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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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Choice of ICV estimation
by Jackson Lee 31 Jan '24

31 Jan '24

External Email - Use Caution Hi there, My question is related to FreeSurfer’s calculations for intracranial volume (ICV): Given the importance to consider ICV as a potential covariate when assessing volumetric differences in ROIs between groups, which ICV output is recommended? FreeSurfer’s recon-all generates eTIV (which is widely used by default in literature, and is a registration-based method). Conversely, the SAMSEG pipeline generates sbTIV (relatively newer approach which is a segmentation-based method). While these two would be the most obvious choice, many papers also consider correcting for supratentorial volume to be an appropriate approach. To some degree, the choice of method would be guided by the research question. However in the most simple of cases (e.g., non-clinical cohorts), what method is recommended? Why would someone, for example, opt to use sbTIV over eTIV? Warm regards, Jackson Lee

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Re: [Freesurfer] Killed procees during running WMH-SynthSeg
by fsbuild 30 Jan '24

30 Jan '24

External Email - Use Caution  We have seen the (Mac or Linux) OS automatically kill resource greedy processes, e.g., commands using large model files.   Increasing the limit on physical RAM usage and/or increasing how much data is swapped out to disk may still not allow the process to run.  There have been some reports of memory leaks in tensorflow/keras python modules, with comments suggesting some issues go away when the GPU’s on the machine are no longer used for data processing.  I don’t know of a reliable workaround right now.  - R. On Jan 30, 2024, at 16:44, Bender, Andrew <BENDERA3(a)ccf.org> wrote:        External Email - Use Caution        Dear Freesurfer Experts, I’m evaluating WMH-SynthSeg for white matter lesion segmentation using the most recent development version, and ran into similar issues reported last month: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/1VwtYiRJfeLutN8gPbBz-bZmM0fMIW8vgmy6E… was running this as CPU only on a Mac Studio (M2 Ultra) with 192GB RAM. I tried is multiple times with 1-8 threads, and the process was killed in each instance. Viewing memory usage through the Mac OS Activity Monitor while running WMH-Synthseg, it appears that memory usage ramps up to >200GB (at which time the process is killed). With system resources consuming ~10GB RAM, it seems there should still be sufficient memory if it only requires ~32GB RAM. Are there any other (i.e., non-documented) options for running the process on CPU only? Any other suggestions are greatly appreciated.. Regardless of specific suggestions you may have, I wanted to bring this to your attention as a potential bug that could produce memory leaks or similar issues. Thanks,Drew   Andrew R. Bender, Ph.D.  |   Staff Neuroimaging ResearchCleveland Clinic Lou Ruvo Center for Brain Health Please consider the environment before printing this e-mailCleveland Clinic is a nonprofit, multispecialty academic medical center that's recognized in the U.S. and throughout the world for its expertise and care. Visit us online at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1wAGnCqYxSltzw75mc2-6ArqL8w0Zro9SfjmjGs… a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Killed procees during running WMH-SynthSeg
by Bender, Andrew 30 Jan '24

30 Jan '24

External Email - Use Caution Dear Freesurfer Experts, I’m evaluating WMH-SynthSeg for white matter lesion segmentation using the most recent development version, and ran into similar issues reported last month: https://secure-web.cisco.com/15YjRoSDCoF2Q2A8SbHg4Jal044A5FQlCGhkswUXxVl-RC… I was running this as CPU only on a Mac Studio (M2 Ultra) with 192GB RAM. I tried is multiple times with 1-8 threads, and the process was killed in each instance. Viewing memory usage through the Mac OS Activity Monitor while running WMH-Synthseg, it appears that memory usage ramps up to >200GB (at which time the process is killed). With system resources consuming ~10GB RAM, it seems there should still be sufficient memory if it only requires ~32GB RAM. Are there any other (i.e., non-documented) options for running the process on CPU only? Any other suggestions are greatly appreciated. Regardless of specific suggestions you may have, I wanted to bring this to your attention as a potential bug that could produce memory leaks or similar issues. Thanks, Drew Andrew R. Bender, Ph.D. | Staff Neuroimaging Research Cleveland Clinic Lou Ruvo Center for Brain Health Please consider the environment before printing this e-mail Cleveland Clinic is a nonprofit, multispecialty academic medical center that's recognized in the U.S. and throughout the world for its expertise and care. Visit us online at http://secure-web.cisco.com/1OkDITwicfyyjVUCL08BSHJwZJEGdzrgLwoI3jy6-6mImmC… for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Re: [Freesurfer] Scratch Directory Permissions Denied
by fsbuild 30 Jan '24

