Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

my email
by giuseppe messina 06 Mar '22

06 Mar '22

External Email - Use Caution hi my email is : giusmex(a)gmail.com thanx -- Giuseppe Messina Dept Neurosurgery Istituto Nazionale Neurologico "Carlo Besta", Milan E-mail giusmex(a)gmail.com

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Update on freeview error with M1 Macs running Monterey (MacOS 12.X)
by fsbuild 05 Mar '22

05 Mar '22

External Email - Use Caution Please check you have your freesurfer license file in a readable location, e.g., you can set the environment variable FS_LICENSE to point to the file license.txt in your home directory.  … in bash or zsh ...$ export FS_LICENSE=$HOME/license.txt… in csh or tcsh ...% setenv FS_LICENSE $HOME/license.txt The current development build of freesurfer now uses a newer version of the Qt distribution compared to the previous 7.2.0 and 7.1.1 releases.  You could try the development build to see if it remedies display issues with freeview on M1 Macs.. The package file  https://secure-web.cisco.com/1ZzEv2RHt0Q6Zowkpf2ipMDHM24zsuJwEJaPkN-sAc1WrZLf0pHDqrMdfHcwcLbdayl4GwciE3HSVe9hZ6mQiXeANHJpN--83bnCvOT7FTKOVmKgEurvQhXDpV-HLpvi7cy9mqEjbrM_QHH5YwMG_kxPyC9lM2wEFIgANTUhY1D78ULhUW3dmG3TLjm4OaYuVYHGjqEmJJD_VxOFIwA4suAJnq9KJ64uV-EQLOjZKIuS8imnZQmL6K9nd3ryadadTMaMdl7M87vojtuhub2Ub-P89vwRo_F2-DW6q4B4nhD_xSFSIMLZobD_0n84OPzF96jmVgKgNPDtsVf8YOoMydQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-darwin-macOS-dev.pkg%26nbsp; will install the development freesurfer distribution as /Applications/freesurfer/dev.  It will not interfere with or clobber your pre-exiting freesurfer 7.X X distributions installed as /Applications/freesurfer/{7.2.0, 7.1.1}. To switch to running the development build, (re)set FREESURFER_HOME in a new terminal window to /Applications/freesurfer/dev and then source the usual script to setup the freesurfer environment, e.g., source $FREESURFER_HOME/{SetUpFreeSurfer.sh, SetUpFreeSurfer.csh} I’ve tested running the freesurfer development build on a 2019 Intel MacBook Pro running Monterey.  That laptop uses an AMD Radeon 5500M graphics card with 4 GB of memory to drive both the laptop display (3072 x 1920 with 24 bit color) and a 2nd monitor (2560 X 1600 with a framebuffer depth of 30 bits).   Neither of those display are 4K resolution.  But I have not seen any issues with freeview displaying graphics on that 2nd monitor with the Intel MacBook Pro running MacOS Monterey, BigSur or Catalina. To completely remove the development build and the package file download you can do,$ sudo bash /Applications/freesurfer/dev/uninstall.sh$ rm -f $HOME/Downloads/freesurfer-darwin-macOS-dev.pkg - R. P.S. There have been reports of 2nd monitors with 4K resolution connected via USB-C cables causing Mac laptops running Monterey and BigSur to crash.  My understanding is that error is from the Mac graphics hardware not detecting the resolution of the 2nd display through that connection.   Switching to a USB-C to HDMI monitor connection fixed the issue for some users.  But I would avoid using a USB-C to USB-C connection for a 2nd monitor with 4K resolution.

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FreeSurfer VitrualBox VM Image password
by Gniewek Aleksandra (STUD) 04 Mar '22

04 Mar '22

External Email - Use Caution Dear all, My name is Aleksandra Gniewek and i am a student of the Warsaw University of Technology at the faculty of Electronics and Information Technology. I study Biomedical Engineering with a specialization in Biomedical Computer Science. I am currently writing an engineering thesis, the topic of which is based on the analysis of the functional examination of the visual cortex in fMRI. In my thesis I would like to use the set of tools included in Freesurfer. Therefore, I would like to request a password for Freesurfer VirtualBox Image to user 'developer', to be able to analyze fMRI photos. I download VM Image from page: < https://secure-web.cisco.com/1JazyfumX6KEWq94pvRyWOVtJLB1ldODBzyd2t-nUzm5RR… > and in accordance with the instructions (from the same page), I write an e-mail asking for a password to 'developer' user in UBUNTU. Thank you for your help. Aleksandra Gniewek [cid:image001.png@01D82FEA.DAC9F170]

