Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

SAMSEG seg output contains holes
by Simon Jones 02 Aug '21

02 Aug '21

External Email - Use Caution Dear all I have tried using SAMSEG in 7.1.1 with 7T MP2RAGE sequence data which has an inv1, inv2 and a uni images and I can create a denoised image which has a more of a traditional T1-weighted appearance. I have got some good looking results combining the uni with the inv2 except for one issue. About 20% have a small hole or slit produced within the frontal lobe. It is like an echo of the frontal sinuses and seems to appear whichever image is input. For others, the hole is outside the brain. Is this just a feature? Thanks for your help Simon

2 1

Analysing HCP Data in freesurfer
by Poortata Shirish Lalwani 30 Jul '21

30 Jul '21

External Email - Use Caution Hello, I am trying to use fsfast to perform 1st level GLM analysis on preprocessed data from the HCP-Aging dataset which happens to be in a different space than fsaverage. I followed the following steps: First I smoothed the data which was in dtseries format wb_command -cifti-smoothing *dtseries.nii 1.27 1.27 COLUMN f.sm3.dtseries.nii -left-surface *L.midthickness_MSMAll.32k_fs_LR.surf.gii -right-surface *R.midthickness_MSMAll.32k_fs_LR.surf.gii Then extracted the left/right surface and volume wb_command -cifti-separate f.sm3.dtseries.nii COLUMN -metric CORTEX_LEFT f.L.func.gii -metric CORTEX_RIGHT f.R.func.gii -volume-all f.mni152.nii Followed by creating a mask for the subcortical analysis mri_binarize --i Atlas_ROIs.2.nii.gz --match 8 10 11 12 13 16 17 18 26 28 47 49 50 51 52 53 54 58 60 --o subcortmask.nii.gz; and creating a global mean .dat file. wb_command -cifti-stats f.sm3.dtseries.nii -reduce MEAN > global.waveform.dat Then I tried to run GLM analysis using FSFast. The subcortical analysis completes without errors, but I am having trouble with the surfaces. Surprisingly, the error seems to be at the Smoothing ACF step because it is trying to perform it on volume even though I have specified that the analysis should be in surface space. Attached are the selx3 log file and analysis info file. Is there something with the analysis specification or in earlier conversion steps? I would appreciate any help with this. Thank you Best, Pia

