Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30071 discussions

FreeSurfer Recon-all error : found no voxels matching id 1
by Khine, Win 08 Jul '25

08 Jul '25

External Email - Use Caution Hi FreeSurfer Developer, I am using FreeSurfer to analyse cortical thickness and ROIs volume. My input MRIs brain format is – nii.gz ( converted from T1 .dicom). I managed to run recon-all without any errors in some of my subjects. But, I am encountering the following error when I run recon-all on the other half of my subjects ( all are the same error) : Recon-all -s subject05_post exited with ERRORS. Error : found no voxels matching id 1 Found : 0 label voxels I have tried both watershed and no skull strip to tackle it. But it still finished with the same error. I have also tried running recon-all in separate stages – autorecon 1 , autorecon 2, autorecon 3 – the error seems to happen in autorecon 2 stage. I have searched the list, and no similar error was reported. Could you help me troubleshoot this error? ( I am also quite new to the field of MRI analysis and using FreeSurfer) I’m using FreeSurfer version 8.0.0 Platform – Mac OS Sequoia version 15.5 , Memory 36 GB, Storage – 370 GB Recon-all log : please see the attached. I have also attached the input nii.gz file to this email. Thank you. Yours sincerely, Dr Win Khine Clinical Research Fellow Imperial College London

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PetSurfer surface-based SUVR
by Mia Anthony 07 Jul '25

07 Jul '25

External Email - Use Caution Hello FS, I have calculated regional SUVR and would like to calculate SUVR on the surface. I have followed the wiki tutorial, including PVC, through smoothing on the surface. The last commands I ran are: mris_fwhm --smooth-only --i all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz --fwhm 5 --o all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --cortex --s fsaverage --hemi lh mris_fwhm --smooth-only --i all.rh.mgx.ctxgm.fsaverage.sm00.nii.gz --fwhm 5 --o all.rh.mgx.ctxgm.fsaverage.sm05.nii.gz --cortex --s fsaverage --hemi rh Do I need to run the mri_glmfit command? For example: mri_glmfit --y all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --surface fsaverage lh --fsgd g1v0.fsgd mri_glmfit --y all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --surface fsaverage rh --fsgd g1v0.fsgd Will the mri_glmfit output provide surface-based SUVR, or will I need to run additional commands after? Thank you, Mia

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Re: Ubuntu 24 release
by fsbuild 07 Jul '25

07 Jul '25

External Email - Use Caution  We hope to have a development build for Ubuntu 24 in the near future. - R. On Jul 7, 2025, at 03:46, Alpay Özcan <ialpayozcan(a)gmail.com> wrote:        External Email - Use Caution        Hello,Any plans for compiling on Ubuntu 26.04? Thanks in advance... --  Alpay Özcan, D.Sc. Professor Electrical & Electronics Eng. Dept., Boğaziçi University Bebek Istanbul 34342 Türkiye Tel: +90 212 359 7427 (or 6414 for Dept.) _______________________________________________ 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/1l2ZjAmSRBzEqngLJIi7nu56UGID6r3V7Bnda0i0LO_Rko…

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Re: Freesurfer installation help
by fsbuild 07 Jul '25

07 Jul '25

External Email - Use Caution  Try using the bash shell (by typing "bash" in the terminal window) and setup the environment with that instead of zsh. mymac[~] bash The default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://secure-web.cisco.com/1D7LUoH_cGGJxXRUBJGiZn5rlB8hoE9OQBmiNugxPvMyZ5… bash-3.2$ export FREESURFER_HOME=/Applications/freesurfer/8.0.0bash-3.2$ source /Applications/freesurfer/8.0.0/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_x86_64-8.0.0-20250205-0f2bd3a --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/8.0.0FSFAST_HOME       /Applications/freesurfer/8.0.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/8.0.0/subjectsMNI_DIR           /Applications/freesurfer/8.0.0/mni if the above works you could try changing your default shell to bash with "chsh -s /bin/bash" - R.

