Freesurfer

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30132 discussions

talairach.m3z question
by Tim Schäfer 14 Feb '19

14 Feb '19

External Email - Use Caution Dear FreeSurfer experts, I have 2 questions on the talairach.m3z file generated by recon-all. 1) What exactly does it contain? I read its the displacement field for a non-linear transform from native space to some freesurfer space. But from which input file (or space) to which other one does it transform? 2) What's the file format? Is there a spec somewhere? Thanks, -- Tim

3 2

GLM - correction for multiple comparisons
by Barletta, Valeria 14 Feb '19

14 Feb '19

Dear Freesurfers, I am performing a GLM analysis on two groups (patients versus controls) and one variable (age). We are using the following option to correct for multiple comparisons: mri_glmfit-sim --glmdir ${glm_dir}/${hemi}_contrast-${contrast}_${surfname_t1} --cache 1.3 pos/abs Is it normal to have those 2 different results when using pos or abs option? (see screenshots) Thank you! Vale

2 2

Re: [Freesurfer] Task Design Question
by Rockhill, Alexander P. 14 Feb '19

14 Feb '19

Hello Freesurfer experts, I am working on designing a task using opt seq to determine the optimal ITI and I had a question about task timing. Does it matter if the stimulus period during a task starts at the start of a TR or that the stimulus presentation lasts uninterrupted an amount of time that is an integer multiple the TR? Thanks in advance for any help. Best, Alex Translational NeuroEngineering Laboratory Division of Neurotherapeutics, Department of Psychiatry Massachusetts General Hospital, Martinos Center 149 13th St Charlestown #2301, Boston, MA 02129

2 1

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

2 1

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. 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1 0

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

1 0

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

1 0

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

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