2 8

Freesurfer quit unexpectedly on Max
by Grace 29 Jul '21

29 Jul '21

External Email - Use Caution Hello, I am on MacOS and unable to load any volumes. I have searched your archives and did not find a comparable response. Do you have any recommendations on how to proceed? I can provide you my institutional email address if needed. This is the error message I get: Process: freeview [1195] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Identifier: com.freesurfer.freeview Version: 0 Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: freeview [1195] User ID: 501 Date/Time: 2021-07-29 16:23:01.109 -0700 OS Version: macOS 11.4 (20F71) Report Version: 12 Bridge OS Version: 5.4 (18P4663) Anonymous UUID: A1410107-8780-F44D-22B0-84D1DAB41E59 Time Awake Since Boot: 4100 seconds System Integrity Protection: enabled Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: EXC_I386_GPFLT Exception Note: EXC_CORPSE_NOTIFY Termination Signal: Segmentation fault: 11 Termination Reason: Namespace SIGNAL, Code 0xb Terminating Process: exc handler [1195] Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 org.qt-project.QtGui 0x0000000111f01bbe QPen::QPen() + 46 1 org.qt-project.QtGui 0x0000000111ed3b15 QPainterState::QPainterState() + 69 2 org.qt-project.QtGui 0x0000000111ea9a01 QRasterPaintEngine::createState(QPainterState*) const + 49 3 org.qt-project.QtGui 0x0000000111ec3978 QPainter::begin(QPaintDevice*) + 248 4 org.qt-project.QtGui 0x0000000111ec3872 QPainter::QPainter(QPaintDevice*) + 242 5 org.qt-project.QtWidgets 0x000000011180e0ed 0x1116b0000 + 1433837 6 org.qt-project.QtWidgets 0x000000011180db70 QMainWindow::event(QEvent*) + 64 7 org.qt-project.QtWidgets 0x00000001116c070d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 8 org.qt-project.QtWidgets 0x00000001116c1b12 QApplication::notify(QObject*, QEvent*) + 594 9 org.qt-project.QtCore 0x000000011238e564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 10 org.qt-project.QtWidgets 0x00000001116f5391 QWidgetPrivate::drawWidget(QPaintDevice*, QRegion const&, QPoint const&, int, QPainter*, QWidgetBackingStore*) + 2929 11 org.qt-project.QtWidgets 0x00000001116ce0bb 0x1116b0000 + 123067 12 org.qt-project.QtWidgets 0x00000001116fc8fd QWidget::event(QEvent*) + 1645 13 org.qt-project.QtWidgets 0x000000011180dc45 QMainWindow::event(QEvent*) + 277 14 org.qt-project.QtWidgets 0x00000001116c070d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 15 org.qt-project.QtWidgets 0x00000001116c1b12 QApplication::notify(QObject*, QEvent*) + 594 16 org.qt-project.QtCore 0x000000011238e564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 17 org.qt-project.QtCore 0x000000011238f79e QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 878 18 libqcocoa.dylib 0x000000011470cd39 0x1146d7000 + 220473 19 libqcocoa.dylib 0x000000011470d4a8 0x1146d7000 + 222376 20 com.apple.CoreFoundation 0x00007fff2059597c __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 21 com.apple.CoreFoundation 0x00007fff205958e4 __CFRunLoopDoSource0 + 180 22 com.apple.CoreFoundation 0x00007fff20595664 __CFRunLoopDoSources0 + 242 23 com.apple.CoreFoundation 0x00007fff2059408c __CFRunLoopRun + 893 24 com.apple.CoreFoundation 0x00007fff2059364c CFRunLoopRunSpecific + 563 25 com.apple.HIToolbox 0x00007fff287d1ab3 RunCurrentEventLoopInMode + 292 26 com.apple.HIToolbox 0x00007fff287d16e6 ReceiveNextEventCommon + 284 27 com.apple.HIToolbox 0x00007fff287d15b3 _BlockUntilNextEventMatchingListInModeWithFilter + 70 28 com.apple.AppKit 0x00007fff22d946f2 _DPSNextEvent + 864 29 com.apple.AppKit 0x00007fff22d92ec5 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1364 30 com.apple.AppKit 0x00007fff22d85239 -[NSApplication run] + 586 31 libqcocoa.dylib 0x000000011470c223 0x1146d7000 + 217635 32 org.qt-project.QtCore 0x0000000112389b7f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 431 33 org.qt-project.QtCore 0x000000011238eb72 QCoreApplication::exec() + 130 34 com.freesurfer.freeview 0x0000000100cd87dd 0x100bd8000 + 1050589 35 libdyld.dylib 0x00007fff204b7f5d start + 1 Thread 1: 0 libsystem_pthread.dylib 0x00007fff20498420 start_wqthread + 0 Thread 2:: QThread 0 libsystem_kernel.dylib 0x00007fff2046d9ca poll + 10 1 org.qt-project.QtCore 0x00000001123e48d0 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 608 2 org.qt-project.QtCore 0x00000001123e60c7 QEventDispatcherUNIX::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 903 3 org.qt-project.QtCore 0x0000000112389b7f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 431 4 org.qt-project.QtCore 0x00000001121c537c QThread::exec() + 140 5 org.qt-project.QtCore 0x00000001121c62f3 0x1121a4000 + 140019 6 libsystem_pthread.dylib 0x00007fff2049c8fc _pthread_start + 224 7 libsystem_pthread.dylib 0x00007fff20498443 thread_start + 15 Thread 3:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x00007fff204672ba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2046762c mach_msg + 60 2 com.apple.CoreFoundation 0x00007fff20595b5f __CFRunLoopServiceMachPort + 316 3 com.apple.CoreFoundation 0x00007fff2059423f __CFRunLoopRun + 1328 4 com.apple.CoreFoundation 0x00007fff2059364c CFRunLoopRunSpecific + 563 5 com.apple.AppKit 0x00007fff22f1a68a _NSEventThread + 124 6 libsystem_pthread.dylib 0x00007fff2049c8fc _pthread_start + 224 7 libsystem_pthread.dylib 0x00007fff20498443 thread_start + 15 Thread 4: 0 libsystem_pthread.dylib 0x00007fff20498420 start_wqthread + 0 Thread 5: 0 libsystem_pthread.dylib 0x00007fff20498420 start_wqthread + 0 Thread 6: 0 libsystem_pthread.dylib 0x00007fff20498420 start_wqthread + 0 Thread 7: 0 libsystem_pthread.dylib 0x00007fff20498420 start_wqthread + 0 Thread 8:: ThreadIOWorker 0 org.qt-project.QtCore 0x0000000112467cd4 0x1121a4000 + 2899156 1 org.qt-project.QtCore 0x0000000112466080 0x1121a4000 + 2891904 2 org.qt-project.QtCore 0x000000011246617e 0x1121a4000 + 2892158 3 org.qt-project.QtCore 0x00000001124558ce 0x1121a4000 + 2824398 4 org.qt-project.QtCore 0x0000000112459eda 0x1121a4000 + 2842330 5 libsystem_c.dylib 0x00007fff203cbd35 __cxa_finalize_ranges + 316 6 libsystem_c.dylib 0x00007fff203cc020 exit + 53 7 com.freesurfer.freeview 0x0000000101e4f87c 0x100bd8000 + 19363964 8 com.freesurfer.freeview 0x0000000101ed84f8 0x100bd8000 + 19924216 9 com.freesurfer.freeview 0x0000000100c4cf2c 0x100bd8000 + 479020 10 com.freesurfer.freeview 0x0000000100c4d5bd 0x100bd8000 + 480701 11 com.freesurfer.freeview 0x0000000100c74cc5 0x100bd8000 + 642245 12 com.freesurfer.freeview 0x0000000100d5f0af 0x100bd8000 + 1601711 13 org.qt-project.QtCore 0x00000001121c62f3 0x1121a4000 + 140019 14 libsystem_pthread.dylib 0x00007fff2049c8fc _pthread_start + 224 15 libsystem_pthread.dylib 0x00007fff20498443 thread_start + 15 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x000096f74be32fa0 rbx: 0x00007f98aa2a4e40 rcx: 0x0000000000000001 rdx: 0x00007f98aa2a4e00 rdi: 0x00007f98aa2a4e40 rsi: 0x000060000024d750 rbp: 0x00007ffeef023d00 rsp: 0x00007ffeef023cd0 r8: 0x000000000000c5c0 r9: 0x00007f98aa008101 r10: 0x0000000000003f01 r11: 0x00007f98aa000000 r12: 0x0000000000000000 r13: 0x0000600003b2e970 r14: 0x0000000000000000 r15: 0x00007ffeef023e10 rip: 0x0000000111f01bbe rfl: 0x0000000000010282 cr2: 0x00007f98aa175608 Logical CPU: 2 Error Code: 0x00000000 Trap Number: 13 Thread 0 instruction stream: 00 00 55 48 89 e5 8b 47-08 48 c7 06 00 00 00 00 ..UH...G.H...... 89 46 08 8b 47 0c 89 46-0c 8b 47 10 89 46 10 5d .F..G..F..G..F.] c3 90 55 48 89 e5 5d c3-90 90 90 90 90 90 90 90 ..UH..]......... 90 90 55 48 89 e5 41 57-41 56 41 55 41 54 53 50 ..UH..AWAVAUATSP 48 89 fb 8b 05 99 68 1c-00 8b 05 93 68 1c 00 85 H.....h.....h... c0 79 1f 48 8b 05 48 68-1c 00 48 8b 00 48 89 03 .y.H..Hh..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 4c 8d 35 31 68 1c-00 4c 89 f7 e8 99 a8 14 ].L.51h..L...... 00 8b 05 5b 68 1c 00 85-c0 0f 85 c3 00 00 00 bf ...[h........... 08 00 00 00 e8 8d b4 14-00 49 89 c7 48 8d 7d d0 .........I..H.}. be 02 00 00 00 ba 01 00-00 00 e8 f3 5c f2 ff bf ............\... 48 00 00 00 e8 6d b4 14-00 49 89 c5 41 c7 45 00 H....m...I..A.E. Thread 0 last branch register state not available. 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0x7fff3fca9fff com.apple.TextInput (1.0 - 1.0) <BC1AA691-A1A5-3368-8267-FA912891F59D> /System/Library/PrivateFrameworks/TextInput.framework/Versions/A/TextInput 0x7fff40daf000 - 0x7fff40ddefff libncurses.5.4.dylib (57) <575D6FE4-911D-39E4-8D19-1CC44687CE6D> /usr/lib/libncurses.5.4.dylib 0x7fff4126b000 - 0x7fff41289fff libCGInterfaces.dylib (544.4) <02C89930-F64D-354E-8C18-F3DDB419DC8D> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib 0x7fff43814000 - 0x7fff43a87fff com.apple.RawCamera.bundle (9.10.0 - 1450.3) <408A3DFB-B3D3-3C15-88BB-16076BDFC74B> /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera 0x7fff46358000 - 0x7fff46363fff libGPUSupportMercury.dylib (18.5.9) <43A9855E-09F8-3F12-8A97-781328A7A758> /System/Library/PrivateFrameworks/GPUSupport.framework/Versions/A/Libraries/libGPUSupportMercury.dylib 0x7fff4798e000 - 0x7fff479cefff com.apple.osanalytics.OSAnalytics (1.0 - 1) <96B8D855-E10D-3E40-884F-DA0BBAE9F48F> /System/Library/PrivateFrameworks/OSAnalytics.framework/Versions/A/OSAnalytics 0x7fff515e5000 - 0x7fff51612fff com.apple.HelpData (2.3 - 201) <3125FBF3-30B7-3237-B001-2692332FF681> /System/Library/PrivateFrameworks/HelpData.framework/Versions/A/HelpData 0x7fff51613000 - 0x7fff5162dfff com.apple.shortcut (2.16 - 118) <1FD9ABCC-0B5B-37DC-9E6E-CC47C128DBB2> /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut 0x7fff5162e000 - 0x7fff516cdfff com.apple.Symbolication (12.5 - 64544.70.1) <B57534E5-43D5-38CA-9A8C-A66EBDFB820A> /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication 