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
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