Freesurfer September 2025

freesurfer@nmr.mgh.harvard.edu

36 participants
42 discussions

Postdoctoral position in neuroimaging studies of neurodevelopmental disorders
by Z S 10 Sep '25

10 Sep '25

External Email - Use Caution *Description: * Our lab (https://secure-web.cisco.com/1_T3NvfJuqYnwjO4JZk_Y_pHCobABv2tYSNO634DlMF30W…) at the University of South Carolina is seeking a postdoctoral fellow to lead projects in neurodevelopmental disorders. This position focuses on investigating how genetic factors and environmental factors (e.g., early life stress) influence human brain developmental trajectory and neurodevelopmental disorders (e.g., autism) using computational models. Our lab explores the mechanisms of atypical brain development and neurodevelopmental disorders (e.g., autism) by leveraging in-house (e.g., high-resolution MRI) and public datasets (e.g., ABCD, HBCD, and etc.) to bridge genetic variation, neural circuitry, exposure (e.g., early life adversity) and psychopathological phenotypes, and treatment outcomes. These innovative projects will leverage state-of-the-art deep computational models and neuroimaging, supported by the brand-new Brain Imaging Center (with high-field 7T MRI) and the Biobehavioral Research Center. *Role: * 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 be able to analyze neuroimaging (MRI) data. 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) You can also submit your application at https://secure-web.cisco.com/1cGcZDxxsp7m-L8EGTHW8C_jvjHLh1i3TSdKniExuCGuNP…

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Re: Recon-all error: synthtrip on Apple M3 Sonoma 14.6.1
by fsbuild 09 Sep '25

09 Sep '25

External Email - Use Caution  If you have not already done so, please try running your commands in the bash shell as shown in the page referenced via the below link (scroll down to MACOS).  So far I've seen no issues running various recon-all tests with 8.0.0 and 8.1.0 on a MacMini running Sequoia 15.5 with an M2 processor and 32GB of RAM using the setups listed on that page.https://secure-web.cisco.com/1GOFWApQpWTzyWax8ZqPYPCfDLKlE61L1LtFzLl80… - R.

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Re: Surfa update
by Hoopes, Andrew 08 Sep '25

08 Sep '25

Thanks Chris, Good point. We can get on this. I’ll investigate putting in a quick fix. The requirement for numpy<2 stems from complications with building cython utilities. I think we should ditch these utilities and instead rely on prebuilt tools (eg scipy). It sacrifices some minor runtime, but will relieve major distribution headache. That project is a bit more involved but hopefully we can get to it soon. Andrew From: Rorden, Chris <RORDEN(a)mailbox.sc.edu> Date: Thursday, August 14, 2025 at 12:22 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>, Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu> Subject: Surfa update External Email - Use Caution Hello Would it be possible to release a version of surfa that uses numpy 2? For examples, the original version of synthsr and the one included with FreeSurfer rely on Python versions that are end of life. I upgraded this to use up to Python 3.13 (latest version supported by TensorFlow), but the Surfa support demand for numpy 1 requires special environment so it does not play well with other tools (surfa pyproject.toml notes 'numpy<2.0’). I really do not want to maintain a separate fork, and if we could upgrade surfa the maintained FreeSurfer project could include versions of these scripts that support maintained versions of Python. For the time being, here is my fork: https://secure-web.cisco.com/1Tj_72h5VBPhEzQKtS8Wnrte2Od2rEUMf2iVThbaWZrFxe… Thanks for all your work, -chris

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Version 7.2 & 7.4
by Taylor, Lisa 08 Sep '25

08 Sep '25

External Email - Use Caution Hi group, I was curious if using both versions of freesurfer 7.2 & 74 would be acceptable? We realized some of our data contained both due to some miscommunication. Would the recommendation be to use just one 7.X version, or are the two similar enough to use concurrently? Lisa

