Freesurfer September 2026

freesurfer@nmr.mgh.harvard.edu

19 participants
24 discussions

Re: FS 8.2.0 on Rocky 9 / RHEL 9
by fsbuild 03 Sep '26

03 Sep '26

External Email - Use Caution The same binaries may not be built and/or installed across different (more recent) versions of operating systems.  It’s not sure why infantfs was not included for rocky9, but for other binaries the 3rd party packages they use are no longer supported (rocky9 uses newer versions of system libraries and/or newer version of the compilers).  It worked for me to install the rocky8 RPM on a rocky9 machine, i.e., I believe binary backwards compatibility allows rocky8 binaries to run on rocky9.  Some of those rocky8 binaries listed might still run on rocky9 if you need them.  You would first need to uninstall the rocky9 rpm. - R. On Sep 1, 2026, at 23:02, Anderson Winkler <anderson.winkler(a)utrgv.edu> wrote:

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FS 8.2.0 on Rocky 9 / RHEL 9
by Anderson Winkler 01 Sep '26

01 Sep '26

External Email - Use Caution Dear all, There are releases of FS 8.2.0 for Rocky 8 and for Rocky 9. We installed the Rocky 8 package on a RHEL 8 system and everything is fine. But when we installed the Rocky 9 package on either a RHEL 9 or Rocky 9 system, FS crashes in the talairach_avi step (command not found). Running a diff between the two installations, it seems many files are missing from the Rocky 9 release. For example, comparing the respective ‘bin’ directories: diff el8/bin el9/bin | grep Only Only in el8/bin: 4dfptoanalyze Only in el8/bin: analyzeto4dfp Only in el8/bin: applyMorph Only in el8/bin: atlassubjects.csh Only in el8/bin: brec Only in el8/bin: brec.awk Only in el8/bin: check_infant_recon_success.csh Only in el8/bin: compute_vox2vox Only in el8/bin: createMorph Only in el8/bin: create_pial_surfaces_mprage_subject.csh Only in el8/bin: create_wm_surfaces_mprage_subject.csh Only in el8/bin: dmri_forrest Only in el8/bin: dmri_group Only in el8/bin: dmri_mergepaths Only in el8/bin: dmri_motion Only in el8/bin: dmri_paths Only in el8/bin: dmri_pathstats Only in el8/bin: dmri_spline Only in el8/bin: dmri_train Only in el8/bin: dmri_trk2trk Only in el8/bin: dmri_vox2vox Only in el8/bin: exportGcam Only in el8/bin: find_cerebral_wm_labels.csh Only in el8/bin: find_neighbors_byAge.csh Only in el8/bin: find_neighbors_byAge_extended.csh Only in el8/bin: find_neighbors_byMI.csh Only in el8/bin: find_neighbors_byMI_extended.csh Only in el8/bin: flip_4dfp Only in el8/bin: gauss_4dfp Only in el8/bin: ifh2hdr Only in el8/bin: imgreg_4dfp Only in el8/bin: infant-container-entrypoint-aws.bash Only in el8/bin: infant-container-entrypoint.bash Only in el8/bin: infant_recon_all Only in el8/bin: mpr2mni305 Only in el8/bin: mri_label_fusion Only in el8/bin: mri_vessel_segment Only in el8/bin: reg_aladin Only in el8/bin: reg_f3d Only in el8/bin: reg_resample Only in el8/bin: run_label_fusion.csh Only in el8/bin: set_babydev_packages.csh Only in el8/bin: set_infant_recon_params.csh Only in el8/bin: surf2vol Only in el8/bin: t4img_4dfp Only in el8/bin: t4imgs_4dfp Only in el8/bin: talairach_avi Only in el8/bin: tal_QC_AZS Only in el8/bin: zero_lt_4dfp Both installations used the ‘dnf' command, but installing with ‘rpm' gives the same result. Have we missed something? Thanks! All the best, Anderson

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SAMSEG lesion threshold
by Jordan Chad 01 Sep '26

01 Sep '26

External Email - Use Caution Hello. I am running run_samseg_long on Freesurfer 8.1.0 with longitudinal MS T1W data and I am trying to resolve lesion undersegmentation. Whenever I lower --threshold manually (e.g., --threshold 0.2), it seems to ignore it, outputting "thresholding posterior of Lesions with threshold: 0.3". To try thresholding manually, I added to the command --save-posteriors and --save-probabilities, but I'm not exactly sure what the outputted "Lesions.mgz" files in the posteriors and probabilities folders represent (and why the "Lesions.mgz" file in the probabilities folder has three frames). Can I please get advice on how to compute lesion volumes and masks at a threshold that is lower than 0.3? Thank you!

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freesurfer
by Risy 01 Sep '26

01 Sep '26

External Email - Use Caution confirm 27d4039ed784228d5250055ea4dba1f573c2b443

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Freesurfer September 2026