Freesurfer August 2024

freesurfer@nmr.mgh.harvard.edu

43 participants
58 discussions

Ubuntu 24.04 compatibility? (libc6 < 2.36, libncurses5)
by Hunter Buchanan 16 Aug '24

16 Aug '24

External Email - Use Caution Hi all! Do we know if a version of Freesurfer compatible with Ubuntu 24.04 is planned for the near future? Attempting to install the 22.04 .deb file on 24.04 shows that dependency libncurses5 is unavailable (manually installing a previous version may fix this) and that libc6 < 2.36 is required, though 2.39 is already installed (this is the tough one). If a 24.04 compatible release is not expected in the near future, do we know of any temporary fixes to get Freesurfer working? Or are we SOL on new servers for now? Thanks in advance!

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Re: [Freesurfer] recon-all terminates at fix topology rh step
by fsbuild 16 Aug '24

16 Aug '24

External Email - Use Caution  You’re using the 7.2.0 release from 2021 whereas the latest release is 7.4.1 from 2023.   Unless you have to stick with the older release because floating point math results could differ with a newer one, then you could try downloading and installing the 7.4.1 release from the links under “7.4.1 Release” at the top of the page, https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloadsOr try just running the subject that fails with the 7.4.1 release to see if it makes a difference. - R.

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recon-all terminates at fix topology rh step
by Dong, Yilei 16 Aug '24

16 Aug '24

External Email - Use Caution Hi Freesurfer Developers, I have one particular subject that terminates at the Fix Topology rh step (screenshot of recon-all-status.log file below) until the job walltime runs out. This problem happens solely for this subject when I submit recon-all just for this 1 subject and also when I do batch submission with multiple other subjects. In batch submission, the 99 other subjects successfully go through recon-all's entire processing stream. For each recon-all job, we allocate 8G. Is there a way to troubleshoot this problem? [cid:fe218087-a1e3-4f1e-b1db-d3f5bf300cd2] Here is other information about my operating system & the freesurfer version. Please let me know if you need anything else! Freesurfer version: freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b Platform: Rocky Linux release 8.8 (Green Obsidian) uname -a: Linux login01 4.18.0-513.24.1.el8_9.x86_64 #1 SMP Thu Apr 4 18:13:02 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux Recon-all log: see attached Sincerely, Yilei

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Re: [Freesurfer] mri_easyreg
by fsbuild 15 Aug '24

15 Aug '24

External Email - Use Caution  When you setup the freesurfer 7.4.1 environment from the terminal, check you see the output below when running bash shell from the terminal.  If you see all the same output, then it should at least work to get the help info from the command… $ bash $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 ————     <—- MAKE SURE YOU SEE THIS EXACT LINESetting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.4.1FSFAST_HOME       /usr/local/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/7.4.1/subjectsMNI_DIR           /usr/local/freesurfer/7.4.1/mniFSL_DIR           /usr/pubsw/packages/fsl/current … then check you see this output ... $ which mri_easyreg/usr/local/freesurfer/7.4.1/bin/mri_easyreg$ file `which mri_easyreg`/usr/local/freesurfer/7.4.1/bin/mri_easyreg: Bourne-Again shell script, ASCII text executable$ which fspython/usr/local/freesurfer/7.4.1/bin/fspython$ fspython --versionPython 3.8.13 … now the help option should work … $ mri_easyreg —help … you may see some warning messages before the help text if your machine does not support cuda for tensorflow … usage: mri_easyreg [-h] [—ref REF] [--ref_seg REF_SEG] [--flo FLO] [--flo_seg FLO_SEG] [--ref_reg REF_REG] [--flo_reg FLO_REG] [--fwd_field FWD_FIELD] [--bak_field BAK_FIELD] [--affine_only]                   [--threads THREADS] EasyReg: deep learning registration simple and easy optional arguments:  -h, --help            show this help message and exit  --ref REF             Reference image .  --ref_seg REF_SEG     Reference SynthSeg segmentation (will be created if it does not exist).  --flo FLO             Floating image.  --flo_seg FLO_SEG     Floating SynthSeg segmentation (will be created if it does not exist).  --ref_reg REF_REG     (optional) Registered referenced.  --flo_reg FLO_REG     (optional) Registetred floating images (in space of reference).  --fwd_field FWD_FIELD                        (optional) Forward field  --bak_field BAK_FIELD                        (optional) Inverse field  --affine_only         (optional) Skips nonlinear part  --threads THREADS     (optional) Number of cores to be used. Default is 1. You can use -1 to use all available cores If you see all the above, then maybe some command options/parameters are causing mri_easyreg to fail.  I’ve asked the mri_easyreg developer to look at your command. - R. On Aug 15, 2024, at 10:23, Sara Ponticorvo <ponti045@umn..edu> wrote:        External Email - Use Caution        Hello,so the command I used is: mri_easyreg --ref MP2RAGE_uni_resampled_2mm.nii.gz --flo sub017_ute_anat.nii.gz --ref_seg mprage_seg.nii --flo_seg ute_seg.nii  The output I get is:Illegal instruction I also tried putting the absolute path to the files, but I get the same output. And, I also tried to get the help (but I'm not sure if there is one) by typing mri_easyreg --h and mri_easyreg --help, but I get the same Illegal instruction output..I'm running it on CentOS Linux 7 server. The output from cat /etc/redhat-releaseCentOS Linux release 7.9.2009 (Core) Thank you for your help!SaraOn Thu, Aug 15, 2024 at 12:45 AM fsbuild <fsbuild(a)contbay.com> wrote: Hello Sara, Please send along the terminal output from running the command so we can see the error. Maybe you could also let us know what version of CentOS you are running, e.g., also include the output from, $ cat /etc/redhat-release - R. On Aug 14, 2024, at 15:32, Sara Ponticorvo <ponti045(a)umn.edu> wrote:         External Email - Use Caution         Hi Freesurfer experts!I am trying to use mri_easyreg. I've installed freesurfer v7.4.1 on my centos machine but when I try to run mri_easyreg I've "Illegal instruction" message. Do you have any suggestion on how to solve it? Thank you,Sara _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh..harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sara Ponticorvo, PhDCenter for Magnetic Resonance ResearchUniversity of Minnesota2021 6th St. S.E.Minneapolis MN 55455 (USA)phone: +1 612 626 2001 (front-desk)e-mail: ponti045@umn.edu _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] mri_easyreg
by fsbuild 15 Aug '24