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RedHat installation
by Gomez-Acebo Ruiz, F. (Fernando) 08 Sep '25

08 Sep '25

External Email - Use Caution Hi, I was wondering if FreeSurfer can be installed in Red Hat systems Thank you, Fernando ________________________________ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ________________________________ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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job openings
by Fischl, Bruce R.,PHD 06 Sep '25

06 Sep '25

From Elizabeth Hillman (now at St Jude): Faculty Positions available! The Department of Imaging Sciences at St Jude Children's Research Hospital is seeking highly innovative faculty at all levels. Our focus is on the development of technologies for quantitative measurement, imaging and analysis across scales and modalities, and their application to accelerating scientific discovery and advancing clinical care. St Jude is a vibrant and inspirational environment where you will be supported to do your best, high-risk, high-reward work, side by side with amazing collaborators. We are committed to maximizing the impact of our work, driven by the belief that no child should die in the dawn of life. More details here: https://lnkd.in/e4qs6Pkx Please submit your application by November 10th 2025.

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Re: Freesurfer 7.4.1 memory usage differences between Ubuntu 20 and Ubuntu 22
by fsbuild 05 Sep '25

05 Sep '25

External Email - Use Caution  As Marinus mentioned, don’t assume 2 different versions of the operating system will have the same memory footprint when they run; newer versions of operating systems often require more memory to run because of added features, processes, code changes, etc. Likewise, for applications running within the OS, memory and resource management may have changed in the newer Ubuntu22 kernel compared to Ubuntu20 such that physical RAM usage and disk space used when swapping the contents of memory in/out to disk may not result in an application having the same resource usage compared to an older version of the OS.https://secure-web.cisco.com/1BOZ3enPr6AhuGeM5g0qnYf74KqxmJXpSwPDwJywRSp… - R.

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recon-all: expert options not applied to mris_inflate
by Mokli, Yahia 04 Sep '25

04 Sep '25

External Email - Use Caution Hello FreeSurfer Team, What I am trying to accomplish: I am running a full recon-all (-all) and trying to control the number of inflation iterations via an expert options file containing: "mris_inflate -n 30" FreeSurfer version and platform: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed Running inside Docker based on Ubuntu 22.04 Command I ran: recon-all -i /data/test/sub-0113_t1_axisAlign.nii.gz -s sub-0113 -all -hires -parallel -openmp 16 -expert /data/test/expert_inflate30.opts Error/output seen: During the Inflation1 stage, the log shows mris_inflate being invoked without the -n flag and with a bare "30" argument: mris_inflate -no-save-sulc 30 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Shortly after, recon-all exits with ERRORS. The recon-all.log file have these lines at the end: #@# Inflation1 lh Thu Sep 4 13:54:46 UTC 2025 /data/subjects/sub-0113/scripts mris_inflate -no-save-sulc 30 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #----------------------------------- #@# Inflation1 rh Thu Sep 4 13:54:46 UTC 2025 /data/subjects/sub-0113/scripts mris_inflate -no-save-sulc 30 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 4083 of (4083 4086) to complete... Waiting for PID 4086 of (4083 4086) to complete... mris_inflate -no-save-sulc 30 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading 30 ** failed to open GIFTI XML file '30.gii' mrisReadGIFTIdanum: ERROR reading gifti 30.gii [INFO] read, cannot find 30, trying 30.gii ... error: No such file or directory error: mris_inflate: could not read surface file 30 mris_inflate -no-save-sulc 30 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading 30 ** failed to open GIFTI XML file '30.gii' mrisReadGIFTIdanum: ERROR reading gifti 30.gii [INFO] read, cannot find 30, trying 30.gii ... error: No such file or directory error: mris_inflate: could not read surface file 30 PIDs (4083 4086) completed and logs appended. Linux 4fa29909686b 6.8.0-78-generic #78-Ubuntu SMP PREEMPT_DYNAMIC Tue Aug 12 11:34:18 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-0113 exited with ERRORS at Thu Sep 4 13:54:46 UTC 2025 Troubleshooting already tried: - Recreated the expert file to ensure ASCII hyphen and LF newline: printf 'mris_inflate -n 30\n' > /data/test/expert_inflate30.opts - Resumed with overwrite -xopts-overwrite -expert /data/test/expert_inflate30.opts - Verified that mris_inflate accepts -n 30 manually:: /usr/local/freesurfer/8.1.0/bin/mris_inflate -no-save-sulc -n 30 in.surf out.surf - Other expert options (e.g., "mris_smooth -seed 9999") are honored and appear correctly in the log Is there a known issue in FreeSurfer 8.1.0 on Ubuntu 22.04 where expert options for mris_inflate are not applied? What is the recommended way to ensure -n 30 is honored? Thank you for your help. Best regards, Yahia Mokli

