Freesurfer March 2026

freesurfer@nmr.mgh.harvard.edu

29 participants
32 discussions

NextBrain atlas at different resolution images
by Gabriella Monopoli 20 Mar '26

20 Mar '26

External Email - Use Caution I would like to ask for your advice regarding the use of NextBrain with MRI datasets acquired at different resolutions and coverage. Specifically, I have: • A 3D T1-weighted image covering the whole brain with 1×1×1 mm voxel size • A second T1-weighted acquisition focused only on the brainstem, with higher resolution (0.5×0.5×0.5 mm) Would it be possible (and methodologically sound) to combine these two datasets within the NextBrain pipeline? In particular, I am interested in whether the high-resolution brainstem scan can be integrated with the whole-brain image to improve segmentation or analysis in that region. If this approach is feasible, I would appreciate any recommendations on preprocessing steps (e.g., registration, resampling, or intensity normalization) to ensure compatibility between the two images. Thank you very much for your help. Best regards, Gabriella Monopoli

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Fwd: FreeSurfer 8.2.0 release
by fsbuild 19 Mar '26

19 Mar '26

External Email - Use Caution Forwarding the notice for the 8.2.0 Freesurfer point release in case it did not previously appear on the list ... - R.- - - - - -  FreeSurfer 8.2.0 is officially released. The release notes are here: https://secure-web.cisco.com/1K36f2h7DHRLJwf0BxzSZ0hoC6TLOiKE5To…, which I have replicated below Stable 8.2.0 Release (Mar 18 2026)FreeSurfer version 8.2.0 can be found here. This is a minor release and will give the same output of recon-all when it is run in the same way. We have stopped supporting CentOS7 and have added support for Rocky 9 Linux, Ubuntu 24 Linux, and MacOS Tahoe (26.1). Note that different combinations of build and execution operating systems can give different results (see "Control of operating system" below). New features: Claustrum segmentation (mri_claustrum_seg) Pituitary and pineal glands segementation (mri_pglands_seg) Control of operating system when running recon-all. Create a file called fs-allowed-os.txt with the allowable operating systems. If recon-all is not run from one of these operating systems, then it will exit with error. See fs-check-os --help for how to use. This, along with FS build version specification (fs-allowed-versions.txt) can go along way towards assuring repeatability. fs-eddy and fs-topup frontend to run FSL eddy and topup corrections for diffusion analysis Bug fixes: Fixes xhemireg (cross-hemisphere surface registration);Fixes gtmseg (now creates segementation with sinus segmentation, arteries, vermis, pons) There was an occasional error in license reading when running mris_volmask that would cause recon-all to crash for no apparent reason when multiple threads were used. 

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FreeSurfer 8.2.0 release
by Douglas N. Greve 19 Mar '26

19 Mar '26

FreeSurfer 8.2.0 is officially released. The release notes are here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes, which I have replicated below doug Stable 8.2.0 Release (Mar 18 2026) FreeSurfer <https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> version 8.2.0 can be found here <https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads>. This is a minor release and will give the same output of recon-all when it is run in the same way. We have stopped supporting CentOS7 and have added support for Rocky 9 Linux, Ubuntu 24 Linux, and MacOS Tahoe (26.1). Note that different combinations of build and execution operating systems can give different results (see "Control of operating system" below). * New features: o Claustrum segmentation (mri_claustrum_seg) o Pituitary and pineal glands segementation (mri_pglands_seg) o Control of operating system when running recon-all. Create a file called fs-allowed-os.txt with the allowable operating systems. If recon-all is not run from one of these operating systems, then it will exit with error. See fs-check-os --help for how to use. This, along with FS build version specification (fs-allowed-versions.txt) can go along way towards assuring repeatability. o fs-eddy and fs-topup frontend to run FSL eddy and topup corrections for diffusion analysis * Bug fixes: o Fixes xhemireg (cross-hemisphere surface registration); o Fixes gtmseg (now creates segementation with sinus segmentation, arteries, vermis, pons) o There was an occasional error in license reading when running mris_volmask that would cause recon-all to crash for no apparent reason when multiple threads were used.

