Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

Re: [Freesurfer] Source freesurfer functions into R Studio Terminal
by fsbuild 06 Oct '21

06 Oct '21

External Email - Use Caution Hello Shrikanth, When you source the freesurfer setup script in your shell, e.g., bash, $ source $FREESURFER_HOME/SetUpFreeSurfer.sh - it sets your PATH, SUBJECTS_DIR and a few other variables.  It’s the addition to PATH of something like /usr/local/freesurfer/7.2.0/bin that enables freesurfer commands to be found, e.g.,  $ which mri_convert$ /usr/local/freesurfer/7.2.0/mri_convert So you could cut and paste the absolute path of a freesurfer command to run in the R environment via the system() command, i.e., use whatever is echoed by the “which” command above in the shell where you run freesurfer. You could also try to use a wrapper script to reproduce setting PATH and the freesurfer environment and run that script in the system() call.   Something like (change path to FREESURFER_HOME as need be), $ vi  fs_from_r.sh — start here —#!/usr/bin/env  bash  export FREESURFER_HOME=/usr/local/freesurfer/7.2.0 source $FREESURFER_HOME/SetUpFreeSurfer..sh  # add any freesurfer commands after this — end here — $ chmod 755 fs_from_r.sh Test run it in your bash sell first to see that it works, $ ./fs_from_r.sh Then see if you can run the fs_from_r.sh script via the R system() command.  You probably need to give the absolute path to the script though. - R. On Oct 6, 2021, at 16:13, Yadav, Shrikanth Muralidhar <SMYADAV(a)mgh.harvard.edu> wrote:Hello Freesurfer Developers,I had a freesurfer-Rstudio issue today which I solved by just working on a Linux shell script. However, I wanted to know if it is possible to send freesurfer related commands from R studio out of curiosity.My Problem:I was trying to use freesurfer commands like mri_convert by sending them through the "system()" function in R.   However, I got a "sh: mri_convert command not found" error. This indicates freesurfer is not sourced into the Linux terminal in the R Session. My Question: Is it possible to run freesurfer related commands from the rstudio terminal? What I did:I looked up this problem online and found a similar example where the user needed the function bedtools. But updating the system path still threw the same error with .In addition, I was able to send commands like "dcm2niix" from R using the system function mentioned above.  I am certain this is a sourcing issue.  Would appreciate any insightThank youShrikanth_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Source freesurfer functions into R Studio Terminal
by Yadav, Shrikanth Muralidhar 06 Oct '21

06 Oct '21

Hello Freesurfer Developers, I had a freesurfer-Rstudio issue today which I solved by just working on a Linux shell script. However, I wanted to know if it is possible to send freesurfer related commands from R studio out of curiosity. My Problem: * I was trying to use freesurfer commands like mri_convert by sending them through the "system()<https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/system>" function in R. * However, I got a "sh: mri_convert command not found" error. This indicates freesurfer is not sourced into the Linux terminal in the R Session. My Question: Is it possible to run freesurfer related commands from the rstudio terminal? What I did: 1. I looked up this problem online and found a similar example<https://stackoverflow.com/questions/26065564/why-cant-i-call-system-functio…> where the user needed the function bedtools. But updating the system path still threw the same error with . 2. In addition, I was able to send commands like "dcm2niix" from R using the system function mentioned above. I am certain this is a sourcing issue. Would appreciate any insight Thank you Shrikanth

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Application portal open for 2022 session of Training in Advanced Statistical Methods in Neuroimaging and Genetics
by ROBERT CARY WELSH 05 Oct '21

