Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30128 discussions

Re: RHEL / Rocky 9 support
by fsbuild 20 Aug '25

20 Aug '25

External Email - Use Caution  The freesurfer development build on Rocky 9 Linux still has some run time bugs and is not entirely tested, so it is not currently fit for real work or public preview/release.  At some point in the near future I anticipate we could send out a notice to the list and ask people to try out the Rocky9 binaries and provide feedback (but not switch from doing work with a current stable freesurfer release like the current 8.1.0 release). - R..

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Freesurfer 8.1.0 failed with hires opton
by Su, Weizhong 18 Aug '25

18 Aug '25

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to use Freesurfer v8.1.0 with -hires option (mris_inflate -n 50), but I get the following error when I run the recon-all command: mris_inflate -no-save-sulc 50 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading 50 ** failed to open GIFTI XML file '50.gii' mrisReadGIFTIdanum: ERROR reading gifti 50.gii [INFO] read, cannot find 50, trying 50.gii ... error: No such file or directory error: mris_inflate: could not read surface file 50\00 Command exited with non-zero status 255 I have tired recon-all without -hires option, and FS finished without any error. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer_ubuntu22-8.1.0_amd64.deb 2) Platform: Ubuntu V22.0.4 3) uname -a: Linux hpc11 5.15.0-105-generic #115-Ubuntu SMP Mon Apr 15 09:52:04 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Another question regarding Freesurfer v8: Is it still good to use T2 for pial surface refinement since FS v8 has used machine learning approach already? Thanks, Wayne

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RHEL / Rocky 9 support
by Mark Janse 18 Aug '25

18 Aug '25

External Email - Use Caution Hi all, Like many institutions, we are migrating our HPC facilities and related workstations from Red Hat Enterprise Linux 7 to 9. I see the most recent RHEL-derived OS you provide builds for is Rocky 8. Are there any plans to make builds for Rocky or RHEL 9 available? RHEL 10 just got released a couple months ago and RHEL 9 is already a couple years old at this point, so it's not super bleeding edge or anything. Kind regards, Mark Janse, M.Sc. Computational Scientist - BioHPC UT Southwestern Medical Center Email: markus.janse(a)utsouthwestern.edu<mailto:markus.janse@utsouthwestern.edu> ________________________________ UT Southwestern Medical Center The future of medicine, today.

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(no subject)
by 田质文 15 Aug '25

15 Aug '25

External Email - Use Caution I need to get the license.txt,please. 广东省智能科学与技术研究院田质文实习生

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Missing endif in recon-all-clinical.sh
by Sebastian Rodrigo 14 Aug '25

14 Aug '25

External Email - Use Caution Dear FreeSurfer Guru, in case you don't already know, "endif" missing after line 185 within recon-all-clinical.sh. Best regards Sebastian

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TIV estimation from Fastsurfer
by Marco Ganzetti 13 Aug '25

13 Aug '25

External Email - Use Caution Dear, I would like to know how to extract the total intracranial volume after running Fastsurfer. The aseg.stats file only report the following regions: # Measure Mask, MaskVol, Mask Volume, 1378561.000000, mm^3 # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1112716.172377, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1095647.392151, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 966887.205081, mm^3 # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 949818.424855, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 58370.262413, mm^3 # Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 235981.558256, mm^3 # Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 231717.193880, mm^3 # Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 467698.752136, mm^3 I don’t see any eTIV. Regards Marco

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Permission Request to Publish FreeSurfer MNI Template Rendering under CC BY
by Matic Kadiš 11 Aug '25

11 Aug '25

External Email - Use Caution Dear FreeSurfer Team, I am a co-author on a manuscript currently in revision for Scientific Reports. One of our figures includes the attached image, which was generated in FreeSurfer (version 7.4.1) from the MNI152 template brain using the default Desikan–Killiany atlas, with the insula highlighted and inflated. The journal requires explicit written permission from the copyright holder to publish this image under a Creative Commons Attribution (CC BY 4.0) license in all formats (print and digital). Their requirements are: * The permission must be in English. * It must explicitly grant Springer Nature Limited permission to publish the image under a CC BY 4.0 open access license. * It must cover publication in all formats (print and digital). * It must be signed by the copyright holder. Could you please confirm whether MGH / the FreeSurfer team holds the copyright for the MNI template and atlas rendering, and if so, provide a signed permission letter meeting these conditions? I am happy to provide any additional details you need. Of course, a different approach to how you usually handle requests like that is also acceptable. Thank you very much for your time and assistance. Best regards, Matic Kadiš [https://secure-web.cisco.com/1iyBRIi0eNVnfRGRv5UF8xLktnjxF21sPChWICxSp1ZNeh… asist. Matic Kadiš, mag. psih. Asistent | Assistant Univerza v Mariboru | University of Maribor Filozofska fakulteta | Faculty of Arts Oddelek za psihologijo | Department of Psychology Koroška cesta 160, 2000 Maribor, Slovenija E: matic.kadis1(a)um.si

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Help
by Gantz, Abbey 10 Aug '25

10 Aug '25

External Email - Use Caution Hello, I’m just contacting to ask for advice with the use of recon-all on a participant that has an abnormally structured brain, specifically a compressed Anterior temporal lobe. Recon-all finished without error, but didn’t completely encapsulate the anatomy properly. I ran recon-all using this code: recon-all -s omni07 -i /mnt/sml_share/OMNI/derivatives/fpp/sub-omni0 7/anat/sub-omni07_space-individual_res-1_desc-preproc_Tlw.nii.gz -all -deface -T2 /mnt/sml. share/OMNI/derivatives/fpp/sub-omni07/anat/sub-omni07_space-individual_res-1_desc-preproc_7 2w.nii.gz -T2pial The final recon-all brain mask.mgz file came out like this: [cid:10e2f9c0-f6e6-4f8f-bf38-405a0b106646] Questions: 1. Are there flags to or steps to manually adjust surface place for such cases? 2. Would you recommend disabling certain steps/running in stages to improve the outcome? Thank you for your help, and let me know if there is anything else I can provide to clarify the issue Abigail Gantz PhD Student | Social Memory Lab Tulane Department of Psychology agantz1(a)tulane.edu

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Issue with Pial and WM Surface Distortion
by Mahta Abbaspour 10 Aug '25

10 Aug '25

External Email - Use Caution Hello FreeSurfer team, While performing QC on my recon-all output, I spotted an issue in a scan where the pial surface intersects with the white matter surface, causing distortions across several slices in that region. I overlaid the filled.mgz and white matter segmentation, and the area appears to be fully filled in both masks, so I'm not quite sure why the surfaces are inaccurate here. I'd appreciate any insights and the best way to edit this. I've attached a few example slices below for reference. [image: image.png] [image: image.png] [image: image.png] [image: image.png]

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Consistent Dura Inclusion in QC
by Mahta Abbaspour 10 Aug '25

10 Aug '25

External Email - Use Caution Hello Freesurfer team, I'm currently performing QC on the FreeSurfer outputs and noticed that in many scans, there’s consistent inclusion of dura near the occipital lobe and cerebellum, spanning approximately 10–40 slices sometimes. No dura is included in the anterior or middle slices. I had two questions: - Do you have any idea why this might be happening? The pial and white matter surfaces look fine throughout. - What would be the best way to address this? Should I manually remove the dura and regenerate the surfaces — though this is quite labor-intensive, especially when it affects many slices — or should I consider adjusting the -h parameter for more aggressive skull stripping? However, brainmask also look fine in all other regions. I’ve attached a screenshot from one of the slices for reference. I’d appreciate any suggestions you might have. Thank you. [image: image.png]

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