External Email - Use Caution
(not familiar yet how to reply on this platform, possible duplicate message,
apologies)
Thank you for your reply.
I have since downloaded and installed 7.4.1 w/ matlab R2019b, and the original
issue disappeared.
I then faced problem 1)
"/Applications/freesurfer/7.4.1//bin/run_SegmentSubfieldsT1Longitudinal.sh:
line 33:
/Applications/freesurfer/7.4.1//bin/SegmentSubfieldsT1Longitudinal.app/Contents/MacOS/SegmentSubfieldsT1Longitudinal:
No such file or directory”.
My solution (temporary, just to check if it ran into further issues) was to
copy over this specific file/app from the 7.2.0 installation over to the 7.4.1
folder structure. Code went through and it ran for about 10 minutes nicely. I
was then faced with problem which ends as 2)
"
minLogLikelihoodTimesPrior =
1.6947e+06
Resolution level 1 iteration 3 deformation iterations 6
/Applications/freesurfer/7.4.1//bin/run_SegmentSubfieldsT1Longitudinal.sh: line
37: 14257 Abort trap: 6
"${exe_dir}"/SegmentSubfieldsT1Longitudinal.app/Contents/MacOS/SegmentSubfieldsT1Longitudinal
$args
Darwin Joaos-MacBook-Pro.local 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"
I imagine error 2 is related to not properly addressing problem 1. Any ideas
how to fix this? This never happened with other freesurfer installations (both
v6.0 and v7.2.0 that I also have installed and both have this file/app for
longitudinal processing) and the error output is not very informative to fix
it. File /run_SegmentSubfieldsT1Longitudinal.sh exists and looks identical to
that of 7.2.0.
Best,
--
João Ramos
On 30 Jan 2024 at 04:12 +0000, fsbuild <fsbu...@contbay.com>, wrote:
>
> 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/15uvAgvDthWGdOGyACM8IRTLNAxSG0yJP-WNrgKEPEI81Dxtj5PSEvEMgO27XZ5BDX_mqAgLKC6d8eVJdp_FJfLOV6gdu0IIjSKvUoJGPAed_WWIB2zaO3nWxmVICKP-vCxi7dJkK6LFL4alfmo9XS5JB5Q3tyDCWaeeI8T9WWBtwYOP0ah1MWO55ApP-IBH4he1CEpoPlQXi5vdOJGihMWvLxzmQcLsyguBd9v_t-N73CAndhTUWDGdi_49-EabIw9C8-7TnWU2nbSFXCcb7tcnRev8Ihoe7t32pA84rR59bk7D_tdHTTzByDfjMtjSH5EEUqGkoO3eCRFJ0eZ7BGQ/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/14G8h6OezbBpedq9hfk_TpIRQ2ASJXOicqLloqWz5RcV2NzGrxoqRVpjxSNR3H7TebrPoiVJu2-GDCYCxzrX6yqKljn4EJZjWJ_fyI63cq3woB5Fg04L8jYbRmtIKhtmMtHvi0hO5_NwSmaRR7CczxIkZFgOTKT_zkadzZVpU73BW-dStf-j8p1ToDsvC_ML9qpzFgp8I0I_faGs-E7JKzICkrBZeolCB3gFo9qPSRctD12HozdKUckB5rVsJxz4KQ72brcyKDO4y8WxJX4Oe_2gKZerwNB9V9RyUWtFmea1DC3A98EL3xE-r0z3PZme5z6aTDV9XVpRA0yB7frEZwA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSubregionSegmentation
> > Cheers,
> > /E
> >
> >
> > --
> > Juan Eugenio Iglesias
> > http://secure-web.cisco.com/1pxIahS4t5IaRxvhOa8ZZ85dRNIoWSkmqhyab4-3o6se_dDdZOLvAzSUv9DAxjiNKNOV0vye0YgEOTtrxwn2vO7iAv5Zb_1zqWpjcpXCyN59ylizQZdJ-I4kBFnj_kniRFUrtVSlvICtbpNbDGMBCP9FbO5bAz19SrS7oG1wRHxW8O1MWPeY8uUyyn-r0uEROSLI-jy7LHuRadVUEBlHRAUZCg70GWTGyslCLRYVg-gpqwAOjrvDIrRewRGwJBKURIHfgP9boOmwi7P3tNxAveARdMMQ2WCmzBx5xDYOVWgUTJRJ060Oj_lqTtJWButmSF6gQBcPfFiAT5ltRfW_42A/http%3A%2F%2Fwww.jeiglesias.com
> >
> > From: freesurfer-boun...@nmr.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 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
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://secure-web.cisco.com/1OSku06PMHQ8LXldRpW_WZEGu_cAbPd6ZC8COQJpEmBywGuG6TypKeClgpflfDE3hg9-urnec10M4y2rklZK5Q7o9pNgIfw3yUKlx6xhtsbyyGx5IwMNRkIGqChKode0OtzucQSAP_SsKCoCKCs8an84PJxGD6mI1FQSQ7aSrRbLZZmy46z4jY3Qvzk0s4Pf3WqOkeQR3E4ZgRRwm99saHIjBkOxq_IJi9OTBslp4lW-c8_QlcTTklxNrEafjEYTBshkL0l3AFqqodplTFwsPMWSaxJcjK-DG9YvBmIQrABRzgONBQ8FaD-g-B_XoQ6JQNbKWz5P2fkanieo_52hL0w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
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