05 Oct '21

External Email - Use Caution Hi folks, We are pleased to announce that the application portal is open for the NIH funded 2022 session of the training course. Due to the ongoing COVID-19 pandemic, we have decided to do virtual again this year. The course is an intensive 2-weeks, about 8 hours per day, so please only apply if you know you will be able to commit to coming to the full course. https://secure-web.cisco.com/1z9PgSzXVnC3wHMB7PHwnulIp26my3AIVqOnL0kKgEUEGX… Because of the limited size, attendance is by application only. In general, applicants must be a US citizen or permanent resident, though we do have the ability to accommodate 1 to 3 individuals that do not meet this criteria. Robert Welsh ------------------------------ Robert Welsh, PhD Associate Professor Course Director, Training in Advanced Statistical Methods in Neuroimaging and Genetics Huntsman Mental Health Institute University of Utah robert.c.welsh(a)utah.edu

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Question about network-wise CV
by Martin Juneja 05 Oct '21

05 Oct '21

External Email - Use Caution Hi FreeSurfer experts, We submitted a paper where we used Yeo's 7-network atlas to estimate the hemispheric mean cortical volume of each network using mri_annotation2label --subject X --hemi lh --annotation Yeo2011_7Networks_N1000 --labelbase Left_7Ns The question from the reviewer is: *did the network-wise hemispheric mean CV refer to the mean CV of all brain regions within the network?* Could you please help address this question? Thanks!

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Missed grey matter of sulci
by McKavanagh, Andrea [amckav] 04 Oct '21

04 Oct '21

External Email - Use Caution Hi all, I am having a problem with some post recon-all edits. The white matter in some of my scans has been over estimated in the aparc+aseg file, labelling some of the white matter (e.g by the lingual gyrus) as hypointensities and/or missing out many sulcui entirely (figure 1). However, the wm.mgz file is accurate picking up only the correct white matter in these areas (figure 2). This is happening, on most of the scans I have processed with recon-all. I am using Freesurfer 7.2.0 on Mac BigSur and have ran the same scans through previous version of Freesurfer (6/7.1) with the same problem occurring. I have read on the archives this has previously been a bug in another version, is this the case here? Or is there another correction step I could try? Any suggestions are welcome :) Thanks, BW Andrea [cid:9B03F6B2-0EEC-4035-8303-7364C1852FBF][cid:7C1283D9-0375-4187-A927-0CFB4B6BD5A9]

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Longitudinal analysis: error "no data found in mri/orig"
by Mary DC 04 Oct '21

04 Oct '21

External Email - Use Caution Hello FreeSurfer developers, I have created the "subjects" folder, and I included a large sample of participants inside the folder. I have performed transversal analysis (CROSS), all successfully. I am now performing a longitudinal analysis with the first 8 subjects: Baseline: 001.mgz; 002.mgz;...; 008.mgz Longitudinal: 109.mgz; 110.mgz;...; 116.mgz I followed the steps: https://secure-web.cisco.com/1TZpE_bQz0tJBdgLnT_voDCZ6eYQJTDqKQRLS1v7fMqRfN… 1) BASE analysis was correctly performed for the 8 subjects, and folders (_base) were created 2) LONG analysis: -First subject with baseline data 001.mgz: LONG analysis finished without errors and A01.long.A01_base was created. -First subject with longitudinal data 109.mgz finished with error. -The rest of the subjects finished with error. *Error message in all cases: * *ERROR: no CROSS run data found in /usr/local/freesurfer/subjects/A01_3/mri/orig/. Make sure to have a volume called 001.mgz there.If you have a second run of data call it 002.mgz, etc.See also: http://secure-web.cisco.com/1TxTwmkGwewO59MpGmT0k8qAqls31H-w6Ys9AObOvl31f6H… <http://secure-web.cisco.com/1TxTwmkGwewO59MpGmT0k8qAqls31H-w6Ys9AObOvl31f6H…>Linux VISUAL 5.4.0-81-generic #91~18.04.1-Ubuntu SMP Fri Jul 23 13:36:29 UTC 2021 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s A01_3.long.A01_base exited with ERRORS at dom oct 3 10:59:53 CEST 2021For more details, see the log file /usr/local/freesurfer/subjects/A01_3.long.A01_base/scripts/recon-all.logTo report a problem, see http://secure-web.cisco.com/1p2mJaCstn9B2xUbzEJL6vTV7W-2WQygHUdN3tVXXu7GPAp… <http://secure-web.cisco.com/1p2mJaCstn9B2xUbzEJL6vTV7W-2WQygHUdN3tVXXu7GPAp…>* However, I think I have correctly named the subjects (001.mgz; 002.mgz; 003.mgz...) and cross-sectional analyses were performed correctly. I can not identify the error. Could you please guide me with this problem? thank you in advance, Best, Mary