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Re: Recon-all clinical vs. FS version 8.0.0
by Zollei, Lilla,Ph.D. 07 Jul '25

07 Jul '25

Hi Stephanie, How old are the subjects in your pediatric cohort? Lilla -------- Forwarded Message -------- Subject: [Freesurfer] Recon-all clinical vs. FS version 8.0.0 Date: Tue, 1 Jul 2025 21:48:43 +0000 From: Stefanie Bradley <stefanie.bradley(a)mail.utoronto.ca><mailto:stefanie.bradley@mail.utoronto.ca> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> External Email - Use Caution Hi there, I am analyzing some pediatric brains with clinical pathology, and I was wondering if I would expect a difference in the reconstructions from regular recon-all (Freesurfer version 8.0.0) vs. recon-all clinical, since they both use SynthSeg from what I understand? Thanks, Stefanie

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Ubuntu 24 release
by Alpay Özcan 07 Jul '25

07 Jul '25

External Email - Use Caution Hello, Any plans for compiling on Ubuntu 26.04? Thanks in advance... -- Alpay Özcan, D.Sc. Professor Electrical & Electronics Eng. Dept., Boğaziçi University Bebek Istanbul 34342 Türkiye Tel: +90 212 359 7427 (or 6414 for Dept.)

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mri_vol2vol bug in fs8.0.0?
by Zahnert, Felix 06 Jul '25

06 Jul '25

Dear experts, I ran into an issue running mri_vol2vol after running bbregister using freesurfer 8. Running the same commands in freesurfer 7.4.1 worked well. bbregister worked in both versions, while mri_vol2vol (8.0.0) resulted in the following error: INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. [...] INFO: using NIfTI-1 sform (sform_code=2) error: File exists error: LTAchangeType: src geometry must be valid Running version 7.4.1 mri_vol2vol using the .dat file generated with bbregister version 8.0.0 worked as well. The commands: # bbregister, where fs8 is the freesurfer directory of the subject (SUBJECTS_DIR has been set to 'structural_dir', in which fs8 is located) reg_file="$out_dir/diff2str.dat" bbregister --s fs8 --mov "$b0" --reg "$reg_file" --fslmat "${reg_file%.dat}.mat" --dti # mri_vol2vol cmd below, working in version 7.4.1, but not in version 8.0.0 # with mov being a map of diffusion metrics in the same space as b0 here mri_vol2vol \ --mov "$mov" \ --targ "$structural_dir/fs8/mri/T1.mgz" \ --o "$output" \ --no-save-reg --reg "$reg_file" I also tried the following prior to mri_vol2vol, which did not help: mri_convert -rl "$b0" -rt nearest "$my_mov" "$my_mov_modified" I encountered the same issue when running mri_vol2vol and bbregister with the identical input as --mov. Might there be a bug in version 8's mri_vol2vol, or am I missing something? Thank you for your help! Best, Felix

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Trouble shooting
by andrew cardona 06 Jul '25

06 Jul '25

External Email - Use Caution Good afternoon, I am reaching out as I am trying to trouble shoot one participant, yet it keeps failing and stating the same error "mri_convert: cant determine type of output volume" we have tried changing the file manually to mgz and it works yet when we run recon all it crashes. We also can run mri_info on the file perfectly fine, we also uninstalled and reinstalled freesurfer itself. Any guidance would be greatly appreciated, thank you! *This is what is outputted when running recon all: * Adding options -fix-ento-wm -transfer-base-bfs -fix-vsinus -fix-mca-dura -fix-ga -fix-acj -synthstrip -synthseg -synthmorph fs-check-version --s sub-1009 --o /tmp/tmp.oai3VJ Wed Jul 2 11:36:48 EDT 2025 setenv SUBJECTS_DIR /home/tur31606(a)tu.temple.edu/freesurfer_output cd /home/tur31606(a)tu.temple.edu /usr/local/freesurfer/8.0.0/bin/fs-check-version --s sub-1009 --o /tmp/tmp.oai3VJ -rwxr-xr-x 1 root root 18565 Feb 3 20:30 /usr/local/freesurfer/8.0.0/bin/fs-check-version freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a $Id$ Linux CLA19571.tu.temple.edu 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux pid 451741 Current FS Version freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a Subject does not have a bstampfile, copying /usr/local/freesurfer/8.0.0/build-stamp.txt Subject FS Version: freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /home/tur31606(a)tu.temple.edu/freesurfer_output Actual FREESURFER_HOME /usr/local/freesurfer/8.0.0 Linux CLA19571.tu.temple.edu 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux /home/tur31606(a)tu.temple.edu/freesurfer_output/sub-1009 mri_convert /data/Project_LITE/Imaging/LITE_PAT/bids/sub-1009/ses-01/anat/sub-1009_ses-01_T1w.nii.gz /home/tur31606(a)tu.temple.edu/freesurfer_output/sub-1009/mri/orig/001.mgz mri_convert /data/Project_LITE/Imaging/LITE_PAT/bids/sub-1009/ses-01/anat/sub-1009_ses-01_T1w.nii.gz /home/tur31606(a)tu.temple.edu/freesurfer_output/sub-1009/mri/orig/001.mgz mri_convert: can't determine type of output volume Command exited with non-zero status 1 @#@FSTIME 2025:07:02:11:36:49 mri_convert N 2 e 0.00 S 0.00 U 0.00 P 100% M 6144 F 0 R 270 W 0 c 0 w 2 I 0 O 0 L 0.30 0.56 0.42 @#@FSLOADPOST 2025:07:02:11:36:49 mri_convert N 2 0.30 0.56 0.42 Linux CLA19571.tu.temple.edu 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-1009 exited with ERRORS at Wed Jul 2 11:36:49 EDT 2025 For more details, see the log file /home/ tur31606(a)tu.temple.edu/freesurfer_output/sub-1009/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1lZL5fd1-LIJV20MkpYIehpHZ9KjK6NT_O2y2M8boj9gcNF… Best, Andrew Cardona

