Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

Re: Running Freesurfer on HPC (Almalinux OS, CycleCloud Compute nodes)
by fsbuild 19 Jun '25

19 Jun '25

External Email - Use Caution I have previously tested freesurfer running on the Expanse/SDSC cluster; I’m not aware of any issues there, e.g., running scripts that depend upon tcsh being installed under bin.  I believe they at least used to use spack to configure packages. I have seen freesufer installed via the freesurfer .rpm or .deb package on a (dedicated) server which is then made available via NFS (read only) mount points into a cluster.  Neither does this setup have issues with the shells, commands, libraries, etc., freesurfer depends upon being installed in their standard locations.  End users should not be writing the results of their subject analyses or any files into the installed freesurfer distribution as part of running freesurfer commands. But the compiled C++ binaries and/or scripts in the freesurfer distribution are not expected to run correctly unless the native linux package tools have been used to install the .rpm or .deb package including installing all the dependencies.   I thought the original poster mentioned they had no issue with freesurfer installed on a stand-alone machine.   If so, I would try and use the installer package the original poster mentioned ran on the stand-alone machine - and try to get that to work in the cluster.   Alternately, the most recent 8.0.0 release freesurfer installer packages are available at the top of this page,https://secure-web.cisco.com/1-2c2DruDJu6g70Z2ppynBgBQqNyhUw_Iet89ZjVB… Short of a standard .deb or .rpm package install, you could as root in a stand-alone container do an interactive install with dpkg, apt, yum, etc… to generate a list of the required packages and then try to manually install/configure your cluster setup from that list.  But we do not test this way (and this is not officially supported). - R.

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Re: Running Freesurfer on HPC (Almalinux OS, CycleCloud Compute nodes)
by fsbuild 19 Jun '25

19 Jun '25

External Email - Use Caution Currently the tcsh scripts assume a normal Linux .rpm or .deb package installation with a dependency on csh/tcsh being installed under /bin.    We do not assume spack, modules, etc. as may be used on clusters is going to configure software images such that it will conflict with that setup.  So the tcsh scripts will not run unless /bin/tcsh exists or maybe an alias would work. If it’s not possible to do a normal install of the .deb or .rpm package to directly install all the system command and library dependencies, then I recommend analyzing the package files to check all the dependencies are otherwise installed. "If: expression syntax errors" can be from executing the wrong shell.  In the case of trying to execute bash scripts, that error might be from running something like  “dash” on an Ubuntu flavor of Linux instead of the full-blown “bash" shell. - R

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Re: Running Freesurfer on HPC (Almalinux OS, CycleCloud Compute nodes)
by Marlene Staginnus 17 Jun '25