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inter-hemispheric registration
by Yu-Chi Chen 03 Oct '21

03 Oct '21

External Email - Use Caution Dear FreeSurfer experts, My current analysis is for analyzing the vertices of the cortical surfaces. I'd like to have the same vertice numbers of the left and right hemispheres and also to retain as much asymmetric feature as possible. I first created the xhemi by using the xhemireg Next, I registered the right hemisphere white surface to the /xhemi/rh.white as following: mri_surf2surf --hemi rh \ --srcsubject ${SUBJECT} \ --trgsubject ${SUBJECT}/xhemi \ --srcsurfval ${SUBJECT}/xhemi/surf/rh.white \ --tval ${SUBJECT}_reg.rh.white But this failed. Could you teach me how to revise the code or is there any other suggestion? Thank you very much. Kind regards, Edward

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Re: [Freesurfer] problem opening freeview (on MacOS Catalina)
by fsbuild 02 Oct '21

02 Oct '21

External Email - Use Caution Hello Elmira, You could try what’s listed in this posting to the freesurfer mailing list, https://secure-web.cisco.com/1yVVItJGPCMsg_Uo7pKlIPolFCr3sddKv2M…, from last month, https://secure-web.cisco.com/16vjmYxwj3UHolWzWQNnuKrRjPTQ2HGAuw….  I’ve copied it below as well. I can’t see from your crash report if you installed the latest 7.2.0 release (via the installer https://secure-web.cisco.com/1cB--DH4LZwahHKKs6NmxADJ9piuaNS…; But if you are not running the latest release, then I would also give that a try. - R. On Oct 2, 2021, at 20:35, Elmira Hassanzadeh <elmitt(a)gmail.com> wrote:Hello FreeSurfer Developers,I installed freesurfer for the first time on my system but although the installation went smoothly I cannot open freeview. Here is the error I receive on terminal (the full log at the end of this message)9800 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" Begin forwarded message:Subject: [Freesurfer] Notes on running freesurfer on MacOS (including M1 Macs running MacOS BigSur 11.6)Date: September 22, 2021 at 21:15:35 EDT To: freesurfer@nmr.mgh.harvard.eduThere have been various postings to the freesurfer mail list about issues running freesurfer on MacOS including M1 Macs.  The information below may help with running freesurfer (Intel) binaries on MacOS including M1 Macs running BigSur (MacOS 11.6).APPLICATION SANDBOXINGThe privacy and security features introduced with macOS Mojave (10.14.X) and subsequently expanded in MacOS Catalina (10.15.X) and BigSur (11.X) means that after installation, binaries and applications are by default “sandboxed” and not allowed access to the disk, networked volumes, etc.. - unless they are given permission.  Permission should only need to be granted once, but this can be cumbersome if many binaries each need permission to run (compared to a single *.app application bundle).The System Preferences GUI can be used to grant disk access to an individual application (bundle): • Open System Preferences • Click the Security & Privacy tab • Click the Privacy tab • On the left hand side menu scroll to and select Full Disk Access  • Click on the (Locked) padlock in the lower left hand corner and enter your password to unlock it • Click the + button under the list of applications in the right hand side menu; navigate using the Finder to the application you want to grant full disk access to; select it; hit the open button           - OR - it may just work to directly drag the application from a Finder window into the right hand side menu • Make sure the box is checked next to the application you added        • Click on the padlock icon to lock out changesThe next time you launch the application, it should have full disk access.So for example you could do the above for the freeview application installed by the freesurfer 7.2.0 Mac installer package as /Applications/freesurfer/7.2.0/Freeview.appSince the binaries and scripts located under /Applications/freesurfer/7.2.0/bin are usually run from the command line using the terminal application, then one option is to grant full disk access to the terminal application.  