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Postdoctoral Research Associate Dept. of Ophthalmology and Visual science University of Illinois at Chicago
by Nasiriavanaki, Zahra,M.D. 04 Mar '22

04 Mar '22

Postdoctoral Research Associate Dept. of Ophthalmology and Visual science University of Illinois at Chicago A post-doctoral position is available in the area of Stem Cell Therapy and Tissue Engineering at the Department of Ophthalmology. The research focuses on generating corneal organoids using novel 3D culture systems. Research experience in stem cell biology and regenerative medicine cell and/or molecular biology is necessary. Key Responsibilities/ Duties: • Collaborate with key personnel to meet research objectives • Collect, analyze, and interpret data • Perform laboratory experiments • Maintain lab notebook with recorded data • Publish original scientific research in peer-review journals • Present research findings at national/international scientific conferences • Other duties as assigned Minimum Qualifications: • Must have a PhD/Doctorate Degree in biology, biomedical engineering, or other related biomedical science fields. • Preference will be given to candidates with expertise in cell culture, immunohistochemical analysis, microscopy, western blot analysis, DNA and RNA purification, PCR, RT-PCR, ELISA, and/or basic bioinformatics. To apply, please send your cover letter describing research interests and accomplishments and CV to Dr. Elmira Jalilian, jalilian(a)uic.edu<mailto:jalilian@uic.edu> The position is supposed to be filled immediately.

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fspalm error
by Janina von der Gablentz 03 Mar '22

03 Mar '22

External Email - Use Caution Hi FreeSurfer community, I try to ues fspalm to correct multiple comparisons for a surface-based thickness analysis. Below is the code I use: python fspalm --glmdir Home/*/lh.group.glmdir --cft 1.3 --cwp .5 --onetail --name palm_onetail_1.3 --iters 1000 --2spaces The analysis starts successfully until runs "palm prep complete". Then it tries to run the generated matlab script. Matlab seems to start correctly. Afterwards I get the following error: Undefined function or variable 'palm', followed by this error: cannot find expected palm output "fsp_clustere_tstat_fewp_c1.mgz" . check for run_palm.m failures I guess there is a communication problem between the terminal and matlab/palm. Palm is included in the matlab path and I'am able to start palm within matlab. Any help with fixing this error would be appreciated. Thanks, Janina

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FW: Neurotechnology Job Opportunity for the BRAIN Initiative
by Fischl, Bruce 02 Mar '22