17 Jun '25

External Email - Use Caution Dear Yujing, Thank you for your response and help. I’m replying to your two points below. 1. make sure ‘tcsh’ is in her PATH I can confirm that I’ve loaded tcsh via the module system and it’s correctly in my PATH. Running which tcsh returns: /apps/fsv2/software/2024a/tcsh/6.24.10-GCCcore-12.3.0/bin/tcsh. Initially, as the system doesn’t have tcsh at /bin/tcsh, this caused errors (e.g., even recon-all --version would fail), but Roberto kindly provided a workaround. Since then, I’ve been able to run recon-all --help and recon-all --version without issues. However, when I try to run the full recon-all command on a subject, it exits within a few seconds due to UpdateNeeded being looked for in an inaccessible location. I’ve included the full console output below for context. This happens regardless of whether I run it from a bash or tcsh shell. 1. It looks like she has ‘/opt/cycle/jetpack/bin/’ in her PATH. Is ‘/campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup’ her Freesurfer install directory? I’m assuming she sourced Freesurfer environment correctly. After sourcing Freesurfer environment correctly, ‘echo $PATH’ should show $FREESURFER_HOME/bin in the very beginning. Also, check if executables in $FREESURFER_HOME/bin have executable permissions. * Yes, /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup is my FreeSurfer installation directory. * I believe I’ve sourced the FreeSurfer environment correctly — I’ve successfully tried sourcing from both bash and tcsh and did not previously have these issues on a local Linux machine. * Running echo $PATH confirms that $FREESURFER_HOME/bin appears at the beginning: /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup/bin:… opt/cycle/jetpack/bin/ is also in my Path but at the very end. Regarding the UpdateNeeded error — when I run which UpdateNeeded, it correctly returns: /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup/bin/UpdateNeeded. So I’m unsure why, at runtime, it's still attempting to use /opt/cycle/jetpack/bin/UpdateNeeded, which leads to the following error: /opt/cycle/jetpack/bin/UpdateNeeded: Permission denied. if: Expression Syntax. Please let me know if there is anything else I can check of provide to help resolves this – and thank you again for your support. Best wishes, Marlene $ recon-all -s sub-315A_T1w -i /campaign/VB-FM5HPC-001/Marlene/Data_tmp/input/sub-315A_T1w.nii -sd $SUBJECTS_DIR -all fs-check-version --s sub-315A_T1w --o /tmp/tmp.eCskko Tue Jun 17 17:43:12 BST 2025 setenv SUBJECTS_DIR /campaign/VB-FM5HPC-001/Marlene/Data_tmp/output cd /campaign/VB-FM5HPC-001/Marlene/Data_tmp/output /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup/bin/fs-check-version --s sub-315A_T1w --o /tmp/tmp.eCskko -rwxr-xr-x 1 ms2290 rce_VB-FM5HPC-001 18565 Jun 17 09:40 /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup/bin/fs-check-version freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 $Id$ Linux nimbus-1-spot-fsv2-2-4 4.18.0-553.50.1.el8_10.x86_64 #1 SMP Tue Apr 15 08:09:22 EDT 2025 x86_64 x86_64 x86_64 GNU/Linux pid 15581 Current FS Version freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 Subject does not have a bstampfile, copying /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup/build-stamp.txt Subject FS Version: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /campaign/VB-FM5HPC-001/Marlene/Data_tmp/output Actual FREESURFER_HOME /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup Linux nimbus-1-spot-fsv2-2-4 4.18.0-553.50.1.el8_10.x86_64 #1 SMP Tue Apr 15 08:09:22 EDT 2025 x86_64 x86_64 x86_64 GNU/Linux /campaign/VB-FM5HPC-001/Marlene/Data_tmp/output/sub-315A_T1w mri_convert /campaign/VB-FM5HPC-001/Marlene/Data_tmp/input/sub-315A_T1w.nii /campaign/VB-FM5HPC-001/Marlene/Data_tmp/output/sub-315A_T1w/mri/orig/001.mgz mri_convert /campaign/VB-FM5HPC-001/Marlene/Data_tmp/input/sub-315A_T1w.nii /campaign/VB-FM5HPC-001/Marlene/Data_tmp/output/sub-315A_T1w/mri/orig/001.mgz reading from /campaign/VB-FM5HPC-001/Marlene/Data_tmp/input/sub-315A_T1w.nii... TR=7.80, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 0.999974, 0.00720242) k_ras = (0, -0.00720242, 0.999974) writing to /campaign/VB-FM5HPC-001/Marlene/Data_tmp/output/sub-315A_T1w/mri/orig/001.mgz... @#@FSTIME 2025:06:17:17:43:13 mri_convert N 2 e 5.88 S 0.03 U 5.81 P 99% M 54872 F 0 R 1094 W 0 c 20 w 109 I 0 O 30376 L 0.07 0.10 0.14 @#@FSLOADPOST 2025:06:17:17:43:19 mri_convert N 2 0.15 0.12 0.14 #-------------------------------------------- #@# MotionCor Tue Jun 17 17:43:20 BST 2025 Found 1 runs /campaign/VB-FM5HPC-001/Marlene/Data_tmp/output/sub-315A_T1w/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... /opt/cycle/jetpack/bin/UpdateNeeded: Permission denied. if: Expression Syntax. From: Huang, Yujing <YHUANG43(a)mgh.harvard.edu> Sent: 17 June 2025 15:50 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Re: Running Freesurfer on HPC (Almalinux OS, CycleCloud Compute nodes) 1. make sure ‘tcsh’ is in her PATH 2. It looks like she has ‘/opt/cycle/jetpack/bin/’ in her PATH. Is ‘/campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup’ her Freesurfer install directory? I’m assuming she sourced Freesurfer environment correctly. https://secure-web.cisco.com/1OPa-utClpZzYVZAm7UT1FwJaDX8H6HzbnM9eZHYpViNrG… https://secure-web.cisco.com/1C3fygtctOGKgwcSFtU7swK_Up5CoYO6M1TZ7S739PLgjU… After sourcing Freesurfer environment correctly, ‘echo $PATH’ should show $FREESURFER_HOME/bin in the very beginning. Also, check if executables in $FREESURFER_HOME/bin have executable permissions. Yujing From: Roberto Scipioni <roberto.scipioni(a)redoakconsulting.co.uk<mailto:roberto.scipioni@redoakconsulting.co.uk>> Sent: Tuesday, June 17, 2025 10:34 AM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Running Freesurfer on HPC (Almalinux OS, CycleCloud Compute nodes) External Email - Use Caution Dear Sir or Madam, I am an HPC admin who has been contacted by a user who has installed the Freesurfer in his local directory. However, she keeps getting errors in using the software., for instance: 1. tcsh ONLY works if it is actually present in /bin . This defeats the purpose of using the HPC and its module environment especially using the Cloud as compute nodes are ephemeral. 1. Update needed is searched in /opt/cycle/jetpack/bin/UpdateNeeded rather than in the Software folder /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup/bin where it is. Is there any obvious reason why this may happen. The user is knowledgeable and she has already trying different environment options like those suggested in: https://secure-web.cisco.com/1CCwHd0B7yIez3RoL6XJ5pWTdKUBQ8lUK_gtbn0lLhpB5C…<https://secure-web.cisco.com/1MlpAewP0l0b-LfNakbZ011g7UhgKbNFb1Xo5kZEtuRQnX…> Your help with this would be greatly appreciated. Kind regards Dr Roberto Scipioni Senior HPC specialist, Red Oak Consulting, UK