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Next brain
by stdp82＠virgilio.it 18 Mar '26

18 Mar '26

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FSL Course 2026 - Registration Open!
by Rezvan Farahibozorg 18 Mar '26

18 Mar '26

External Email - Use Caution Dear all, We are pleased to announce that registration is now open for FSL Course 2026, which will be held in-person June 22nd – 26th in Bordeaux, France. You can find details and registration info here: https://secure-web.cisco.com/1lRouTZj_k816TyLEwr9s3-hdo3Tcw5XhR7SjcGOlawI_B… Spots on the course are limited and will be allocated on a first-come-first-served basis. Please register early to avoid disappointment. Both new and existing users of FSL are welcome on the course, as it aims to cover both basic and more advanced features of FSL. This intensive course covers the theory and practice of functional, structural, diffusion and resting state brain image analysis. Background concepts and the practicalities of analyses are taught in detailed lectures. These lectures are interleaved with hands-on practical sessions, where attendees learn how to carry out analysis for themselves on real data. The contents covered in the course are primarily aimed at applications in basic science and clinical research (not clinical practice). Please note that the only option to attend the course in 2026 will be this in person course. To strike a balance between broad accessibility and the benefits of in-person interaction, the FSL Course intends to follow an approximately alternating pattern of fully in-person and fully online courses. We hope to see you at the course! The FSL Course team

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segmentHA_T2.sh ERROR:cannot find transform file
by Chunling Hu 16 Mar '26

16 Mar '26

External Email - Use Caution Freesurfer experts, I encountered an issue while using segmentHA_T2.sh. I am using Freesurfer 7.3, and the command I executed was: segmentHA_T1.sh SUB01 /home/huchunling/HP5T/SUB01_PID_20260313_132311_0037_43/sPID202603131323110037-0301-00001-000001-01.nii T2 1 Referring to the solution provided in a previous email, I ensured that the input file is a single frame rather than a multi‑frame image. Therefore, I need your help to identify where the problem lies. Best regards, Chunling Hu The error message I received is as follows: ------------------------------ USER huchunling HOST fox-c06 PROCESSID 2744600 PROCESSOR x86_64 OS Linux Linux fox-c06 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:03:14 UTC 2 x86_64 x86_64 x86_64 GNU/Linux ------------------------------ #-------------------------------------------- #@# Hippocampal Subfields processing (T1+T2) left 2026年 03月 16日星期一 13:34:54 CST ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/opt/fox_cloud/share/app/imaging/freesurfer7.3/MCRv97//runtime/glnxa64:/opt/fox_cloud/share/app/imaging/freesurfer7.3/MCRv97//bin/glnxa64:/opt/fox_cloud/share/app/imaging/freesurfer7.3/MCRv97//sys/os/glnxa64:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/thinlinc/lib64:/opt/thinlinc/lib:/opt/fox_cloud/share/app/imaging/freesurfer7.3/MCRv97//sys/opengl/lib/glnxa64:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/sge/lib/lx-amd64:/opt/fox_cloud/share/app/imaging/c3d/lib:/opt/fox_cloud/share/app/imaging/ImageMagick6.9/lib:/opt/fox_cloud/share/app/imaging/ANTs/install/lib:/opt/fox_cloud/share/app/imaging/dcm2nii/build/lib:/opt/fox_cloud/share/app/imaging/Slicer/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/openmpi-2.0.1/lib:/opt/fox_cloud/share/app/imaging/itksnap-3.6.0/lib:/opt/fox_cloud/share/app/imaging/OpenBLAS:/opt/fox_cloud/share/app/imaging/R:/opt/thinlinc/lib64:/opt/thinlinc/lib Registering norm.mgz to additional volume makeIsotropic WARNING: not different enough, won't reslice! CostFunctions::centroid is NAN (empty image? n = 0 ) ERROR: cannot find transform file /home/huchunling/HP5T/OUTPUT/freesurfer_subjects/SUB01/mri/transforms/T1_to_T2.v22.lta gzip: /home/huchunling/HP5T/OUTPUT/freesurfer_subjects/SUB01/tmp/hippoSF_T1T2_v22_T2_left//T2resampledLikeT1.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or a character vector. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1T2_autoEstimateAlveusML (line 192) MATLAB:badSwitchExpression Command exited with non-zero status 249 @#@FSTIME 2026:03:16:13:34:54 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 22.89 S 3.89 U 7.50 P 49% M 1468976 F 0 R 705152 W 0 c 399 w 16444 I 0 O 288120 L 0.20 0.33 0.40 @#@FSLOADPOST 2026:03:16:13:35:17 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 0.65 0.43 0.44 Linux fox-c06 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:03:14 UTC 2 x86_64 x86_64 x86_64 GNU/Linux T2 hippocampal subfields exited with ERRORS at 2026年 03月 16日星期一 13:35:17 CST