02 Mar '22

FYI From: Talley, Edmund (NIH/NINDS) [E] <talleye(a)ninds.nih.gov> Sent: Wednesday, March 2, 2022 1:08 PM To: Talley, Edmund (NIH/NINDS) [E] <talleye(a)ninds.nih.gov> Subject: Neurotechnology Job Opportunity for the BRAIN Initiative External Email - Use Caution I’m writing with information on a rare opening for a Neurotechnology Program Director to manage projects for the BRAIN Initiative. This is a dream job for anyone who wants to shape the development of cutting edge methods to understand the brain. The Brain Research through Advancing Innovative Neurotechnologies® Initiative (BRAIN Initiative), along with the NINDS Division of Neuroscience, is seeking exceptional candidates for the position of Neurotechnology Program Director (Health Scientist Administrator -13/14 or 15). This is a unique opportunity to advance the Neurotechnology portfolio for the BRAIN Initiative, a historic multi-billion-dollar effort to transform neuroscience by developing the technologies of the future. It offers collaborations with highly motivated, skilled, and scientifically curious colleagues from 10 NIH Institutes and Centers and from partner agencies such as NSF and DARPA. It requires extensive engagement and outreach to the research community to assess trends, communicate priorities, and identify new opportunities. Responsibilities include developing new programs, making funding recommendations, and direct managerial oversight of grants and research cooperative agreements. The position will be responsible for overseeing a portfolio of grants and cooperative agreements to support these scientific areas: neural interface technologies that record, modulate, or stimulate neural activity; novel materials and neural interface devices; and biotechnologies applied to the nervous system (including development of hardware, software, and computational techniques). Candidates should possess a doctoral degree and post-doctoral training, with expertise in research towards understanding and applying neural engineering concepts and technologies. We encourage applications from candidates who enjoy working collaboratively and bring a diverse perspective to neural engineering research. Job Post Link: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.ninds.nih.gov/About-NINDS/Jobs-At-NINDS/Health-Scientist-Admini…<https://secure-web.cisco.com/1FD1ESrT1kjS-AWTaloEZcV0Ogwza0WFHR-fbr8INZau1k…> Please send a letter of interest and curriculum vitae to Dr. Ned Talley at Edmund.Talley(a)nih.gov<mailto:Edmund.Talley@nih.gov>. Edmund (Ned) Talley, Ph.D. Program Director, National Inst. of Neurological Disorders and Stroke (NINDS) 6001 Executive Boulevard, Rockville MD 20852 Phone: 301-496-1917, Email: Edmund.Talley(a)nih.gov<mailto:Edmund.Talley@nih.gov> Alert: For BRAIN FOAs that require a Plan for Enhancing Diverse Perspectives (PEDP), applications without this new component will be withdrawn prior to review. Evaluation of the PEDP will be made during peer review as part of the scorable criteria and will be used to inform funding decisions. For more information: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://braininitiative.nih.gov/about/plan-enhancing-diverse-perspectives-p…<https://secure-web.cisco.com/18IFisnOCyk7RxokcMWlgoxS-RgdLRCD9bKVPSupLtv-6e…>

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Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames!
by Knut J Bjuland 02 Mar '22

02 Mar '22

External Email - Use Caution Dear Freesurfer experts, I get this error when I am running FreeSurfer. Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /home/knutjb/subjects/test/mri/orig/001.mgz has 4 frames If this is a multi-frame MEMPRAGE image, use mri_concat --rms to combine echo frames. It has a t1_sag_mprage sequence, and it also give this waning filesare not found to be different and cannot be sorted. In addition, I get these errors when importing using recon-all -i file -all -s test INFO: Found 770 files in //20210224_151919/5_t1_sag_mprage INFO: Scanning for Series Number 5 Scanning Directory INFO: found 768 files in series INFO: loading series header info. When I am running mri_concat --rms I am able to run recon-all -all. Your sincerely, Knut Jørgen Bjuland

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mri_binarize error when using trac-all -prep
by Thorn, Kathryn 02 Mar '22

02 Mar '22

External Email - Use Caution Hello Freesurfer Experts, I am currently attempting to process a single subject via Tracula v7.2. Previously, I used v6.0 to process this same dataset through all three steps of Tracula (prep, bedp, and path) with equivalent parameters with no errors. First, I ran recon-all -all on this subject which finished without error. Then I ran segmentThalamicNuclei.sh per instructions on the first page of the Tracula user guide - also finished without error. Then I passed the outputs of these steps onto trac-all -prep. tract-all -prep exits with errors after about a minute. The command is unable to find the file aparc+aseg+thalnuc.nii.gz. This traces back to an error with mri_binarize: mri_binarize --i /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/aparc+aseg.mgz --o /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz ERROR: must specify minimum and/or maximum threshold or match values aparc+aseg+thalnuc.nii.gz cannot be found because it is never created. However, all expected outputs previous to this file are created in the correct locations and trac-all -prep seems to be able to find all of the initial files I supply to it. I've attached the full trac-all -prep output as well as the config file I used for full context. Is there some threshold I need to specify in the config file? I looked at a complete example config file and I don't see any field related to this, but perhaps I'm missing something. Or is this perhaps due to some error in my data? Any ideas? Thank you! Kayti Thorn (she/her) Database Specialist Medical University of South Carolina Department of Neurology Center for Biomedical Imaging 135 Cannon St. CS101 Charleston, SC 29425

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Linear mixed model for longitudinal data
by Julian Macoveanu 02 Mar '22

