Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30128 discussions

T1 + DTI for thalamus segmentation Tensorflow version
by Jörg Stadler 26 Nov '25

26 Nov '25

External Email - Use Caution Hi, I try to run the https://secure-web.cisco.com/1OB24sXJsXKpFV3_YZf2OoUc5HIGSgT5Os8CiD0Kw5KeUJ… code, but I got stuck. I created a conda env with tensorflow 2.20, this gives me a ValueError: Unrecognized keyword arguments passed to BatchNormalization: {'fused': False} Same with tensorflow 2.16. It seems, that the 'fused' parameter was removed after version 2.4. Tensorflow 2.4 was available under python 3.6, but with conda create -n freesurfer python=3.6 and pip install tensorflow==2.4.0 I can only install versions from 2.16 onwards. Version 2.4 is not available. Removing the {'fused': False} gives me an error at input_shape = last_tensor.shape.as_list()[1:] ^^^^^^^^^^^^^^^^^ AttributeError: 'list' object has no attribute 'shape' How can I solve this dependency problem? Jörg

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Using the Glasser Cortical Atlas
by Carly McIntyre-Wood 25 Nov '25

25 Nov '25

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FreeSurfer 8.X Container?
by AmirHussein Abdolalizadeh 25 Nov '25

25 Nov '25

External Email - Use Caution Hi Freesurfer users/experts, I am looking for a containerized version of FreeSurfer 8.X. If none is available, please let me know if there are any plans to release it as a containerized version. Many people use high-performance clusters for their FreeSurfer analysis, which makes the recent FreeSurfer a bit not HPC-user-friendly; for example, the new recon-all requires 80GB RAM, so it must run on an HPC, but switching to the "cuda" version of some Python commands requires sudo - which is not often given to the HPC users. Best, Amir

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FreeSurfer License Request
by Yuxuan Dai 21 Nov '25

21 Nov '25

External Email - Use Caution Hello, I would like to request a FreeSurfer license key for academic research use. Name: Yuxuan Dai Affiliation: Zhejiang University Email: fischdai2333(a)gmail.com Thank you!

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HistoAtlasSegmentation NextBrain with FS 8.1
by La Rosa, Francesco 18 Nov '25

18 Nov '25

External Email - Use Caution Good morning, I have been trying to run the HistoAtlasSegmentation<https://secure-web.cisco.com/1ZIvtpmNUrrYqX7_h4BlvrEnYVZIRoEE4tdMenRNNTEsEz…> with either FS 8 or FS 8.1. The command fails with both versions as it seems that the FireANTs scripts (eg. segment_fireants.py') are not included in the released code. Could you help me with that? Thanks, Francesco

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[Job alert] Research Assistant in Neuroimaging & Computational Neuroscience
by Julie Ottoy 17 Nov '25

17 Nov '25

External Email - Use Caution Dear colleagues, The Ottoy & Goubran labs at the Sunnybrook Research Institute, University of Toronto, are seeking a motivated Research Assistant to work on a range of projects at the intersection of Alzheimer’s disease, cerebrovascular disease, and neuroinflammation. Our interdisciplinary teams lead the computational and neuroimaging analyses for several cutting-edge imaging studies and clinical trials at Sunnybrook focused on Alzheimer’s disease. You will be involved with a broad range of tasks, including the computational analysis of our recently funded CIHR project (focused on developing new imaging biomarkers and studying the intersection between immune-vascular dysfunction and pathology in Alzheimer’s disease). Other tasks will include processing/statistical analysis of medical images (MRI and PET), optimizing computational pipelines, building an imaging database, maintaining repositories, leveraging cutting-edge techniques to analyze biomarkers (including 7T MRI), and contributing to publications. We collaborate with a diverse and multidisciplinary team of researchers, including computer scientists, physicists, neurologists, radiologists, and psychologists, within a dynamic and collegial environment. *Main responsibilities:* 1. Management and analysis of human neuroimaging data, including structural, functional, and diffusion MRI, and PET. 2. Developing and optimizing neuroimaging pipelines and computational tools to analyze data from various dementia cohorts, including those from our international collaborators. 3. Contributing to research projects, international collaborations, grant writing, and publishing papers. 4. Writing and submitting REB applications and other administrative tasks. 5. Presenting at conferences and workshops. *Qualifications:* · Post-secondary degree in computer science, biomedical engineering, bioinformatics, computational neuroscience, or a related discipline (M.Sc. preferred). · Computer programming experience, with demonstrated skills in Python. · Intermediate knowledge of Linux, including shell scripting. · Proven ability to work independently as well as collaboratively. · Excellent verbal and written communication skills in English. *Assets:* · Python software packaging, virtual environments, High-Performance Computing (Slurm), Docker, Jupyter/IPython. · Working knowledge of neuroimaging software and toolkits (e.g., Freesurfer, FSL, ITK, MRtrix, fMRIPrep) - if no knowledge in this domain, please explain your interest in the cover letter. · Experience with systems architecture/imaging databases for computational pipeline design. · Experience with version control systems, such as Git. · Prior research experience (course-based allowed). · Experience with biostatistics/statistical analysis and Python/R or equivalent software. · Experience with Machine Learning model development and evaluation. *To apply for this position, please follow the link <https://secure-web.cisco.com/162vLYxn2JXvJnm87wEL21h9fpwgnbHZKa7tOOco4vBBom…>*

