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License Registration Error "Spammer, go away!"
by Peng Wang 14 Feb '19

14 Feb '19

External Email - Use Caution Please help! Repost with a better title.

3 3

-so unknown in mri_surf2vol?
by Boris Rauchmann 14 Feb '19

14 Feb '19

External Email - Use Caution My_pc$ mri_surf2vol --o 0021_thickness-in-volume.nii.gz --subject 0021 \ --so $SUBJECTS_DIR/0021/surf/lh.white $SUBJECTS_DIR/0021/surf/lh.thickness \ --so $SUBJECTS_DIR/0021/surf/rh.white $SUBJECTS_DIR/0021/surf/rh.thickness ERROR: Option --so unknown Why it returns that —so is unknown? Exactly this line is given as an example on: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol#ArgumentsforBothMeth… <https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol#ArgumentsforBothMeth…> Thanks, Boirs

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Unexpected termination of freeviewer
by Lykke Silfwerbrand 14 Feb '19

14 Feb '19

External Email - Use Caution Hi, I used freeviewer a few weeks ago without any problems, but now that I want to continue my analysis it terminates as a try to load a volume or a surface. (same computer, same setting) I have tried the “sudo -E fs_update” and to disable SIP, freeviewer still terminates the same way with the same error message, see below. Any help is much appreciated! Lykke PhD candidate Neuro Science Uppsala University Process: Freeview [1713] Path: /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview Identifier: com.yourcompany.Freeview Version: ??? Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: Freeview [1713] User ID: 271794372 Date/Time: 2019-02-14 16:48:18.395 +0100 OS Version: Mac OS X 10.14.3 (18D109) Report Version: 12 Bridge OS Version: 3.0 (14Y674) Anonymous UUID: A7073C18-5895-3A14-4551-409200FFED72 Time Awake Since Boot: 2500 seconds System Integrity Protection: disabled Crashed Thread: 9 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 libobjc.A.dylib 0x00007fff6605e681 search_method_list(method_list_t const*, objc_selector*) + 78 1 libobjc.A.dylib 0x00007fff6605e614 getMethodNoSuper_nolock(objc_class*, objc_selector*) + 98 2 libobjc.A.dylib 0x00007fff66060a73 lookUpImpOrForward + 328 3 libobjc.A.dylib 0x00007fff66060494 _objc_msgSend_uncached + 68 4 com.apple.AppKit 0x00007fff3747e426 -[NSView(NSInternal) _allocAuxiliary] + 227 5 com.apple.AppKit 0x00007fff374b241c -[NSView initWithFrame:] + 36 6 com.apple.AppKit 0x00007fff374bd14f -[NSNextStepFrame initWithFrame:styleMask:owner:] + 74 7 com.apple.AppKit 0x00007fff374bb709 -[NSWindow _commonInitFrame:styleMask:backing:defer:] + 610 8 com.apple.AppKit 0x00007fff374baf5e -[NSWindow _initContent:styleMask:backing:defer:contentView:] + 1202 9 com.apple.AppKit 0x00007fff374baaa6 -[NSWindow initWithContentRect:styleMask:backing:defer:] + 45 10 QtGui 0x0000000120ba003f QMacInputContext::reset() + 30319 11 QtGui 0x0000000120b9fedc QMacInputContext::reset() + 29964 12 QtGui 0x0000000120b9289a QWidgetPrivate::setWindowLevel() + 810 13 QtGui 0x0000000120b8ffb1 QWidgetPrivate::createWindow_sys() + 145 14 QtGui 0x0000000120b900bf qt_mac_window_for(QWidget const*) + 159 15 QtGui 0x0000000120b923b1 QWidgetPrivate::setModal_sys() + 145 16 QtGui 0x0000000120c4b698 QWidget::create(long, bool, bool) + 360 17 QtGui 0x0000000120c4c909 QWidget::setVisible(bool) + 121 18 com.yourcompany.Freeview 0x000000010fe7241c FloatingStatusBar::ShowProgress() + 60 19 com.yourcompany.Freeview 0x000000010fe26aab FloatingStatusBar::qt_metacall(QMetaObject::Call, int, void**) + 251 20 QtCore 0x00000001208ede99 QObject::event(QEvent*) + 1081 21 QtGui 0x0000000120c4d83e QWidget::event(QEvent*) + 78 22 QtGui 0x0000000120bf315d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 189 23 QtGui 0x0000000120bf918d QApplication::notify(QObject*, QEvent*) + 349 24 QtCore 0x00000001207f34dc QCoreApplication::notifyInternal(QObject*, QEvent*) + 124 25 QtCore 0x00000001208e10cb QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 731 26 com.apple.CoreFoundation 0x00007fff39f08395 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 27 com.apple.CoreFoundation 0x00007fff39f0833b __CFRunLoopDoSource0 + 108 28 com.apple.CoreFoundation 0x00007fff39eebdd1 __CFRunLoopDoSources0 + 195 29 com.apple.CoreFoundation 0x00007fff39eeb37a __CFRunLoopRun + 1219 30 com.apple.CoreFoundation 0x00007fff39eeac64 CFRunLoopRunSpecific + 463 31 com.apple.HIToolbox 0x00007fff39181ab5 RunCurrentEventLoopInMode + 293 32 com.apple.HIToolbox 0x00007fff391817eb ReceiveNextEventCommon + 618 33 com.apple.HIToolbox 0x00007fff39181568 _BlockUntilNextEventMatchingListInModeWithFilter + 64 34 com.apple.AppKit 0x00007fff3743c363 _DPSNextEvent + 997 35 com.apple.AppKit 0x00007fff3743b102 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1362 36 com.apple.AppKit 0x00007fff37435165 -[NSApplication run] + 699 37 QtGui 0x0000000120bae174 QDesktopWidget::resizeEvent(QResizeEvent*) + 12724 38 QtCore 0x00000001208dfa34 QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 68 39 QtCore 0x00000001208dfd54 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 180 40 QtCore 0x00000001208e137c QCoreApplication::exec() + 188 41 com.yourcompany.Freeview 0x000000010ff03f58 main + 6232 42 com.yourcompany.Freeview 0x000000010fe24974 start + 52 Thread 1: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796 Thread 2: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796 Thread 3: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796 Thread 4: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796 Thread 5:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x00007fff6727617a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff672766d0 mach_msg + 60 2 com.apple.CoreFoundation 0x00007fff39eebfde __CFRunLoopServiceMachPort + 337 3 com.apple.CoreFoundation 0x00007fff39eeb52d __CFRunLoopRun + 1654 4 com.apple.CoreFoundation 0x00007fff39eeac64 CFRunLoopRunSpecific + 463 5 com.apple.AppKit 0x00007fff37444f89 _NSEventThread + 160 6 libsystem_pthread.dylib 0x00007fff67330305 _pthread_body + 126 7 libsystem_pthread.dylib 0x00007fff6733326f _pthread_start + 70 8 libsystem_pthread.dylib 0x00007fff6732f415 thread_start + 13 Thread 6: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796 Thread 7: 0 libsystem_pthread.dylib 0x00007fff6732f3f8 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796 Thread 8:: CVDisplayLink 0 libsystem_kernel.dylib 0x00007fff672797de __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff67333593 _pthread_cond_wait + 724 2 com.apple.CoreVideo 0x00007fff3bd2be90 CVDisplayLink::runIOThread() + 722 3 libsystem_pthread.dylib 0x00007fff67330305 _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff6733326f _pthread_start + 70 5 libsystem_pthread.dylib 0x00007fff6732f415 thread_start + 13 Thread 9 Crashed: 0 dyld 0x0000000128c4e456 __abort_with_payload + 10 1 dyld 0x0000000128c4dc4d abort_with_payload_wrapper_internal + 82 2 dyld 0x0000000128c4dc7f abort_with_payload + 9 3 dyld 0x0000000128c0baea dyld::halt(char const*) + 343 4 dyld 0x0000000128c0bc17 dyld::fastBindLazySymbol(ImageLoader**, unsigned long) + 170 5 libdyld.dylib 0x00007fff67128c1a dyld_stub_binder + 282 6 ??? 0x00000001204dd018 0 + 4836937752 7 com.yourcompany.Freeview 0x000000010fead0df LayerMRI::LoadVolumeFromFile() + 399 8 com.yourcompany.Freeview 0x000000010ff79ea1 ThreadIOWorker::run() + 1361 9 QtCore 0x00000001208275b5 QThread::setPriority(QThread::Priority) + 469 10 libsystem_pthread.dylib 0x00007fff67330305 _pthread_body + 126 11 libsystem_pthread.dylib 0x00007fff6733326f _pthread_start + 70 12 libsystem_pthread.dylib 0x00007fff6732f415 thread_start + 13 Thread 9 crashed with X86 Thread State (64-bit): rax: 0x0000000002000209 rbx: 0x0000000000000000 rcx: 0x000070000787ea48 rdx: 0x000070000787eeb0 rdi: 0x0000000000000006 rsi: 0x0000000000000004 rbp: 0x000070000787ea90 rsp: 0x000070000787ea48 r8: 0x000070000787eab0 r9: 0x0000000000000000 r10: 0x0000000000000098 r11: 0x0000000000000246 r12: 0x0000000000000098 r13: 0x000070000787eeb0 r14: 0x0000000000000004 r15: 0x0000000000000006 rip: 0x0000000128c4e456 rfl: 0x0000000000000246 cr2: 0x000000012519c000 Logical CPU: 0 Error Code: 0x02000209 Trap Number: 133 ----- När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Submission deadline for #BrainTC extended
by Kivisaari Sasa 14 Feb '19

