Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: Freesurfer Digest, Vol 271, Issue 4
by fsbuild 04 Sep '26

04 Sep '26

External Email - Use Caution The Freesdurfer release page,https://secure-web.cisco.com/1aFSeUS1wPG9NyqX8ojDowAxZz8EG0dwH-X32J5_0… - shows the Freesurfer 7.4.1 release from June 2023 was never tested on MacOS Tahoe, i.e., the latest release at the time was MacOS 13 (Ventura).7.4.1 releaseLinux OS: CentOS7, CentOS8, Ubuntu18, Ubuntu20, Ubuntu22 release notes Mac OS: 10.15; 11.X, 12.X, 13.X (Intel binaries only running under Rosetta).The 7.4.1 binaries were built for Intel processors. Even if you are running 7.4.1 on MacOS Tahoe with older Mac hardware using an Intel processor it might be something is working differently on MacOS Tahoe.  If you are running Freesurfer 7.4.1 Intel binaries on newer Mac hardware with an M1, M2, M3, M3 processor, then you are running those binaries thru the rosetta emulation environment.  That might also cause something not to work as expected.  Unless you absolutely have to continue to use 7.4.1, e.g., continuity for processing some subject data, then I suggest you try running the same commands with the most recent Freesurfer release which is 8.2.0 from March of 2026.8.2.0 release Linux OS: CentOS7, Rocky8, Rocky9, Ubuntu22, Ubuntu24 release notes Mac OS: 13.X (Ventura), 14.X (Sonoma), 15.X (Sequoia) 25.1 (Tahoe) with separate Intel and arm64 installers. Mac M1, M2, M3, M4 ... processor equipped arm64 machines should have 32G+ RAM to use the new/faster recon-all setup and its associated commands. Otherwise you may revert the recon-all process to the pre-8.X version.For older Mac hardware using an Intel processor you would install,https://secure-web.cisco.com/1s39BkWvbDcqfN0R06Xfq48pjE1wm1GEgpPfyT… For newer Mac hardware with the M1, M2, M3, M4 processors you would install,https://secure-web.cisco.com/1V650weNcDy0Hq_ZmZWvWJ175ESlBVJ8cYL8TV… - R. On Sep 4, 2026, at 16:05, Rachel Sharkey <rachel.sharkey1(a)ucalgary.ca> wrote:

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Re: Freesurfer Digest, Vol 271, Issue 4
by Rachel Sharkey 04 Sep '26

04 Sep '26

External Email - Use Caution Freesurfer Version: 7.4.1 R Studio Version: 2022.07.1 R Version: 4.4.1 Operating System: macOS Tahoe 26.6.2 I also went back through the output in terminal and there is an indexing error. Here is the start of what gets printed into the terminal: subject sub-F03019_ses-30D_T1W hemi lh SUBJECTS_DIR /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap ColorTable /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/SecondErrorTest_editedColour.txt AnnotName ctab.hand.edited.R.output2 nlables 34 LabelThresh 0 0.000000 Loading /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/sub-F03019_ses-30D_T1W/surf/lh.orig Index Offset 0 0 reading /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/aparc-labels-left/lh.bankssts.label 1 10657952 caudalanteriorcingulate 1 reading /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/aparc-labels-left/lh.caudalanteriorcingulate.label 2 10723488 caudalmiddlefrontal 2 reading /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/aparc-labels-left/lh.caudalmiddlefrontal.label 3 10854560 cuneus 3 reading /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/aparc-labels-left/lh.cuneus.label 4 10920096 entorhinal 4 reading /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/aparc-labels-left/lh.entorhinal.label 5 10985632 fusiform What I can't figure out is where the mis-indexed numbers are coming from because I can't see anything in the text file , this is what the first few rows of that looks like (this is a version with colours edited but the same issue happens when I use autogenerated colours): 0 unknown 160 160 160 0 1 bankssts 160 160 161 0 2 caudalanteriorcingulate 160 160 162 0 3 caudalmiddlefrontal 160 160 163 0 4 corpuscallosum 160 160 164 0 5 cuneus 160 160 165 0 6 entorhinal 255 239 0 0 7 fusiform 160 160 167 0 8 inferiorparietal 160 160 168 0 9 inferiortemporal 160 160 169 0 If I figure out anything else I will update this thread. Thanks Rachel Rachel J. Sharkey, Ph.D. (she/her) Research Associate, Sport Injury Prevention Research Centre Faculty of Kinesiology, University of Calgary I would like to acknowledge that I reside within the traditional territories of the peoples of Treaty 7, which includes the Blackfoot Confederacy, comprising the Siksika, Piikani, and Kainai First Nations, the Tsuut’ina First Nation, the Stoney Nakoda First Nations, including the Chiniki, Bearspaw, and Wesley First Nations. The City of Calgary is also home to Métis Nation of Alberta, Region III. ________________________________ From: freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: September 4, 2026 2:20 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 271, Issue 4 [△EXTERNAL] Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: mris_label2annot generates the wrong labels (fsbuild) ---------------------------------------------------------------------- Message: 1 Date: Thu, 03 Sep 2026 22:50:21 +0200 From: fsbuild <fsbuild(a)contbay.com> Subject: [Freesurfer] Re: mris_label2annot generates the wrong labels To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <ccb75858b67361700c730091c38ad60f(a)trashmail.com> Content-Type: multipart/alternative; boundary="_=_swift_1788468621_85c59db5602a01fe6dfd79a894c93d31_=_" External Email - Use Caution It would be useful to know the version of freesurfer you are running as well as the operating system version.  The behavior might not be the same in different (more recent) freesurfer versions. - R. On Sep 3, 2026, at 16:14, Rachel Sharkey <rachel.sharkey1(a)ucalgary.ca> wrote: -------------- next part -------------- A message part incompatible with plain text digests has been removed ... 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mris_label2annot generates the wrong labels
by Rachel Sharkey 04 Sep '26