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[Job alert] Postdoctoral Fellow in Neuroimaging for Alzheimer’s disease
by Julie Ottoy 17 Nov '25

17 Nov '25

External Email - Use Caution Dear colleagues, The Ottoy & Goubran labs at the Sunnybrook Research Institute (SRI), University of Toronto, are seeking a motivated postdoctoral fellow to lead a fully-funded, innovative project at the intersection of Alzheimer’s disease, cerebrovascular disease, and neuroinflammation. You will leverage cutting-edge biomarkers and neuroimaging techniques, including 7T MRI, in a dynamic, collegial environment. The main project will focus on employing structural and functional magnetic resonance imaging, both at high- and ultra-high-resolution MRI, to study immune-vascular and neuronal dysfunction in Alzheimer’s disease. We will leverage existing large dementia cohorts, as well as a novel cohort to be acquired at SRI. We closely collaborate with a diverse and multidisciplinary team of researchers, including computer scientists, physicists, neurologists, radiologists, and psychologists. We encourage new approaches and ideas, as well as independent projects that align with current studies that involve immune-vascular contributions to dementia. SRI is the research arm of Sunnybrook Health Sciences Centre (SHSC), a teaching hospital fully affiliated with the University of Toronto. It is a world-renowned research institute known for developing innovative diagnostic and therapeutic imaging technologies. SRI employs over 300 scientists and clinician-scientists, along with more than 1,300 research staff. Working with scientists are more than 600 highly skilled biomedical and research personnel, as well as over 450 postdoctoral fellows and other trainees. SRI possesses state-of-the-art imaging facilities and computational resources, including one 1.5T (GE) and three 3T (GE, Philips, Siemens) research-dedicated MRI systems, a research MRI-PET system (Siemens), a system for MRI-guided focused ultrasound brain treatments, a fully electronically steered phased array system for MRI-guided focused ultrasound for extracranial treatments, a combined X-ray / MRI suite dedicated to research on image-guided interventions, a research CT scanner, a 7T small-bore MRI system, a vertical 7T NMR system, a GE Spinlab polarizer for 13C MRI research, a wide range of ultrasound machines, and a local HPC system. A new 7T human MRI system has recently been installed (the first in Toronto) and will be used in our projects. *Main responsibilities:* 1. Lead study design, data acquisition, and analyses for a novel project on early-stage fluid and imaging biomarkers for Alzheimer's disease & cerebral amyloid angiopathy at 3T and 7T MRI. 2. Develop neuroimaging pipelines and computational tools to analyze data from various dementia cohorts, including those from our international collaborators. 3. Write scientific manuscripts and fellowship applications. You will develop key skills for academic independence, including grant writing, supervision of students/staff, and presenting at international conferences. 4. Present findings at international conferences and workshops. 5. Collaborate on various other projects focused on neurodegenerative disorders in the labs. *Required Qualifications/Special Skills: * • PhD obtained within the last 5 years or a graduating PhD candidate in computer science, biomedical engineering, biophysics, neuroscience, or a related discipline • Experience with neuroimaging (MRI and PET) • Strong understanding of Alzheimer’s disease and/or cerebral small vessel disease pathophysiology • Proficiency with programming languages (Python/R/MATLAB, Bash) and imaging software (e.g., Freesurfer, FSL, MRtrix, fMRIPrep). • Strong research record, including multiple first-author papers and presentations • Excellent verbal and written communication skills in English • Proven ability to work independently as well as collaboratively This is a fully funded position. Stipend levels are in line with experience and CIHR stipend levels, including health and dental benefits. A 2-year minimum commitment is required. *To apply for this position, please follow the link <https://secure-web.cisco.com/1bsObucDalwjex5nhuCIRxGby1uYroLYH7fXI_AbUSoPAG…>*

