Freesurfer April 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
217 discussions

Re: [Freesurfer] Fixing a left/right flip
by Dan Grupe 26 Apr '17

26 Apr '17

I took a look at the xhemireg script and I feel like editing this to serve my purposes might be too tall of an order. However, I think I have a processing stream that will work — I want to make sure there’s nothing problematic about it. 1. Run recon-all on the properly oriented T1 images through -segmentation 2. Take the old hand-edited wm.mgz file [containing extensive hand-edits] and left/right flip this file (using mri_convert to change LIA to RIA) 3. Visually confirm alignment of this hand-edited, flipped wm.mgz file. It turns out this brain was shifted by 1 voxel in the left/right direction; I manually adjusted this after converting the file to COR-format, and then converted back to .mgz and visually confirmed proper alignment. 4. Drop this hand-edited, L/R flipped and 1-voxel-shifted wm.mgz file into the subject/mri directory from running recon-all in (#1), then proceed with recon-all -autorecon2-wm -autorecon3 Is there anything inherently flawed about this approach? Are there any other files that I also need to flip (i.e., wm.seg.mgz or anything else?) thanks, Dan On 4/17/17 6:48 PM, Douglas Greve wrote: you can try xhemireg. it is kind of meant to do this kind of thing, but not to the extent that you need it. If you know a little programming, you can try to edit the script so that it does everything. On 4/17/17 6:43 PM, Dan Grupe wrote: > Hi all, > > After running a bunch of subjects through FreeSurfer and making > extensive manual edits to the white matter masks, we discovered that > the data were left/right flipped during the dicom-to-nifti conversion > process. I hope to maintain these manual edits while processing data > in the proper orientation and running them through the rest of the > pipeline. Is this possible to do? > > An old thread from 10 years ago directed me to this page: > https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal that > offered some tips on how to go about this. However, after confirming > that the volume was reversed running recon-all -autorecon1 in a new > directory, I encountered an error message: > > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > > This problem does not arise when running the same command on a copy of > this subject’s non-flipped data. > > Are there different steps that I should be following to rectify the > problem? Or can you help me troubleshoot this error? > > Best, > Dan

1 0

Filling in missing ventricles in WM
by Shane Schofield 26 Apr '17

26 Apr '17

Hi Freesurfer Experts and Antonin, About an earlier question on XL Defects I have used your suggestions to check the orig.nofix surfaces and I think the skull and missing ventricle voxels are causing the problem. Picture pasted. I have removed the WM voxels in the skull, filled in the ventricles by adding WM voxels (brush value = 255 ), and ran the commandrecon-all -s subject -autorecon2-wm -autorecon3 Recon-all was completed successfully and the surfaces look good. However, the aseg volume in the lateral ventricles are still wrong.At the crosshair, the WM value is 255 and the ASEG value is 0. Should I be editing the aseg now? Or should I be doing something else to the wm.mgz? Appreciate your tips!Best Wishes,Shane

3 5

Freesurfer version from recon-all output files
by Diogo Duarte 25 Apr '17

25 Apr '17

Hi everyone, How can I find the freesurfer version used (recon-all) from the resulting files? This would be necessary for keeping freesurfer versions consistent. Thank you, Diogo