If you are comfortable with the security risk this poses, then you can use the steps above to navigate to and add /System/Applications/Utilities/Terminal.app to the list of applications with full disk access.FREESURFER LICENSE FILEThe format of older freesurfer license files may cause a runtime error, e.g., segfault on MacOS.  Getting a new license file from https://secure-web.cisco.com/1av48oNjCEWiUav-Caf0a-qMQEIPDIIn17u3… prevent this error.You can set the environment variable FS_LICENSE to set the path to the license file.  For example, if you set that path to be $HOME/license.txt, then there is no need to use sudo/admin privileges to place a license file in an installed freesurfer distribution under /Applications.… assume you downloaded license.txt to your Downloads folder …$ cd $HOME$ pwd/Users/myuid$ cp -p -f  ~/Downloads/license.txt .$ export FS_LICENSE=$HOME/license.txt   <— add appropriate export to your shell init file for whatever shell you set the Terminal.app to runMATLAB INSTALLATION ON M1 MACSThe Freesurfer 7.2.0 distribution includes the script /Applications/freesurfer/7.2.0/bin/fs_install_mcr to install the Matlab R2014b run time environment.  While the 7.2.0 release was built and tested with R2014b, this release is too old to be supported on M1 Macs and may cause run time errors.  This will be addressed in a future freesurfer release.RUNNING INTEL BINARIES ON M1 MACSThe Freesurfer distribution is currently Intel binary only.Apple provides the built-in Rosetta2 emulation environment to translate applications built for Intel (x86_64) to run on the the M1 hardware (arm64) in real-time.   Or the system detects "on the fly" if the binary is built for x86_64, and then automatically runs Rosetta2 to translate the x86_64 instructions to arm64 instructions and runs them on the M1 chip.  The translation process may take longer for some binaries compared to others.On an M1 Mac, when you open the terminal window and see the shell prompt, you are by default running the arm64 version of zsh.  As soon as you give a command to launch/run an Intel binary, Rosetta2 kicks in with the translation process.While existing freesurfer bash scripts should run under zsh, it is always a safe bet to run the bash shell directly (which was the default shell in older versions of MacOS), e.g,$ bashThe default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://secure-web.cisco.com/136dfBL41xqA3SFJn4-yT5lJiei5PUSVUcA2CFhfBcne5N… reset the SHELL environment to reflect bash ...userid@developer-Mac:~> export SHELL=/bin/bashuserid@developer-Mac:~> echo $SHELL/bin/bashIf you prefer bash, it’s easier to set that as your default shell via the command line or via the GUI..  See https://secure-web.cisco.com/1oLu13zgRriywPCM-aoCk7xWrEkSuYPaNNnEEum2CS-1VsPdfCccnkpn7KCwvJj0oiCy2a84uTD92aCIZSxURL8BCNS5aSXiKMVfF3LX6Et-g4HpYEHZuPFMuuLJyPdBg11qotcIOZ5wVZ6_Xg0JC3v41NlqGnbrP3PVVfT5eaZFXcwiuEcFPzn4yXvDXupn7PMhukBR7VIDJYfS0lltOUoWhfNp6jFoBohvhFmruw0fJzrL5Z5M87_8ooykS1cDG9Rv6lg1cJ48rFkCT-FrPUA/https%3A%2F%2Fsupport.apple.com%2Fen-us%2FHT208050%C2%A0%28e.g.., change /bin/zsh to /bin/bash).Users who only want to run Intel binaries sometimes go a step further.  Instead of running the arm64 version of “/bin/bash” (which allows for running both arm64 binaries and x86_64 binaries via Rosetta2 from the same parent shell), they instead directly run the Intel version of “/bin/bash” by invoking bash as,$ arch -x86_64 /bin/bashWhen running the x86_64 version of a shell then only Intel binaries can run as child processes.- R.._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] problem opening freeview
by Elmira Hassanzadeh 02 Oct '21