0x7fff5dca8000 - 0x7fff5e137fff com.apple.driver.AppleIntelKBLGraphicsMTLDriver (16.4.5 - 16.0.4) <994BBF27-F4D5-3561-BC2E-FECC0C460C76> /System/Library/Extensions/AppleIntelKBLGraphicsMTLDriver.bundle/Contents/MacOS/AppleIntelKBLGraphicsMTLDriver 0x7fff5eec8000 - 0x7fff5feaffff com.apple.driver.AppleIntelKBLGraphicsGLDriver (16.4.5 - 16.0.4) <844E918A-E28D-3FF0-B391-2E3F3FFA0F68> /System/Library/Extensions/AppleIntelKBLGraphicsGLDriver.bundle/Contents/MacOS/AppleIntelKBLGraphicsGLDriver 0x7fff6965e000 - 0x7fff69662fff libmetal_timestamp.dylib (31001.189) <89A82967-B14D-3109-B45E-34717156E60E> /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/31001/Libraries/libmetal_timestamp.dylib 0x7fff6baa9000 - 0x7fff6baaffff libCoreFSCache.dylib (200.9) <12A2A7E7-39F7-30A5-AC0B-E09947417D3E> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib 0x7fff6bab0000 - 0x7fff6bab4fff libCoreVMClient.dylib (200.9) <F8C4D017-075A-37B2-AE8D-8CEB5FE1BC9B> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib 0x7fff6bab5000 - 0x7fff6bac4fff com.apple.opengl (18.5.9 - 18.5.9) <1422D0CA-C3E2-3309-8897-018E651CB74E> /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL 0x7fff6bac5000 - 0x7fff6bac7fff libCVMSPluginSupport.dylib (18.5.9) <AC7D4088-7CA8-3A0B-9B55-08427083C382> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib 0x7fff6bac8000 - 0x7fff6bad0fff libGFXShared.dylib (18.5.9) <76ABDB4A-3687-39E0-B8FB-125717742431> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib 0x7fff6bad1000 - 0x7fff6bb04fff libGLImage.dylib (18.5.9) <750C938A-9F4F-3BAD-8D3F-03EF619F28AD> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib 0x7fff6bb05000 - 0x7fff6bb41fff libGLU.dylib (18.5.9) <4A77F717-2BBC-3439-AE10-694E82C0A184> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib 0x7fff6bb42000 - 0x7fff6bcd5fff libGLProgrammability.dylib (18.5.9) <811C33B6-9856-3D1F-8947-3899496630BD> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib 0x7fff6bcd6000 - 0x7fff6bce0fff libGL.dylib (18.5.9) <95D5C72E-9352-39EC-83B1-6BB295A83462> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib 0x7fff6bce1000 - 0x7fff6be5efff GLEngine (18.5.9) <F8809EE9-15B0-36EC-8F33-12B869822B72> /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine 0x7fff6be5f000 - 0x7fff6be87fff GLRendererFloat (18.5.9) <F4858214-65AC-3CEF-834D-7A13370D9C5D> /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat 0x7fff6d120000 - 0x7fff6d178fff com.apple.opencl (4.6 - 4.6) <769BB23D-09E5-3A3A-B2EA-310157AA206D> /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL 0x7fff6e222000 - 0x7fff6e229fff com.apple.agl (3.3.4 - AGL-3.3.3) <23E38B10-2F27-3BB2-B78D-C28189C21601> /System/Library/Frameworks/AGL.framework/Versions/A/AGL 0x7fff7791e000 - 0x7fff77925fff libRosetta.dylib (203.46) <0A17EAFC-15E9-37FE-8EE2-DE0F7F220AD8> /usr/lib/libRosetta.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 0 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=801.5M resident=0K(0%) swapped_out_or_unallocated=801.5M(100%) Writable regions: Total=910.5M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=910.5M(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 512K 4 Activity Tracing 256K 1 CG backing stores 2880K 6 CG image 136K 14 CoreAnimation 53.9M 32 CoreGraphics 12K 2 CoreImage 56K 5 CoreUI image data 3256K 24 Foundation 16K 1 Kernel Alloc Once 8K 1 MALLOC 268.2M 94 MALLOC guard page 32K 8 MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) STACK GUARD 56.0M 9 Stack 12.1M 9 VM_ALLOCATE 228K 24 __DATA 258.9M 365 __DATA_CONST 17.1M 200 __DATA_DIRTY 793K 118 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 504.0M 25 __OBJC_RO 70.2M 1 __OBJC_RW 2480K 2 __TEXT 297.6M 362 __UNICODE 588K 1 mapped file 230.6M 29 shared memory 768K 17 =========== ======= ======= TOTAL 2.1G 1357 TOTAL, minus reserved VM space 1.7G 1357 Model: MacBookAir8,2, BootROM 1554.120.19.0.0 (iBridge: 18.16.14663.0.0,0), 2 processors, Dual-Core Intel Core i5, 1.6 GHz, 8 GB, SMC Graphics: kHW_IntelUHDGraphics617Item, Intel UHD Graphics 617, spdisplays_builtin Memory Module: BANK 0/DIMM0, 4 GB, LPDDR3, 2133 MHz, 0x802C, 0x4D5435324C3531324D3634443450512D3039 Memory Module: BANK 1/DIMM0, 4 GB, LPDDR3, 2133 MHz, 0x802C, 0x4D5435324C3531324D3634443450512D3039 AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x843), wl0: Feb 15 2021 23:32:14 version 9.30.444.10.32.5.61 FWID 01-89152cbf Bluetooth: Version 8.0.5d7, 3 services, 27 devices, 1 incoming serial ports Network Service: Wi-Fi, AirPort, en0 USB Device: USB 3.0 Bus USB Device: Apple T2 Bus USB Device: Apple Internal Keyboard / Trackpad USB Device: Headset USB Device: Ambient Light Sensor USB Device: FaceTime HD Camera (Built-in) USB Device: Apple T2 Controller Thunderbolt Bus: MacBook Air, Apple Inc., 47.5 Best regards, Grace Nie

