Dear Joao, I’ll defer to our software specialists, but another option may be trying the Python version: https://surfer.nmr.mgh.harvard.edu/fswiki/SubregionSegmentation Cheers, /E

-- Juan Eugenio Iglesias http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of João Ramos jnpramos@outlook.com Date: Monday, January 29, 2024 at 4:26 PM To: 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 joao HOST Joaos-MBP.lan PROCESSID 17239 PROCESSOR x86_64 OS Darwin Darwin 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 + 242 1 libobjc.A.dylib 0x00007ff80e60a321 objc_exception_throw + 48 2 CoreFoundation 0x00007ff80ebbd134 -[NSObject(NSObject) __retain_OA] + 0 3 CoreFoundation 0x00007ff80ea85643 ___forwarding___ + 1379 4 CoreFoundation 0x00007ff80ea85058 _CF_forwarding_prep_0 + 120 5 Foundation 0x00007ff80f9e8abf -[NSProcessInfo arguments] + 203 6 CoreFoundation 0x00007ff80eb8aa75 __getDefaultArguments_block_invoke + 101 7 libdispatch.dylib 0x00007ff80e82159a _dispatch_client_callout + 8 8 libdispatch.dylib 0x00007ff80e8227cb _dispatch_once_callout + 20 9 CoreFoundation 0x00007ff80eb8a486 _addBackstopValuesForIdentifierAndSource + 636 10 CoreFoundation 0x00007ff80ea5183d __81-[_CFXPreferences(SourceAdditions) withNamedVolatileSourceForIdentifier:perform:]_block_invoke + 151 11 CoreFoundation 0x00007ff80eb8a145 -[_CFXPreferences withNamedVolatileSourceForIdentifier:perform:] + 241 12 CoreFoundation 0x00007ff80ea58400 -[CFPrefsSearchListSource addNamedVolatileSourceForIdentifier:] + 98 13 CoreFoundation 0x00007ff80ebc4c3b __108-[_CFXPreferences(SearchListAdditions) withSearchListForIdentifier:container:cloudConfigurationURL:perform:]_block_invoke.160 + 310 14 CoreFoundation 0x00007ff80ebc4908 -[_CFXPreferences withSearchLists:] + 60 15 CoreFoundation 0x00007ff80ea52e58 __108-[_CFXPreferences(SearchListAdditions) withSearchListForIdentifier:container:cloudConfigurationURL:perform:]_block_invoke + 278 16 CoreFoundation 0x00007ff80ebc4a80 -[_CFXPreferences withSearchListForIdentifier:container:cloudConfigurationURL:perform:] + 349 17 CoreFoundation 0x00007ff80ea63210 -[_CFXPreferences copyDictionaryForApp:withContainer:] + 119 18 CoreFoundation 0x00007ff80ea63160 __CFXPreferencesCopyCurrentApplicationStateWithDeadlockAvoidance + 158 19 Foundation 0x00007ff80fc5dee6 $s10Foundation11LocaleCacheV11preferencesAA0B11PreferencesV_SbtyFTf4d_n + 54 20 Foundation 0x00007ff80fc5ce23 $s10Foundation11LocaleCacheV15currentNSLocaleAA08_NSSwiftB0CyF + 99 21 Foundation 0x00007ff80fe3ecda $sSo8NSLocaleC10FoundationE8_currentABvgZTo + 26 22 CoreFoundation 0x00007ff80ea630ae CFLocaleCopyCurrent + 24 23 libmwi18n.dylib 0x0000000101a90cd9 _ZN2fl4i18n6LcInit17getLocaleValueOSXEv + 25 24 libmwi18n.dylib 0x0000000101a9041c _ZN2fl4i18n6LcInit12getLocaleOSXEv + 28 25 libmwi18n.dylib 0x0000000101a8fcbc _ZN2fl4i18n6LcInit7initOSXEv + 28 26 libmwi18n.dylib 0x0000000101a8f9f0 _ZN2fl4i18n6LcInit16lcInitializationEbRb + 48 27 libmwi18n.dylib 0x0000000101a95a3d _ZN2fl4i18n11MwLocaleCtx16initGlobalLocaleEb + 93 28 libmwi18n.dylib 0x0000000101a95158 _ZN2fl4i18n11MwLocaleCtx14initLocaleMgmtEv + 1176 29 libmwi18n.dylib 0x0000000101a97ce7 _ZN2fl4i18n16initLcMgmtSystemEv + 135 30 libut.dylib 0x0000000101c2ad2e _ZN2fl4i18n15init__mllc_initEi + 78 31 libut.dylib 0x0000000101c2ae59 _ZN14static_managerIN2fl4i18n13LcInitTriggerEED1Ev + 57 32 dyld 0x00007ff80e656fca ___ZZNK5dyld46Loader25findAndRunAllInitializersERNS_12RuntimeStateEENK3$_0clEv_block_invoke + 182 33 dyld 0x00007ff80e698584 ___ZNK5dyld313MachOAnalyzer18forEachInitializerER11DiagnosticsRKNS0_15VMAddrConverterEU13block_pointerFvjEPKv_block_invoke.175 + 133 34 dyld 0x00007ff80e68c913 ___ZNK5dyld39MachOFile14forEachSectionEU13block_pointerFvRKNS0_11SectionInfoEbRbE_block_invoke + 543 35 dyld 0x00007ff80e63a07f _ZNK5dyld39MachOFile18forEachLoadCommandER11DiagnosticsU13block_pointerFvPK12load_commandRbE + 249 36 dyld 0x00007ff80e68badc _ZNK5dyld39MachOFile14forEachSectionEU13block_pointerFvRKNS0_11SectionInfoEbRbE + 176 37 dyld 0x00007ff80e68e104 _ZNK5dyld39MachOFile32forEachInitializerPointerSectionER11DiagnosticsU13block_pointerFvjjRbE + 116 38 dyld 0x00007ff80e6982ba _ZNK5dyld313MachOAnalyzer18forEachInitializerER11DiagnosticsRKNS0_15VMAddrConverterEU13block_pointerFvjEPKv + 390 39 dyld 0x00007ff80e653cfc _ZNK5dyld46Loader25findAndRunAllInitializersERNS_12RuntimeStateE + 222 40 dyld 0x00007ff80e6595cb _ZNK5dyld416JustInTimeLoader15runInitializersERNS_12RuntimeStateE + 21 41 dyld 0x00007ff80e653ef1 _ZNK5dyld46Loader23runInitializersBottomUpERNS_12RuntimeStateERN5dyld35ArrayIPKS0_EE + 181 42 dyld 0x00007ff80e653ed3 _ZNK5dyld46Loader23runInitializersBottomUpERNS_12RuntimeStateERN5dyld35ArrayIPKS0_EE + 151 43 dyld 0x00007ff80e653ed3 _ZNK5dyld46Loader23runInitializersBottomUpERNS_12RuntimeStateERN5dyld35ArrayIPKS0_EE + 151 44 dyld 0x00007ff80e653ed3 _ZNK5dyld46Loader23runInitializersBottomUpERNS_12RuntimeStateERN5dyld35ArrayIPKS0_EE + 151 45 dyld 0x00007ff80e657040 _ZZNK5dyld46Loader38runInitializersBottomUpPlusUpwardLinksERNS_12RuntimeStateEENK3$_1clEv + 98 46 dyld 0x00007ff80e653f87 _ZNK5dyld46Loader38runInitializersBottomUpPlusUpwardLinksERNS_12RuntimeStateE + 93 47 dyld 0x00007ff80e67596d _ZN5dyld44APIs25runAllInitializersForMainEv + 317 48 dyld 0x00007ff80e63f241 _ZN5dyld4L7prepareERNS_4APIsEPKN5dyld313MachOAnalyzerE + 3397 49 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_long Darwin 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 subfields exited with ERRORS at Mon Jan 29 20:55:30 WET 2024

-- João Ramos