Freesurfer

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30076 discussions

Finishing LeftHemi LGI and Not Starting RightHemi on Linux HPC
by Toms, Robert 04 May '26

04 May '26

External Email - Use Caution Dear FreeSurfer Team, I'm currently testing an LGI pipeline using FreeSurfer 8.0.0's -localGI recon-all command on our university's Linux-based computing cluster, aiming to get LGI statistics from 12,000ish subjects. We've got it successfully working for the most part, but we've run into the following issue: We currently run 50 subjects at a time in parallel (using TAC Launcher) across 4 nodes. In each batch of 50, 4 subjects (1 on each node) finish the left hemisphere of the -localGI command, and never start the right hemisphere process. They maintain the IsRunning.lh+rh file in their scripts directory, where it stays after the computation times out and is ended by the SLURM system. The other 46 complete both the lh and rh with no problems, apart from the occasional failure due to an MRI artifact. We've tried shrinking the batch sizes, looking for missing files, and checking matlab dependencies, and haven't been able to figure out the problem, though we've ruled out it being a memory issue. We've also separated these one-hemisphere-run folks out and tried running just the right hemisphere -localGI command on them. Few if any of these go through. I've checked the mailing list and haven't found anything relevant—any ideas? I've attached recon-all logs and IsRunning files from one of these groups of 4, as well as an additional recon-all log from an attempted right hemisphere rerun. Thank you for your time and attention, Robert Toms --------------------------------- Lab Manager, DAMMI Lab School of Brain & Behavioral Sciences University of Texas at Dallas ---------------------------------

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claustrum segmentation
by Vittorio Rispoli 03 May '26

03 May '26

External Email - Use Caution Dear FreeSurfer Developers, I am interested in a tool for automated claustrum segmentation for a dataset of 1x1x1mm in-vivo T1. Does the command "mri_claustrum_seg" provide an analysis with identical performance of what "mri_histo_atlas_segment_fireants" does in term of claustrum volumetric analysis and segmentation? Thanks in advance Best Vittorio

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Large discrepancy in left and right volumes of perirhinal cortices on FreeSurfer 7.1.1- Dissertation Help
by Schade, Rachel 28 Apr '26

28 Apr '26

External Email - Use Caution Dear FreeSurfer Developers, I was examining the perirhinal regions from BA_exvivo_thresh.stats when I noted a significant discrepancy between the left and right hemispheres, particularly obvious on the perirhinal volumes. On a set of 166 older adults, I found the following discrepancy: Left Mean (SD) Left Range Right Mean (SD) Right Range Volume 1694.01 (473.09) 872–3087 943.80 (244.34) 514–1638 Thickness 2.83 (0.27) 2.18 - 3.72 2.98 (0.31) 2.25 - 3.76 Surface Area 492.47 (83.31) 329 - 703 259.76 (38.55) 170 - 357 As you can see the mean and range are almost double that of the right for volume and surface area, though thickness seems relatively unaffected. I have included my colleague who looked at one participant with the most extreme asymmetry and found the following, where it looks like the entorhinal cortex is overlapping the perirhinal. Attached is a screen shot. I am using this for my dissertation due in a month and would love to know if this is a bug that could be resolved. Thank you for your time! Best. Rachel [UF] Rachel Schade Doctoral Candidate Public Health & Health Professions | Clinical & Health Psychology University of Florida rschade1(a)ufl.edu<mailto:rschade1@ufl.edu>

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Re: need license.txt urgently
by fsbuild 27 Apr '26

27 Apr '26

External Email - Use Caution Please try filling out and submitting the form at, https://secure-web.cisco.com/1T2tXCzg9gdR2IrrwN7O4uIv2RG-stuYEFyrM7wVo-on6U… The license file will be mailed to the email address you provide. - R. On 4/26/26 14:22, 马婧 (majing20000714(a)gmail.com) wrote:         External Email - Use Caution         I am so sorry to bother you.But I need FreeSurfer license.txt urgently for academic use.Thank you for your help. Name: MA JING Institution: JUNTENDO University  Email: majing20000714(a)gmail.com _______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1V5q9v0KJD9gU1usgVlg9iDjqzyifOArj_r7gCpnIJ3vxq… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1v4afNXIwJMdtkMisJBAXPZW0i6xnjRAMDRTibxQ-93nOu… <https://secure-web.cisco.com/1dWhB7785W_Lw1N9t1WR5J1NlBRCOpPLTHSjxx5pQO9IPApq-2EX3XFSwiND5tR4OycQ92gx9X_AENRTzLdj79jPwGB7beqLkqTVrfLvNlycVpvwo1SYdb99ZJv0HW9Bt5lr50qAH3mvt9YvJtoUWTXdwR5PGW3KWl2kZp3pL7-4xpIQvjWKnQDoYh9MOXMAjwpBymMVIxCuF0mcNSIL7_BmjSGHXgnH76DfTayaFbE2Bt2TQlLyXrphYhOjoYplYk1SG0TMdTW2qalvsvYVFSX58kwI1KhNk7ygGzPgrUxkjZmK7Wu4zBz4e__PPK9RiOUVVgEr2tK2UKQZprwaBBA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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reply
by Lepus Li 27 Apr '26

27 Apr '26

External Email - Use Caution confirm b54752357af3c9c3243ab66e4ca4f9805f5d93ec

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Confirm
by 許嘉琪 27 Apr '26

27 Apr '26

External Email - Use Caution confirm b54752357af3c9c3243ab66e4ca4f9805f5d93ec ᐧ

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need license.txt urgently
by 马婧 26 Apr '26

26 Apr '26

External Email - Use Caution I am so sorry to bother you.But I need FreeSurfer license.txt urgently for academic use.Thank you for your help. Name: MA JING Institution: JUNTENDO University Email: majing20000714(a)gmail.com

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confirm
by 許嘉琪 26 Apr '26

26 Apr '26

External Email - Use Caution confirm f7ac57421691dbb0f3dd3d33588d33bf4bc5878b ᐧ

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Dockerhub image missing python3
by Dan Fitch 24 Apr '26

24 Apr '26

External Email - Use Caution Hi folks, In the freesurfer/freesurfer:8.2.0 image from Dockerhub, straightforward `recon-all -all ...` runs have: env: 'python3': No such file or directory in STDERR. I'm running on a HTCondor cluster so I'm getting STDERR and STDOUT in separate files and can't see where this is exactly. It's the first line output to STDERR, followed by a bunch of INFO: using NIfTI-1 sform (sform_code=1) threshold mask volume at 0.001 ... that looks normal. When I converted the Dockerfile to a singularity conf and created my own rockylinux:9 8.2.0 container, I didn't see this issue. I've confirmed that going into the container in writable mode and running `yum install python3` fixes it. (As a side note, recent updates being released as in-place patches with the same version number [instead of using minor version changes] is a bit confusing in places like dockerhub. I'm sure you all have a reason for doing it this way, but there are disadvantages too.) Dan Fitch Research Engineer University of Wisconsin-Madison Institute on Aging

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7t
by Miriam Taza 23 Apr '26

23 Apr '26

External Email - Use Caution Hello, Im wondering if you know if sclimbic would work well on 7T data? Thanks Miriam

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