02 Oct '21

External Email - Use Caution Hello FreeSurfer Developers, I installed freesurfer for the first time on my system but although the installation went smoothly I cannot open freeview. Here is the error I receive on terminal (the full log at the end of this message) 9800 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" The updated freeview release ( https://secure-web.cisco.com/1y14448N7lhraUps4TzeJUZTN0gN1Kb2wgC5Fqp-PulqpL…) didn't solve the issue. pls advise. best, Elmira *Full log:* Process: freeview [9651] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Identifier: com.freesurfer.freeview Version: 0 Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: freeview [9651] User ID: 501 Date/Time: 2021-10-02 18:42:06.674 -0400 OS Version: Mac OS X 10.15.7 (19H1419) Report Version: 12 Anonymous UUID: 39AC47F0-5292-5D7A-4E1E-60752339F3AB Sleep/Wake UUID: 7B20900C-3E6D-4AFD-B3C9-7A1209E9F1F8 Time Awake Since Boot: 30000 seconds Time Since Wake: 19000 seconds System Integrity Protection: enabled Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x000000006149584e Exception Note: EXC_CORPSE_NOTIFY Termination Signal: Segmentation fault: 11 Termination Reason: Namespace SIGNAL, Code 0xb Terminating Process: exc handler [9651] VM Regions Near 0x6149584e: --> __TEXT 0000000107f69000-0000000109562000 [ 22.0M] r-x/rwx SM=COW /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Application Specific Information: dyld: in dlsym() Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 com.freesurfer.freeview 0x0000000108131df8 0x107f69000 + 1871352 1 org.qt-project.QtWidgets 0x0000000118a106ed QWidget::event(QEvent*) + 1117 2 org.qt-project.QtWidgets 0x0000000118b21c45 QMainWindow::event(QEvent*) + 277 3 org.qt-project.QtWidgets 0x00000001189d470d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 4 org.qt-project.QtWidgets 0x00000001189d5b12 QApplication::notify(QObject*, QEvent*) + 594 5 org.qt-project.QtCore 0x000000011969f564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 6 org.qt-project.QtWidgets 0x0000000118a2ea74 0x1189c4000 + 436852 7 org.qt-project.QtWidgets 0x00000001189d470d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 8 org.qt-project.QtWidgets 0x00000001189d5b12 QApplication::notify(QObject*, QEvent*) + 594 9 org.qt-project.QtCore 0x000000011969f564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 10 org.qt-project.QtGui 0x0000000118f9ba74 QGuiApplicationPrivate::processGeometryChangeEvent(QWindowSystemInterfacePrivate::GeometryChangeEvent*) + 516 11 org.qt-project.QtGui 0x0000000118f9c420 QGuiApplicationPrivate::processWindowScreenChangedEvent(QWindowSystemInterfacePrivate::WindowScreenChangedEvent*) + 736 12 org.qt-project.QtGui 0x0000000118f7ac33 bool QWindowSystemInterfacePrivate::handleWindowSystemEvent<QWindowSystemInterface::SynchronousDelivery>(QWindowSystemInterfacePrivate::WindowSystemEvent*) + 115 13 libqcocoa.dylib 0x000000011b701c77 0x11b6e3000 + 126071 14 libqcocoa.dylib 0x000000011b6fb862 0x11b6e3000 + 100450 15 libqcocoa.dylib 0x000000011b6fb2eb 0x11b6e3000 + 99051 16 org.qt-project.QtGui 0x0000000118fa51dc QWindowPrivate::create(bool, unsigned long long) + 140 17 org.qt-project.QtWidgets 0x00000001189fde31 QWidgetPrivate::create() + 1201 18 org.qt-project.QtWidgets 0x00000001189fcb22 QWidget::create(unsigned long long, bool, bool) + 322 19 org.qt-project.QtWidgets 0x0000000118b224d7 QMainWindow::setUnifiedTitleAndToolBarOnMac(bool) + 55 20 com.freesurfer.freeview 0x0000000108122037 