Freesurfer

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30070 discussions

mri_vol2surf with "--vol2surf" argument generating error with non-FreeSurfer surfaces
by James Hengenius 19 Jun '25

19 Jun '25

External Email - Use Caution Hi FS list, I have some infant native space cortical surfaces generated by another software package. I would like to 'paint' them with some volumetric ROIs also in the native space. I noticed that mri_vol2surf has the "--vol2surf" option, which does not require typical FS output directory structure. I first converted the vtk surfaces from the other software to FS format. Here, the left hemi surface is called lh.pial and the corresponding volume is subject-168-T1w-iso.mgz (also used as regheader volume). I'm trying abs distance projection with 5mm distance, no projmap (0 as dummy var), and nearest neighbor interp. I get the errors below. My first guess is that using the native volume as the 'reg' argument is the issue, but any feedback is welcome! Searched a bit, but the "could not allocate xforms" error only comes up in one other thread on the listserv, and it's about mri_convert, not mri_vol2surf. Thanks, Jim H. mri_vol2surf --vol2surf \ /mnt/f/iBEAT_longitudinal_format/1433/1433_V2/subject-168-T1w-iso.mgz \ /mnt/f/iBEAT_longitudinal_format/1433/1433_V2/surf/lh.pial \ 0 \ 5 \ 0 \ /mnt/f/iBEAT_longitudinal_format/1433/1433_V2/subject-168-T1w-iso.mgz \ novsm \ 0 \ /mnt/f/iBEAT_longitudinal_format/1433/1433_V2/surf/lh.surf_ROIs error: Cannot allocate memory error: LTAalloc(1085915240): could not allocate xforms -- Jim Hengenius Research Associate Paus Research Group CHU Sainte-Justine Research Centre My Google Calendar <http://secure-web.cisco.com/1fTLLOHBUxeHr_93Qy3ygesltkiuCLo-hiJm1MHYChZYxiu…>

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Fs-FAST preprocessing error
by Hibah Chughtai 19 Jun '25

19 Jun '25

External Email - Use Caution Hello Freesurfer Developers, I am currently running the fs-FAST preprocessing command, and this is a frequent error that I keep running into across various datasets of ours. DOF = 0 I have searched the listserv in order to find any possible solutions for my query, but to no avail. Another curious issue that comes up is when I re-run the preproc-sess command after the above error, it proceeds without issue and completes the process, which has further confused me as to what the possible issue could be. Attached is the terminal session output for you to take a look at. Thank you so much for all your help! Best, Hibah

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Nonhomogenous PVC with mri_gtmpvc
by Finn, Quentin 19 Jun '25

19 Jun '25

External Email - Use Caution Freesurfer experts, I have an older PET scanner that has a nonhomogenous FWHM, varying in the z-dimension (it's 5.1 x 5.1 x 5.6 ) How should I input this FWHM into mri_gtmpvc to get accurate PVC results ? Thanks so much! -qf Houston Methodist. Leading Medicine. Houston Methodist Hospital has been named the Best Hospital in Texas for 13 years in a row by U.S. News & World Report and recognized on the Honor Roll eight times. For more than 100 years, we have provided patients with the highest quality care, the most advanced technology and the best patient experience. That’s the difference between practicing medicine and leading it. houstonmethodist.org twitter.com/MethodistHosp facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Vertex-wise cortical thickness analysis using longitudinal stream (across 3 groups and 2 timepoints)
by Jackson Lee 19 Jun '25

19 Jun '25

External Email - Use Caution Dear FreeSurfer community, I'm currently working on a study involving three groups, each with two timepoints, and I'm interested in analysing vertex-wise cortical thickness using FreeSurfer's longitudinal pipeline. I have already run recon-all, -base, and -long for all subjects. I would appreciate any clarification or recommendations on the following points: * Is it appropriate to perform vertex-wise group comparisons after longitudinal processing using mri_glmfit * Are there any recommended workflows or examples for group X timepoint interaction analysis at the vertex level? * Is it possible to conduct linear mixed-effects models (LME) at the vertex level within FreeSurfer (e.g., random intercepts for subject), or would this require extracting thickness data and performing the analysis externally (e.g., in R or Python)? * Can QDEC handle longitudinal vertex-wise analyses involving multiple groups and timepoints, or is it more suitable for simpler designs? I'd love to know if others have implemented similar longitudinal vertex-wise analyses and whether you used QDEC, custom scripts, or external tools! Warm regards, Jackson Lee

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FSGD file query
by Muskan Khetan 19 Jun '25

19 Jun '25

External Email - Use Caution Hi, I have a question related to setting up the FSGD file for my analysis. Specifically, I’m looking into the effects of hormone levels on the brain in a single group (i.e., not comparing different classes). My model includes both continuous and categorical covariates. From what I’ve gathered, most examples on the FreeSurfer website focus on group comparisons, which isn't the focus of my analysis. Therefore, I’ve set up an FSGD file with only one class (see the attached screenshot for reference). In this file: - Variables like soft_A, soft_B, soft_C, child_raceMixed, and child_raceWhite are *categorical covariates*. - Since these are covariates and not grouping factors, I haven’t created separate classes for them. I believe this approach is appropriate, but I wanted to confirm whether that understanding is correct. Additionally, regarding the contrast file: - My contrast vector is 0 1 0 0 0 0 0 0 0 0 0, where the number of elements matches the number of variables in my model (including the intercept). - As I’m specifically interested in the effect of E2_mean, I’ve set its position to 1 and all others (including covariates and intercept) to 0. Is this the correct way to set up the FSGD and contrast files for this type of single-group analysis? Thank you in advance for your guidance. Best, Muskan

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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 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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