Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30130 discussions

Error in SegmentSubfieldsT1Longitudinal (line 2148)
by Annchen Knodt 03 Sep '24

03 Sep '24

External Email - Use Caution Hello, I'm running the longitudinal hippocampal subfields module in ~300 individuals - it ran fine in most but with 8 i'm running into an error with the right hemisphere, which seems to be similar to the one posted in this unresolved thread<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg74844.html>, though my exact error is: In an assignment A(:) = B, the number of elements in A and B must be the same. Error in SegmentSubfieldsT1Longitudinal (line 2148) My environment: $ cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos7_x86_64-dev-20171219-d5d1e74 $ cat /etc/os-release NAME="AlmaLinux" VERSION="9.4 (Seafoam Ocelot)" ID="almalinux" ID_LIKE="rhel centos fedora" VERSION_ID="9.4" PLATFORM_ID="platform:el9" ... I can tell which of the 6 timepoints each of the 8 subjects are failing on, and i don't see anything particularly different about the input images from the failing tp, so i'm not sure what's going on or where to begin troubleshooting. I have tried simply re-running and gotten the same result. Attaching an example log file. Any help is appreciated - thanks!! Annchen

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atlas for subregional precentral gyrus
by Woo-Suk Tae 02 Sep '24

02 Sep '24

External Email - Use Caution Dear FreeSurfer developers, Thank you for developing such an excellent imaging analysis package. Among Freesurfer's parcellation atlases, is there one that divides the precentral gyrus into areas for the tongue (pharynx), face, hand, and arm, etc., or one that separates the superior, middle, and inferior frontal gyri? If not, are there any plans to develop such an atlas in the future?" Woo-Suk Tae Seoul, Korea -------------------------------------------------------------------- Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Korea University College of Medicine, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6077 email: woosuk.tae(a)gmail.com, w <woosuk.tae(a)kumc.or.kr>stae(a)korea.ac.kr --------------------------------------------------------------------

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Re: [Freesurfer] When release a version for ubuntu24?
by fsbuild 02 Sep '24

02 Sep '24

External Email - Use Caution  We should have a development build on Ubuntu 24 available in the near future. - R. On Sep 2, 2024, at 04:49, Chunling Hu <huchunling99(a)gmail.com> wrote:        External Email - Use Caution        Hi, group.I am using ubuntu24 now, but the latest FreeSurfer version is only suitable for ubuntu22. I wonder when you will release a version for ubuntu24? Thanks,Hu Chunling_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

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When release a version for ubuntu24?
by Chunling Hu 02 Sep '24

02 Sep '24

External Email - Use Caution Hi, group. I am using ubuntu24 now, but the latest FreeSurfer version is only suitable for ubuntu22. I wonder when you will release a version for ubuntu24? Thanks, Hu Chunling

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Re: [Freesurfer] Help with samseg
by fsbuild 30 Aug '24

30 Aug '24

External Email - Use Caution If you are working on a silicon (not Intel) Mac with an M1, M2, M3 processor, then try downloading and installing the development build of freesurfer for the silicon Mac,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-m… you may not get the same numerical results with this newer 2024 build compared to the 7.3.2 release from 2022, but you will get any/all the latest updates/fixes with the 2024 build. - R. On Aug 30, 2024, at 19:20, Cacciaguerra, Laura, M.D., Ph.D. <Cacciaguerra.Laura(a)mayo.edu> wrote:        External Email - Use Caution        Hello everyone,I am trying to segment MS lesions with "samseg" (FreeSurfer version 7.3.2), but it ends immediately with the following error: "zsh: illegal hardware instruction  run_samseg --input T1.nii --input T2.nii  --lesion" Have tried to run the command without the option --lesion and it works, so I guess the error is somehow linked to that option? Thank you in advance for your help,All the best,Laura_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Help with samseg
by Cacciaguerra, Laura, M.D., Ph.D. 30 Aug '24

30 Aug '24

External Email - Use Caution Hello everyone, I am trying to segment MS lesions with "samseg" (FreeSurfer version 7.3.2), but it ends immediately with the following error: "zsh: illegal hardware instruction run_samseg --input T1.nii --input T2.nii --lesion" Have tried to run the command without the option --lesion and it works, so I guess the error is somehow linked to that option? Thank you in advance for your help, All the best, Laura

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Skullstripping Issues / Estimated ICV Concern
by Carly McIntyre-Wood 29 Aug '24

29 Aug '24

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Longitudinal base processing error
by Maximo, Jose Omar 28 Aug '24

28 Aug '24

External Email - Use Caution Hello all, I am using the longitudinal pipeline and keep getting the following error when generating the base for one of our subjects. I have 3 timepoints I am including. I have checked the nu.mgz and orig.mgz files for both the base and each time point. Everything looks fine with the exception of the nu.mgz for timepoint 1 (which is a solid white and looks like a mask). Could this be the problem? I have re-run recon-all for that cross sectional subject, but the image remains the same. Attached the full recon-all.log from the base output. 3d normalization pass 1 of 2 error: MRInormFindControlPoints: could not find enough control points error: MRInormFindControlPoints failed @#@FSTIME 2024:08:16:18:05:30 mri_normalize N 10 e 10.45 S 0.04 U 10.40 P 99% M 434992 F 0 R 10859 W 0 c 4 w 11 I 0 O 0 L 1.14 0.90 0.57 @#@FSLOADPOST 2024:08:16:18:05:40 mri_normalize N 10 1.19 0.92 0.58 Linux c0235 3.10.0-1160.24.1.el7.x86_64 #1 SMP Thu Mar 25 21:21:56 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Best, Jose O. Maximo, Ph.D. | Scientist II Department of Psychiatry and Behavioral Neurobiology Heersink School of Medicine UAB | The University of Alabama at Birmingham Sparks Center 1059 | 1720 7th Ave S | Birmingham, AL 35233 P: 205.934.4245 | jomaximo(a)uabmc.edu<mailto:jomaximo@uabmc.edu><mailto:jomaximo@uabmc.edu> <mailto:jomaximo@uabmc.edu> <jomaximo(a)uabmc.edu>

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Question on hippocampus segmentation algorithm
by Savoia, Alice (Stud. FPN) 27 Aug '24

27 Aug '24

External Email - Use Caution Hi everyone! I have segmented the hippocampus subfields using the segmentation tool provided by the latest version of FreeSurfer. I am now looking at the pictures and I have a few questions: * In some cases, the hp tail takes a bit of the thalamus, does the size of the tail or its borders affect the subfields. This to know if we should exclude the participant or if we can just exclude the tail from t he analysis * How the algorithm works? I also have provided a picture as an example. Thank you for the help.

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FSGD Error
by Recht, Grace Owen 26 Aug '24

26 Aug '24

External Email - Use Caution Hello there, I am attempting to run the runGLMs.sh script and I am receiving the error message: ERROR: gdfRead: reading <path to FSGD file> is not formatted properly. The first string is ‘GroupDescriptorFile’, should be ‘GroupDescriptorFile’ It looks like the .fsgd file is correct – I can attach if necessary! I have searched the archive and it looks like one other person posted about it a while back with no conclusion that I can see. I am using FreeSurfer 7.4.1 using Linux i42.red.uits.iu.edu 4.18.0-553.8.1.el8_10.x86_64 #1 SMP Fri Jun 14 03:19:37 EDT 2024 x86_64 x86_64 x86_64 GNU/Linux Thank you for your time and help! Sincerely, Grace Grace Recht, MA PhD Student Clinical Neurotrauma Lab Department of Kinesiology | School of Public Health Indiana University – Bloomington gorecht(a)iu.edu

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