02 Mar '22

External Email - Use Caution Dear all, This is my first attempt to analyze longitudinal structural data with freesurfer, and I just do my best to follow the tutorial. I have some things not clear, so any help would be appreciated. We have a longitudinal study design with 2 groups, healthy and patients who were scanned at baseline a second time following a variable time interval (6 to 36 months). We want to investigate whether the patient’s cortical thickness/volume progresses differently compared to controls (group-by-time interaction effects). I chose to analyze the data with LME due to variable follow-up time, having only 50% of the patients with a second scan, and also having family members within and between groups. Questions 1) To account for familial relationship, should I add a family ID as covariate that stays in the design matrix X and count this covariate as random effect when the model is fitted? Like this: lhstats = lme_mass_fit_Rgw(X,[1 2 3],Y,ni,lhTh0,lhRgs,lhsphere); Where the first 3 covariates in X are counted as random effects: 1 the intercept, 2 follow-up time and 3 family ID. The X would further include group, age, sex, TIV, and group*time, the last one being the interaction term we want to assess using CM.C = [0 0 0 0 0 0 0 1]. Does the X and CM look good to address our research question? 2) It is unclear to me how to perform correction for multiple comparisons and assess what is significant. I follow this procedure after constructing X: [lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2 3],Y,ni,lhcortex,3); [lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere,lhRe,lhTh0,lhcortex,2,95); lhstats = lme_mass_fit_Rgw(X,[1 2 3],Y,ni,lhTh0,lhRgs,lhsphere); F_lhstats = lme_mass_F(lhstats,CM); dvtx = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0): The dvtx is not empty but has 130 vertexes that survive. What I don’t understand, when constructing the sig.mgh map it appears the dvtx is not used: fs_write_fstats(F_lhstats,mri,'sig.mgh','sig'); How can I be sure when I import sig.mgh in Freeview I only look at the vertexes surviving multiple comparison? 3) Given a few clusters showing an interaction effect which are saved as sig.mgh and overlaid on surface in freeview, how do I know (visualize) what is going on in these clusters, like which of the group means go up or down? (I use FS71 and tksurfer not working). Is it here that printing out and plotting the betas (of the interaction term) are useful for? 4) I have a hypothesis to find differences in prefrontal cortex, at which step would I apply a PFC mask? I have constructed a PFC.label file by adding corresponding label files. Thank you, Julian

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Re: [Freesurfer] Advice? Re: Freeview 7.1.1 won't start on Mac: segmentation fault
by fsbuild 02 Mar '22

