Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30051 discussions

FreeSurfer 8.2.0 release
by Douglas N. Greve 23 Mar '26

23 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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FreeSurfer 8.2.0 expert options bug in recon-all / rca-surfreg
by Sofoklis Goulis 22 Mar '26

22 Mar '26

External Email - Use Caution Hello, I encountered two reproducible bugs in the latest release, Stable 8.2.0 (March 18 2026), when running recon-all with an expert options file on a 0.7 mm 7T MP2RAGE dataset. First, the run crashes after mris_sphere because recon-all evaluates if($XOptsFile), which expands to the expert-options path and triggers tcsh’s "if: Expression Syntax." error. A suggested fix would be to replace if($XOptsFile) with if($#XOptsFile). After patching this locally, recon-all proceeds further but then passes --expert to rca-surfreg, which currently recognizes -expert but not --expert, causing a second crash with "ERROR: Flag --expert unrecognized". A suggested fix would be to add support for --expert in rca-surfreg, for example: case "--expert": case "-expert": These issues were reproduced with an expert options file containing only mris_inflate -n 60. I have also registered the bug on GitHub and am emailing here for completeness. Best regards, Sophocles Goulis Postdoctoral Research Fellow Max Planck UCL Centre for Computational Psychiatry and Ageing Department of Imaging Neuroscience UCL Queen Square Institute of Neurology University College London, London, UK

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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

1 0

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

18 Mar '26

1 0

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.

1 0

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

12 Mar '26

1 0

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