2 2

Re: [Freesurfer] FS 6.0 Freeview
by 吕元媛 25 Apr '17

25 Apr '17

Dear Experts, I have the same problem with Freeview. I recently installed FS 6.0 on macOS Sierra (16E195). I have ran the command “sudo -E fs_update” in terminal. When I start with Freeview app, load a volume, it will immediately crash. I attach the problem report in the end. The only way to run freeview is from the terminal, but I cannot use the shortcuts with the Option (Alt) key, but other ones with Ctrl and Command functions well. I also have a warning message from the terminal window when I load a volume in this way. Freeview[694:13734] modalSession has been exited prematurely - check for a reentrant call to endModalSession: I tried to reinstall the OS but it didn’t work. Best, Yuanyuan ----------------------------- Process: Freeview [1050] Path: /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview Identifier: com.yourcompany.Freeview Version: ??? Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: Freeview [1050] User ID: 501 Date/Time: 2017-04-25 22:01:12.682 +0200 OS Version: Mac OS X 10.12.4 (16E195) Report Version: 12 Anonymous UUID: A853EAA1-CE03-1F51-19F0-A51C358DA386 Time Awake Since Boot: 2100 seconds System Integrity Protection: enabled Crashed Thread: 7 Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000 Exception Note: EXC_CORPSE_NOTIFY Termination Reason: DYLD, [0x4] Symbol missing Dyld Error Message: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Thread 0:: Dispatch queue: com.apple.main-thread 0 com.apple.CoreGraphics 0x00007fffd60c376c argb32_mark + 13240 1 com.apple.CoreGraphics 0x00007fffd60c6862 argb32_image + 1954 2 com.apple.CoreGraphics 0x00007fffd6490486 RIPLayerBltImage + 1039 3 com.apple.CoreGraphics 0x00007fffd61309da ripc_RenderImage + 228 4 com.apple.CoreGraphics 0x00007fffd6136199 ripc_EndLayer + 1411 5 com.apple.CoreGraphics 0x00007fffd6481bf5 CGContextEndTransparencyLayer + 53 6 com.apple.coreui 0x00007fffe1983dcb -[CUITextEffectStack drawGlyphs:inContext:usingFont:atPositions:count:lineHeight:inBounds:atScale:] + 1833 7 com.apple.coreui 0x00007fffe195dfd4 CUIRenderer::DrawStyledGlyphsAtPositions(CGContext*, __CFDictionary const*, __CTFont const*, unsigned short const*, CGPoint const*, unsigned long, double) + 2188 8 com.apple.coreui 0x00007fffe195fbfe CUIDrawStyledGlyphsAtPositions + 275 9 com.apple.HIToolbox 0x00007fffd51fa204 _HIThemeCUIDrawStyledGlyphsAtPositions + 88 10 com.apple.HIToolbox 0x00007fffd51f998c TCoreTextEngine::DrawThemeTextBox(THIThemeTextInfo*, CGRect const&, unsigned int, CGContext*) + 2220 11 com.apple.HIToolbox 0x00007fffd51f9014 ___ZN10DataEngine11DrawTextBoxEPKvPK6CGRectP15HIThemeTextInfoP9CGContext_block_invoke + 262 12 com.apple.HIToolbox 0x00007fffd51f8ce8 DataEngine::DrawTextBox(void const*, CGRect const*, HIThemeTextInfo*, CGContext*) + 1412 13 com.apple.HIToolbox 0x00007fffd51f874c HIThemeDrawTextBox + 490 14 com.apple.HIToolbox 0x00007fffd51f7d21 HIMenuBarView::DrawTextTitle(MenuData*, CGRect const*, __CFString const*, unsigned short, CGContext*, bool, bool) + 379 15 com.apple.HIToolbox 0x00007fffd51f317b HIMenuBarView::DrawOnce(CGRect, CGRect, bool, bool, CGContext*) + 1599 16 com.apple.HIToolbox 0x00007fffd51f2a44 HIMenuBarView::DrawSelf(short, __HIShape const*, CGContext*) + 554 17 com.apple.HIToolbox 0x00007fffd51f246c HIMenuBarView::DrawWithoutCustomization(short, __HIShape const*, CGContext*) + 