Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30071 discussions

recon-all fails with "Invalid FreeSurfer license key" when executed via Docker SDK but works interactively
by Óscar Peña-Nogales 16 Oct '25

16 Oct '25

External Email - Use Caution Hi all, I’m running recon-all inside a Docker container, but it fails with the following error when launched programmatically through an SDK: ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://secure-web.cisco.com/1caZqJPIIzERnX6myZfn7lHvJljbS0zsXzR6nmSo47CLhLQ… to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. The command used by the SDK looks like this: docker run -v /usr/local/lib/python3.10/dist-packages/xxxx/execution/communication.patch:/usr/local/lib/python3.11/dist-packages/xxxx/sdk/communication.py:ro \ --cap-drop=NET_RAW -dt --name analysis_1420668 --entrypoint /bin/bash \ --cpus=4 --memory=16384m \ europe-west3-docker.pkg.dev/xxxx/freesurfer_530:dev-1.0 \ /xxxx/entrypoint.sh --project 2289 --analysis 1420668 \ --token xxxx --url https://secure-web.cisco.com/1_ZG55biN3BILRStBLxIfao5TAMons8aRRsmdYirMJ90Ow… \ --tool-path tool:run However, when I start the container manually (e.g., docker run -it ... /bin/bash) and run recon-all inside it directly, the license is detected and validated correctly. So the license.txt file at /usr/local/freesurfer/license.txt itself appears to be valid. This suggests the issue is related to *how the container is executed by the SDK or entrypoint*, possibly involving the entrypoint script /xxx/entrypoint.sh altering the environment before recon-all starts. The Docker container has: Ubuntu 22.04 Python 3.11 Has anyone seen a similar issue where FreeSurfer fails to validate the license only when invoked non-interactively? Are there specific environment variables or checks that recon-all performs which might differ when running under /bin/bash -c or through an SDK wrapper? Any insights or debugging suggestions would be greatly appreciated. Thanks!

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Hippocampal subfield segmentation
by Tricia Merkley 14 Oct '25

14 Oct '25

External Email - Use Caution Hello FreeSurfer Developers, We are visually reviewing the output of the hippocampal subfield segmentation, and there are a few subjects that show a gap in the segmentation. For some, this may be due to variation in intensities in the region, but for others we are unable to tell why this may happen. Please see the two attached examples, with and without the segmentation. This was run with FS v7.1.0. Any idea why this may happen? Should we be concerned about the accuracy of the segmentation, or does it accurately represent the neuroanatomy for these individuals (potentially normal variation vs. pathology)? Thanks, Tricia Merkley

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Raw Cortical Thickness Oscillations/Periodicity
by Jonathan P Dyke 10 Oct '25

10 Oct '25

External Email - Use Caution Hi. We have a question about the raw cortical thickness (CT) data exported from FS with read_curv. As an example, I loaded in the "bert" sample dataset, read the left hand cortical thicknesses and then dumped to a text file (attached). This comes straight from the FS Wiki (https://secure-web.cisco.com/1xTVjn_11mS7O8kpk-Z_1qWqdnYVJGSS8DDdmA7uqHC1a7…) Q. How can I make a histogram of cortical thickness? A: In Matlab you can use the read_curv() function, as in the example below. * thick = read_curv ('/usr/local/freesurfer/subjects/bert/surfer/lh.thickness'); hist (thick,100); Notice that there are many zero values that refer to areas where there's no cortical surface. The best procedure is to create a new array without the zero values and then make the histogram. The matlab code are just in these three lines. thick = read_curv(bert); fileID2 = fopen(outfile,'w'); fprintf(fileID2,'%s \n',thick); The first image below shows the first 500 thicknesses in the array while the second image shows the first 5,000. There is a distinct oscillation/periodicity in the data that is written out. We were wondering if this has to do with the way that FS rasters across the brain going from sulci to gyri, etc? If the data is placed in a histogram, in a normal control subject we do get and expect a Gaussian distribution. Please let us know! Thanks, Jon [cid:image001.png@01DC39D4.C0D9EE30] [cid:image002.png@01DC39D4.C0D9EE30] Jonathan P. Dyke, Ph.D., DABMP (MRI) Professor of Physics Research in Radiology Weill Cornell Medicine Citigroup Biomedical Imaging Center 516 East 72nd Street, New York, NY 10021 T: (212) 746-5781 jpd2001(a)med.cornell.edu<mailto:jpd2001@med.cornell.edu> https://secure-web.cisco.com/10j0E5YHOxocBnWfcrDQ216C6nsc2hKJWtNPtq-wJom6Ys…<https://secure-web.cisco.com/1Lnkj1qw7ihDOCfmxSKCVFoSzRb4AchVJ4tZveXJcU8yLE…> https://secure-web.cisco.com/1Vk4ZlA8td_XcHqE_xIWYF3DPPZztt5RTvnCLZOXo3Xbv-… https://secure-web.cisco.com/11foGvXt-9ehohguhfB8iiX-faywHX81Sf7kmgUKGn3FBA…

