Freesurfer January 2024

freesurfer@nmr.mgh.harvard.edu

70 participants
111 discussions

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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converting preprecessed functional surface data to gifti
by wangzhiwei3233 26 Jan '24

26 Jan '24

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 ----------------------------------------------- Zhiwei Wang（王志伟), Associate Investigator International Center for Primate Brain Research Center for Excellence in Brain and Intelligence Technology Institute of Neuroscience,Chinese Academy of Sciences Room 215, Building #5, 500 Qiangye Road, Shanghai, 201602,China

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recon-all ends prematurely without error
by Weisholtz, Daniel S.,MD 25 Jan '24

25 Jan '24

Hello FreeSurfer team, I have been using FreeSurfer for some time without difficulty, but I recently encountered a problem that I cannot overcome. When I run recon-all using a command like this: recon-all -s b047test -i /Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz the process terminates in just a few seconds without error. The output reads as follows: fs-check-version --s b047test --o /var/folders/44/ndjzqbx515991v_9vt0j8spr0000gq/T//tmp.IMS2K1 Thu Jan 25 12:35:02 EST 2024 setenv SUBJECTS_DIR /Users/danielweisholtz/Coregistration/subjects cd /Users/danielweisholtz /Applications/freesurfer/7.4.1/bin/fs-check-version --s b047test --o /var/folders/44/ndjzqbx515991v_9vt0j8spr0000gq/T//tmp.IMS2K1 -rwxr-xr-x 1 root wheel 18565 Jun 14 2023 /Applications/freesurfer/7.4.1/bin/fs-check-version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 $Id$ Darwin i.partners.org<http://i.partners.org> 21.6.0 Darwin Kernel Version 21.6.0: Mon Aug 22 20:19:52 PDT 2022; root:xnu-8020.140.49~2/RELEASE_ARM64_T6000 arm64 pid 6977 Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /Applications/freesurfer/7.4.1/build-stamp.txt Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /Users/danielweisholtz/Coregistration/subjects Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 Darwin i.partners.org<http://i.partners.org> 21.6.0 Darwin Kernel Version 21.6.0: Mon Aug 22 20:19:52 PDT 2022; root:xnu-8020.140.49~2/RELEASE_ARM64_T6000 arm64 /Users/danielweisholtz/Coregistration/subjects/b047test \n mri_convert /Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz /Users/danielweisholtz/Coregistration/subjects/b047test/mri/orig/001.mgz \n mri_convert /Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz /Users/danielweisholtz/Coregistration/subjects/b047test/mri/orig/001.mgz INFO: using NIfTI-1 qform reading from /Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz... INFO: This is an unsigined short. TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) writing to /Users/danielweisholtz/Coregistration/subjects/b047test/mri/orig/001.mgz... ~/Coregistration/subjects/b047test/mri/transforms ~/Coregistration/subjects/b047test ~/Coregistration/subjects/b047test Started at Thu Jan 25 12:35:02 EST 2024 Ended at Thu Jan 25 12:35:06 EST 2024 #@#%# recon-all-run-time-hours 0.001 recon-all -s b047test finished without error at Thu Jan 25 12:35:06 EST 2024 done The subject folder is created along with some of the files, but not much is actually there. I had been using FreeSurfer 7.2.0 but I upgraded to 7.4.1, and this did not resolve the problem. Initially, I thought the problem was with the source file I was using, but I tested it with an MRI that I had previously used successfully with recon-all, and I got the same error. So something seems to have changed with my system that is causing this problem. I am running FreeSurfer on a Mac using MacOS 12.6. Many thanks for any assistance you can provide. Sincerely, Dan Weisholtz

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Intensity Representation
by ERNEST KISSI 25 Jan '24

25 Jan '24

External Email - Use Caution Dear Freesurfer Team, I registered a Macromolecular Proton Fraction (MPF) map on T1 image using multimodal registration in FSL and used freesurfer for the parcellation as instructed by one of your colleagues. I want to really confirm that whether the intensity is from the MPF as the T1 just provides the anatomical information and the MPF has the information for the myelination. Upon, a discussion with a colleague. He said that when MPF images are registered on T1 images, the intensity represents the MPF values, not the T1 values. This is because the registration process only transforms the spatial coordinates of the MPF images to match the T1 images, but does not alter the signal intensity or contrast of the MPF images. Therefore, the registered MPF images still reflect the macromolecular proton fraction of the brain tissue. Testing it in fsl, the intensity reflects that of the MPF. And a similar process has been found in a article but in their case they used mri_vol2vol. I want to confirm this since I used your software for the analysis. Thank you for your time.

2 1

Extra Large Defect T1
by Flemister, Abeoseh B. 25 Jan '24

25 Jan '24

External Email - Use Caution Hi Freesurfer team, I have gotten this error message on a successful run before: An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://secure-web.cisco.com/1kY22AwBCARfSQUY7cjfeplC3gw9EQSf1L_ErLh8Y6XncM… Try following those instructions while running recon-all on a T1.nii.gz structural scan. I read the link and it seems I have to use the wm.mgz file I get from the freesurfer run, but I was wondering if there is any preprocessing I can do to the T1 scan to prevent it? Thanks, Abeoseh Flemister

2 1

File extension .area failures
by James Bartolotti 23 Jan '24

23 Jan '24

External Email - Use Caution The MR data on network drives at our institute were recently migrated to a new server. After the migration, recon-all in freesurfer fails to complete. The issue is that freesurfer generates files with the extension ".area", including lh.area and rh.area, but the .area extension is forbidden on the server and the files will not be created. Has anyone ever had issues with an .area extension? Are there any possible workarounds to change the .area extension used by freesurfer? James Bartolotti, Ph.D. (he/him/his) Senior Scientist Structure and Function Unit, Hoglund Biomedical Imaging Center University of Kansas Medical Center jbartolotti2(a)kumc.edu<mailto:jbartolotti@ku.edu>

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