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Running Freesurfer on HPC (Almalinux OS, CycleCloud Compute nodes)
by Roberto Scipioni 17 Jun '25

17 Jun '25

External Email - Use Caution Dear Sir or Madam, I am an HPC admin who has been contacted by a user who has installed the Freesurfer in his local directory. However, she keeps getting errors in using the software., for instance: 1. tcsh ONLY works if it is actually present in /bin . This defeats the purpose of using the HPC and its module environment especially using the Cloud as compute nodes are ephemeral. 2. Update needed is searched in /opt/cycle/jetpack/bin/UpdateNeeded rather than in the Software folder /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup/bin where it is. Is there any obvious reason why this may happen. The user is knowledgeable and she has already trying different environment options like those suggested in: https://secure-web.cisco.com/1MlpAewP0l0b-LfNakbZ011g7UhgKbNFb1Xo5kZEtuRQnX… Your help with this would be greatly appreciated. Kind regards Dr Roberto Scipioni Senior HPC specialist, Red Oak Consulting, UK

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FW: Postdoc position in neuroimaging-genomics studies
by Sennott, Liam Ricker 16 Jun '25

16 Jun '25

Posted on behalf of zhiq.sha(a)gmail.com<mailto:zhiq.sha@gmail.com> From: Z S <zhiq.sha(a)gmail.com> Date: Monday, June 16, 2025 at 10:11 AM To: freesurfer-owner(a)nmr.mgh.harvard.edu <freesurfer-owner(a)nmr.mgh.harvard.edu> Subject: Postdoc position in neuroimaging-genomics studies External Email - Use Caution Zhiqiang Sha's lab (https://shazhiqiang.wixsite.com/sha-lab<https://secure-web.cisco.com/1p-qub4e6wW7OPjQDli2Uf0lBCwFDQ_MqAxO2RDtQj5zbt…>) at the University of South Carolina is seeking an exceptional postdoctoral fellow to lead projects in neuroimaging-genomics/transcriptomics. This position focuses on investigating how genetic factors (e.g., genomics) and environmental factors (e.g., early life stress) influence brain development and neurodevelopmental disorders such as autism spectrum disorder. Research will integrate both in-house datasets and large-scale public resources. Our lab investigates the neurophysiological mechanisms underlying neurodevelopmental disorders by integrating multimodal biomedical data from both in-house and public datasets (e.g., UK Biobank, ABCD, HBCD, and etc.), including neuroimaging, genomics, and transcriptomics. These innovative projects will leverage state-of-the-art computational models and AI algorithms, supported by the brand-new Brain Imaging Center (with high-field 7T MRI) and the Biobehavioral Research Center. As a postdoctoral fellow, you will lead this interdisciplinary project and benefit from close mentorship and collaborative opportunities in a supportive and productive research environment. You will have full access to (1) rich in-house and public datasets; (2) advanced neuroimaging platforms (3T and 7T MRI); (3) biobehavioral and clinical research resources. You will conduct a range of neuroimaging and genomics-based analyses, design and implement computational models, and lead manuscript preparation. The role also includes: (1) collaborating with international research collaborators; (2) presenting work at international conferences and institutional seminars. What we offer: We assist postdoctoral researchers in applying for internal and external grants and provide structured mentorship tailored to each individual's career goals. Our lab fosters a collaborative and productive environment, and we actively support postdocs in building their academic networks, generating high-quality research publications, and securing independent faculty positions. Requirements: The ideal candidate will hold a Ph.D. in neuroscience, bioinformatics, biomedical sciences, psychology, or a related field. A strong interest in programming is essential (e.g., Python, R, Matlab, or Linux). The successful applicant will be highly motivated, possess strong analytical and problem-solving skills. Excellent communication skills and the ability to work both independently and collaboratively in an interdisciplinary research environment are also required. How to apply: submit your CV to Dr. Zhiqiang Sha (zsha(a)mailbox.sc.edu<mailto:zsha@mailbox.sc.edu>). We encourage applications from individuals of all backgrounds who are passionate about neuroscience.

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Re: Query related to controlling for ICV in the models for surface area and thickness
by Douglas N. Greve 14 Jun '25

14 Jun '25

I'm not sure what you mean. Can you elaborate? On 6/11/2025 5:09 PM, kingwai.chu(a)gmail.com wrote: > > External Email - Use Caution > > Hi Doug, > > What about the argument of using eTIV^(2/3) makes the scaling > dimensionless? > > Best, > > King-Wai > > *From:*Douglas N. Greve <dgreve(a)mgh.harvard.edu> > *Sent:* Wednesday, June 11, 2025 4:09 PM > *To:* freesurfer(a)nmr.mgh.harvard.edu > *Subject:* [Freesurfer] Re: Query related to controlling for ICV in > the models for surface area and thickness > > Yes, it is recommended. The exact form it should take is in dispute, > namely whether you should correct by the eTIV or the eTIV.^(2/3). The > second is motivated by the idea of a sphere whose surface area grows > with the 2/3 power of the volume. But cortex is not a sphere -- it is > folded, so the area can grow faster than 2/3 power. I usually just > scale by eTIV. When you run mris_preproc, you can add the --etiv > option and it will do the scaling for you. > > On 6/11/2025 4:05 AM, Muskan Khetan wrote: > > * External Email - Use Caution * > > Dear Team members, > > I have a question regarding vertex-wise analysis using FreeSurfer. > In my current analysis, I’m looking at the effects of an > independent variable on cortical thickness and surface area across > the brain. > > I understand that forROI-based surface area analyses, it is > typically recommended to control for total brain volume (TBV) or > intracranial volume (ICV), as surface area is correlated with > these global brain size measures. However, I’m unsure whether this > recommendation applies tovertex-wise analysesas well or whether > anyunderlying preprocessing stepsin FreeSurfer account for brain > size differences automatically. > > Could you please advise on whether TBV or ICV should be included > as covariates in vertex-wise surface area models? And more > broadly, under what circumstances is it advisable to control for > global brain size in vertex-wise analysis? > > Any insights would be greatly appreciated. > > Best, > > Muskan > > > > _______________________________________________ > > Freesurfer mailing list --freesurfer(a)nmr.mgh.harvard.edu > > To unsubscribe send an email tofreesurfer-leave(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.… <https://secure-web.cisco.com/1zgqCqj4qntd9bt8wznuUVVVTiFZuyVa-TmLzp-uKKBcf3…> >