82 18 com.apple.HIToolbox 0x00007fffd51f240b HIMenuBarView::DrawingDelegateHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*) + 249 19 com.apple.HIToolbox 0x00007fffd51d5d85 DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 1708 20 com.apple.HIToolbox 0x00007fffd51d4ff6 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 428 21 com.apple.HIToolbox 0x00007fffd51d4e3f SendEventToEventTargetWithOptions + 43 22 com.apple.HIToolbox 0x00007fffd51f1f9f HIView::SendDraw(short, OpaqueGrafPtr*, __HIShape const*, CGContext*) + 337 23 com.apple.HIToolbox 0x00007fffd51f194d HIView::RecursiveDrawComposited(__HIShape const*, __HIShape const*, unsigned int, HIView*, CGContext*, unsigned char, double) + 565 24 com.apple.HIToolbox 0x00007fffd51f1bfd HIView::RecursiveDrawComposited(__HIShape const*, __HIShape const*, unsigned int, HIView*, CGContext*, unsigned char, double) + 1253 25 com.apple.HIToolbox 0x00007fffd51f13b5 HIView::DrawComposited(short, OpaqueGrafPtr*, __HIShape const*, unsigned int, HIView*, CGContext*) + 975 26 com.apple.HIToolbox 0x00007fffd51f0fd4 HIView::Render(unsigned int, CGContext*) + 54 27 com.apple.HIToolbox 0x00007fffd52072e2 FlushWindowObject(WindowData*, void**, unsigned char) + 771 28 com.apple.HIToolbox 0x00007fffd5206d45 FlushAllBuffers(__CFRunLoopObserver*, unsigned long, void*) + 373 29 com.apple.CoreFoundation 0x00007fffd5cbbdd7 __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ + 23 30 com.apple.CoreFoundation 0x00007fffd5cbbd47 __CFRunLoopDoObservers + 391 31 com.apple.CoreFoundation 0x00007fffd5c9c1a9 CFRunLoopRunSpecific + 393 32 com.apple.HIToolbox 0x00007fffd51fdebc RunCurrentEventLoopInMode + 240 33 com.apple.HIToolbox 0x00007fffd51fdbf9 ReceiveNextEventCommon + 184 34 com.apple.HIToolbox 0x00007fffd51fdb26 _BlockUntilNextEventMatchingListInModeWithFilter + 71 35 com.apple.AppKit 0x00007fffd3798e24 _DPSNextEvent + 1120 36 com.apple.AppKit 0x00007fffd3f1485e -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 2796 37 com.apple.AppKit 0x00007fffd378d7ab -[NSApplication run] + 926 38 QtGui 0x000000011594e174 QDesktopWidget::resizeEvent(QResizeEvent*) + 12724 39 QtCore 0x0000000115685a34 QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 68 40 QtCore 0x0000000115685d54 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 180 41 QtCore 0x000000011568737c QCoreApplication::exec() + 188 42 com.yourcompany.Freeview 0x0000000104cb5f58 main + 6232 43 com.yourcompany.Freeview 0x0000000104bd6974 start + 52 Thread 1: 0 libsystem_kernel.dylib 0x00007fffeb52e44e __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fffeb618695 _pthread_wqthread + 1426 2 libsystem_pthread.dylib 0x00007fffeb6180f1 start_wqthread + 13 Thread 2: 0 libsystem_kernel.dylib 0x00007fffeb52e44e __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fffeb618502 _pthread_wqthread + 1023 2 libsystem_pthread.dylib 0x00007fffeb6180f1 start_wqthread + 13 Thread 3: 0 libsystem_pthread.dylib 0x00007fffeb6180e4 start_wqthread + 0 1 libsystem_blocks.dylib 0x00007fffeb433bdc _Block_object_assign + 358 Thread 4: 0 libsystem_kernel.dylib 0x00007fffeb52e44e __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fffeb618695 _pthread_wqthread + 1426 2 libsystem_pthread.dylib 0x00007fffeb6180f1 start_wqthread + 13 Thread 5:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x00007fffeb52634a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fffeb525797 mach_msg + 55 2 com.apple.CoreFoundation 0x00007fffd5c9d4e4 __CFRunLoopServiceMachPort + 212 3 com.apple.CoreFoundation 0x00007fffd5c9c971 __CFRunLoopRun + 1361 4 com.apple.CoreFoundation 0x00007fffd5c9c1c4 CFRunLoopRunSpecific + 420 5 com.apple.AppKit 0x00007fffd38e62d2 _NSEventThread + 205 6 libsystem_pthread.dylib 0x00007fffeb6189af _pthread_body + 180 7 libsystem_pthread.dylib 0x00007fffeb6188fb _pthread_start + 286 8 libsystem_pthread.dylib 0x00007fffeb618101 thread_start + 13 Thread 6: 0 libsystem_pthread.dylib 0x00007fffeb6180e4 start_wqthread + 0 1 libsystem_blocks.dylib 0x00007fffeb433bdc _Block_object_assign + 358 Thread 7 Crashed: 0 dyld 0x00000001187399ee __abort_with_payload + 10 1 dyld 0x000000011873943b abort_with_payload_wrapper_internal + 90 2 dyld 0x0000000118739464 abort_with_payload + 9 3 dyld 0x0000000118714793 dyld::halt(char const*) + 361 4 dyld 0x000000011871489e dyld::fastBindLazySymbol(ImageLoader**, unsigned long) + 139 5 libdyld.dylib 0x00007fffeb3fb282 dyld_stub_binder + 282 6 ??? 0x000000011528a018 0 + 4649951256 7 com.yourcompany.Freeview 0x0000000104c5f0df LayerMRI::LoadVolumeFromFile() + 399 8 com.yourcompany.Freeview 0x0000000104d2bea1 ThreadIOWorker::run() + 1361 9 QtCore 0x00000001155cd5b5 QThread::setPriority(QThread::Priority) + 469 10 libsystem_pthread.dylib 0x00007fffeb6189af _pthread_body + 180 11 libsystem_pthread.dylib 0x00007fffeb6188fb _pthread_start + 286 12 libsystem_pthread.dylib 0x00007fffeb618101 thread_start + 13 Thread 7 crashed with X86 Thread State (64-bit): rax: 0x0000000002000209 rbx: 0x0000000000000004 rcx: 0x0000700004e05b38 rdx: 0x0000700004e05fb0 rdi: 0x0000000000000006 rsi: 0x0000000000000004 rbp: 0x0000700004e05b90 rsp: 0x0000700004e05b38 r8: 0x0000700004e05bb0 r9: 0x0000000000000000 r10: 0x0000000000000098 r11: 0x0000000000000246 r12: 0x0000000000000098 r13: 0x0000700004e05fb0 r14: 0x0000000000000006 r15: 0x0000000000000000 rip: 0x00000001187399ee rfl: 0x0000000000000246 cr2: 0x000000011e046000 Logical CPU: 0 Error Code: 0x02000209 Trap Number: 133 Binary Images: 0x104bd0000 - 0x106331fe7 +com.yourcompany.Freeview (???) <5C1FDB24-A795-321E-BA3D-393141B59E3B> /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview 0x11527c000 - 0x115289fff +libgomp.1.dylib (2) <E0C76B2B-0EC6-364E-AACD-42C7AAE73F23> /Applications/freesurfer/Freeview.app/Contents/Frameworks/libgomp.1.dylib 0x115293000 - 0x1154eafe7 +QtScript (4.7.4) <22C41B2A-3C52-B7E9-37A8-EF71E48EE9FB> /Applications/freesurfer/Freeview.app/Contents/Frameworks/QtScript.framework/Versions/4/QtScript 0x115546000 - 0x1157ceff7 +QtCore (4.7.4) <9EB52EC3-3C0F-0A45-1CE6-227EB7069767> /Applications/freesurfer/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/4/QtCore 0x115834000 - 0x1158e0fe7 +QtScriptTools (4.7.4) <1863C4B7-A7BB-9ACE-A1A5-F728893B45A6> /Applications/freesurfer/Freeview.app/Contents/Frameworks/QtScriptTools.framework/Versions/4/QtScriptTools 0x11590f000 - 0x1162f4fef +QtGui (4.7.4) <8B10C74D-0789-C563-FA0E-3192DAE669E6> /Applications/freesurfer/Freeview.app/Contents/Frameworks/QtGui.framework/Versions/4/QtGui 0x1164cf000 - 0x11659ffef +QtOpenGL (4.7.4) <132C4069-CFF6-2DC4-C0FE-3A6E7121AD28> /Applications/freesurfer/Freeview.app/Contents/Frameworks/QtOpenGL.framework/Versions/4/QtOpenGL 0x1165cf000 - 0x11664afd7 +libstdc++.6.dylib (7.20) <45707038-B56E-375D-A43A-53DB80CDAFAD> /Applications/freesurfer/Freeview.app/Contents/Frameworks/libstdc++.6.dylib 