30 Jan '24

External Email - Use Caution  Is SUBJECTS_DIR for Freesurfer being set to live under a temporary scratch directory initially created by and then subsequently used by Matlab? If so, maybe Freesurfer is deleting files and/or changing file permissions there - causing Matlab to subsequently complain.   I would not expect multiple programs writing to the same directory tree to work together if they use different file permissions, privileges, and/or perform independent clean/delete functions in shared directories. - R. On Jan 9, 2024, at 14:47, Michael Ruvalcaba <michaelruvalcaba(a)berkeley.edu> wrote:        External Email - Use Caution        Hello,I am trying to run the recon -all function in my MATLAB pipeline using Freesurfer 6.0.0 and I have no issues with it. However, when I run the recon -all step using Freesurfer 7.2.0 and run the following command (the recon -all step finishes without error by the way):ft_read_mri([subdir '3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']);I get the following error: /bin/bash: /scratch/tp746feb5d_1e83_4141_b25d_1824a1cb209e.load_mgh.m.mgh: Permission deniedThe issue is there is no scratch file and it looks like between version 6.0.0 and 7.2.0 there is some extra lines of code that uses a scratch directory (which 6.0.0 doesn't)Does anyone have any input on this? I hope this made sense!Best,Michael Ruvalcaba_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] converting preprecessed functional surface data to gifti
by wangzhiwei3233 30 Jan '24

30 Jan '24

External Email - Use Caution Dear Yujing,Thank you for your response. I attempted the command again as follows:mris_convert -f $funcfile ${SUBJECTS_DIR}/fsaverage/surf/${hemi}.white ./$fname.gii This time, no errors were reported. However, upon comparison, it appears that the output gii file is identical (same file size) to the output from the following command line: mri_convert $funcfile ./$fname.gii (Note: mri_convert, not mris_convert) The content of the output file is as follows: <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE GIFTI SYSTEM "http://secure-web.cisco.com/1ZsaOdcZAGrRVO6b3WNQl_96LvzvlzYCF31TcDIPCvUjwn-…"> <GIFTI Version="1.0" NumberOfDataArrays="1"> <MetaData> <MD> <Name><![CDATA[UserName]]></Name> <Value><![CDATA[wzw]]></Value> </MD> <MD> <Name><![CDATA[Date]]></Name> <Value><![CDATA[Tue Jan 30 11:31:22 2024]]></Value> </MD> <MD> <Name><![CDATA[gifticlib-version]]></Name> <Value><![CDATA[gifti library version 1.09, 28 June, 2010]]></Value> </MD> </MetaData> <LabelTable/> <DataArray Intent="NIFTI_INTENT_NONE" DataType="NIFTI_TYPE_FLOAT32" ArrayIndexingOrder="RowMajorOrder" Dimensionality="1" Dim0="163842" Encoding="GZipBase64Binary" Endian="LittleEndian" ExternalFileName="" ExternalFileOffset=""> <MetaData/> <Data>eJysunV4ldfWtxsh7u7utuLua95xJ8RICQQnFA1OCQQIWjQ4xYsXdyheNDR4sKLBKSSEIkkg+Z69r+vd17fP6dnvOd975j9rZeVZz5xzzDF+4/(.....more lines like this, not shown ) It appears that there is no vertex coordinate information in it. I am uncertain whether the output result file is correct. What should the output file look like? My ultimate goal is to perform GLM analysis in SPM using these gii data. The 'gifti' function in SPM can read the output gii file, but it contains only values (cdata: 163842×1 single), as I split the frames, so the frame is "×1". This leads to errors in further analysis. I also converted the pial surface to gii and read it using the 'gifti' function in SPM; it contained three fields: faces: [327680×3 int32] mat: [4×4 double] vertices: [163842×3 single] It seems that there is no problem with converting the pial surface to gii, but there is an issue with converting functional surface data to gii. Best, zhiwei Date: Fri, 26 Jan 2024 13:29:24 +0000 From: "Huang, Yujing" <YHUANG43(a)mgh.harvard.edu> Subject: Re: [Freesurfer] converting preprecessed functional surface data to gifti To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <MN2PR04MB5982358D1DE7CF24B4127E7C9D792(a)MN2PR04MB5982.namprd04.prod.outlook.com> Content-Type: text/plain; charset="utf-8" How does your command line look like? To convert functional file, use ?-f <function-file>?. You also need to specify surface file. Best, Yujing From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of wangzhiwei3233 Sent: Friday, January 26, 2024 4:39 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] converting preprecessed functional surface data to gifti External Email - Use Caution Dear Freesurfer experts, How can I convert the preprecessed functional surface data to gifti format(gii)? I tried mris_convert, but I encountered the following error. error: freadFloat: fread failed Your assistance would be highly appreciated. Best regards, zhiwei