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Re: any updates on installing on Ubuntu 24?
by fsbuild 12 Jun '25

12 Jun '25

External Email - Use Caution   Recent freesurfer releases list the supported OS’s on the web page,https://secure-web.cisco.com/14dxuu_DbHG9-OdhIKIO4mT7TZRdP453JQfldXjZ0… While Ubuntu24 is not listed for 8.0.0, it is on the list to support for future releases. Recent changes in Linux OS’s prevent binary backwards compatibility when upgrading to Rocky9, CentOS9, Ubuntu 24. - R. On Jun 12, 2025, at 13:59, William Graves <william.graves(a)rutgers.edu> wrote:        External Email - Use Caution        Dear FreeSurfer experts, In searching your email list archive, I saw a message from Feb 5 of this year about known issues with installing FreeSurfer on Ubuntu 24. Any updates on whether those issues have been resolved? I ask because when I download and try to install the .deb package for freesurfer 8.0, I get this: Unpacking freesurfer (8.0.0) ...dpkg: dependency problems prevent configuration of freesurfer: freesurfer depends on libncurses5; however:  Package libncurses5 is not installed. freesurfer depends on libc6 (<< 2.36); however:  Version of libc6:amd64 on system is 2.39-0ubuntu8.4. freesurfer depends on libicu70 (>= 70.1-1~); however:  Package libicu70 is not installed. dpkg: error processing package freesurfer (--install): dependency problems - leaving unconfiguredProcessing triggers for libc-bin (2.39-0ubuntu8.4) ...Errors were encountered while processing: freesurfer I’d appreciate any insight you could give! Best,Will --- William W. Graves, Ph.D. Associate Professor, Department of Psychology Rutgers, The State University of New Jersey Smith Hall, Room 337 101 Warren Street, Newark, NJ  07102 http://secure-web.cisco.com/1NPzbSguN782gCrsIkTAvR6KDkkdSIQ9Rze0CwYkPXW7LPQ… _______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1V0E1aPavCVV45TGCyLOq0zPzHsNXPELJIyxY000FGU3PO…

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any updates on installing on Ubuntu 24?
by William Graves 12 Jun '25

12 Jun '25

External Email - Use Caution Dear FreeSurfer experts, In searching your email list archive, I saw a message from Feb 5 of this year about known issues with installing FreeSurfer on Ubuntu 24. Any updates on whether those issues have been resolved? I ask because when I download and try to install the .deb package for freesurfer 8.0, I get this: Unpacking freesurfer (8.0.0) ... dpkg: dependency problems prevent configuration of freesurfer: freesurfer depends on libncurses5; however: Package libncurses5 is not installed. freesurfer depends on libc6 (<< 2.36); however: Version of libc6:amd64 on system is 2.39-0ubuntu8.4. freesurfer depends on libicu70 (>= 70.1-1~); however: Package libicu70 is not installed. dpkg: error processing package freesurfer (--install): dependency problems - leaving unconfigured Processing triggers for libc-bin (2.39-0ubuntu8.4) ... Errors were encountered while processing: freesurfer I’d appreciate any insight you could give! Best, Will --- William W. Graves, Ph.D. Associate Professor, Department of Psychology Rutgers, The State University of New Jersey Smith Hall, Room 337 101 Warren Street, Newark, NJ 07102 http://secure-web.cisco.com/10xSdrnQwPN0s0wFvnWgnpsjwfLF9AmsaUlcaB4xmPD1xZ5…

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Please stop copying me on these emails. I no longer require updates on this matter.
by Joseph 12 Jun '25

12 Jun '25

External Email - Use Caution Please stop copying me on these emails. I don't require updates on this matter.

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Computational Neuroscience Post Doc job opening
by Thomas Funck 12 Jun '25

12 Jun '25

External Email - Use Caution Hi everyone, We currently have a job opening for a Post Doctoral Fellow in computational neuroscience, specifically for neural mass modeling. The position is based in New York City and is for 3 years. Please see the attached pdf for job details. Feel free to reach out if you have any questions or want to discuss further! Cheers, Thomas Funck, PhD Research Scientist Child Mind Institute This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message and any attachments

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