x107253000 + 662750 24 freeview 0x1073e10ea 0x107253000 + 1630442 25 QtCore 0x119bd6619 0x119bb4000 + 140825 26 libsystem_pthread.dylib 0x7ff81a00d1d3 _pthread_start + 125 27 libsystem_pthread.dylib 0x7ff81a008bd3 thread_start + 15 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000f5c047f594c0 rbx: 0x00007fa3a200d040 rcx: 0x0000000000000000 rdx: 0x0000000000005000 rdi: 0x00007fa3a200d040 rsi: 0x0000600001625720 rbp: 0x00007ff7b8ca8c80 rsp: 0x00007ff7b8ca8c50 r8: 0x0000000000001d30 r9: 0x00000000000001d2 r10: 0x0000000000000410 r11: 0x00000000ffffffff r12: 0x00007ff7b8ca8e10 r13: 0x000060000315eda0 r14: 0x0000000000000000 r15: 0x00007ff7b8ca8e10 rip: 0x000000011926b4be rfl: 0x0000000000010282 cr2: 0x0000000107445000 Logical CPU: 8 Error Code: 0x00000000 Trap Number: 13 Thread 0 instruction stream: ee 3e f9 ff eb c0 66 66-66 2e 0f 1f 84 00 00 00 .>....fff....... 00 00 55 48 89 e5 53 50-48 89 fb 48 8b 46 18 48 ..UH..SPH..H.F.H 8b 70 58 e8 6a 53 ff ff-48 89 d8 48 83 c4 08 5b .pX.jS..H..H...[ 5d c3 55 48 89 e5 41 57-41 56 41 55 41 54 53 50 ].UH..AWAVAUATSP 48 89 fb 8b 05 59 92 22-00 8b 05 53 92 22 00 85 H....Y."...S.".. c0 79 1f 48 8b 05 08 92-22 00 48 8b 00 48 89 03 .y.H....".H..H.. [f0]ff 00 48 83 c4 08 5b-41 5c 41 5d 41 5e 41 5f ...H...[A\A]A^A_ <== 5d c3 b9 01 00 00 00 31-c0 f0 48 0f b1 0d e8 91 ]......1..H..... 22 00 75 21 8b 05 18 92-22 00 85 c0 74 2d 31 c9 ".u!...."...t-1. b8 01 00 00 00 f0 48 0f-b1 0d cc 91 22 00 74 b3 ......H.....".t. e9 f6 00 00 00 48 8d 3d-be 91 22 00 e8 49 d8 19 .....H.=.."..I.. 00 8b 05 eb 91 22 00 85-c0 75 d3 bf 08 00 00 00 ....."...u...... Binary Images: 0x107253000 - 0x1088fafff com.freesurfer.freeview (*) <2d93be07-b47e-3b61-92dc-947be65a61af> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview 0x1183d4000 - 0x11881afff org.qt-project.QtWidgets (5.15) <b432d666-dcab-320a-8496-78a67f554c0e> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtWidgets.framework/Versions/5/QtWidgets 0x118f7c000 - 0x119465fff org.qt-project.QtGui (5.15) <cbcec35a-ee54-354f-9c2b-188ac6b2790d> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtGui.framework/Versions/5/QtGui 0x119bb4000 - 0x11a124fff org.qt-project.QtCore (5.15) <c723812a-f7a5-3001-98d5-e60e8daa6ffb> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/5/QtCore 0x1180fd000 - 0x11826bfff libqcocoa.dylib (*) <d4ab240b-4535-3aec-b72b-5ffc4750e4e5> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/platforms/libqcocoa.dylib 0x117fba000 - 0x118019fff org.qt-project.QtDBus (5.15) <f6c498cb-9925-350d-b597-6c3f102e09d5> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtDBus.framework/Versions/5/QtDBus 0x118032000 - 0x11805dfff org.qt-project.QtPrintSupport (5.15) <be399b08-503c-39e3-acac-268a9d866624> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtPrintSupport.framework/Versions/5/QtPrintSupport 0x1182fd000 - 0x118322fff libqmacstyle.dylib (*) <5b9adb30-04ac-325f-bb42-6e40df6d7e6a> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/styles/libqmacstyle.dylib 0x1182c8000 - 0x1182cdfff libqico.dylib (*) <6a858a22-8e2e-3f6d-b9ac-438c4749c8b7> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqico.dylib 0x118dcf000 - 0x118e33fff libqjpeg.dylib (*) <18b65be7-2104-3d96-9a0c-95dc8839ae72> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqjpeg.dylib 0x118333000 - 0x118339fff libqmacheif.dylib (*) <f878d1f1-c295-3e94-b5ea-d53a00776427> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqmacheif.dylib 0x1182de000 - 0x1182e3fff libqmacjp2.dylib (*) <6ebf7c32-c2dc-32ab-bd6f-e79f35b8095f> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqmacjp2.dylib 0x11833e000 - 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VM freesurfer version
by Federico Uquillas 20 Apr '23