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FS-FAST starting from surface data?
by Sam Hutchinson 09 Oct '25

09 Oct '25

External Email - Use Caution Hello FreeSurfer Developers, I am trying to compare (1) data for which I have only the BOLD time courses in native surface-space vertices, with (2) data where I have run the whole FS-FAST process from start to finish, computing contrasts in both surface and volume. For the fairest comparison, I would like to run all the surface data from (1) through the same preprocessing and contrast calculations which I used to create the surface contrast maps in (2). Is it possible to run the FS-FAST steps starting from surface time courses? Something like starting from f.lh.nii.gz instead of f.nii.gz. Thanks!! Sam

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Re: recon-all fails with "Invalid FreeSurfer license key" when executed via Docker SDK but works interactively
by fsbuild 08 Oct '25

08 Oct '25

External Email - Use Caution  When you create the container, copy the license.txt file into the home directory ($HOME) of the userid that will run the commands, and then define the environment variable FS_LICENSE to be $HOME/license.txt in the shell..  Or when the container comes up you want the environment variable FS_LICENSE to point to the absolute path to the license.txt file. - R. On Oct 8, 2025, at 05:04, Óscar Peña-Nogales <opennog@gmail..com> wrote:

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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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Waiting for PID error.
by Sambamoorthy, Sowmya 30 Sep '25

30 Sep '25

External Email - Use Caution Dear Experts, One of my recon-all seems to be in a hung state. Started the recon at 10AM and its still going on - we have other brains that typically finish within 4 hrs. These are the last few entries from the recon-all log. Should I kill this process? What could be the root cause for this state? Any help appreciated. TIA! -Sowmya 280/300: dt: 0.9000, rms radial error=124.996, avgs=0 285/300: dt: 0.9000, rms radial error=124.336, avgs=0 290/300: dt: 0.9000, rms radial error=123.681, avgs=0 295/300: dt: 0.9000, rms radial error=123.030, avgs=0 300/300: dt: 0.9000, rms radial error=122.383, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 152036.29 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00112 epoch 2 (K=40.0), pass 1, starting sse = 54086.27 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/13 = 0.00388 epoch 3 (K=160.0), pass 1, starting sse = 32919.19 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/14 = 0.00615 epoch 4 (K=640.0), pass 1, starting sse = 27218.02 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/15 = 0.00710 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.1488 hours FSRUNTIME@ mris_sphere 0.1488 hours 4 threads #VMPC# mris_sphere VmPeak 2099556 mris_sphere done PIDs (2329613 2329616) completed and logs appended. #@# Fix Topology lh Tue Sep 30 11:59:56 CDT 2025 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 fmri102_114 lh #@# Fix Topology rh Tue Sep 30 11:59:56 CDT 2025 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 fmri102_114 rh Waiting for PID 2398610 of (2398610 2398617) to complete...

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Error with segmentHA_T2.sh on FreeSurfer 7.4.1
by Rashid, Shams 29 Sep '25

29 Sep '25

External Email - Use Caution Dear FreeSurfer experts, I am running into a problem with hippocampal subfield segmentation with T2 input on a newly installed FreeSurfer 7.4.1 and I really need help. On this subject, recon-all and segmentHA_T1.sh completed successfully, but when I ran segmentHA_T2.sh, I get the following error after a few minutes of processing: ------ writing to T2corrected.mgz... set final LTA type to 1 ERROR: tried to read 51314688, actually read 0 Index in position 1 exceeds array bounds. Error in applyCropping (line 15) Error in segmentSubjectT1T2_autoEstimateAlveusML (line 935) MATLAB:badsubscript Command exited with non-zero status 249 ------ This instance of FreeSurfer 7.4.1 is running on Ubuntu 22.04.5 running on VirtualBox 7.1.8 on a Windows 11 Pro for Workstations. I have tried segmentHA_T2 with two different T2 input images (axial and coronal), and get the same error both times. The images open OK on Matlab. Not sure if this is a problem with the Matlab runtime. I have installed (and re-installed) Matlab runtime R2019b using fs_install_mcr 2019b. I have attached the log files for segmentHA_T2 (and also recon-all, which worked OK). I would greatly appreciate your help. Thank you very much! Best regards, Shams -- Shams Rashid, PhD Instructor Diagnostic, Molecular and Interventional Radiology BioMedical Engineering & Imaging Institute (BMEII) Icahn School of Medicine at Mount Sinai 1470 Madison Ave 1st floor, S1-116 New York, NY 10029

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