Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30091 discussions

Error when transforming aal.nii to lh.aal.label
by haidong wang 27 Apr '17

27 Apr '17

Hello FS experts, I want to get the thickness of 90 ROIs of AAL using freesurfer. I use the following commands to transform aal.nii to lh.aal.label. 1.bbregister --s sub_con_sub01 --mov ch2.nii --t1 --init-fsl --reg register_vol2surf.dat 2.mri_vol2surf --mov aal.nii --reg register_vol2surf.dat --hemi lh --out_type mgh --o lh.aal.mgh --interp nearest 3.mri_cor2label --i lh.aal.mgh --id 1 --l ./lh.aal.label --surf sub_con_sub01 4.mri_label2label --srclabel lh.aal.label --srcsubject fsaverage --trgsubject sub_con_sub01 --trglabel lh.aal.label --regmethod surface --hemi lh 5.mris_anatomical_stats -l lh.aal.label -t lh.thickness -b -f sub_con_sub01/stats/lh.aal.stats sub_con_sub01 lh 6.aparcstats2table --hemi lh --subjects sub_con_sub01 --parc aal --meas thickness -t ./aal_thickness.txt The result is that there is no measurement in the produced document named lh.aal.stats. I am also confused about how to set id in mri_cor2label.Could you please give me some suggestions? I am looking forwad for your prompt reply. Yours, Haidong The attachment is the screenshot of my working directory. Here is the error: mri_cor2label --i lh.aal.mgh --id 1 --l ./lh.aal.label --surf sub_con_sub01 $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri lh.aal.mgh ------- Vox2RAS of input volume ----------- -1.000 0.000 0.000 75659.000; 0.000 0.000 1.000 -0.500; 0.000 -1.000 0.000 0.500; 0.000 0.000 0.000 1.000; Scanning the volume Found 6451 label voxels Writing label file ./lh.aal.label LabelWrite: saving to ./lh.aal.label Centroid: -9707.33 -0.50 0.50 mri_cor2label completed SUCCESSFULLY admi@admi:~/Desktop/freesurfer_thickness$ mri_label2label --srclabel lh.aal.label --srcsubject fsaverage --trgsubject sub_con_sub01 --trglabel lh.aal.label --regmethod surface --hemi lh srclabel = lh.aal.label srcsubject = fsaverage trgsubject = sub_con_sub01 trglabel = lh.aal.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/admi/Desktop/freesurfer_thickness FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6451 points in source label. Starting surface-based mapping Reading source registration /home/admi/Desktop/freesurfer_thickness/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/admi/Desktop/freesurfer_thickness/sub_con_sub01/surf/lh.white Reading target registration /home/admi/Desktop/freesurfer_thickness/sub_con_sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). ERROR: there is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres or the surface has been changed since the label was created. Label point 0: vno = -1, max = 163842

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NEW ANIMAL MODELS TO UNDERSTAND THE BRAIN symposium - 15th May 2017 - Nouzilly, Loire Valley, France
by Frederic Andersson 27 Apr '17

27 Apr '17

We are pleased to announce the 2nd edition of the NAMUB workshop (NEW ANIMAL MODELS TO UNDERSTAND THE BRAIN) in Nouzilly, Loire Valley, France, 2017 15th may. This symposium will present new insights on neurophysiology and in vivo neuroimaging in sheep and pigs. These animals present serious advantages compared to rodents, because in addition to their larger size, their brain is gyrencephalic. Therefore, sheep and pigs are interesting alternative to non-human primates, even more with in vivo imaging tools that are now available to investigate such large animals. By this way, it is possible to perform longitudinal studies to investigate the impact of environment on brain development, these animal models offering new ways for preclinical and therapeutic investigations. The aim of this symposium is to demonstrate how these animals are suitable experimental models to perform preclinical studies in alternative to non-human primates. Parkinson disease, stroke and brain development will be illustrated. Organization Committee Elodie Chaillou (Physiologie de la Reproduction et des Comportements, UMR Inra-CNRS-Université François-Rabelais Tours), Frédéric Andersson (Imagerie et Cerveau, UMR Inserm U930 - Université François-Rabelais Tours), Martine Migaud (Physiologie de la Reproduction et des Comportements, UMR Inra-CNRS-Université François-Rabelais Tours), Yves Tillet (Physiologie de la Reproduction et des Comportements, UMR Inra-CNRS-Université François-Rabelais Tours). Contact and information : elodie.chaillou(a)inra.fr Download the poster [PDF - 594 Ko] <http://sfrneuroimagerie.univ-tours.fr/medias/fichier/affiche-15mai-2017_149…> http://sfrneuroimagerie.univ-tours.fr/fonctionnement/new-animal-models-to-u… <http://sfrneuroimagerie.univ-tours.fr/fonctionnement/new-animal-models-to-u…> PRELIMINARY PROGRAMME: 8:45 - Coffee 9:15 - Introduction of the meeting. E. Chaillou (INRA - Physiologie de la Reproduction et des Comportements, Nouzilly) Session 1 – Diffusion MRI. F. Andersson (INSERM Imagerie et Cerveau, Tours) 9:35 - Diffusion MRI. T. Dyrby (DIG, Copenhagen - Denmark) 10:10 - Impact of early rearing experience on brain development in sheep infant. E. Chaillou (INRA - Physiologie de la Reproduction et des Comportements, Nouzilly, France) 10:45 - Sheep brain connectivity. C. Poupon (NeuroSpin, CEA Saclay, France) 11:15 - Coffee Session 2 – Technical developments H. Adriaensen (INRA - Physiologie de la Reproduction et des Comportements, Nouzilly, France) 11:40 - Use of MPIOs as a contrast agent in sheep. L. Butruille (INRA - Physiologie de la Reproduction et des Comportements, Nouzilly, France) 12:05 - Adenoassociated virus vector for brain manipulations. D. Zelena (Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary) 12:30 - Segmentation of sheep brain images using local probabilistic atlases coupled with topological information G. Galisot (Laboratoire d’Informatique, Université François Rabelais de Tours) 12:55 - Virtual slides for big brain : Services and system. B. Damart (Excilone® Elancourt France) 13:05 - Stereotactic neurosurgery based on 3D imagery (m2e, Inomed, Inra, Inserm). C. Destrieux (INSERM, Imagerie et Cerveau, Tours, France) 13:15 - Lunch Session 3 – Model of neurological troubles 14:35 - Sheep, a model for Batten disease; J. Morton (Department of Physiology, Development and Neuroscience, Cambridge, United Kingdom) 15:10 - Sheep, a model for neurovascular pathology; B. Nitzsche (Fraunhofer Institute, Leipzig Germany). Session 4 – Brain anatomy Y .Tillet (INRA - Physiologie de la Reproduction et des Comportements, Nouzilly, France) 15:45 - The Göttingen minipig telencephalon. C. Bjarkam (Department of neurobiology, University of Aarhus, Denmark) 16:20 - Atlas of the sheep cortex. S. Love (INSERM, Imagerie et Cerveau, Tours, France) Conclusion 16:45 - M. Migaud (INRA - Physiologie de la Reproduction et des Comportements, Nouzilly, France) Regards,