02 Mar '22

External Email - Use Caution Hello Sam, While your crash report is from a Qt process (and not a WindowServer process), you might want to be aware there have been various reports of external monitors connected to Mac laptops causing crashes because the video hardware may not sense the correct resolution or refresh rate of external monitors through a USB-C to USB-C connection.  Some crashes were fixed by by using a USB-C (mac output) to HDMI (monitor input) connection.  Upgrading to Monterey apparently made things worse, https://secure-web.cisco.com/1DBOKcevsj0nBhREsCU8v_3geVkkvJnxbx… - R.. On Mar 1, 2022, at 23:08, Sam Buck Johnson <samjohns(a)stanford.edu> wrote:        External Email - Use Caution        Thanks very much Adam and Ruopeng,I believe that the external monitor was what was causing the error! Freeview seems to work normally now that I have detached it and am working only with my laptop's native display. I can only imagine how long it would have taken for me to discover this on my own.Thanks again,SamOn Mar 1, 2022, at 5:01 PM, Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:You can also download the latest build of freeview here:MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1p3g1aUfMpv-5OYWryXOH2Klul9BV737w-VN8f… Mar 1, 2022, at 7:44 PM, Adam Martersteck <acmarter(a)gmail.com> wrote:        External Email - Use Caution        Hi Sam,I can tell from your crash report you have a LG HDR 4K, 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) plugged in.You might try unplugging any external monitors and just having your native laptop display on then starting FreeView and seeing if it works.I had the same issue; see here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/10i4ZuCFZN8GuKB-DWCevEuF86X5PdpwHzWu9e… unresolved. Can open FreeView fine without a monitor plugged in but get a segmentation fault whenever I'm using an external display.-AdamOn Tue, Mar 1, 2022 at 4:04 PM Sam Buck Johnson <samjohns(a)stanford.edu> wrote:        External Email - Use Caution        Dear Freesurfer experts,I am writing to request technical assistance with freeview. I use freesurfer and freeview in my current research, where they are very valuable tools. However, upon upgrading my macbook's OS to macOS Monterey, Version 12.2.1, I now am unable to open freeview; it quits immediately upon starting. The error message indicates a segmentation fault, and in fact my error (and the error message) appears to be exactly the same as the one encountered by Alex White in this thread: https://secure-web.cisco.com/1IXdnFyTKmN2mh6oaF1iVQ3_Ho1Z9szlP… have been in correspondence with Alex, and he mentioned that you were able to help him resolve the issue, but that it required you to send him a patched version of freeview (or freesurfer?). I have the identical problem on freeview 7.1.1 and 7.2.0, but if possible I would prefer to continue working with your latest version, 7.2.0.Please do let me know if further information could help you understand this issue better. For the time being, I have copied the error message that prints to terminal and the full error report, both below.Any help/advice is much appreciated.Sincerely,Sam JohnsonPostdoctoral ScholarYeatman Brain and Education Lab, Stanford University GSE-----# terminal error message:(base) samjohns@DNab40bbcb 7.2.0 % freeview/Applications/freesurfer/7.2.0/bin/freeview: line 2:  1968 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"# full crash report-------------------------------------Translated Report (Full Report Below)-------------------------------------Process:               freeview [1673]Path:                  /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeviewIdentifier:            com.freesurfer.freeviewVersion:               ???Code Type:             X86-64 (Translated)Parent Process:        Exited process [1672]Responsible:           Terminal [1587]User ID:               502Date/Time:             2022-03-01 15:12:51.8713 -0800OS Version:            macOS 12.2.1 (21D62)Report Version:        12Anonymous UUID:        DCA45306-7159-2569-6BDE-CF94BEE1E522Time Awake Since Boot: 1200 secondsSystem Integrity Protection: enabledCrashed Thread:        0  Dispatch queue: com.apple.main-threadException Type:        EXC_BAD_ACCESS (SIGSEGV)Exception Codes:       KERN_INVALID_ADDRESS at 0x0000545845545f67Exception Codes:       0x0000000000000001, 0x0000545845545f67Exception Note:        EXC_CORPSE_NOTIFYTermination Reason:    Namespace SIGNAL, Code 11 Segmentation fault: 11Terminating Process:   exc handler [1673]VM Region Info: 0x545845545f67 is not in any region.  