0x107f69000 + 1806391 21 com.freesurfer.freeview 0x000000010811c24e 0x107f69000 + 1782350 22 com.freesurfer.freeview 0x00000001080612a3 0x107f69000 + 1016483 23 libdyld.dylib 0x00007fff6ce55cc9 start + 1 Thread 1: 0 libsystem_pthread.dylib 0x00007fff6d055b68 start_wqthread + 0 Thread 2:: Dispatch queue: com.apple.dock.fullscreen 0 dyld 0x000000011b974a22 ImageLoader::trieWalk(unsigned char const*, unsigned char const*, char const*) + 202 1 dyld 0x000000011b97e580 ImageLoaderMachOCompressed::findShallowExportedSymbol(char const*, ImageLoader const**) const + 112 2 dyld 0x000000011b9781f5 ImageLoaderMachO::findExportedSymbol(char const*, bool, char const*, ImageLoader const**) const + 37 3 dyld 0x000000011b970c9a ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 254 4 dyld 0x000000011b970d3e ImageLoader::findExportedSymbolInDependentImagesExcept(char const*, ImageLoader const**, ImageLoader const**&, ImageLoader const**, ImageLoader const**) const + 418 5 dyld 0x000000011b970e5a ImageLoader::findExportedSymbolInImageOrDependentImages(char const*, ImageLoader::LinkContext const&, ImageLoader const**) const + 88 6 dyld 0x000000011b96e54f dlsym_internal + 401 7 libdyld.dylib 0x00007fff6ce41a09 dlsym + 195 8 com.apple.SkyLight 0x00007fff62202025 __loginframework_vtable_block_invoke + 357 9 libdispatch.dylib 0x00007fff6cdfc658 _dispatch_client_callout + 8 10 libdispatch.dylib 0x00007fff6cdfd7de _dispatch_once_callout + 20 11 com.apple.SkyLight 0x00007fff62203a55 SLSCopyCurrentSessionPropertiesInternalBridge + 366 12 com.apple.SkyLight 0x00007fff620e8ed3 SLSessionCopyCurrentDictionary + 12 13 com.apple.AppKit 0x00007fff3015bd3a -[NSDockConnection _makeConnectionIfNeededWithRetryInterval:onDemand:] + 47 14 com.apple.AppKit 0x00007fff3015bcff __35-[NSDockConnection startConnection]_block_invoke.41 + 45 15 libdispatch.dylib 0x00007fff6cdfb6c4 _dispatch_call_block_and_release + 12 16 libdispatch.dylib 0x00007fff6cdfc658 _dispatch_client_callout + 8 17 libdispatch.dylib 0x00007fff6ce01c44 _dispatch_lane_serial_drain + 597 18 libdispatch.dylib 0x00007fff6ce025d6 _dispatch_lane_invoke + 363 19 libdispatch.dylib 0x00007fff6ce0bc09 _dispatch_workloop_worker_thread + 596 20 libsystem_pthread.dylib 0x00007fff6d056a3d _pthread_wqthread + 290 21 libsystem_pthread.dylib 0x00007fff6d055b77 start_wqthread + 15 Thread 3: 0 libsystem_pthread.dylib 0x00007fff6d055b68 start_wqthread + 0 Thread 4: 0 libsystem_pthread.dylib 0x00007fff6d055b68 start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000061495846 rbx: 0x00007ffee7c95168 rcx: 0x0000000000010000 rdx: 0x0000000118a106dd rdi: 0x000000011ba06ac0 rsi: 0x00007ffee7c94208 rbp: 0x00007ffee7c93cc0 rsp: 0x00007ffee7c93cb0 r8: 0x0000000000000000 r9: 0x00000000fffffc00 r10: 0x000000011b9fba30 r11: 0x000000011969f5b0 r12: 0x00007fc5ce510ff0 r13: 0x00007ffee7c95168 r14: 0x00007ffee7c94208 r15: 0x00007ffee7c94208 rip: 0x0000000108131df8 rfl: 0x0000000000010207 cr2: 0x000000006149584e Logical CPU: 2 Error Code: 0x00000004 (no mapping for user data read) Trap Number: 14 Binary Images: 0x107f69000 - 0x109561ff7 +com.freesurfer.freeview (0) <5D2F3B3B-4E77-33B0-BCD0-96FC46B58202> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview 0x1189c4000 - 0x118e02ff7 +org.qt-project.QtWidgets (5.12 - 5.12.7) <EF671B84-7965-3C74-89DF-09C3FA9096CA> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtWidgets.framework/Versions/5/QtWidgets 0x118f65000 - 0x1193b1fe7 +org.qt-project.QtGui (5.12 - 