Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30063 discussions

FSL Course 2024 - Registration Open!
by Rezvan Farahibozorg 02 Feb '24

02 Feb '24

External Email - Use Caution Dear all, We are pleased to announce that registration is now open for FSL Course 2024, which will be held in-person June 17th – 21st in Osaka, Japan, co-hosted by the Riken Center for Biosystems Dynamics Research. You can find details and registration info here: https://secure-web.cisco.com/1XjftPTbYPnuuxZuh9bpnzw23-chW6Fq0WMjf2PrkFqhs2… Spots on the course are limited and will be allocated on a first-come-first-served basis. Please register early to avoid disappointment. Both new and existing users of FSL are welcome on the course, as it aims to cover both basic and more advanced features of FSL. This intensive course covers the theory and practice of functional, structural, diffusion and resting state brain image analysis. Background concepts and the practicalities of analyses are taught in detailed lectures. These lectures are interleaved with hands-on practical sessions, where attendees learn how to carry out analysis for themselves on real data. The contents covered in the course are primarily aimed at applications in basic science and clinical research (not clinical practice). Please note that the only option to attend the course in 2024 will be this in person course. To strike a balance between broad accessibility and the benefits of in-person interaction, the FSL Course intends to follow an approximately alternating pattern of fully in-person and fully online courses. We hope to see you at the course! The FSL Course team

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Euler number calculation from number of holes
by Melissa Thalhammer 01 Feb '24

01 Feb '24

External Email - Use Caution Dear FreeSurfer experts, I want to calculate Euler numbers for QC but I am not sure how to get them. I read some posts here and figured out that I get the number of holes in a surface with mris_euler_number -o $OUTPUT_FILE $subject/surf/?h.orig.nofix. Is it correct that I need to calculate the Euler number subsequently as the sum of holes of both surfaces and then Euler_number=(number_of_holes*(-2)) -2 ? Best, Melissa

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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

1 0

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.

1 0

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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