Bytes after previous region: 92257060675432  Bytes before following region: 12815019253913      REGION TYPE                    START - END         [ VSIZE] PRT/MAX SHRMOD  REGION DETAIL      commpage (reserved)        1000000000-7000000000   [384.0G] ---/--- SM=NUL  ...(unallocated)--->  GAP OF 0x5f9000000000 BYTES      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-/rwx SM=PRV  Thread 0 Crashed::  Dispatch queue: com.apple.main-thread0   freeview                                   0x104ec0ff8 0x104ce2000 + 19619761   QtWidgets                                  0x12046c6ed QWidget::event(QEvent*) + 11172   QtWidgets                                  0x12057dc45 QMainWindow::event(QEvent*) + 2773   QtWidgets                                  0x12043070d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 2694   QtWidgets                                  0x120431b12 QApplication::notify(QObject*, QEvent*) + 5945   QtCore                                     0x12266e564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 2126   QtWidgets                                  0x12048aa74 0x120420000 + 4368527   QtWidgets                                  0x12043070d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 2698   QtWidgets                                  0x120431b12 QApplication::notify(QObject*, QEvent*) + 5949   QtCore                                     0x12266e564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 21210  QtGui                                      0x1211e2a74 QGuiApplicationPrivate::processGeometryChangeEvent(QWindowSystemInterfacePrivate::GeometryChangeEvent*) + 51611  QtGui                                      0x1211e3420 QGuiApplicationPrivate::processWindowScreenChangedEvent(QWindowSystemInterfacePrivate::WindowScreenChangedEvent*) + 73612  QtGui                                      0x1211c1c33 bool QWindowSystemInterfacePrivate::handleWindowSystemEvent<QWindowSystemInterface::SynchronousDelivery>(QWindowSystemInterfacePrivate::WindowSystemEvent*) + 11513  libqcocoa.dylib                            0x121eb4c77 0x121e96000 + 12607114  libqcocoa.dylib                            0x121eae862 0x121e96000 + 10045015  libqcocoa.dylib                            0x121eae2eb 0x121e96000 + 9905116  QtGui                                      0x1211ec1dc QWindowPrivate::create(bool, unsigned long long) + 14017  QtWidgets                                  0x120459e31 QWidgetPrivate::create() + 120118  QtWidgets                                  0x120458b22 QWidget::create(unsigned long long, bool, bool) + 32219  QtWidgets                                  0x12057e4d7 QMainWindow::setUnifiedTitleAndToolBarOnMac(bool) + 5520  freeview                                   0x104eaf497 0x104ce2000 + 188943121  freeview                                   0x104ea950e 0x104ce2000 + 186497422  freeview                                   0x104de279a 0x104ce2000 + 105052223  dyld                                       0x2158184fe start + 462Thread 1:: com.apple..rosetta.exceptionserver0   runtime                                 0x7ff7ffc578e4 0x7ff7ffc53000 + 186601   runtime                                 0x7ff7ffc64928 0x7ff7ffc53000 + 719762   runtime                                 0x7ff7ffc660a4 0x7ff7ffc53000 + 77988Thread 2:0   runtime                                 0x7ff7ffc75814 0x7ff7ffc53000 + 141332Thread 3:0   runtime                                 0x7ff7ffc75814 0x7ff7ffc53000 + 141332Thread 4::  Dispatch queue: com.apple.dock.fullscreen0   dyld                                       0x215824e0c dyld4::Loader::LoaderRef::loader(dyld4::RuntimeState const&) const + 681   dyld                                       0x21582cdb1 dyld4::PrebuiltLoader::dependent(dyld4::RuntimeState const&, unsigned int, dyld4::Loader::DependentKind*) const + 952   dyld                                       0x215828a1e dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 5323   dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 5934   dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 5935   dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 5936   dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 5937   dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 5938   dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 5939   dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 59310  dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 59311  dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 59312  dyld                                       0x215828a5b dyld4::Loader::hasExportedSymbol(Diagnostics&, dyld4::RuntimeState&, char const*, dyld4::Loader::ExportedSymbolMode, dyld4::Loader::ResolvedSymbol*, dyld3::Array<dyld4::Loader