Re: [Freesurfer] longitudinal hippocampal segmentation error in Mac OS Sonoma + Freesurfer 7.2.0

29 Jan 2024


      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. &nbsp; Although The MathWorks does not support R2019b on MacOS Sonoma, I think we tested the 7.4.1 release on BigSur, Monterey and Ventura. &nbsp;So it may work on Sonoma. &nbsp;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/1rsGw8GzmRUK9yxME6fi8OiEwksVSolguqiea92G44m3nZ8...
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=$FREESURFER_HOME &nbsp;./fs_install_mcr &nbsp;R2019b
… answer y to any installer questions ...
The script should output how to set the environment variable LD_LIBRARY_PATH to pick up the The MathWorks libraries. &nbsp;That might include a setting something like,&nbsp;$ 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.&nbsp;
On Jan 29, 2024, at 21:02, Iglesias Gonzalez, Juan E. &lt;JIGLESIASGONZALEZ@mgh.harvard.edu&gt; 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-SRa... Eugenio Iglesiashttp://http://secure-web.cisco.com/1xkFYctwFMfhxok7RYaJbrw5crH_Wnw2ywE2VZjqP... &lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt; on behalf of João Ramos &lt;jnpramos@outlook.com&gt;Date:&nbsp;Monday, January 29, 2024 at 4:26 PMTo:&nbsp;Freesurfer@nmr.mgh.harvard.edu &lt;Freesurfer@nmr.mgh.harvard.edu&gt;Subject:&nbsp;[Freesurfer] longitudinal hippocampal segmentation error in Mac OS Sonoma + Freesurfer 7.2.0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;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)&nbsp;&nbsp;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&nbsp; &nbsp;CoreFoundation&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80eb17d86 __exceptionPreprocess + 2421&nbsp; &nbsp;libobjc.A.dylib&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80e60a321 objc_exception_throw + 482&nbsp; &nbsp;CoreFoundation&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80ebbd134 -[NSObject(NSObject) __retain_OA] + 03&nbsp; &nbsp;CoreFoundation&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80ea85643 ___forwarding___ + 13794&nbsp; &nbsp;CoreFoundation&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80ea85058 _CF_forwarding_prep_0 + 1205&nbsp; &nbsp;Foundation&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80f9e8abf -[NSProcessInfo arguments] + 2036&nbsp; &nbsp;CoreFoundation&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; 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&nbsp;0x00007ff80e698584 ___ZNK5dyld313MachOAnalyzer18forEachInitializerER11DiagnosticsRKNS0_15VMAddrConverterEU13block_pointerFvjEPKv_block_invoke.175 + 13334&nbsp;&nbsp;dyld&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80e68c913 ___ZNK5dyld39MachOFile14forEachSectionEU13block_pointerFvRKNS0_11SectionInfoEbRbE_block_invoke + 54335&nbsp;&nbsp;dyld&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80e63a07f _ZNK5dyld39MachOFile18forEachLoadCommandER11DiagnosticsU13block_pointerFvPK12load_commandRbE + 24936&nbsp;&nbsp;dyld&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80e68badc _ZNK5dyld39MachOFile14forEachSectionEU13block_pointerFvRKNS0_11SectionInfoEbRbE + 17637&nbsp;&nbsp;dyld&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80e68e104 _ZNK5dyld39MachOFile32forEachInitializerPointerSectionER11DiagnosticsU13block_pointerFvjjRbE + 11638&nbsp;&nbsp;dyld&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80e6982ba _ZNK5dyld313MachOAnalyzer18forEachInitializerER11DiagnosticsRKNS0_15VMAddrConverterEU13block_pointerFvjEPKv + 39039&nbsp;&nbsp;dyld&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80e653cfc _ZNK5dyld46Loader25findAndRunAllInitializersERNS_12RuntimeStateE + 22240&nbsp;&nbsp;dyld&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80e6595cb _ZNK5dyld416JustInTimeLoader15runInitializersERNS_12RuntimeStateE + 2141&nbsp;&nbsp;dyld&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80e653ef1 _ZNK5dyld46Loader23runInitializersBottomUpERNS_12RuntimeStateERN5dyld35ArrayIPKS0_EE + 18142&nbsp;&nbsp;dyld&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80e653ed3 _ZNK5dyld46Loader23runInitializersBottomUpERNS_12RuntimeStateERN5dyld35ArrayIPKS0_EE + 15143&nbsp;&nbsp;dyld&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80e653ed3 _ZNK5dyld46Loader23runInitializersBottomUpERNS_12RuntimeStateERN5dyld35ArrayIPKS0_EE + 15144&nbsp;&nbsp;dyld&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80e653ed3 _ZNK5dyld46Loader23runInitializersBottomUpERNS_12RuntimeStateERN5dyld35ArrayIPKS0_EE + 15145&nbsp;&nbsp;dyld&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80e657040 _ZZNK5dyld46Loader38runInitializersBottomUpPlusUpwardLinksERNS_12RuntimeStateEENK3$_1clEv + 9846&nbsp;&nbsp;dyld&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80e653f87 _ZNK5dyld46Loader38runInitializersBottomUpPlusUpwardLinksERNS_12RuntimeStateE + 9347&nbsp;&nbsp;dyld&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80e67596d _ZN5dyld44APIs25runAllInitializersForMainEv + 31748&nbsp;&nbsp;dyld&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0x00007ff80e63f241 _ZN5dyld4L7prepareERNS_4APIsEPKN5dyld313MachOAnalyzerE + 339749&nbsp;&nbsp;dyld&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;/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&nbsp;--&nbsp;João Ramos_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] longitudinal hippocampal segmentation error in Mac OS Sonoma + Freesurfer 7.2.0