Freesurfer October 2025

freesurfer@nmr.mgh.harvard.edu

36 participants
33 discussions

Intra cranial volume as a covariate
by Alan Francis 07 Oct '25

07 Oct '25

External Email - Use Caution Hi Freesurfer group: I have been using ICV as a covariate in all my analyses. Can CORTEX VOLUME be a better measure of covariance? If not, why? Thanks, Alan -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* Dr. Alan N. Francis Assistant Professor of Neuroscience Director: Neuroimaging & Neuromodulation Research Lab Institute of Neuroscience University of Texas, School of Medicine Rio Grande Valley, Texas.

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Freesurfer 7.4.1 memory usage differences between Ubuntu 20 and Ubuntu 22
by Suzanne Witt 03 Oct '25

03 Oct '25

External Email - Use Caution Hello, I have previously been running Freesurfer 7.4.1 Ubuntu 20 from a Docker container on a GCP n1-highmem-4 machine (4 CPUs, 26GB RAM, 207GB Disk, 32GB Swap) with no issues. I recently updated the Docker image to install Freesurfer 7.4.1 Ubuntu 22 from the official distribution, and now “recon-all” is getting stuck after mri_nu_correct.mni completes and at the very start of “mri_add_xform_to_header -c /usr/local/freesurfer/subjects/05/mri/transforms/talairach.xfm nu.mgz nu.mgz”. Currently, in order to get Freesurfer 7.4.1 Ubuntu 22 to run to completion, I am having to launch the jobs on a GCP n1-highmem-8 machine (8 CPUs, 52GB RAM, 207GB Disk, 32GB Swap). I am not seeing anything in either the release notes or the message boards to suggest that the Ubuntu 22 version of Freesurfer 7.4.1 has additional memory requirements compared with the Ubuntu 20 version. I have tested reducing both of the omp threads and itk threads from 4 to 2. I am also not running with the “parallel” flag. Are there any other options that can be used to reduce the memory usage of the Ubuntu 22 version of Freesurfer 7.4.1? I’ve attached a typical log file showing the recon-all workflow getting stuck at the “mri_add_xform_to_header” step. cheers. Suzanne T. Witt, PhD Scientific Solutions Engineer suzannewitt(a)flywheel.io<mailto:suzannewitt@flywheel.io> she/her flywheel.io<https://secure-web.cisco.com/1lauWKjXr4_chpBjaaXEv16-WgEUjyLdWrrdE7rj4CoASO…> [A close-up of a logo Description automatically generated] Sign up to receive our monthly updates<https://secure-web.cisco.com/1yipTZHLgLQzEDOTwlegpN9Mp4brS1wWsbahzxQ9yRI6Gu…>

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Job Vacancy - Two Postdoctoral Researcher positions at the Max Planck Institute for biological Cybernetics, Germany
by jonas.bause＠tuebingen.mpg.de 01 Oct '25

01 Oct '25

External Email - Use Caution Dear all, The High Field Magnetic Resonance Department at the Max Planck Institute for biological Cybernetics, Tuebingen, Germany, is currently seeking for two postdoctoral researchers. One position is available immediately and the other is available in January 2026. Depending on the project, the researchers will support the development of functional and structural human neuroimaging methods for the prefrontal cortex, anterior insula, or hippocampus using our 9.4 Tesla and 3 Tesla MRI scanners. They will work closely with the corresponding PIs of the two projects. Ideal candidates will have experience in performing MR scans independently and a strong expertise in (ultra-high field) fMRI and/or DTI. They should either have completed or be near completing a PhD in physics, neuroscience, biomedical engineering or similar. You can find more details about the positions, requirements, and application process on our website: <https://secure-web.cisco.com/1D2GyOf1mBTJAWowVLMSumUxjrkZwHn7fgAhifzx1166dp…> https://secure-web.cisco.com/1D2GyOf1mBTJAWowVLMSumUxjrkZwHn7fgAhifzx1166dp… <https://secure-web.cisco.com/18p3mFtE1-ZQ2Wqix7SWygDud0XR1fsv3QxXXgDtNraWT9…> https://secure-web.cisco.com/18p3mFtE1-ZQ2Wqix7SWygDud0XR1fsv3QxXXgDtNraWT9… The department for High Field Magnetic Resonance offers a world-leading research environment with access to the latest cutting-edge MRI hardware (incl. a Siemens 9.4T Magnetom Plus and Prisma 3T for humans as well as a Bruker 14.1T small animal system) and other excellent research facilities (EEG, eye-tracking, fMRI-TMS). Thanks to our own RF lab, numerous different coils optimized for specific MR research questions are available. MR image reconstruction can be performed using dedicated servers. The institute’s compute cluster is also available for signal simulations, (f)MRI pre-processing and other computationally intensive tasks. In addition, state-of-the-art stimulation equipment and physiological monitoring devices are available for all MR scanners. Tuebingen is a picturesque university town with a rich history nestled in beautiful landscapes in southwestern Germany, approximately 50 kilometers from Stuttgart. The institute is part of the Tuebingen NeuroCampus, which has more than 100 active groups. It offers a vibrant community of international researchers and an enriching environment of collaboration. The Max Planck Society seeks to employ more handicapped people and strongly encourages them to apply. Furthermore, we actively support the compatibility of work and family life. The Max Planck Society also seeks to increase the number of women in leadership positions and strongly encourages qualified women to apply. The Max Planck Society strives for gender equality and diversity. Please feel free to contact me if you have any questions. Jonas Bause, PhD Max-Planck-Institute for biological Cybernetics Department for Highfield Magnetic Resonance Max-Planck-Ring 11 72076 Tuebingen Germany

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Freesurfer October 2025