Freesurfer September 2026

freesurfer@nmr.mgh.harvard.edu

19 participants
24 discussions

License.txt not received after registration (live outside US)
by 李亚锋 18 Sep '26

18 Sep '26

External Email - Use Caution Dear FreeSurfer team, I registered for a FreeSurfer license key via the registration page on 2026-09-17, using the email address liyafengna(a)foxmail.com. I have subscribed to and confirmed the freesurfer mailing list successfully (I received the confirmation and welcome messages), but I have not received any email containing the license.txt file. I have checked both my inbox and spam folder. Could you please advise whether the license email can be resent to a different address? I can provide an alternative address (e.g. a Gmail account) if delivery to the current domain is blocked. Registration details: Name: Yafeng Li Institution: Shenzhen University Country: China Platform: Linux/Intel Thank you very much. Best regards, Yafeng Li

2 1

lack of cerebellum in freesurfer clinical
by Aimee Flores 10 Sep '26

10 Sep '26

External Email - Use Caution Dear freesurfer team, I am running the freesurfer clinical and we found that it does not extract the cerebellum by design. However, for coregistering the t1 to other imaging modalities it would be important to have a whole brain mask. I wonder if there is any solution for this. Best wishes, Aimee Flores -- 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/19oI9BK5igUPkhRSoXPEfneexkjWlRWfv0N0paLp_Caws-… X: https://secure-web.cisco.com/1ZGkNThsM86iaEcfI1-ga8G_72WN0Ve518MR_ojtBII6jh… LinkedIn: http://secure-web.cisco.com/1TjxqTx_gQ9JRdOa14ckrvdeMhX5xdy2MqNOBlVgvzH_kgp… YouTube: https://secure-web.cisco.com/1d6ZS7_sRE3xPAYpp6ozaS6svy1FpF4rRnneu_CBmfoJxp… Website: https://secure-web.cisco.com/1g_n3ZldRmGbDnDtQUnSDsiQtXnPhjges8BccTPyFMKRug…

2 1

FreeSurfer license registration – repeated 504 Gateway Timeout
by masahiro.joko＠fujita-hu.ac.jp 10 Sep '26

10 Sep '26

External Email - Use Caution Dear FreeSurfer Support Team, I am trying to obtain a FreeSurfer license.txt file for non-profit acade mic research, but the registration form repeatedly returns a “504 Gatew ay Timeout” after submission. I have tried the registration form multiple times, but no license email has arrived. Name: Masahiro Joko Institution: Fujita Health University, Japan Intended use: Non-profit academic research Operating system: Linux / Ubuntu 24.04 on WSL2 FreeSurfer version: 8.2.0 Could you please advise how I can obtain the license.txt file, or issue one manually if possible? Thank you very much for your assistance. Best regards, Masahiro Joko

1 0

mri_gtmpvc error: segmentation ROIs disappear in PET space
by Qassim Alkassir 08 Sep '26