2 2

Error in hippocampal subfields longitudinal processing
by Kaija Sander 29 Jul '21

29 Jul '21

External Email - Use Caution Hello all, I am attempting to obtain the hippocampal subfields segmentation in a small longitudinal dataset (18 participants, 2 time points each). I have successfully been able to run recon-all, recon-all -base and recon-all -long (or at least, these steps appear to be completed without errors). However, when trying to run segmentHA_T1_long.sh, I encountering the following error (I have also attached the full log file of one of the subjects): Open file failed because file '/tmp/MCR_511464988/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m' has invalid content. Details: 'file is closed.failbit is set.' The file "/tmp/MCR_511464988/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m" cannot be executed. Error in SegmentSubfieldsT1Longitudinal (line 1795) What is strange is that this has only happened for a couple of subjects, and has worked fine for the few others I did. Does anyone have any suggestions of what might be going wrong and how to fix it? Thank you very much, Kaija FreeSurfer version: freesurfer-local-build-dev-20200116 Platform: Ubuntu 18.04.5

3 9

Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly
by fsbuild 29 Jul '21

29 Jul '21

External Email - Use Caution If you have not already done so, see if you get a different result by double clicking on the Freeview.app icon under /Applications/freesurfer/7.2.0 with the mouse. You can try this variation on what's been previously suggested. 1) run a bash shell $ bash 2) setup freesurfer environment $ export FREESURFER_HOME=/Applications/freesurfer/7.2.0 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.2.0 FSFAST_HOME       /Applications/freesurfer/7..2.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.2.0/subjects MNI_DIR           /Applications/freesurfer/7.2.0/mni 3) Locate your license file (I name mine license.txt) in your home directory and check you can read its contents, $ export FS_LICENSE=$HOME/license.txt $ cat $FS_LICENSE .... check the output ... .... first line should contain email address ... .... followed by 3 more lines ... 4) set environment variable for debug $ export QT_DEBUG_PLUGINS=1 5) run freeview with no arguments $ which freeview /Applications/freesurfer/7.2.0/bin/freeview $ freeview .... an empty freeview window should appear and persist on the screen ... At this point the last few lines of output in the terminal window should now be: Got keys from plugin meta data ("svg", "svgz", "svg.gz") QFactoryLoader::QFactoryLoader() checking directory path "/Applications/freesurfer/7.2.0/Freeview.app/Contents/MacOS/iconengines" ... QFactoryLoader::QFactoryLoader() checking directory path "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/accessible" ... QFactoryLoader::QFactoryLoader() checking directory path "/Applications/freesurfer/7.2.0/Freeview.app/Contents/MacOS/accessible" ... 6) Use the freeview application "File" pull down menu to select "load volume".  In the window that comes up, click on the yellow folder icon to the r.h.s of the folder/file entry box under "Select Volume File".  In the Finder window that comes up, navigate to /Applications/freesurfer/7.2.0/subjects/bert/mri and select the brain.mgz file.  Click on OPEN. That path/filename will appear in the load volume text entry box.  Don't check/change any of the options for loading the volume and click OK. The steps above worked for me to load that volume using an Intel MacPro laptop with the 7.2.0 release running under either MacOS 10.15.7 (Catlaina) or MacOS 11.4 (Big Sur) w/o freeview exiting or producing any further output in the terminal window.  If it fails on your machine, you could send along the Qt debug output after the lines listed above.  Please do not send the output from cat'ing your license file though. - R.On Jul 28, 2021, at 14:53, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Please check in “energy saver” preferences that “automatic graphics switching” is not selected so that high performance graphics is always used.- R.On Jul 28, 2021, at 14:36, Sahil Bajaj <sahil.brain(a)gmail.com> wrote:        External Email - Use Caution        Hi Freesurfer team,I am also having a similar issue from the last few weeks. I hope we will get a solution soon.Thanks,Sahil On Wed, Jul 28, 2021 at 11:15 AM Tom Parker <tomparker59(a)gmail.com> wrote:        External Email - Use Caution        I have just installed Freesurfer 7.2.0 for Mac. When I attempt to open Freeview it crashes. Full details of error messages below.Any advice to correct would be much appreciated.Many thanks!_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-UOGTt3HFDlHvIM_e7oJsIyW0px6D2XV4xw3F… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Medical Imaging Analyst Position - Department of Radiology
by Sneha Pandya 29 Jul '21