0x1166cc000 - 0x1166dbfe7 +libgcc_s.1.dylib (1) <327095EF-0073-34FF-9EB4-9033971EDC74> /Applications/freesurfer/Freeview.app/Contents/Frameworks/libgcc_s.1.dylib 0x118096000 - 0x118139ff7 ColorSyncDeprecated.dylib (502.2) <FDB3BCCA-7C71-3DAA-9AB2-528E0CC60616> 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/Applications/freesurfer/Freeview.app/Contents/PlugIns/imageformats/libqtiff.dylib 0x119f4b000 - 0x11a0f1fff GLEngine (14.0.16) <E67A2652-EEBB-38BF-9FF2-6C64ED0ABA9B> /System/Library/Frameworks/OpenGL.framework/Resources/GLEngine.bundle/GLEngine 0x11a130000 - 0x11a67fff7 com.apple.driver.AppleIntelBDWGraphicsGLDriver (10.24.45 - 10.2.4) <0DF3C2D6-C8B7-3B99-84DF-D0339ECAD006> /System/Library/Extensions/AppleIntelBDWGraphicsGLDriver.bundle/Contents/MacOS/AppleIntelBDWGraphicsGLDriver 0x11a89d000 - 0x11a8c7fff GLRendererFloat (14.0.16) <768ADC3B-C0E6-3936-801C-35990D62CAE7> /System/Library/Frameworks/OpenGL.framework/Resources/GLRendererFloat.bundle/GLRendererFloat 0x11de8d000 - 0x11df0cfff com.apple.driver.AppleIntelBDWGraphicsMTLDriver (10.24.45 - 10.2.4) <445AA610-11DF-3FA7-A535-189FE60E3D7B> /System/Library/Extensions/AppleIntelBDWGraphicsMTLDriver.bundle/Contents/MacOS/AppleIntelBDWGraphicsMTLDriver 0x11fc27000 - 0x11fc28ff1 +cl_kernels (???) <D020EA37-E023-4AAE-B6A5-BDA701B4D575> cl_kernels 0x11fc2b000 - 0x11fd11fff unorm8_bgra.dylib (2.8.5) <BC3B5906-663C-306B-8E2E-9C2B7720161D> /System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries/ImageFormats/unorm8_bgra.dylib 0x7fffd08c9000 - 0x7fffd0c0efff com.apple.RawCamera.bundle (7.02 - 899) <EB92C4A8-6A1D-349A-8107-59B265512B2A> /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera 0x7fffd2440000 - 0x7fffd2444ffb com.apple.agl (3.3.1 - AGL-3.3.1) <EEB77D74-9B6B-331F-B103-5A62A029BCE2> /System/Library/Frameworks/AGL.framework/Versions/A/AGL 0x7fffd2774000 - 0x7fffd2774fff com.apple.Accelerate (1.11 - Accelerate 1.11) <E559CE70-1A9A-3C5C-9FB7-C51FDF82F03C> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate 0x7fffd2775000 - 0x7fffd278cffb libCGInterfaces.dylib (331.5) <E0CA9D83-7F26-3D65-9249-F9231C1CB7DB> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib 0x7fffd278d000 - 0x7fffd2ca6feb 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/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLinearAlgebra.dylib 0x7fffd323c000 - 0x7fffd3242fff libQuadrature.dylib (3) <EF56C8E6-DE22-3C69-B543-A8648F335FDD> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libQuadrature.dylib 0x7fffd3243000 - 0x7fffd3257ff7 libSparseBLAS.dylib (1185.50.4) <67BA432E-FB59-3C78-A8BE-ED4274CBC359> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparseBLAS.dylib 0x7fffd3258000 - 0x7fffd33dffe7 libvDSP.dylib (600) <02EC87E3-EA41-36DF-8696-B84E7551168E> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib 0x7fffd33e0000 - 0x7fffd3492ffb libvMisc.dylib (600) <1093AAB8-090A-3A6C-9E52-583B081079D2> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib 0x7fffd3493000 - 0x7fffd3493fff 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0x7fffeb433ff7 libsystem_blocks.dylib (67) <10DC5404-73AB-35B3-A277-A8AFECB476EB> /usr/lib/system/libsystem_blocks.dylib 0x7fffeb434000 - 0x7fffeb4c1fef libsystem_c.dylib (1158.50.2) <B03F8915-1E9B-3C84-AED5-68E2E0031630> /usr/lib/system/libsystem_c.dylib 0x7fffeb4c2000 - 0x7fffeb4c5ffb libsystem_configuration.dylib (888.51.2) <872C8A42-0871-3424-830B-84E587A75D27> /usr/lib/system/libsystem_configuration.dylib 0x7fffeb4c6000 - 0x7fffeb4c9fff libsystem_coreservices.dylib (41.4) <FD0915E8-9C43-3FCB-94E0-33C45DF028CD> /usr/lib/system/libsystem_coreservices.dylib 0x7fffeb4ca000 - 0x7fffeb4e2fff libsystem_coretls.dylib (121.50.4) <EC6FCF07-DCFB-3A03-9CC9-6DD3709974C6> /usr/lib/system/libsystem_coretls.dylib 0x7fffeb4e3000 - 0x7fffeb4e9fff libsystem_dnssd.dylib (765.50.9) <FF02A197-7CEF-3684-8155-E5E225051E44> /usr/lib/system/libsystem_dnssd.dylib 0x7fffeb4ea000 - 0x7fffeb513ff7 libsystem_info.dylib (503.50.4) <611DB84C-BF70-3F92-8702-B9F28A900920> /usr/lib/system/libsystem_info.dylib 0x7fffeb514000 - 0x7fffeb536ff7 libsystem_kernel.dylib (3789.51.2) <FC51D7B0-8292-3F6A-9231-64340B237EB7> /usr/lib/system/libsystem_kernel.dylib 0x7fffeb537000 - 0x7fffeb57efe7 libsystem_m.dylib (3121.6) <A790C9A5-DD24-32F5-8FD7-33BFCE79AC87> /usr/lib/system/libsystem_m.dylib 0x7fffeb57f000 - 0x7fffeb59dff7 libsystem_malloc.dylib (116.50.8) <48D1BBA3-914E-3C65-AF70-C33B4A1B5233> /usr/lib/system/libsystem_malloc.dylib 0x7fffeb59e000 - 0x7fffeb5f7ffb libsystem_network.dylib (856.50.56) <FDE14243-4328-3EFD-824C-C0D314D7B540> /usr/lib/system/libsystem_network.dylib 0x7fffeb5f8000 - 0x7fffeb601ff3 libsystem_networkextension.dylib (563.50.32) <D5381DA9-529C-3588-BE16-A2245DE93423> /usr/lib/system/libsystem_networkextension.dylib 0x7fffeb602000 - 0x7fffeb60bff3 libsystem_notify.dylib (165.20.1) <B8160190-A069-3B3A-BDF6-2AA408221FAE> /usr/lib/system/libsystem_notify.dylib 0x7fffeb60c000 - 0x7fffeb614fe7 libsystem_platform.dylib (126.50.8) <5940EAB7-84D6-34DC-9B38-111648B2B589> 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/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: 1454 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=310.6M resident=0K(0%) swapped_out_or_unallocated=310.6M(100%) Writable regions: Total=409.5M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=409.5M(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= ATS (font support) 32.0M 7 ATS (font support) (reserved) 4K 2 reserved VM address space (unallocated) Accelerate framework 384K 4 Activity Tracing 256K 2 CG backing stores 6812K 5 CG image 196K 20 CoreUI image data 1156K 8 CoreUI image file 176K 4 Kernel Alloc Once 8K 2 MALLOC 110.6M 52 MALLOC guard page 48K 11 Memory Tag 242 12K 2 OpenCL 16K 3 STACK GUARD 56.0M 9 Stack 11.6M 9 VM_ALLOCATE 88K 17 __DATA 254.5M 263 __GLSLBUILTINS 2588K 2 __IMAGE 528K 2 __LINKEDIT 126.5M 24 __TEXT 184.1M 257 __UNICODE 556K 2 mapped file 47.0M 17 shared memory 16.4M 16 =========== ======= ======= TOTAL 851.2M 716 TOTAL, minus reserved VM space 851.2M 716 Model: MacBookPro12,1, BootROM MBP121.0167.B24, 2 processors, Intel Core i5, 2.7 GHz, 8 GB, SMC 2.28f7 Graphics: Intel Iris Graphics 6100, Intel Iris Graphics 6100, Built-In Memory Module: BANK 0/DIMM0, 4 GB, DDR3, 1867 MHz, 0x80AD, 0x483943434E4E4E424C54414C41522D4E5544 Memory Module: BANK 1/DIMM0, 4 GB, DDR3, 1867 MHz, 0x80AD, 0x483943434E4E4E424C54414C41522D4E5544 AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x133), Broadcom BCM43xx 1.0 (7.21.171.124.1a2) Bluetooth: Version 5.0.4f18, 3 services, 27 devices, 1 incoming serial ports Network Service: Wi-Fi, AirPort, en0 Serial ATA Device: APPLE SSD SM0256G, 251 GB USB Device: USB 3.0 Bus USB Device: BUP Slim WH USB Device: Bluetooth USB Host Controller Thunderbolt Bus: MacBook Pro, Apple Inc., 27.1

