External Email - Use Caution At this point, I think your best bet is to install and run the freesurfer 7..4.1 release from June 2023 which was tested with R2019b. Although The MathWorks does not support R2019b on MacOS Sonoma, I think we tested the 7.4.1 release on BigSur, Monterey and Ventura. So it may work on Sonoma. The 7.2.0 release from 2021 is too old to have been tested on newer versions of MacOS. You can install the 7.4.1 release with the pkg installer,https://secure-web.cisco.com/1rsGw8GzmRUK9yxME6fi8OiEwksVSolguqiea92G44m3nZ8vkR_pUdXoEEyyZGxT5kLITfqkOgn9K5Yi6uB4BWVSsfdeQgcNv2po-t8b5umyOs0BOD2M0pUfv1H0RRvI_KeZ3icjBIVvwrzWk7U_0QdriOPTDw8UtNebc9olqbl0vWKqGg0u37yGtGA5Gb7vy2EgH6Mys3HaeqSXocPinchKl5s4zKYgHxK_nchQ9XBHFmgQuUtdO-UnZ3Nmq-ou5cKbJ2c14SCGnIR8WJtJKI9XZAPGysNTrsd1RpoBNpaki-KGHp8CRNiOK1iDt4nFlLSwUXejfepae4z2VhG_54A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg After installing 7.4.1, you should run the fs_install_mcr_script provided in the freesurfer distribution to install and setup R2019b using the instructions below. - R.
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1 $ cd $FREESURFER_HOME/bin $ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b … answer y to any installer questions ... The script should output how to set the environment variable LD_LIBRARY_PATH to pick up the The MathWorks libraries. That might include a setting something like, $ export LD_LIBRARY_PATH=$FREESURFER_HOME/MCRv97/bin/glnxa64:$LD_LIBRARY_PATH Please make sure you have otherwise removed any references to your previous matlab R2016 environment from PATH, LD_LIBRARY_PATH, etc. On Jan 29, 2024, at 21:02, Iglesias Gonzalez, Juan E. <jiglesiasgonza...@mgh.harvard.edu> wrote:Dear Joao,I’ll defer to our software specialists, but another option may be trying the Python version:https://secure-web.cisco.com/1gPJbJkeAwLxRG5ISVgM2USwM6OoyR8xf1PZE6EvMJf-SRaA9EGrMIWMtoTGH7aMT86QE3DlUA-XL1cyKUT3DHiXT0ma5mZHgd8ElXQmslT_wo-B2jePlem_KHUlWQToIJfu88U9chsrSFPXs215vnwwuXBvNTLJVE_lh4T6cIBV8QanuQVm3e3BjQ2EaXcYC6lhhkrsO-307Mn1YWFWI0xkVANXmWcY12KiGHnlfDB4oQwY-GjBYbyVDhcDlyZNNNweBWf11saa25eKp5Psjr8CU3zE-iQlD181J1MMo6K2lE_R2hvTnJn_7VjLF8-XpGoq_UscsjzCYr00bk4ySXg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSubregionSegmentationCheers,/E --Juan Eugenio Iglesiashttp://http://secure-web.cisco.com/1xkFYctwFMfhxok7RYaJbrw5crH_Wnw2ywE2VZjqP-qYTzxO45GiX_q_jHOGkqPmOQY12cjT47WY_TNufoQOmeAFinHtebu_tDtkJJVMmB96rzEQOlCZI1k2mTTmKDvUzHaDMbEkw4eLcStBv9BFy5ovxP_UcPTbUqlRjlE6blbq8D5Fv7VSm30vX9EUttKo8iDtVUGfS2XjFHB6gAGXA1URsH0JKHt7Q7dflcHZH_NjOHpx0Yn-QKiwXl_S6b6qeUhvyqWOImXysYCX2OZ2FK_hd1KwrVcATlaLNfRrLWT-3UAWR26hK9Kd627pXbyVKblH7o-d5_SZJqNciPeKwBQ/http%3A%2F%2Fwww.jeiglesias.com%C2%A0From%3A%C2%A0freesurfer-bounces%40nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of João Ramos <jnpra...@outlook.com>Date: Monday, January 29, 2024 at 4:26 PMTo: Freesurfer@nmr.mgh.harvard.edu <Freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] longitudinal hippocampal segmentation error in Mac OS Sonoma + Freesurfer 7.2.0 External Email - Use Caution Dear all,I would appreciate your help in an issue I am having and one that I have not found a reference to regarding Freesurfer. Basically, I have run all of the longitudinal Freesurfer pipeline and I am now interested in running the longitudinal hippocampal / amygdala segmentation code (segmentHA_T1_long.sh), though I am faced with an error (log below). I have searched and this happens on various settings with no pattern that I could recognize (apart from iOS app development), and it was also pointed out on a mathworks forum post regarding matlab 2016 on a Mac OS Sonoma (which is my operating system, and this version of freesurfer uses matlab r2014b). Would this be possible to run within Mac OS Sonoma (v14.2.1, with current freesurfer version 7.2.0) or should I run a linux instance with freesurfer install and everything?Thank you!