29 Jul '21

External Email - Use Caution The Division of Medical Nuclear Physics in the Department of Radiology at Weill Cornell Medicine is seeking a full-time Medical Imaging Analyst to support its active research program in PET and Nuclear Medicine. Interested individuals must have at least a master’s degree in medical imaging, medical physics, physics, math, engineering, or related fields. Programming and statistical analysis skills are a must. Good understanding of medical imaging and experience with compartmental kinetic modeling is highly desired. The qualified candidate must have: • excellent written and oral communication skills. • strong ability to identify, analyze, and solve problems. • ability to carry out analysis for multiple projects simultaneously. • ability to effectively communicate with multiple principal investigators. To apply, please email a cover letter, research interests, CV, and names of three references to: Sadek Nehmeh, Ph.D., D.A.B.R. Chief of PET and Nuclear Physics Associate Professor of Medical Physics in Radiology Weill Cornell Medicine New York, New York 10065-4870 E-mail: san2028(a)med.cornell.edu<mailto:san2028@med.cornell.edu> Diversity is one of Weill Cornell Medicine’s core values and is essential to achieving excellence in patient care, research, and education. We welcome applications from candidates who share our commitment to fostering a culture of fairness, equity, and belonging. Weill Cornell Medicine is an Equal Employment Opportunity Employer, providing equal employment opportunities to all qualified applicants without regard to race, sex, sexual orientation, gender identity, national origin, color, age, religion, protected veteran or disability status, or genetic information.

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Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly
by fsbuild 28 Jul '21

28 Jul '21

External Email - Use Caution Please check in “energy saver” preferences that “automatic graphics switching” is not selected so that high performance graphics is always used. - R. On Jul 28, 2021, at 14:36, Sahil Bajaj <sahil.brain(a)gmail.com> wrote:        External Email - Use Caution        Hi Freesurfer team,I am also having a similar issue from the last few weeks. I hope we will get a solution soon.Thanks,Sahil On Wed, Jul 28, 2021 at 11:15 AM Tom Parker <tomparker59(a)gmail.com> wrote:        External Email - Use Caution        I have just installed Freesurfer 7.2.0 for Mac. When I attempt to open Freeview it crashes. Full details of error messages below.Any advice to correct would be much appreciated.Many thanks!_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Mac install of Freesurfer 7.2.0 - Freeview quits unexpectedly
by Tom Parker 28 Jul '21