3 3

mri_convert: the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks?
by Maria Hakonen 25 Apr '17

25 Apr '17

Dear Freesurfer experts, Could someone please let me know what is the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks of mri_covert? >From the internet and by typing mri_convert on the command line I only managed to find the following information: -iis, --in_i_size <size> -ijs, --in_j_size <size> -iks, --in_k_size <size> -iid, --in_i_direction <R direction> <A direction> <S direction> -ijd, --in_j_direction <R direction> <A direction> <S direction> -ikd, --in_k_direction <R direction> <A direction> <S direction> However, I don't still understand what is the effect of those argumnents in the following command: mri_convert gre_000.bfloat data.mgh -iid 1 0 0 -ijd 0 -1 0 -ikd 0 0 1 -iis 5 -ijs 5 -iks 5 Are the arguments describing the direction and voxelsize of .bfloat? Best, Maria

2 2

mri_cvs_register failure from missing shared lib
by Michael Waskom 25 Apr '17

25 Apr '17

Hi, I had mri_cvs_register die on me when it couldn't find a shared library. Relevant bit is (full log is attached): mris_resample: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory Freesurfer bugr info: -------------------- FREESURFER_HOME: /hsgs/software/freesurfer/5.3.0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: Red Hat Enterprise Linux Server release 6.3 (Santiago) Kernel info: Linux 2.6.32-358.6.2.el6.x86_64 x86_64 ---------------------- Any thoughts on how to proceed? Thanks! Michael

3 4

Relation between Segmentation Volumes and number of pixels in Aseg+aparc.mgz
by Gamaliz 25 Apr '17