const*>*) const + 59313  dyld                                       0x215837b4c dyld4::APIs::dlsym(void*, char const*) + 65614  SkyLight                                0x7ff811fbf581 __loginframework_vtable_block_invoke + 60515  libdispatch.dylib                       0x7ff80ccd8cc9 _dispatch_client_callout + 816  libdispatch.dylib                       0x7ff80ccd9ec1 _dispatch_once_callout + 2017  SkyLight                                0x7ff811fc0de5 SLSCopyCurrentSessionPropertiesInternalBridge + 36618  SkyLight                                0x7ff811e6a097 SLSessionCopyCurrentDictionary + 1219  AppKit                                  0x7ff80f9e04ee -[NSDockConnection _makeConnectionIfNeededWithRetryInterval:onDemand:] + 4720  AppKit                                  0x7ff8101b9720 __35-[NSDockConnection startConnection]_block_invoke.37 + 4521  libdispatch.dylib                       0x7ff80ccd7ad8 _dispatch_call_block_and_release + 1222  libdispatch.dylib                       0x7ff80ccd8cc9 _dispatch_client_callout + 823  libdispatch.dylib                       0x7ff80ccdecee _dispatch_lane_serial_drain + 69624  libdispatch.dylib                       0x7ff80ccdf7c8 _dispatch_lane_invoke + 36625  libdispatch.dylib                       0x7ff80cce97e1 _dispatch_workloop_worker_thread + 75826  libsystem_pthread.dylib                 0x7ff80ce8f074 _pthread_wqthread + 32627  libsystem_pthread.dylib                 0x7ff80ce8dffb start_wqthread + 15Thread 5:0   runtime                                 0x7ff7ffc75814 0x7ff7ffc53000 + 141332Thread 6:0   runtime                                 0x7ff7ffc75814 0x7ff7ffc53000 + 141332Thread 7:0   runtime                                 0x7ff7ffc75814 0x7ff7ffc53000 + 141332Thread 0 crashed with X86 Thread State (64-bit):  rax: 0x0000545845545f5f  rbx: 0x000000031e5aac00  rcx: 0x0000000000010000  rdx: 0x000000012046c6dd  rdi: 0x00007ff815d4f000  rsi: 0x000000031e5a9c78  rbp: 0x000000031e5a9730  rsp: 0x000000031e5a9720   r8: 0x0000000000000000   r9: 0x0000000000000000  r10: 0x00000001220129e0  r11: 0x00007ff80f8c8bb9  r12: 0x00007ff175745090  r13: 0x000000031e5aac00  r14: 0x000000031e5a9c78  r15: 0x000000031e5a9c78  rip: 0x0000000104ec0ff8  rfl: 0x0000000000000203 tmp0: 0x0000000115a9c01c tmp1: 0x000000012046c6ed tmp2: 0x0000000120a3c1e8Binary Images:       0x104ce2000 -        0x106349fff com.freesurfer.freeview (*) <35cc1656-e7ff-32a5-8ec9-9faf896f9915> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview       0x120420000 -        0x12085efff org.qt-project.QtWidgets (5.12) <ef671b84-7965-3c74-89df-09c3fa9096ca> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtWidgets.framework/Versions/5/QtWidgets       0x122484000 -        0x1229b9fff org.qt-project.QtCore (5.12) <ae294ca9-b3ec-3f0e-b67a-509a13c0c913> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/5/QtCore       0x1211ac000 -        0x1215f8fff org.qt-project.QtGui (5.12) <9cc34b01-ae4a-3ff2-ac1b-de08b8fbbbae> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtGui.framework/Versions/5/QtGui       0x121e96000 -        0x121ffcfff libqcocoa.dylib (*) <14bc2336-68e6-3ace-b3a9-f21152a64785> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/platforms/libqcocoa.dylib       0x215813000 -        0x21587efff dyld (*) <7de33963-bbc5-3996-ba6e-f1d562c17c95> /usr/lib/dyld    0x7ff7ffc53000 -     0x7ff7ffc82fff runtime (*) <faca02c7-0a4c-3629-a746-55ddcfee9116> /usr/libexec/rosetta/runtime    0x7ff811d55000 -     0x7ff8120eafff com.apple.SkyLight (1.600.0) <eab4373e-52ca-38d7-963a-9f5bd71824e9> /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight    0x7ff80ccd6000 -     0x7ff80cd1cfff libdispatch.dylib (*) <67d92c93-aa68-34c2-964b-23e8a8d32098> /usr/lib/system/libdispatch.dylib    0x7ff80f86e000 -     0x7ff8106fffff com.apple.AppKit (6.9) <9d3ab204-4858-3120-b002-5c38b02edec4> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit    0x7ff80ce8c000 -     0x7ff80ce97fff libsystem_pthread.dylib (*) <ee564342-d8f2-396d-b642-40092cf34d82> /usr/lib/system/libsystem_pthread.dylib               0x0 - 0xffffffffffffffff ??? (*) <00000000-0000-0000-0000-000000000000> ???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: 0VM Region Summary:ReadOnly portion of Libraries: Total=964.1M resident=0K(0%) swapped_out_or_unallocated=964.1M(100%)Writable regions: Total=1.