28 Jul '21

External Email - Use Caution I have just installed Freesurfer 7.2.0 for Mac. When I attempt to open Freeview it crashes. Full details of error messages below. Any advice to correct would be much appreciated. Many thanks! Error message on the terminal line 2: 77482 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“ Error following clicking on freeviw app: Full error report: Process: freeview [77560] Path: /Applications/freesurfer/Freeview.app/Contents/MacOS/freeview Identifier: com.freesurfer.freeview Version: 0 Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: freeview [77560] User ID: 503 Date/Time: 2021-07-28 17:12:46.904 +0100 OS Version: macOS 11.4 (20F71) Report Version: 12 Bridge OS Version: 3.0 (14Y908) Anonymous UUID: BA169BD1-5C1C-BF02-1EA0-32FC6DD703EA Time Awake Since Boot: 110000 seconds System Integrity Protection: enabled Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: EXC_I386_GPFLT Exception Note: EXC_CORPSE_NOTIFY Termination Signal: Segmentation fault: 11 Termination Reason: Namespace SIGNAL, Code 0xb Terminating Process: exc handler [77560] Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 com.freesurfer.freeview 0x0000000103522164 0x1034bc000 + 418148 1 com.freesurfer.freeview 0x000000010369b004 0x1034bc000 + 1961988 2 org.qt-project.QtWidgets 0x0000000113fda6ed QWidget::event(QEvent*) + 1117 3 org.qt-project.QtWidgets 0x00000001140ebc45 QMainWindow::event(QEvent*) + 277 4 org.qt-project.QtWidgets 0x0000000113f9e70d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 5 org.qt-project.QtWidgets 0x0000000113f9fb12 QApplication::notify(QObject*, QEvent*) + 594 6 org.qt-project.QtCore 0x0000000114c69564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 7 org.qt-project.QtWidgets 0x0000000113ff8a74 0x113f8e000 + 436852 8 org.qt-project.QtWidgets 0x0000000113f9e70d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 9 org.qt-project.QtWidgets 0x0000000113f9fb12 QApplication::notify(QObject*, QEvent*) + 594 10 org.qt-project.QtCore 0x0000000114c69564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 11 org.qt-project.QtGui 0x0000000114565a74 QGuiApplicationPrivate::processGeometryChangeEvent(QWindowSystemInterfacePrivate::GeometryChangeEvent*) + 516 12 org.qt-project.QtGui 0x0000000114566420 QGuiApplicationPrivate::processWindowScreenChangedEvent(QWindowSystemInterfacePrivate::WindowScreenChangedEvent*) + 736 13 org.qt-project.QtGui 0x0000000114544c33 bool QWindowSystemInterfacePrivate::handleWindowSystemEvent<QWindowSystemInterface::SynchronousDelivery>(QWindowSystemInterfacePrivate::WindowSystemEvent*) + 115 14 libqcocoa.dylib 0x0000000116fd7c77 0x116fb9000 + 126071 15 libqcocoa.dylib 0x0000000116fd1862 0x116fb9000 + 100450 16 libqcocoa.dylib 0x0000000116fd12eb 0x116fb9000 + 99051 17 org.qt-project.QtGui 0x000000011456f1dc QWindowPrivate::create(bool, unsigned long long) + 140 18 org.qt-project.QtWidgets 0x0000000113fc7e31 QWidgetPrivate::create() + 1201 19 org.qt-project.QtWidgets 0x0000000113fc6b22 QWidget::create(unsigned long long, bool, bool) + 322 20 org.qt-project.QtWidgets 0x00000001140ec4d7 QMainWindow::setUnifiedTitleAndToolBarOnMac(bool) + 55 21 com.freesurfer.freeview 0x0000000103689497 0x1034bc000 + 1889431 22 com.freesurfer.freeview 0x000000010368350e 0x1034bc000 + 1864974 23 com.freesurfer.freeview 0x00000001035bc79a 0x1034bc000 + 1050522 24 libdyld.dylib 0x00007fff204b7f5d start + 1 Thread 1: 0 libsystem_pthread.dylib 0x00007fff20498420 start_wqthread + 0 Thread 2: 0 libsystem_pthread.dylib 0x00007fff20498420 start_wqthread + 0 Thread 3: 0 libsystem_pthread.dylib 0x00007fff20498420 start_wqthread + 0 Thread 4: 0 libsystem_pthread.dylib 0x00007fff20498420 start_wqthread + 0 Thread 5: 0 libsystem_pthread.dylib 0x00007fff20498420 start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x9e667f3bcdba483f rbx: 0x00007ffeec742010 rcx: 0x00007fff2a5baaea rdx: 0x0000000113fda6dd rdi: 0x00007fff81563828 rsi: 0x00007ffeec741088 rbp: 0x00007ffeec740b20 rsp: 0x00007ffeec740b10 r8: 0x0000000000000000 r9: 0x00000000fffffe00 r10: 0x0000000000000002 r11: 0x0000000114c695b0 r12: 0x00007fa21d5177a0 r13: 0x00007ffeec742010 r14: 0x00007ffeec741088 r15: 0x00007ffeec741088 rip: 0x0000000103522164 rfl: 0x0000000000010202 cr2: 0x0000000103522150 Logical CPU: 2 Error Code: 0x00000000 Trap Number: 13 Thread 0 instruction stream: 01 48 89 df e8 65 9c 3a-01 48 8b 43 08 48 8b 4b .H...e.:.H.C.H.K 28 48 8b 40 10 48 8b 40-28 8b 51 20 f7 d2 03 50 (H.@.H.@(.Q ...P 20 03 51 18 8b 40 14 ff-c0 48 c1 e2 20 48 09 d0 .Q..@...H.. H.. 48 89 45 f0 48 8d 75 f0-48 89 df e8 28 9c 3a 01 H.E.H.u.H...(.:. 48 83 c4 08 5b 5d c3 0f-1f 44 00 00 55 48 89 e5 H...[]...D..UH.. 48 83 ec 10 48 8b 47 08-48 8b 4f 28 48 8b 40 10 H...H.G.H.O(H.@. [48]8b 40 28 44 8b 40 18-8b 70 20 8b 51 20 f7 d2 H.@(D.@..p .Q .. <== 44 29 c6 01 d6 03 71 18-8b 40 14 ff c0 44 01 c6 D)....q..@...D.. 48 c1 e6 20 48 09 f0 48-89 45 f8 48 8d 75 f8 e8 H.. H..H.E.H.u.. d4 9b 3a 01 48 83 c4 10-5d c3 66 90 55 48 89 e5 ..:.H...].f.UH.. 53 50 48 89 fb 48 8b 7f-38 e8 4e 98 3a 01 48 89 SPH..H..8.N.:.H. df e8 ac 9b 3a 01 48 8b-43 30 48 8b 78 18 48 83 ....:.H.C0H.x.H. Thread 0 last branch register state not available. 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0x7fff6e229fff com.apple.agl (3.3.4 - AGL-3.3.3) <23E38B10-2F27-3BB2-B78D-C28189C21601> /System/Library/Frameworks/AGL.framework/Versions/A/AGL External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 0 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=745.8M resident=0K(0%) swapped_out_or_unallocated=745.8M(100%) Writable regions: Total=822.3M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=822.3M(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 256K 2 Activity Tracing 256K 1 CG backing stores 4320K 12 CoreUI image data 228K 2 Foundation 16K 1 Kernel Alloc Once 8K 1 MALLOC 180.7M 39 MALLOC guard page 32K 8 MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) STACK GUARD 56.0M 6 Stack 10.5M 6 VM_ALLOCATE 112K 28 __DATA 257.4M 325 __DATA_CONST 11.9M 170 __DATA_DIRTY 549K 99 __FONT_DATA 4K 1 __LINKEDIT 503.9M 23 __OBJC_RO 70.2M 1 __OBJC_RW 2480K 2 __TEXT 241.9M 321 __UNICODE 588K 1 mapped file 93.6M 27 shared memory 752K 14 =========== ======= ======= TOTAL 1.8G 1091 TOTAL, minus reserved VM space 1.4G 1091 Model: MacBookPro13,2, BootROM 429.120.4.0.0, 2 processors, Dual-Core Intel Core i5, 2.9 GHz, 8 GB, SMC 2.37f25 Graphics: kHW_IntelIrisGraphics550Item, Intel Iris Graphics 550, spdisplays_builtin Memory Module: BANK 0/DIMM0, 4 GB, LPDDR3, 2133 MHz, 0x802C, 0x4D5435324C3531324D3332443250462D3039 Memory Module: BANK 1/DIMM0, 4 GB, LPDDR3, 2133 MHz, 0x802C, 0x4D5435324C3531324D3332443250462D3039 AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x157), Broadcom BCM43xx 1.0 (7.77.111.1 AirPortDriverBrcmNIC-1680.8) Bluetooth: Version 8.0.5d7, 3 services, 27 devices, 1 incoming serial ports Network Service: Wi-Fi, AirPort, en0 USB Device: USB3.0 Hub USB Device: USB 3.0 Bus USB Device: USB2.0 Hub USB Device: Keyboard Hub USB Device: Apple Keyboard USB Device: USB-C Digital AV Multiport Adapter USB Device: Apple T1 Controller Thunderbolt Bus: MacBook Pro, Apple Inc., 41.2 Thunderbolt Bus: MacBook Pro, Apple Inc., 41.2