20 Apr '23

External Email - Use Caution Hello, We’d like to set up the virtual machine version of freesurfer, but need a password to unzip the ova.7z file. Would you be able to send it when you get a chance? Thank you so much! Best regards, Fred

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postdoctoral position available at the University of Toronto Brain, Body, and Perception Research Program
by Jamie Feusner 20 Apr '23

20 Apr '23

External Email - Use Caution A postdoctoral scholar position is available in the Brain, Body, and Perception Research Program<https://secure-web.cisco.com/126geZ6_OJj3kUtThXneP0QJoUZa5jB1o6agC2nk_iMhtQ…> at the University of Toronto and Centre for Addiction and Mental Health to study neural and behavioural phenotypes associated with visual perception, body processing, emotion, and reward. Description: Our clinical neuroscience lab studies brain and behavioural phenotypes across disorders of body image including body dysmorphic disorder and eating disorders. We are passionate and committed to understanding these understudied disorders to improve treatment strategies, and we have produced seminal research studies in the field. Our group uses neuroimaging (fMRI, EEG, diffusion MRI, and structural MRI), neuromodulation (TMS), and physiological tools (ECG, eye-tracking, and psychophysics). We also develop and use novel digital 3D tools to assess body experiences in those with gender dysphoria as well as in those with disorders of body image. We employ machine learning and other computational techniques for modelling behavioural, physiological, and neural responses and for predicting clinical outcomes. Our research is funded by the U.S. NIH and foundation grants. The University of Toronto and the Centre for Addiction and Mental Health have a wealth of neuroimaging and clinical resources and career development support. You will be joining a productive and collaborative group using advanced neuroimaging techniques and creative software and hardware development that is grounded in strong clinical understandings of the phenomenology of psychiatric and other populations. The PI (Dr. Feusner) will provide mentoring and guidance including grant writing for developing independent projects. Requirements: Ph.D. or M.D./Ph.D. in neuroscience, cognitive science, computer science, engineering, biostatistics, physics, psychology, or related fields. We are looking for candidates with experience in analyzing fMRI data – including statistical analysis software such as FSL, AFNI, SPM, or others. The successful applicant will be able to function independently, work on more than one project at a time in a team setting, and lead and mentor students and research assistants. The successful applicant will have excellent computing and programming skills (Matlab, Python, R, bash scripting), verbal English skills, and writing skills. To apply: Please send your CV and either a research statement (1-2 pages) or cover letter that describes your research experience, your specific interests in this position, and how this position fits with your career goals to Dr. Jamie Feusner: jamie.feusner(a)utoronto.ca<mailto:jamie.feusner@utoronto.ca> Or, apply here: https://secure-web.cisco.com/1fBSvDw6WRCe3BpBumwp2GuL1E07L87aInyzeb0Zwtu9pO…

1 0

Hippocampal/amygdala subfields hemisphere error
by Hemond, Christopher 19 Apr '23

19 Apr '23

External Email - Use Caution Dear experts, I'm getting an error running the longitudinal hippocampal/amygdala subfields analysis and hoping for help. I've been able to complete this analysis without problems for all but one of my subjects. The issue is that only the left hemisphere will be processed (but successfully). Cross-sectional hippocampal/amygdala subfield processing works fine, and the quality of the scans and recon-all output looks good. I've tried several times to re-process the data but to no avail. I get the following error message: ... Wrote image to file image_tp_2.mgz This file does not contain MRI parameters Unable to perform assignment because the left and right sides have a different number of elements. Error in SegmentSubfieldsT1Longitudinal (line 2136) MATLAB:matrix:singleSubscriptNumelMismatch Any ideas on what I might be doing wrong? I couldn't find this specific error in the forums. Thanks very much, Chris (running freesurfer-darwin-macOS-7.3.2-20220804-6354275) The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, transmission, re-transmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer.

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