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Request to Remove Email Addresses from FreeSurfer Mailing List
by 강다정 12 Mar '26

12 Mar '26

External Email - Use Caution Hello, I am contacting you because I have been receiving FreeSurfer-related emails every day. It seems that the emails are being sent to the following addresses. Please take the necessary action so that these addresses are removed from the mailing list. danbidan2443(a)gmail.com / doramisister(a)naver.com The notifications arrive during the early morning hours, and the alerts are disturbing my sleep. I would appreciate it if you could check and resolve this issue. Thank you.

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Request to Remove Email Addresses from FreeSurfer Mailing List
by 강다정 12 Mar '26

12 Mar '26

1 0

FREESURFER: undefined variable
by Wales, Ryan 12 Mar '26

12 Mar '26

External Email - Use Caution Hi, I’m trying to run FreeSurfer (v. 7.2.0) longitudinally, first creating the base template for my sample subject across both timepoints, using: recon-all -base sub_01-tp sub-01_ses-01_t1 -tp sub-01_ses-02_t1 -all Both cross-sectional timepoints were previously run separately. Just after ‘mri_pretess’ finishes, I encounter the error: “FREESURFER: Undefined variable”. I’m running FreeSurfer on my organization’s HPC, and I’ve ensured that SUBJECTS_DIR and FREESURFER_HOME are both set appropriately. I found another post with the same error, but they also had “nu_correct: Command not found”, unlike me. Both of us are using v. 7.2.0. https://secure-web.cisco.com/1KfETP9AssoehTvJ3VhjCNZJJg3rReFE0UsHzbxBF1de4x… Can’t figure this one out. Thanks all! Best, Ryan Wales ________________________________ Confidentiality Notice: This electronic mail transmission and any documents, files, or previous email messages attached to it may contain confidential information and are intended solely for the use of the individual or entity to which they are addressed. If you are not the intended recipient, or a person responsible for delivering such information to the intended recipient, you are hereby notified that any further review, disclosure, copying, dissemination, distribution, or use of any of the information contained in or attached to this email transmission is strictly prohibited. If you have received this message in error, please notify the sender immediately by email, discard any paper copies, and delete all electronic files of the message. Thank you for your cooperation.

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use of a custom annot for mri_segstats
by Simone Cauzzo 12 Mar '26

12 Mar '26

External Email - Use Caution Hi all I am running Freesurfer 7.4 I am trying to extract QSM values at different cortical depths, and obtain statistics for the 400 Schaefer regions. my code is mri_vol2surf --mov [QSM coregistered to orig_nu.mgz ] \ --regheader $sub \ --hemi lh \ --surf white \ --o outputsurf.mgh \ --projfrac 0.2 mri_segstats --annot subjid lh 400Parcels_Yeo2011_17Networks \ --i outputsurf.mgh \ --sum outputstats.stats I get the following errors Reading annotation $SUBJECTS_DIR/$sub /label/lh.400Parcels_Yeo2011_17Networks.annot error: No such file or directory error: # elements (137017) in $SUBJECTS_DIR/$sub/label/lh.400Parcels_Yeo2011_17Networks.annot and # vertices (137601) don't match ... trying local annot error: No such file or directory error: # elements (137017) in $SUBJECTS_DIR/$sub/label/lh.400Parcels_Yeo2011_17Networks.annot and # vertices (137601) don't match The annot file is there, I checked, and that's verified by the fact that apparently it knows how many vertices are there. Moreover, it totally worked when I tried this command to extract anatomical stats from the same parcel mris_anatomical_stats -a $SUBJECTS_DIR/$sub /label/lh.400Parcels_Yeo2011_17Networks.annot -f $SUBJECTS_DIR/$sub/stats/$hemi.$parc.stats $sub $hemi Do you have any idea of what is going on? The volume [QSM coregistered to orig_nu.mgz ] was created by applying the QSM 2 T1 rigid transform with ants antsApplyTransform, with orig_nu.mgz as reference volume, which provided a new QSM volume that looks aligned to orig_nu.mgz and on the same grid. It is not a problem of this file since I tried producing an mgh file with orig_nu.mgz as --mov volume and the error persists. Thank you for your help Simone Cauzzo

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Freesurfer March 2026