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Next brain atlas on ex vivo MRI
by Yasmine Salman 17 Nov '25

17 Nov '25

External Email - Use Caution Dear FreeSurfer developers, I am trying to run the command mri_histo_atlas_segment_fireants INPUT_SCAN OUTPUT_DIRECTORY GPU THREADS MODE SIDE from NexBrain atlas on my ex vivo left hemisphere scan called EX_VIVO_18. I therefore use the following command : mri_histo_atlas_segment_fireants T2.nii EX_VIVO_18 1 -1 hemi left And I get this answer back : "Incorrect number of arguments. Usage: mri_histo_atlas_segment_fireants INPUT_SCAN OUTPUT_DIRECTORY GPU THREADS [BF_MODE] Or, for help mri_histo_atlas_segment_fireants --help" which corresponds to the SynthMorph version, which is designed for in vivo MRI. I therefore do not know how to run the "real" ex vivo MRI command. Thanks in advance, Yasmine

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Re: QDEC license error
by fsbuild 15 Nov '25

15 Nov '25

External Email - Use Caution The system libraries have changed on newer versions of Linux such that the freesurfer 6 binaries can no longer read the license file.  Freesurfer 6 was released in 2017 at the time when CentOS6 (RedHat 6) and MacOS 10..7 were still relatively current.  Some 8 years later, the encryption, etc., libraries have changed on current Linux OS’s.  Also, qdec has been deprecated (no longer supported) in the subsequent 7.X and 8.X freesurfer releases where the alternative is to use freeview and commands like mris_surf2surf mri_glmfit, mri_glmfit-sim, etc., for stream processing.  Any license you download now should work with the 7.X and 8.X releases. If you already have experience using a version of a Linux OS where you were able to run the 6.0 release using your own personal or perhaps your institutions license file, then I would try and duplicate that setup.  That may mean you need to use a container or VM to host that older version of the Linux OS where FS6 could read the license file on top of a newer version of Linux OS, i.e., if the original system where FS6 ran is no longer available. - R. On Nov 15, 2025, at 21:02, Henry Do <minhhiep.do(a)sydney.edu.au> wrote:        External Email - Use Caution        Hi Freesurfer expert, I am having an error with the QDEC. I am using Freesurfer v6.0 stable and it keeps giving me error when I do the analyze. I can load the qdec table and all other commands still run fine but when I did the analyze, it gave this error. I have converted the license.txt to $FREESURFER_HOME/.license like previous suggestion but doesn't work. Writing to /home/henrydo/subjects/qdec/Untitled/contrasts.sig.mgh--------------------------------------------------------------------------ERROR: Invalid FreeSurfer license key found in license file /home/henrydo/software/freesurfer/.license  If you are outside the NMR-Martinos Center,  go to http://secure-web.cisco.com/1ZlyBXRvfJ4TIBTtdtGuv0qPMrQ2CslRKxOtpCD… get a valid license file (it's free).  If you are inside the NMR-Martinos Center,  make sure to source the standard environment.--------------------------------------------------------------------------  I want to use QDEC to see which subjects will have impacts on different regions. If possible, I would like to have instruction how to do visualize it without qdec.  Many thanks,Henry_______________________________________________Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.eduTo unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/

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QDEC license error
by Henry Do 15 Nov '25

15 Nov '25

External Email - Use Caution Hi Freesurfer expert, I am having an error with the QDEC. I am using Freesurfer v6.0 stable and it keeps giving me error when I do the analyze. I can load the qdec table and all other commands still run fine but when I did the analyze, it gave this error. I have converted the license.txt to $FREESURFER_HOME/.license like previous suggestion but doesn't work. Writing to /home/henrydo/subjects/qdec/Untitled/contrasts.sig.mgh -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /home/henrydo/software/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://secure-web.cisco.com/1ZMUb3rLIKtbUCpTz2aOiKX5ZTHQDVKbpcuykvo5CNFCnYX… to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- I want to use QDEC to see which subjects will have impacts on different regions. If possible, I would like to have instruction how to do visualize it without qdec. Many thanks, Henry

1 0

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