04 Sep '26

External Email - Use Caution Hi Everyone, I ran some regionwise statistics based on aparc cortical thickness regions. I want to generate a new annot file that displays the statistical results back onto the aparc surface. So, the only thing that needs to change is the RGB values in the ctab file. I am not attempting to change any region boundaries, just the color. 1. I ran mri_annotation2label to extract a label folder from aparc 2. I have tried 2 methods for generating the ctab file. I have tried hand editing a text file to match the LUT format, and I have used the R package freesurfer formats to read and write the colourtable. 3. I used mris_label2annot to generate a new annot file But even when I simply extract the labels and ctab and make NO edits, when I load the resulting annot file into Freeview, it misplaces the labels by one (the lateral occipital in the original becomes lateral orbitofrontal in the new version, the middle temporal is labelled as the parahippocampal etc). The first item in the colortable is indexed at 0 and is labelled unknown. I have copied my code below, I have not hand edited these outputs in any way, they come directly out of the original annot file. These all run without throwing an error, the issue is only apparent when I load the annot file in freesurfer and check the labels with the cursor. Annotation2Label: mri_annotation2label --subject sub-F03019_ses-30D_T1W --hemi lh --ctab ThirdErrorTest --outdir ThirdErrorTest R Code to generate the colour table: library('freesurferformats') testannot = read.fs.annot('/Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/sub-F03019_ses-30D_T1W/label/lh.aparc.annot') testcolortable = colortable.from.annot(testannot) head(testcolortable) print(testcolortable) write.table(testcolortable, file='/Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/ErrorTest.txt', sep=" ", row.names = FALSE) write.fs.colortable('/Volumes/SHredMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/SecondErrorTest.txt',testcolortable) Label 2 Annot: --s sub-F03019_ses-30D_T1W --h lh --ctab /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/SecondErrorTest.txt --ldir /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/aparc-labels-left --annot ctab.test2 --sd /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap I have attached the version of the ctab file generated in R. Thanks Rachel Rachel J. Sharkey, Ph.D. (she/her) Research Associate, Sport Injury Prevention Research Centre Faculty of Kinesiology, University of Calgary I would like to acknowledge that I reside within the traditional territories of the peoples of Treaty 7, which includes the Blackfoot Confederacy, comprising the Siksika, Piikani, and Kainai First Nations, the Tsuut’ina First Nation, the Stoney Nakoda First Nations, including the Chiniki, Bearspaw, and Wesley First Nations. The City of Calgary is also home to Métis Nation of Alberta, Region III.

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Re: mris_label2annot generates the wrong labels
by fsbuild 03 Sep '26

03 Sep '26

External Email - Use Caution It would be useful to know the version of freesurfer you are running as well as the operating system version.  The behavior might not be the same in different (more recent) freesurfer versions. - R. On Sep 3, 2026, at 16:14, Rachel Sharkey <rachel.sharkey1(a)ucalgary.ca> wrote:

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

03 Sep '26

External Email - Use Caution I would not say “ignore” the rocky9 installer. The rocky9 binaries should run more efficiently on rocky9 than the rocky8 binaries.   If you don’t need to run what you listed, then I would default to using the rocky9 installer, e.g., what you listed is not necessary to run recon-all or freeview on rocky9.  You will eventually need to abandon the rocky8 binaries as they are not expected to work going forward on newer OS’s like rocky10 (which is the current release). You can install only 1 instance of the freesurfer package using the .rpm installers.   So I would install the rocky9 .rpm on rocky9 and make that the default for users.  You could then manually unpack the rocky8 rpm, and copy the contents somewhere such that you can access it as a fallback on the rocky9 machine in case someone needs to try and run those older binaries. - R. On Sep 3, 2026, at 02:54, Anderson Winkler <anderson.winkler(a)utrgv.edu> wrote:

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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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Fwd: Correction caused error in aseg
by Aimee Flores 30 Aug '26