15 Aug '24

External Email - Use Caution Hello Sara, Please send along the terminal output from running the command so we can see the error. Maybe you could also let us know what version of CentOS you are running, e.g., also include the output from, $ cat /etc/redhat-release - R. On Aug 14, 2024, at 15:32, Sara Ponticorvo <ponti045(a)umn.edu> wrote:        External Email - Use Caution        Hi Freesurfer experts!I am trying to use mri_easyreg. I've installed freesurfer v7.4.1 on my centos machine but when I try to run mri_easyreg I've "Illegal instruction" message. Do you have any suggestion on how to solve it? Thank you,Sara _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Calculating gray matter volume and BPF from Samseg output
by Maaike Romme 15 Aug '24

15 Aug '24

External Email - Use Caution Dear all, For the past few days I have been trying to use the output from the Samseg tool to generate more volume metrics, such as gray matter volume. Unfortunately, I am not getting any output other than what I already get from Samseg. I tried running mri_segstats, but that also gave me the same volumes I already had. I was wondering if there is another tool within freesurfer to calculate these volumes for which I do not need to run the recon-all tool due to time constraints. Thank you in advance. Best regards, Maaike Romme

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mri_easyreg
by Sara Ponticorvo 14 Aug '24

14 Aug '24

External Email - Use Caution Hi Freesurfer experts! I am trying to use mri_easyreg. I've installed freesurfer v7.4.1 on my centos machine but when I try to run mri_easyreg I've "Illegal instruction" message. Do you have any suggestion on how to solve it? Thank you, Sara

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Comparison of "segment_subregions" and "recon-all"
by Yoonho Hwang 14 Aug '24

14 Aug '24

External Email - Use Caution Hi Iglesias, Okay. I got it. Thank you for informing me. I will try it. Sincerely, Yoonho -- *Hwang, Yoonho* *Research professor* *Institute of Human Genomic Study,* *College of Medicine, Korea University* *#123, Jeokgeum-ro, Danwon-gu, Ansan-si, Gyeonggi-do, **15355, Republic of Korea.* *Email: ken.lmstar11(a)gmail.com <ken.lmstar11(a)gmail.com>*

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Re: [Freesurfer] freesurfer version 6 on Debian
by fsbuild 13 Aug '24

13 Aug '24

External Email - Use Caution  Debian 9 looks like it was the current version when Freesurfer 6 was released in 2017 for CentOS6 and MacOS.    But even if Freesurfer 6 runs on Debian 9, it’s not expected to run on current versions of Debian or CentOS because of system library changes that can break binary backwards compatibility.    I suggest you create a CentOS6 VirtualBox VM or Docker container and then install/run Freesurfer 6 in that.   You should be able to use Virtualbox or Docker to host CentOS6 on current versions of Linux, MacOS and Windows. - R. On Aug 13, 2024, at 14:57, Gregory Book <gregory.a.book(a)gmail.com> wrote:        External Email - Use Caution        Is there a way to install freesurfer6 on Debian? I see only CentOS packages available for freesurfer6. Or, is there a way to build from source on Debian?_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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freesurfer version 6 on Debian
by Gregory Book 13 Aug '24

13 Aug '24

External Email - Use Caution Is there a way to install freesurfer6 on Debian? I see only CentOS packages available for freesurfer6. Or, is there a way to build from source on Debian?

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Freesurfer August 2024