2 1

Samseg.stats file to table
by AJ 28 Jul '21

28 Jul '21

External Email - Use Caution Hi, I was wondering if there is a simple command for generating a table from all the SamsegOutput/stats files across all subjects. When I use the asegstats2table, I get index error: list index out of range. I guess this has to do with the structure of files in the samsegOutput/stats versus the aseg.stats file? Thank you. AJ

1 0

Hippocampal Subfield Definition Errors
by Franchesca Kuhney 28 Jul '21

28 Jul '21

External Email - Use Caution Hello, I've run into an issue with the longitudinal hippocampus/amygdala segmentation (segmentHA_T1_long.sh). All of the commands ran properly and I got the outputs listed on the FreeSurfer wiki but, upon QAing the segmentations, I realized that a few subjects hippocampal segmentations were a poor fit. It appears that the segmentation includes their parahippocampal gyrus. I'm wondering if you have any recommendations for how to fix these either manually or automatically? Thank you! Kindly, Franchesca *Franchesca Kuhney, M.A.* *(she/her)* Clinical Psychology Doctoral Student University of Illinois at Chicago Behavioral Sciences Building | Rm 3019 1007 W. Harrison St. | Chicago, IL 60607 ----- *Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.* *The information included in the email may be confidential and is meant only for the use of the intended recipient.* *If you received this communication in error, please notify the sender immediately and destroy the original information.*

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