14 Feb '19

External Email - Use Caution Dear colleagues, the deadline for submitting abstracts to the 3rd annual Brain Twitter Conference has been extended - the new deadline is 20th February. The line-up of keynotes is now: prof. Jay van Bavel, New York University (social neuroscience) prof Paul Thompson, University of Southern California (connectivity / ENIGMA project) prof. Russ Poldrack, Stanford University (reproducible neuroscience) prof. Alice Proverbio, University Milano-Bicocca (emotions, neuroaesthetics) prof. Stephani Jones, Brown University (brain network dynamics) In previous years, the conference has had a potential reach of hunderds of thousands of Twitter users, and is a great event to present your research internationally, both for fellow neuroscientists, but with the general public able to see the debates. The conference takes place at #brainTC in Twitter on 14th March, and it is part of the international Brain Awareness Week. Follow @RealBrainTC for updates and submit your abstract at http://brain.tc . on behalf of the organising team, Sasa Kivisaari

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Re: [Freesurfer] dt_recon issue
by fsbuild 13 Feb '19

13 Feb '19

External Email - Use Caution Hello Daniel. It looks like you need a slash in front of Volumes for the path after —I/Volumes - R. On Feb 13, 2019, at 14:44, Daniel Davidson Callow <dcallow(a)umd.edu> wrote:        External Email - Use Caution        Hello,I am trying to run dt_recon on my dti data using the following script.dt_recon --debug --i Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtreconwith the following errorecho "ERROR: cannot find $InputVol"echo ERROR: cannot find Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcmERROR: cannot find Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcmgoto error_exit ;the DICOM files are named image000001.dcm through image000065.dcmThese were 64 gradient images acquired on a SIEMENS scanner with 1 bo image. Any advice on how I should structure this command would be greatly appreciated!Daniel CallowPhD Student, Neuroscience and Cognitive ScienceExercise for Brain Health LabUniversity of Maryland, College Parkdcallow@umd.edu443-254-6298_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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dt_recon issue
by Daniel Davidson Callow 13 Feb '19

13 Feb '19

External Email - Use Caution Hello, I am trying to run dt_recon on my dti data using the following script. dt_recon --debug --i Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon with the following error echo "ERROR: cannot find $InputVol" echo ERROR: cannot find Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm ERROR: cannot find Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm goto error_exit ; the DICOM files are named image000001.dcm through image000065.dcm These were 64 gradient images acquired on a SIEMENS scanner with 1 bo image. Any advice on how I should structure this command would be greatly appreciated! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow(a)umd.edu <dcallow(a)gmail.com> 443-254-6298

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Registrations with freesurfer voxel space and posterior map of thalamic nuclei segmentation results
by Sherry Shen 13 Feb '19

13 Feb '19

External Email - Use Caution Hello Freesurfer Developers, I got the posterior map of thalamic nuclei segmentation by setting the environment parameter: export WRITE_POSTERIORS=1 I found the posterior map is of different dimension. In my case, posterior map is of [173, 117,116] dimension with 0.5mm voxel resolution. However, the segmentation label ThalamicNuclei.v10.T1 is of [187,117,112] 0.5mm and ThalamicNuclei.v10.T1.FSvoxelSpace is of [256,256,256] 1mm. How can I align posterior map with the other two? Thank you, Sherry

1 0

FreeSurfer Registration Error
by Peng Wang 13 Feb '19

13 Feb '19

External Email - Use Caution Whatever I filled the form I got "Spammer. Go away!" message. Please help!

2 2

Re: [Freesurfer] problem using recon-all
by Shachar Gal 13 Feb '19

13 Feb '19

External Email - Use Caution Hey Tim, I tried to run the “-E fs_update”, and got this message: rsync -zbrlv --progress --suffix=.1550066275_bak rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-D… /Applications/freesurfer receiving file list ... rsync: change_dir "/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in pub) failed: No such file or directory (2) 0 files to consider sent 4 bytes received 9 bytes 8.67 bytes/sec total size is 0 speedup is 0.00 rsync error: some files could not be transferred (code 23) at /BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-52.200.1/rsync/main.c(1404) [receiver=2.6.9] Does the indicate I should disable SIP, or is it a different issue? Thanks, Shachar

2 2

Different aseg and aparc stats with Freesurfer 5.3 and 6.0
by Ranila Bhoyroo 13 Feb '19

13 Feb '19

External Email - Use Caution Hello Experts, I was working with some data pre-processed using freesurfer v5.3 - i think this was done on linux. Recently I pre-processed the dataset using v6.0 on an imac. I extracted cortical thickness and surface area from both hemispheres. The data is different for each version. What worries me is that I am correlating the neural metrics with some behavioral data and this gives me different results. My sample size is only 20. Some advice would be very helpful. Thanks. Cheers, *Ranila *

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