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longitudinal hippocampal segmentation error in Mac OS Sonoma + Freesurfer 7.2.0
by João Ramos 29 Jan '24

29 Jan '24

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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Re: [Freesurfer] conversion of D-K atlas
by Fischl, Bruce R.,PHD 29 Jan '24

29 Jan '24

Hi Anna The DK atlas (or DKT?) gets written into the aparc+aseg.mgz volume, but the DKT parts of it only consist of cortex. The subcortical labels are the normal ones (caudate, putamen, etc...) Cheers Bruce From: Arkhipova Anna, MUDr. <Anna.Arkhipova(a)fnol.cz> Sent: Monday, January 29, 2024 10:21 AM To: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu>; Freesurfer(a)nmr.mgh.harvard.edu; fischl <fischl(a)nmr.mgh.harvard.edu> Cc: phlustik(a)upol.cz; Jasenská Monika, Ing. <Monika.Jasenska(a)fnol.cz> Subject: Re: conversion of D-K atlas External Email - Use Caution Hello Bruce, Thank you very much for helping us. Basically, we would like to replicate the methodology of Poudel 2021, the study I sent to you in the last email. If you can have a look at Figure2 in the paper: we are now at the step (ii) and we need to apply the D-K atlas (including the subcortical regions) to the parcellation of our fMRI data. This step should extract BOLD time-courses from 82 regions "as per DK atlas". Since finding the D-K atlas (in 3D space as a Nifti file) through other authors wasn't succeeded, we were trying to convert the D-K atlas from Freesurfer to Nifti file ourselves. Then, in order to run recon-all, as you have suggested, a member of our team found and tried the command I copied in the last email, but we are not sure if it was the right one, because we see the name Talairah (see screenshot, on the right bottom). I hope my explanation makes sense to you. Best regards, Anna ________________________________ From: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Sent: January 19, 2024 4:17:43 PM To: Arkhipova Anna, MUDr.; Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>; fischl Cc: phlustik(a)upol.cz<mailto:phlustik@upol.cz>; Jasenská Monika, Ing. Subject: RE: conversion of D-K atlas Upozornění: Tento e-mail přišel z externí e-mailové adresy. Dbejte zvýšené opatrnosti při otvírání příloh a odkazů v textu mailu, nezadávejte svoje přihlašovací údaje. Maybe you can give us more details about what you are trying to do? Generate an fMRI time-series that is the average response in each cortical parcel? And subcortical structure? The subcortical segmentation is not Talairach, although I'm not sure that is relevant. Generating the average time series should be pretty straightforward if that is what you want (although Doug will know the commands better than I do) Cheers Bruce From: Arkhipova Anna, MUDr. <Anna.Arkhipova(a)fnol.cz<mailto:Anna.Arkhipova@fnol.cz>> Sent: Friday, January 19, 2024 10:08 AM To: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>>; Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>; fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Cc: phlustik(a)upol.cz<mailto:phlustik@upol.cz>; Jasenská Monika, Ing. <Monika.Jasenska(a)fnol.cz<mailto:Monika.Jasenska@fnol.cz>> Subject: Re: conversion of D-K atlas External Email - Use Caution Hi Bruce, thank you a lot for your kind reply. Unfortunately, we've got further question, since we tried the following command: recon-all -sd $PWD/surf -all -i ./Mprage.nii.gz -s $PWD -parallel -openmp $num_cores and acquired a cortical-level parcellation according to the D-K atlas, but the subcortical parcellation was produced (we think) automatically