25 Apr '17

I wrote an algorithm which uses the number of pixels per region in the aseg+aparc.mgz file. As this file has 1x1x1mm3 I was expecting the number of pixels to match very closely the value of the volume; as each pixel represents a 1 mm3 cube.(I did the same for cortical volume and got a similar result, with an even larger discrepancy). The aseg.stats file lists the nVoxel value, and it is basically the volume rounded up. here are some sample values for subcortical regions: Left-Lateral-Ventricle Volume (mm3): 7829.8 Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396 Left-Inf-Lat-Vent Volume (mm3):594 Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569 Left-Cerebellum-White-Matter Volume (mm3):12668 Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz):12203 Left-Cerebellum-Cortex Volume (mm3):44113.2 Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz): 43804 Left-Thalamus-Proper Volume (mm3):5752.8 Left-Thalamus-Proper(number of Pixels in aseg+aparc.mgz): 5899 Pretty much the values are close to the volume, but different enough to be significant. I wonder why this discrepancy.

2 5

Additional processing flags when using the longitudinal pipeline
by Gustav Mårtensson 25 Apr '17

25 Apr '17

Hi, I have a question regarding the longitudinal pipeline. We are following the workflow summary as outlined in https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing, essentially: 1. recon-all -all -s <tpNid> -i path_to_tpN_dcm 2. recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all 3. recon-all -long <tpNid> <templateid> -all We tend to run -all -mprage -qcache -hippocampal-subfields-T1 -brainstem-structures in our cross-sectional process. Should we use all (or part of) these options for step 2 and 3? We are running on Ubuntu 16.04 LTS with FS version freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. Thank you for your help! Gustav Mårtensson -- Gustav Mårtensson | PhD student Division of Clinical Geriatrics Department of Neurobiology, Care Sciences and Society Karolinska Institutet ___________________________________ Karolinska Institutet – a medical university

2 1

summary 500 samples FS results
by shi yao wang 24 Apr '17

24 Apr '17

Dear FS expert, We have running around 500 samples by FS. I am wondering if there are easy way to summary these data. i.e., generate mean of cortical thickness. thanks Shiyao

3 2

Re: [Freesurfer] volume in native space of .vtk file in mni152 space
by Antonin Skoch 24 Apr '17

24 Apr '17

Dear Corinna, I am not sure what is (or whether is) something wrong with your commands, but in any case I would be cautious of interpretation of results using such method, mainly from following reasons: 1. mni152reg uses 12 DOF whole-brain registration. You cannot expect to get perfect alignment of subcortical regions using such crude transform. To obtain more precise transform, I would use either registration targeted specifically to subcortical regions (e.g. using first_flirt in FSL, which is, however, still affine only), or use mri_cvs_register. 2. Due to no reasonable contrast within thalamus to allow to distinguish the nuclei using even state-of-the-art MR imaging, such registration-based atlas method would by necessity be a simple transfer of predefined atlas onto the subject space, with no information to guide the alignment within the thalamus itself (it would basically be a best-guiess of where these nuclei might be, with no scope for subject-specific refinement). Antonin Skoch Hi al, Just wondering if anyone has any suggestionsto my previous question as to why the volume from mni152 space would be rotated, even though the MNI152 to subject T1 alignment looks good? As a recap, here are my commands: mni152reg --s ${subject} --1 tkregister2 --mov ${subj_dir}/mri/mni152.orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz --reg ${reg_file} mri_vol2vol --mov ${subj_dir}/mri/orig.mgz --targ /home/Documents/thalamus/AtlasMNI152/left-vols-1mm/global.nii.gz --reg ${reg_file} --inv --o ${out_dir}/lh_global.nii.gz tkmedit -f subject/mri/orig.mgz -aux ${out_dir}/lh_global.nii.gz -ov ${out_dir}/lh_global.nii.gz -fminmax .5 1

2 1

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Freesurfer April 2017