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Interaction effects in QDEC
by Heidi Foo 26 Apr '17

26 Apr '17

Hi all, I was wondering how I could test for interaction effects between a categorical variable and a continuous variable using QDEC. Is there a way to do so? Thank you. Best Regards, Heidi Foo

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Extract time courses corresponding to a brain structure from an stc file
by Maria Hakonen 26 Apr '17

26 Apr '17

Dear Freesurfer experts, I would like to extract time courses of certain brain structures from the stc file in Matlab. Could someone please let me know how I can determine the lables of 10242 verices of my stc file? Or is there some matlab function that gives the time course of a barin structure. Best, Maria

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fs6.0 mri_surf2surf failure
by Dongnandi 26 Apr '17

26 Apr '17

Dear FS experts, I'm trying to transform some files from fsaverage space to fsaverage5 space using mri_surf2surf(fs version: 6.0), however, it is weird that the results turn out to be all zeros on the fsaverage5 surface, the command line I used if : mri_surf2surf -srcsubject fsaverage -sval ${hemi}.fsaverage.nii.gz -hemi ${hemi} --cortex -trgsubject fsaverage5 -tval ${hemi}.fsaverage5.nii.gz -surfreg sphere.reg. There is no error reported. The strange thing is that it works well using FS5.3, it failed after I update to FS 6.0. Any suggestion of solving this? Many thanks! Best! Dong

3 2

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

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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

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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) 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/usr/lib/system/libsystem_platform.dylib 0x7fffeb615000 - 0x7fffeb61fff7 libsystem_pthread.dylib (218.51.1) <62A84A68-431D-3B54-A7B6-31367CCF2884> /usr/lib/system/libsystem_pthread.dylib 0x7fffeb620000 - 0x7fffeb623ff7 libsystem_sandbox.dylib (592.50.47) <87A2327D-B7A1-3E4C-A85D-D3D9484003DB> /usr/lib/system/libsystem_sandbox.dylib 0x7fffeb624000 - 0x7fffeb625ff3 libsystem_secinit.dylib (24.50.4) <F78B847B-3565-3E4B-98A6-F7AD40392E2D> /usr/lib/system/libsystem_secinit.dylib 0x7fffeb626000 - 0x7fffeb62dffb libsystem_symptoms.dylib (532.50.47) <9CF6A47C-8343-3E85-9C27-A8D98E726A8B> /usr/lib/system/libsystem_symptoms.dylib 0x7fffeb62e000 - 0x7fffeb641ff7 libsystem_trace.dylib (518.51.1) <E1D540D8-CC88-3901-92BA-FC4B802FE0E8> /usr/lib/system/libsystem_trace.dylib 0x7fffeb642000 - 0x7fffeb647ffb libunwind.dylib (35.3) <3D50D8A8-C460-334D-A519-2DA841102C6B> /usr/lib/system/libunwind.dylib 0x7fffeb648000 - 0x7fffeb671ff7 libxpc.dylib (972.50.27) <ABC45890-DA23-3A4A-B50B-1384BD4CBBDF> /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

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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

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