according to the Talairach atlas (see attached). Actually, we would like to get time-series in 82 brain regions as per D-K atlas, which should generate a vector of size 82x1 according to the methodology of Poudel et al. J Neural Eng. 2021. However, as you wrote that D-K atlas is only cortical, would you think that it is possible at all (to get cortical + subcortial via D-K)? Or have we proceeded wrongly? We are sorry for repeatedly bothering you.. (We have tried to contact for the atlas both prof. Killiany and dr. Desikan, who sadly passed away, and also asked dr. Poudel himself, but he suggested a different atlas (we are not sure why) without subcortical regions.) Thank you very much again! Best regards, Anna and lab team ________________________________ From: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Sent: January 9, 2024 3:48:23 PM To: Arkhipova Anna, MUDr.; Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>; fischl Cc: phlustik(a)upol.cz<mailto:phlustik@upol.cz> Subject: RE: conversion of D-K atlas Upozornění: Tento e-mail přišel z externí e-mailové adresy. Dbejte zvýšené opatrnosti při otvírání příloh a odkazů v textu mailu, nezadávejte svoje přihlašovací údaje. Hi Anna Parcellation is more than just format conversion - you need to map it onto the details of an individual subject's anatomy. In addition, the DKT atlas is only cortical. If you want subcortical regions in addition you should run recon-all as it will produce both. Cheers Bruce From: Arkhipova Anna, MUDr. <Anna.Arkhipova(a)fnol.cz<mailto:Anna.Arkhipova@fnol.cz>> Sent: Tuesday, January 9, 2024 6:14 AM To: Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>; fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Cc: phlustik(a)upol.cz<mailto:phlustik@upol.cz> Subject: conversion of D-K atlas External Email - Use Caution Dear prof. Fischl, We would like to kindly ask a question, if there is a way to convert Fressurfer Atlas Desikan-Killiany (lh and rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs) to Nifti file for parcellation of our resting-state fMRI data. Although we have tried script mri_convert, we obtained only cortical regions, but we need also subcortical regions. Would it be anyhow possible? Thank you so much in advance. Sincerely yours, Anna Arkhipova, MD fMRI laboratory Department of Neurology, Faculty of Medicine and Dentistry Palacky University and University hospital Olomouc Czech Republic The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline<https://secure-web.cisco.com/1Jks6aGDbVRK45MXX_bng2dSYKT5jA6CUTif0iwWA4-fH6…> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 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Error in mri_seg_overlap
by Sorby-Adams, Annabel 27 Jan '24

27 Jan '24

Hi Freesurfers, I am trying to compute DICE scores between 2 WMH-SynthSeg masks from a low-field image and high-field counterpart. I have co-registered the original images and used mri_binarize to isolate the WMH segmentations from other brain structures. I then used reg_resample to transform the binarized masks to the same space using the CPP from the coregistration. However, when I then try to run mri_seg_overlap I am getting an error that ‘error: input volumes must have matching dimensions’. When I load the binarized masks in freeview, they appear to be in the same space, and the LUT label for both is 1. Is there a way I can force mri_seg_overlap to compute the DICE in this instance/anything else I can do? I have attached 2 examples of the co-registered images for reference. Any advice appreciated! Annabel

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