08 Sep '26

External Email - Use Caution Hello, I am using PETSurfer/mri_gtmpvc for PET quantification in the WRAP Alzheimer's cohort. I am encountering a reproducible error when regions present in gtmseg.mgz have no voxels after the segmentation is mapped into PET space. I searched the mailing-list archives and found a previous discussion of the same error message involving segid 29. In our data, however, the affected labels differ between subjects, so I wanted to ask what the recommended general approach is. What I am trying to accomplish ------------------------------ We are processing motion-corrected, frame-averaged 11C-PiB PET images with PETSurfer. Our PET images are approximately: Matrix: 128 x 128 x 63 Voxel size: 2.574 x 2.574 x 2.425 mm Voxel volume: 16.07 mm^3 The corresponding gtmseg.mgz images have: Voxel size: 0.5 x 0.5 x 0.5 mm Voxel volume: 0.125 mm^3 Command ------- The relevant mri_gtmpvc options generated by our PETSurfer workflow are: mri_gtmpvc \ --psf 0 \ --no-tfe \ --seg gtmseg.mgz \ --default-seg-merge \ --auto-mask 10 0.01 \ --mgx 0.01 \ --no-reduce-fov \ --no-rescale \ --save-input \ ... I have attached the full PETSurfer log from a representative failed subject. It contains the complete generated command and output. Exact error ----------- For example: ERROR: creating region for nthseg=22, segid=78, Left-WM-hypointensities It may be that there are no voxels for this seg when mapped into the input space. I initially encountered this problem in another subject for segid 79 (Right-WM-hypointensities). Before changing the segmentation or adding replacement rules, I tested four additional independent PiB subjects using the same unmodified workflow. gtmseg completed successfully for all four subjects. PETSurfer completed successfully for one subject and failed during mri_gtmpvc for three subjects. Results ------- The regions producing mri_gtmpvc errors were: Subject SegID Region GTM vol PET vox ---------------------------------------------------------------- WRAP1 78 Left-WM-hypointensities 6 mm^3 0 WRAP1 79 Right-WM-hypointensities 5 mm^3 0 WRAP2 31 Left-choroid-plexus 6 mm^3 0 WRAP2 78 Left-WM-hypointensities 21 mm^3 0 WRAP2 79 Right-WM-hypointensities 1 mm^3 0 WRAP3 78 Left-WM-hypointensities 2 mm^3 0 We also have an informative within-subject comparison in WRAP3: segid 78: GTM volume = 2 mm^3 PET-space representation = 0 voxels mri_gtmpvc reports an error for segid 78 segid 79: GTM volume = 46 mm^3 PET-space representation = 1 voxel mri_gtmpvc does not report an error for segid 79 For the failing labels, we directly counted the voxels in both gtmseg.mgz and the PET-space segmentation at: no_pvc_6.0fwhm/aux/seg.nii.gz In every case listed above, the label is present in gtmseg.mgz but has zero voxels in the PET-space segmentation. This makes us suspect that the immediate failure occurs when a region retained in the GTM definition receives no voxel representation after mapping the segmentation onto the much coarser PET grid. One detail that of note was that total region volume alone does not determine whether a label survives. For example, segid 78 in WRAP2 occupies 21 mm^3 in gtmseg.mgz, which is greater than the volume of one PET voxel (16.07 mm^3), but it still maps to zero PET voxels. Questions --------- 1. What is the recommended PETSurfer/mri_gtmpvc approach when a valid region in gtmseg.mgz has zero voxels after mapping into PET space? 2. For segids 78 and 79 (Left/Right-WM-hypointensities), is --merge-hypos intended for this situation? 3. We also see the same problem for segid 31 (Left-choroid-plexus). Should choroid plexus be merged/replaced for GTM analysis, or should this be handled differently? 4. More generally, should very small regions be merged before GTM construction, or is there another recommended way to handle regions that disappear at PET resolution? Additional FreeSurfer context ----------------------------- The anatomical FreeSurfer reconstructions were originally generated with FreeSurfer 8. The PETSurfer/gtmseg environment currently uses FreeSurfer 7.4.0. Because the FreeSurfer 8 reconstructions did not contain the classical talairach.m3z expected by the FreeSurfer 7.4 gtmseg, we generated talairach.m3z using FreeSurfer 7.4 mri_ca_register. gtmseg subsequently completes successfully for all subjects tested. The error described above occurs later during mri_gtmpvc. 1) FreeSurfer version: freesurfer-linux-ubuntu20_x86_64-7.4.0-20230510-e558e6e 2) Platform: Ubuntu Linux, x86_64 3) uname -a: Linux hpclogin.sri.utoronto.ca 5.4.0-132-generic #148-Ubuntu SMP Mon Oct 17 16:02:06 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 4) PETSurfer log: See attached. I have attached the PETSurfer log from WRAP2, which demonstrates the failure for three different labels (31, 78, and 79). Thank you, Qassim Alkassir

1 0

WM segmentation in tutorial Subj001
by Bélinda Boudi 08 Sep '26

08 Sep '26

External Email - Use Caution Hello Freesurfer team, I am working through the Freesurfer tutorial using the "Subj001" dataset. I ran recon-all using Freesurfer 8.2.0 on macOS. While looking through wm.mgz I noticed what appears to be a small region of white matter in an unusual location that is also included within the pial surface (see the attached pictures). Interestingly, it also does not appear in brainmask.mgz. I was wondering if you could help me understand what this represents and if it is something I should address. If it does need to be corrected, I am unsure which volume I should edit. I thought of deleting the relevant voxels from wm.mgz, but I would be concerned about affecting the surface reconstruction. I was wondering what you would recommend as the appropriate way to correct this, if any correction is needed. Thank you for your help. Best, Belinda Boudi

1 0

Extract additional scalar metrics along reconstructed white matter pathways
by Durgerian, Sally 07 Sep '26

07 Sep '26

External Email - Use Caution Hello, I have run TRACULA on a group of subjects, and have text output for standard DTI metrics. I would like to see what difference it makes to do free water correction on the data by evaluating the FWC metrics along the same paths created in TRACULA. A google search of this question suggested that there is an extscalar option in TRACULA that I can use, but I don't see it in any of the documentation. Am I being led down the garden path by AI, or is this a thing? If so, how do I use it? Thanks, Sally [cid:37544fa9-a649-4fc9-a44c-85d8e5f0c3de] Sally Durgerian Senior Research Engineer | Division Of Radiology Cleveland Clinic | 9500 Euclid Ave. | Cleveland, OH 44195 (414) 364-7091 | DURGERS(a)ccf.org Please consider the environment before printing this e-mail Cleveland Clinic is a nonprofit, multispecialty academic medical center that's recognized in the U.S. and throughout the world for its expertise and care. Visit us online at http://secure-web.cisco.com/1Y0P0wokYL5ZNdbMxGt9sslPpjXazl-6TTCS2mNWS3v6z3q… for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

1 0

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:

1 0

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 ... Name: not available Type: text/html Size: 1214 bytes Desc: not available ------------------------------ Subject: Digest Footer _______________________________________________ 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/1SSy-AVc3jCHndfEUPE-ClcbYJ35UQHAsyQn5ysfFSCGjM… ------------------------------ End of Freesurfer Digest, Vol 271, Issue 4 ****************************************** 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/1X4PL_D4Jz-Wht6k3xyROEBaYGjntfWZUHm44oVmLNEx-h… <https://secure-web.cisco.com/1X4PL_D4Jz-Wht6k3xyROEBaYGjntfWZUHm44oVmLNEx-h…> . 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.

1 0

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.

2 1

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:

1 0

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer September 2026