Freesurfer February 2024

freesurfer@nmr.mgh.harvard.edu

58 participants
83 discussions

mri_watershed and improvements of skullstripping
by Michelangelo Fabbrizzi 01 Feb '24

01 Feb '24

External Email - Use Caution Dear Freesurfer experts, I am new to FS, and I would have couple of questions. I used in sequence: A- recon-all -i sub-01_T1w.nii.gz -s sub-01_recon -autorecon1 B- recon-all -skullstrip -wsthresh 5 -clean-bm -s sub-01_recon C- recon-all -skullstrip -clean-bm -gcut -subjid sub-01_recon The brainmask.mgz obtained is good (no skull, brain is okay), however if I now use mri_watershed to obtain the bem surfaces, it looks the brainmask.mgz is not used and it is created a new one called ws.mgz that still contain some piece of skull that generate wrong BEM surfaces; even using -h 5 the result is not optimal: mri_watershed -h 5 -useSRAS -surf /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/sub-01_recon /Users/michelangelo/Test_skullstripping/sub-01_recon/mri/T1.mgz /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/ws.mgz I am wondering: - how can I force the mri_watershed command to use the brainmask.mgz already created after step C above, instead of creating a new one? - is it possible to use the -gcut command also for mri_watershed? Thanks, appreciated, Miche

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Re: [Freesurfer] longitudinal hippocampal segmentation error in Mac OS Sonoma + Freesurfer 7.2.0
by fsbuild 01 Feb '24

01 Feb '24

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/1rsGw8GzmRUK9yxME6fi8OiEwksVSolguqie… 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. <JIGLESIASGONZALEZ(a)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/1gPJbJkeAwLxRG5ISVgM2USwM6OoyR8xf1PZE6… Eugenio Iglesiashttp://http://secure-web.cisco.com/1xkFYctwFMfhxok7RYaJbrw5crH_Wnw2… <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of João Ramos <jnpramos@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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Query Regarding White Matter Hypointensity Volume Calculation
by Liang Zhao 01 Feb '24

01 Feb '24

External Email - Use Caution Dear FreeSurfer Team, I hope this email finds you well. I am reaching out to seek clarification regarding the WMH-SynthSeg function in FreeSurfer. I am interested in utilizing the WMH-SynthSeg function for the computation of white matter hypointensity. However, I am uncertain whether the resulting volume values undergo any form of normalization, such as division by intracranial volume, etc. Currently, I lack information on whether the obtained values are comparable across different subjects. Could you please provide insights or guidance on how the volume values are processed or standardized in WMH-SynthSeg? Understanding this aspect is crucial for ensuring the comparability of results across diverse study participants. I appreciate your dedication to the development of FreeSurfer and look forward to your valuable insights. Best regards, Liang Zhao Nanjing Medical University

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Freesurfer February 2024