30 Aug '26

External Email - Use Caution Dear Freesurfer course team, I hope everything is going great in Boston. My name is Aimee Flores and I took the freesurfer course online last June. I have a follow-up question about freesurfer brainmask correction. Is it possible that after a brainmask correction the aseg file gets distorted so that it seems like a sulci is displaced? Do you know what could be causing this and any possible solutions? Best wishes, Aimee Flores ----- Forwarded Message ----- From: "Nastya Asmolova" <asmolova(a)cbs.mpg.de> To: "Aimee Flores" <flores(a)cbs.mpg.de> Sent: Monday, August 10, 2026 1:19:49 PM Subject: Re: Correction successful? Dear Aimee, Thank you so much for following up! Unfortunately, M1 is still shifted com[pared to the uncorrected one. I'm attaching the screenshots and the log file Best, Nastya ----- Original Message ----- > From: "Aimee Flores" <flores(a)cbs.mpg.de> > To: "Anastasiia Asmolova" <asmolova(a)cbs.mpg.de> > Sent: Monday, August 10, 2026 1:00:00 PM > Subject: Correction successful? > Dear Nastya, > > Did the run from the person modified segmentation in M1 correction worked out? > otherwise to ask the freesurfer team as would be nice to know how to > troubleshooting it in case it happens again. > > Best wishes, > Aimee > > -- > PhD candidate at Charité – Universitätsmedizin Berlin > Neurology Department. Max Planck Institute for Human Cognitive and Brain > Sciences. > Stephanstrasse 1a, 04103 Leipzig, Germany. > Tel: +49(0)3419940-2256 > Neurotech Stroke project > Instagram: https://secure-web.cisco.com/1YS5lXrLnMNM_5TlAI27ASFSPVjgKOjoFupQFsrcuDRUQ5… > X: https://secure-web.cisco.com/1qM3WEUFoDUa_NdeSPS-F92GXo3K6ZNvyETk_3Dn2hQXiq… > LinkedIn: http://secure-web.cisco.com/1WO5sk1ictowpW-cjnUecvx5sCaCN6NYsK3ucWO5RXOhE5O… > YouTube: https://secure-web.cisco.com/1iKg9eDxIJY1kgP9trmCk0m-U-G7o7FRuHXUI8xUHdc40x… > Website: https://secure-web.cisco.com/1LPLCxKWlInoXoLNKDsec0-6p03LF7lkf1plcabzzhB1JU… -- PhD candidate at Charité – Universitätsmedizin Berlin Neurology Department. Max Planck Institute for Human Cognitive and Brain Sciences. Stephanstrasse 1a, 04103 Leipzig, Germany. Tel: +49(0)3419940-2256 Neurotech Stroke project Instagram: https://secure-web.cisco.com/1YS5lXrLnMNM_5TlAI27ASFSPVjgKOjoFupQFsrcuDRUQ5… X: https://secure-web.cisco.com/1qM3WEUFoDUa_NdeSPS-F92GXo3K6ZNvyETk_3Dn2hQXiq… LinkedIn: http://secure-web.cisco.com/1WO5sk1ictowpW-cjnUecvx5sCaCN6NYsK3ucWO5RXOhE5O… YouTube: https://secure-web.cisco.com/1iKg9eDxIJY1kgP9trmCk0m-U-G7o7FRuHXUI8xUHdc40x… Website: https://secure-web.cisco.com/1LPLCxKWlInoXoLNKDsec0-6p03LF7lkf1plcabzzhB1JU… -- PhD candidate at Charité – Universitätsmedizin Berlin Neurology Department. Max Planck Institute for Human Cognitive and Brain Sciences. Stephanstrasse 1a, 04103 Leipzig, Germany. Tel: +49(0)3419940-2256 Neurotech Stroke project Instagram: https://secure-web.cisco.com/1YS5lXrLnMNM_5TlAI27ASFSPVjgKOjoFupQFsrcuDRUQ5… X: https://secure-web.cisco.com/1qM3WEUFoDUa_NdeSPS-F92GXo3K6ZNvyETk_3Dn2hQXiq… LinkedIn: http://secure-web.cisco.com/1WO5sk1ictowpW-cjnUecvx5sCaCN6NYsK3ucWO5RXOhE5O… YouTube: https://secure-web.cisco.com/1iKg9eDxIJY1kgP9trmCk0m-U-G7o7FRuHXUI8xUHdc40x… Website: https://secure-web.cisco.com/1LPLCxKWlInoXoLNKDsec0-6p03LF7lkf1plcabzzhB1JU… -- PhD candidate at Charité – Universitätsmedizin Berlin Neurology Department. Max Planck Institute for Human Cognitive and Brain Sciences. Stephanstrasse 1a, 04103 Leipzig, Germany. Tel: +49(0)3419940-2256 Neurotech Stroke project Instagram: https://secure-web.cisco.com/1YS5lXrLnMNM_5TlAI27ASFSPVjgKOjoFupQFsrcuDRUQ5… X: https://secure-web.cisco.com/1qM3WEUFoDUa_NdeSPS-F92GXo3K6ZNvyETk_3Dn2hQXiq… LinkedIn: http://secure-web.cisco.com/1WO5sk1ictowpW-cjnUecvx5sCaCN6NYsK3ucWO5RXOhE5O… YouTube: https://secure-web.cisco.com/1iKg9eDxIJY1kgP9trmCk0m-U-G7o7FRuHXUI8xUHdc40x… Website: https://secure-web.cisco.com/1LPLCxKWlInoXoLNKDsec0-6p03LF7lkf1plcabzzhB1JU…

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