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trouble with recon-all FLAIRpial flag
by Mojdeh Zamyadi 06 Jul '25

06 Jul '25

External Email - Use Caution Hi FreeSurfer developers, I'm attempting to use FLAIR images to improve the segmentation quality of some of my subjects after successfully running recon-all -all with the T1 images. After QCing the initial results some segmentation needed improvement which is why I am trying to use the FLAIR images on the recon-all -all results with T1. This is the command I am using: recon-all -s ${subject_id}_T1 -FLAIRpial -autorecon2 -autorecon3 but I am getting errors at the "mris_place_surface" stage. I have also tried manually running mri_normalize first and then running recon-all with the -FLAIRpial flag (command below), but I still get the same errors. mri_normalize $SUBJECTS_DIR/${subject_id}_T1/mri/FLAIR.mgz $SUBJECTS_DIR/${subject_id}_T1/mri/FLAIR.norm.mgz I have attached my recon-all.log file here in case it's of any use. Additional info: 1- recon-all --version freesurfer-macOS-darwin_x86_64-8.0.0-20250205-0f2bd3a 2-Mac info: ProductName: macOS ProductVersion: 15.5 BuildVersion: 24F74 3- uname -a Darwin iMac.local 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:53:26 PDT 2025; root:xnu-11417.121.6~2/RELEASE_X86_64 x86_64 Also, a note that we have been able to run recon-all v6 with -FLAIR flag on the same subject on an older Mac system. I would appreciate any insights you might have to how to improve my results using Flair images using v8 of FreeSurfer. Thanks, Mojdeh Zamyadi, MSc (she/her) Research Coordinator (Imaging) Centre for Youth Bipolar Disorder Centre for Addiction and Mental Health 80 Workman Way, Toronto 416-535-8501 ext. 33278 Twitter: @CYBDatCAMH<https://secure-web.cisco.com/1YOInhbSeEqszoMsC5o-oTzaa5eOkFEeEi14Qwx4Faci68…> Website: camh.ca/CYBD<https://secure-web.cisco.com/1-8ab9JMFlspDu1rE_5j9UF0W-Y4o0EXEfZACxBbGkZC9N…> [cid:image001.png@01D3E3D3.C62144B0] If you are in crisis or need urgent help: * Call the Kids Help Phone: 1-800-668-6868 or text 686868 * In Toronto, contact the Youthdale Crisis Service Line: 416-363-9990 * Go to a local hospital emergency room * Call 911 CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. AVIS DE CONFIDENTIALIT? : Ce message ?lectronique, ainsi que tout fichier qui y est joint, est reserve ? l'usage exclusif du destinataire vis? et peut contenir des renseignements confidentiels et privil?gi?s. Toute lecture, utilisation, divulgation ou distribution non autoris?e est interdite. Si vous n'?tes pas le destinataire vis?, veuillez en aviser l'exp?diteur par retour de courriel et d?truire toutes les copies du message original.

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Mask-to-eTIV > 1
by Krystalyn Edwards-Calma 06 Jul '25

06 Jul '25

External Email - Use Caution Aloha, I am using Version 7.4.1. After running recon-all for multiple subjects, I noticed the Brain mask is larger than the intracranial volume (Mask-to-eTIV > 1). I attempted multiple different skull stripping methods, however, the mask-to-eTIV is always > 1. Any suggestions on how to fix this? Mahalo for your help. Malama pono, Krystalyn Edwards-Calma

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