5.12.7) <9CC34B01-AE4A-3FF2-AC1B-DE08B8FBBBAE> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtGui.framework/Versions/5/QtGui 0x1194b5000 - 0x1199eaff7 +org.qt-project.QtCore (5.12 - 5.12.7) <AE294CA9-B3EC-3F0E-B67A-509A13C0C913> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtCore.framework/Versions/5/QtCore 0x11b6e3000 - 0x11b849fff +libqcocoa.dylib (0) <14BC2336-68E6-3ACE-B3A9-F21152A64785> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/platforms/libqcocoa.dylib 0x11b896000 - 0x11b8f4fff +org.qt-project.QtDBus (5.12 - 5.12.7) <3D9A10D9-CB4E-3A1B-8664-BD25993D5FF3> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtDBus.framework/Versions/5/QtDBus 0x11b90d000 - 0x11b936ff7 +org.qt-project.QtPrintSupport (5.12 - 5.12.7) <9AB0608C-8F2E-3FC1-B144-04ECEC6FA634> /Applications/freesurfer/*/Freeview.app/Contents/Frameworks/QtPrintSupport.framework/Versions/5/QtPrintSupport 0x11b95e000 - 0x11b9f0267 dyld (750.7) <0191F040-B591-3082-B8D9-498DC11D3BB5> /usr/lib/dyld 0x11de04000 - 0x11de29fff +libqmacstyle.dylib (0) <05CC7ADD-D833-3744-93D6-D859235085A3> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/styles/libqmacstyle.dylib 0x11de3a000 - 0x11de40ff3 +libqgif.dylib (0) <B67892CC-B844-3404-B289-B572937D144D> /Applications/freesurfer/*/Freeview.app/Contents/PlugIns/imageformats/libqgif.dylib 0x11de44000 - 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/usr/lib/system/libsystem_symptoms.dylib 0x7fff6d06f000 - 0x7fff6d085ff2 libsystem_trace.dylib (1147.120.1) <BC141783-66D9-3137-A783-211B38E49ADB> /usr/lib/system/libsystem_trace.dylib 0x7fff6d087000 - 0x7fff6d08cff7 libunwind.dylib (35.4) <42B7B509-BAFE-365B-893A-72414C92F5BF> /usr/lib/system/libunwind.dylib 0x7fff6d08d000 - 0x7fff6d0c2ffe libxpc.dylib (1738.140.3) <8DA7D88F-AE2F-3BCF-8426-8D041E57A9AA> /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: 752927 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=615.2M resident=0K(0%) swapped_out_or_unallocated=615.2M(100%) Writable regions: Total=818.4M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=818.4M(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 256K 2 Activity Tracing 256K 1 CG backing stores 2200K 4 CoreImage 24K 2 CoreUI image data 116K 1 Foundation 4K 1 Kernel Alloc Once 8K 1 MALLOC 179.4M 40 MALLOC guard page 32K 8 MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) STACK GUARD 56.0M 5 Stack 10.0M 5 VM_ALLOCATE 84K 12 __DATA 268.3M 306 __DATA_CONST 20K 1 __FONT_DATA 4K 1 __LINKEDIT 392.8M 22 __OBJC_RO 32.3M 1 __OBJC_RW 1908K 2 __TEXT 222.4M 299 __UNICODE 564K 1 mapped file 55.7M 17 shared memory 640K 15 =========== ======= ======= TOTAL 1.6G 748 TOTAL, minus reserved VM space 1.2G 748 Model: MacBookPro12,1, BootROM 427.140.8.0.0, 2 processors, Dual-Core Intel Core i7, 3.1 GHz, 16 GB, SMC 2.28f7 Graphics: kHW_IntelIris6100Item, Intel Iris Graphics 6100, spdisplays_builtin Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1867 MHz, 0x80CE, 0x4B3445424533303445422D45474346202020 Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1867 MHz, 0x80CE, 0x4B3445424533303445422D45474346202020 AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x133), Broadcom BCM43xx 1.0 (7.77.111.1 AirPortDriverBrcmNIC-1615.4) Bluetooth: Version 7.0.6f8, 3 services, 27 devices, 1 incoming serial ports Network Service: Wi-Fi, AirPort, en0 Serial ATA Device: APPLE SSD SM0512G, 500.28 GB USB Device: USB 3.0 Bus USB Device: Bluetooth USB Host Controller USB Device: 2.4G Keyboard Mouse Thunderbolt Bus: MacBook Pro, Apple Inc., 27.1 > >