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.2G(100%)                                VIRTUAL   REGION REGION TYPE                        SIZE    COUNT (non-coalesced) ===========                     =======  ======= Accelerate framework               256K        2 Activity Tracing                   256K        1 CG backing stores                 5056K        8 ColorSync                          228K       25 CoreGraphics                         8K        2 CoreUI image data                  152K        1 Foundation                          16K        1 Kernel Alloc Once                    8K        1 MALLOC                           216.2M       34 MALLOC guard page                  192K        9 MALLOC_MEDIUM (reserved)         240.0M        2         reserved VM address space (unallocated)MALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)Rosetta Arena                     4096K        2 Rosetta Generic                    736K      181 Rosetta IndirectBranch             512K        1 Rosetta JIT                      128.0M        1 Rosetta Return Stack               100K       10 Rosetta Thread Context             100K       10 STACK GUARD                         20K        5 Stack                             11.1M        7 Stack Guard                       56.0M        2 VM_ALLOCATE                       8280K       29 VM_ALLOCATE (reserved)               4K        1         reserved VM address space (unallocated)__DATA                           262.5M      320 __DATA_CONST                      12.2M      173 __DATA_DIRTY                       539K       99 __FONT_DATA                          4K        1 __LINKEDIT                       704.8M       29 __OBJC_RO                         81.8M        1 __OBJC_RW                         3136K        2 __TEXT                           259.3M      332 __UNICODE                          588K        1 dyld private memory               1024K        1 mapped file                        5.1G      429 shared memory                      848K       22 unshared pmap                     5504K        3 ===========                     =======  ======= TOTAL                              7.4G     1749 TOTAL, minus reserved VM space     6.8G     1749 -----------Full Report-----------{"app_name":"freeview","timestamp":"2022-03-01 15:12:52.00 -0800","app_version":"","slice_uuid":"35cc1656-e7ff-32a5-8ec9-9faf896f9915","build_version":"","platform":1,"bundleID":"com.freesurfer.freeview","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.2.1 (21D62)","incident_id":"78ED639A-5BDF-48BF-88B6-8A9AE3997115","name":"freeview"}{  "uptime" : 1200,  "procLaunch" : "2022-03-01 15:12:51.6463 -0800",  "procRole" : "Background",  "version" : 2,  "userID" : 502,  "deployVersion" : 210,  "modelCode" : "MacBookPro17,1",  "procStartAbsTime" : 30601251608,  "coalitionID" : 1327,  "osVersion" : {    "train" : "macOS 12.2.1",    "build" : "21D62",    "releaseType" : "User"  },  "captureTime" : "2022-03-01 15:12:51.8713 -0800",  "incident" : "78ED639A-5BDF-48BF-88B6-8A9AE3997115",  "bug_type" : "309",  "pid" : 1673,  "procExitAbsTime" : 30606634548,  "translated" : true,  "cpuType" : "X86-64",  "procName" : "freeview",  "procPath" : "\/Applications\/freesurfer\/*\/Freeview.app\/Contents\/MacOS\/freeview",  "bundleInfo" : {"CFBundleIdentifier":"com.freesurfer.freeview"},  "storeInfo" : {"deviceIdentifierForVendor":"61B48C8D-0860-568E-953B-3DE776CD3C66","thirdParty":true},  "parentProc" : "Exited process",  "parentPid" : 1672,  "coalitionName" : "com.apple.Terminal",  "crashReporterKey" : "DCA45306-7159-2569-6BDE-CF94BEE1E522",  "responsiblePid" : 1587,  "responsibleProc" : "Terminal",  "sip" : "enabled",  "vmRegionInfo" : "0x545845545f67 is not in any region.  Bytes after previous region: 92257060675432  Bytes before following region: 12815019253913\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",  "isCorpse" : 1,  "exception" : {"codes":"0x0000000000000001, 0x0000545845545f67","rawCodes":[1,92738097012583],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000545845545f67"},  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"exc handler","byPid":1673},  "vmregioninfo" : "0x545845545f67 is not in any region.  Bytes after previous region: 92257060675432  Bytes before following region: 12815019253913\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},  "faultingThread" : 0,  "threads" : [{"triggered":true,"id":21764,"threadState":{"r13":{"value":13394160640},"rflags":{"value":515},"rax":{"value":92738097012575},"rosetta":{"tmp2":{"value":4842570216},"tmp1":{"value":4836476653},"tmp0":{"value":4658413596}},"r14":{"value":13394156664},"rsi":{"value":13394156664},"r8":{"value":0},"rdx":{"value":4836476637,"symbolLocation":1101,"symbol":"QWidget::event(QEvent*)"},"r10":{"value":4865468896},"r9":{"value":0},"r15":{"value":13394156664},"rbx":{"value":13394160640},"r11":{"value":140703389486009,"symbolLocation":0,"symbol":"-[NSView 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