--------------------------------USER joaoHOST Joaos-MBP.lanPROCESSID 17239PROCESSOR x86_64OS DarwinDarwin Joaos-MBP.lan 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:54:10 PST 2023; root:xnu-10002.61.3~2/RELEASE_X86_64 x86_64------------------------------#--------------------------------------------#@# Longitudinal Hippocampal Subfields processing (T1) left Mon Jan 29 20:55:28 WET 2024------------------------------------------Setting up environment variables---DYLD_LIBRARY_PATH is .:/Applications/freesurfer/7.2.0//MCRv84//runtime/maci64:/Applications/freesurfer/7.2.0//MCRv84//bin/maci64:/Applications/freesurfer/7.2.0//MCRv84//sys/os/maci64:/Applications/freesurfer/7.2.0//lib/gcc/lib:*** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: '-[__NSCFString stringByStandardizingPath]: unrecognized selector sent to instance 0x600002e281b0'*** First throw call stack:(0 CoreFoundation 0x00007ff80eb17d86 __exceptionPreprocess + 2421 libobjc.A.dylib 0x00007ff80e60a321 objc_exception_throw + 482 CoreFoundation 0x00007ff80ebbd134 -[NSObject(NSObject) __retain_OA] + 03 CoreFoundation 0x00007ff80ea85643 ___forwarding___ + 13794 CoreFoundation 0x00007ff80ea85058 _CF_forwarding_prep_0 + 1205 Foundation 0x00007ff80f9e8abf -[NSProcessInfo arguments] + 2036 CoreFoundation 0x00007ff80eb8aa75 __getDefaultArguments_block_invoke + 1017 libdispatch.dylib 0x00007ff80e82159a _dispatch_client_callout + 88 libdispatch.dylib 0x00007ff80e8227cb _dispatch_once_callout + 209 CoreFoundation 0x00007ff80eb8a486 _addBackstopValuesForIdentifierAndSource + 63610 CoreFoundation 0x00007ff80ea5183d __81-[_CFXPreferences(SourceAdditions) withNamedVolatileSourceForIdentifier:perform:]_block_invoke + 15111 CoreFoundation 0x00007ff80eb8a145 -[_CFXPreferences withNamedVolatileSourceForIdentifier:perform:] + 24112 CoreFoundation 0x00007ff80ea58400 -[CFPrefsSearchListSource addNamedVolatileSourceForIdentifier:] + 9813 CoreFoundation 0x00007ff80ebc4c3b __108-[_CFXPreferences(SearchListAdditions) withSearchListForIdentifier:container:cloudConfigurationURL:perform:]_block_invoke.160 + 31014 CoreFoundation 0x00007ff80ebc4908 -[_CFXPreferences withSearchLists:] + 6015 CoreFoundation 0x00007ff80ea52e58 __108-[_CFXPreferences(SearchListAdditions) withSearchListForIdentifier:container:cloudConfigurationURL:perform:]_block_invoke + 27816 CoreFoundation 0x00007ff80ebc4a80 -[_CFXPreferences withSearchListForIdentifier:container:cloudConfigurationURL:perform:] + 34917 CoreFoundation 0x00007ff80ea63210 -[_CFXPreferences copyDictionaryForApp:withContainer:] + 11918 CoreFoundation 0x00007ff80ea63160 __CFXPreferencesCopyCurrentApplicationStateWithDeadlockAvoidance + 15819 Foundation 0x00007ff80fc5dee6 $s10Foundation11LocaleCacheV11preferencesAA0B11PreferencesV_SbtyFTf4d_n + 5420 Foundation 0x00007ff80fc5ce23 $s10Foundation11LocaleCacheV15currentNSLocaleAA08_NSSwiftB0CyF + 9921 Foundation 0x00007ff80fe3ecda $sSo8NSLocaleC10FoundationE8_currentABvgZTo + 2622 CoreFoundation 0x00007ff80ea630ae CFLocaleCopyCurrent + 2423 libmwi18n.dylib 0x0000000101a90cd9 _ZN2fl4i18n6LcInit17getLocaleValueOSXEv + 2524 libmwi18n.dylib 0x0000000101a9041c _ZN2fl4i18n6LcInit12getLocaleOSXEv + 2825 libmwi18n.dylib 0x0000000101a8fcbc _ZN2fl4i18n6LcInit7initOSXEv + 2826 