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Re: [Freesurfer] matlab: command not found - How can I solve this?
by fsbuild 01 Oct '21

01 Oct '21

External Email - Use Caution Hello Camila, Did you try using the script fs_install_mcr, e.g., in the linux 7.2.0 release as freesurfer/7.2.0/bin/fs_install_mcr to install Matlab R2014b ?   Please note that there is a currently an issue with running it on M1 Macs. - R. On Oct 1, 2021, at 15:51, Camila Fernandes da Silva <camila.fernandes.silva(a)usp.br> wrote:        External Email - Use Caution        Hey, I'm totally new into Freesurfer and I need some help with my Matlab.I tried to do "recon-all -s <.....>/ -lgi But as you can see, It shows an error related to matlab...I tried everything! But nothing is working.I have heard that we should modify the startup.m file...But, what am I supposed to do with it?I'm using the Freesurfer 7.1.0 version-----------------------------------------------------------------------#@# Local Gyrification Index lh Fri Oct  1 15:25:01 EDT 2021 mris_compute_lgi --i lh.pial matlab: Command not found.matlab5: Command not found.ERROR: Matlab is required to run mris_compute_lgi!Command exited with non-zero status 1@#@FSTIME  2021:10:01:15:25:01 mris_compute_lgi N 2 e 0.01 S 0.00 U 0.01 P 94% M 2784 F 0 R 736 W 0 c 11 w 15 I 0 O 0 L 0.05 0.12 0.10@#@FSLOADPOST 2021:10:01:15:25:01 mris_compute_lgi N 2 0.05 0..12 0.10Linux developer-VirtualBox 5.4.0-87-generic #98~18.04.1-Ubuntu SMP Wed Sep 22 10:45:04 UTC 2021 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s controle01_T1 exited with ERRORS at Fri Oct  1 15:25:01 EDT 2021For more details, see the log file /home/developer/freesurfer/controle01_T1/scripts/recon-all.logTo report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1vxWcbz-IO91ksjI-7f0BIIkVTrTYBYHERFTGDy… FernandesLicenciatura em Física - IFUSP_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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