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Recon-all error: synthtrip on Apple M3 Sonoma 14.6.1
by Diedrich, Lukas 03 Sep '25

03 Sep '25

External Email - Use Caution Hello Freesurfer developers, I’m attempting to run the recon-all pipeline but it exited with ERRORS during synthtrip. I’ve attached the recon-all.log. 1) FreeSurfer version: freesurfer-macOS-darwin_arm64-8.1.0-20250718-f30dfed 2) Platform: macOS Sonoma 14.6.1 3) Command: recon-all -s NVR-1 -sd /Volumes/INTENSO/Projects/NeuroVR+/MRI/recon/NVR-1_recon -i /Volumes/INTENSO/Projects/NeuroVR+/MRI/Nifti/NVR-1_nii/5_t1_tfl3d_sag_ti1090_fa9_tr2700_09mm_p2.nii.gz -T2 /Volumes/INTENSO/Projects/NeuroVR+/MRI/Nifti/NVR-1_nii/6_t2_space_sag_081x081x09mm_p2.nii.gz -T2pial -all Error: \n mri_synthstrip --threads 1 -i /Volumes/INTENSO/Projects/NeuroVR+/MRI/recon/NVR-1_recon/NVR-1/mri/orig.mgz -o /Volumes/INTENSO/Projects/NeuroVR+/MRI/recon/NVR-1_recon/NVR-1/mri/synthstrip.mgz \n if: Empty if. then: Command not found. Configuring model on the CPU Running SynthStrip model version 1 Input image read from: /Volumes/INTENSO/Projects/NeuroVR+/MRI/recon/NVR-1_recon/NVR-1/mri/orig.mgz Processing frame (of 1): 1 Killed 4) recon-all.log: see attached Looking forward to your help Lukas Diedrich ________________________________ Dr. rer. nat. Lukas Diedrich Postdoctoral researcher Non-invasive Brain Stimulation (NBS) Lab Department of Neurology University Medical Center Göttingen, Germany +49 551 39 64838 | lukas.diedrich(a)med.uni-goettingen.de [cid:94c3b536-7fb1-4ae8-8dc3-a0d660d38d74@med.uni-goettingen.de]

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Fixing Misclassified Ventricles During QC
by Ran Yan 02 Sep '25

02 Sep '25

External Email - Use Caution Hi Freesurfer team, I am new to FreeSurfer and am currently doing QC using FreeSurfer (v.8). I wanted to check what the best approach is to correcting the following participant (screenshot attached). It appears that the participant had very large ventricles (?), which have been misclassified (as indicated by FreeSurfer drawing the white and pial surfaces around them). My initial thought was to add control points or manually fill the ventricles in WM.mgz, but I wanted to check first, since this issue is widespread across the brain volumes. Many thanks for your help! Sincerely, Rachel -- *Ran (Rachel) Yan* She/her Ph.D. Candidate in Developmental Psychology University of Michigan 530 Church St. | East Hall 2048 | Ann Arbor, MI | 48109-1043

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Freesurfer September 2025