libmwi18n.dylib 0x0000000101a8f9f0 _ZN2fl4i18n6LcInit16lcInitializationEbRb + 4827 libmwi18n.dylib 0x0000000101a95a3d _ZN2fl4i18n11MwLocaleCtx16initGlobalLocaleEb + 9328 libmwi18n.dylib 0x0000000101a95158 _ZN2fl4i18n11MwLocaleCtx14initLocaleMgmtEv + 117629 libmwi18n.dylib 0x0000000101a97ce7 _ZN2fl4i18n16initLcMgmtSystemEv + 13530 libut.dylib 0x0000000101c2ad2e _ZN2fl4i18n15init__mllc_initEi + 7831 libut.dylib 0x0000000101c2ae59 _ZN14static_managerIN2fl4i18n13LcInitTriggerEED1Ev + 5732 dyld 0x00007ff80e656fca ___ZZNK5dyld46Loader25findAndRunAllInitializersERNS_12RuntimeStateEENK3$_0clEv_block_invoke + 18233 dyld 0x00007ff80e698584 ___ZNK5dyld313MachOAnalyzer18forEachInitializerER11DiagnosticsRKNS0_15VMAddrConverterEU13block_pointerFvjEPKv_block_invoke.175 + 13334 dyld 0x00007ff80e68c913 ___ZNK5dyld39MachOFile14forEachSectionEU13block_pointerFvRKNS0_11SectionInfoEbRbE_block_invoke + 54335 dyld 0x00007ff80e63a07f _ZNK5dyld39MachOFile18forEachLoadCommandER11DiagnosticsU13block_pointerFvPK12load_commandRbE + 24936 dyld 0x00007ff80e68badc _ZNK5dyld39MachOFile14forEachSectionEU13block_pointerFvRKNS0_11SectionInfoEbRbE + 17637 dyld 0x00007ff80e68e104 _ZNK5dyld39MachOFile32forEachInitializerPointerSectionER11DiagnosticsU13block_pointerFvjjRbE + 11638 dyld 0x00007ff80e6982ba _ZNK5dyld313MachOAnalyzer18forEachInitializerER11DiagnosticsRKNS0_15VMAddrConverterEU13block_pointerFvjEPKv + 39039 dyld 0x00007ff80e653cfc _ZNK5dyld46Loader25findAndRunAllInitializersERNS_12RuntimeStateE + 22240 dyld 0x00007ff80e6595cb _ZNK5dyld416JustInTimeLoader15runInitializersERNS_12RuntimeStateE + 2141 dyld 0x00007ff80e653ef1 _ZNK5dyld46Loader23runInitializersBottomUpERNS_12RuntimeStateERN5dyld35ArrayIPKS0_EE + 18142 dyld 0x00007ff80e653ed3 _ZNK5dyld46Loader23runInitializersBottomUpERNS_12RuntimeStateERN5dyld35ArrayIPKS0_EE + 15143 dyld 0x00007ff80e653ed3 _ZNK5dyld46Loader23runInitializersBottomUpERNS_12RuntimeStateERN5dyld35ArrayIPKS0_EE + 15144 dyld 0x00007ff80e653ed3 _ZNK5dyld46Loader23runInitializersBottomUpERNS_12RuntimeStateERN5dyld35ArrayIPKS0_EE + 15145 dyld 0x00007ff80e657040 _ZZNK5dyld46Loader38runInitializersBottomUpPlusUpwardLinksERNS_12RuntimeStateEENK3$_1clEv + 9846 dyld 0x00007ff80e653f87 _ZNK5dyld46Loader38runInitializersBottomUpPlusUpwardLinksERNS_12RuntimeStateE + 9347 dyld 0x00007ff80e67596d _ZN5dyld44APIs25runAllInitializersForMainEv + 31748 dyld 0x00007ff80e63f241 _ZN5dyld4L7prepareERNS_4APIsEPKN5dyld313MachOAnalyzerE + 339749 dyld 0x00007ff80e63e31f start + 1839)libc++abi: terminating due to uncaught exception of type NSException/Applications/freesurfer/7.2.0//bin/run_SegmentSubfieldsT1Longitudinal.sh: line 33: 17311 Abort trap: 6 /Applications/freesurfer/7.2.0//bin/SegmentSubfieldsT1Longitudinal.app/Contents/MacOS/SegmentSubfieldsT1Longitudinal /Users/joaoramos/Downloads/Patients/patients_freesurfer/ 0.333333333333333333333333333333333333 /Applications/freesurfer/7.2.0//average/HippoSF/atlas/AtlasMesh.gz /Applications/freesurfer/7.2.0//average/HippoSF/atlas/AtlasDump.mgz /Applications/freesurfer/7.2.0//average/HippoSF/atlas/compressionLookupTable.txt 0.05 0.05 left L-BFGS long.v21 '/Applications/freesurfer/7.2.0//bin/fs_run_from_mcr /Applications/freesurfer/7.2.0//bin/' 0 Colombo_long Colombo_2018_T1.long.Colombo_long Colombo_2021_T1.long.Colombo_longDarwin Joaos-MBP.lan 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:54:10 PST 2023; root:xnu-10002.61.3~2/RELEASE_X86_64 x86_64longitudinal subfields exited with ERRORS at Mon Jan 29 20:55:30 WET 2024 -- João Ramos_______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
