Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

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

2 2

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

2 1

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.

3 2

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

2 3

QC recon- all and manual editing
by Mahta Abbaspour 06 Jul '25

06 Jul '25

External Email - Use Caution Hi, I recently attended your FreeSurfer course in June and found it incredibly helpful—thank you! I’m currently working on a research project on AD patients and have been performing quality control on my FreeSurfer outputs using version 8.0.0. I’d really appreciate your input on a few slices I came across, as I wasn’t sure whether they require manual correction. In this image, do you think the pial surface (red line) near both hippocampus (light blue) are undersegmented? [cid:1f744d31-7e4a-40c3-959e-09280cea965e] This is also another screenshot of the same brain. The pial surface on the left placed inside the WM surface. It's just 1-2 slices but I was wondering what's the best approach to these types of error. [cid:173d0154-9a5e-49f2-a430-c68849f64d80] Thank you for your time. Best

4 3

ASLPrep Recon-all Error
by 岳昊 06 Jul '25

06 Jul '25

External Email - Use Caution Dear FreeSurfer Developers, I am a neuroscience student currently working on analyzing ASL MRI data using ASLPrep. I am encountering difficulties running recon-all during the preprocessing pipeline. Specifically, I am running the command recon-all, and the exact error message displayed is Cmdline: recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -rh-only -openmp 8 -subjid sub-OAS30001 -sd /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer Stdout: ERROR: Flag -rh-only unrecognized. I encountered an issue similar to one reported on GitHub, suggesting a FreeSurfer version incompatibility. Attempts to resolve this by using FreeSurfer version freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c and freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b did not resolve the original issue. Upgrading to FreeSurfer version freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 resulted in a complete failure of ASLPrep. For your reference, the following information may be relevant: 1).FreeSurfer Version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c, and freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b and freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460. 2).Platform: Red Hat Enterprise Linux 8.5 (Ootpa) 3).uname -a: Linux cn77042 4.18.0-348.cn.x86_64 #1 SMP Wed Sep 14 10:27:16 CST 2022 x86_64 x86_64 x86_64 GNU/Linux 4).recon-all.log and the crash file: Please find those files attached to this email. Any guidance you could provide in resolving this issue would be greatly appreciated. Thank you for your time and assistance. Sincerely, Hao Yue

2 1

Recon-all clinical vs. FS version 8.0.0
by Stefanie Bradley 02 Jul '25

02 Jul '25

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

2 4

Re: Freesurfer Digest, Vol 257, Issue 14
by Sunniva Fenn-Moltu 02 Jul '25

02 Jul '25

External Email - Use Caution Please unsubscribe me! Dr Sunniva Fenn-Moltu (she/her) Postdoctoral Research Associate Department of Forensic and Neurodevelopmental Science Institute of Psychiatry, Psychology & Neuroscience King’s College London 16 De Crespigny Park, Denmark Hill, London, SE5 8AF ________________________________ From: freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: 02 July 2025 15:23 To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 257, Issue 14 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: Recon-all clinical vs. FS version 8.0.0 (Iglesias Gonzalez, Juan E.) ---------------------------------------------------------------------- Message: 1 Date: Wed, 2 Jul 2025 14:23:09 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Subject: [Freesurfer] Re: Recon-all clinical vs. FS version 8.0.0 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <PH0PR04MB83888D5F6E0D1EB14A99250EFD40A(a)PH0PR04MB8388.nam prd04.prod.outlook.com> Content-Type: multipart/alternative; boundary="_000_PH0PR04MB83888D 5F6E0D1EB14A99250EFD40APH0PR04MB8388namp_" Oh, I see. They are fairly different in the way that they try to place cortical surfaces. Recon-all uses T1 intensities directly, and only works with high-resolution near-isotropic T1w scans. Recon-all-clinical uses machine learning and is compatible with scans of any contrast and resolution, BUT is less accurate than recon-all if you actually do have 1mm T1 data. So, I would try recon-all first. Cheers, /Eugenio -- Juan Eugenio Iglesias https://secure-web.cisco.com/1K25c8GgtPaI1iQbFYGnNILxny8Ubj0djw1dmJIKkZgr4F…<http://secure-web.cisco.com/19dk633J8cDfEYmJaTrtHSBYKUttUKjsNwNDCuKAZXv-UO6…> From: Stefanie Bradley <stefanie.bradley(a)mail.utoronto.ca> Date: Wednesday, July 2, 2025 at 09:24 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Re: Recon-all clinical vs. FS version 8.0.0 External Email - Use Caution Hi Eugenio, Thanks for your response. I was more wondering if the standard recon-all pipelines (v8.0) are the same for recon-all clinical, since it seems like recon-all in version 8 uses Synthseg by default. My population is children aged 4-6 years old with cerebral palsy. The T1-weighted scans are MPRAGE, 0.8mm isotropic. Thanks, Stefanie ________________________________ From: Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Sent: Tuesday, July 1, 2025 8:35 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Re: Recon-all clinical vs. FS version 8.0.0 Dear Stefanie, What type of pathology are we discussing? What ages? What MRI sequence and resolution? Cheers, /Eugenio -- Juan Eugenio Iglesias https://secure-web.cisco.com/1HDqa2YX4Xwt8w_hiXJZ0lyV8Spi72Rzf-J41A6uWqy-QZ…<http://secure-web.cisco.com/19dk633J8cDfEYmJaTrtHSBYKUttUKjsNwNDCuKAZXv-UO6…> From: Stefanie Bradley <stefanie.bradley(a)mail.utoronto.ca> Date: Tuesday, July 1, 2025 at 5:49 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Recon-all clinical vs. FS version 8.0.0 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 -------------- next part -------------- A message part incompatible with plain text digests has been removed ... Name: not available Type: text/html Size: 9120 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/16ZFvrQdiKvIMaN8sLwQCpZ5El4XcFlkr9LTv_lvSf5Sst…<https://secure-web.cisco.com/1FaXldm9wavkFtAeZNwhtQHIAHc_ug45xZRaK9ok8MHFwZ…> ------------------------------ End of Freesurfer Digest, Vol 257, Issue 14 ******************************************* 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/1J1nT1TwyoO_2Tr4jiVBN3lxFttvA_lJZiD86hSfFhaQbF…<https://secure-web.cisco.com/1LGU4CR67sZ5KdtF2pZUdbVJLT5XFwciQ4V1hEMiMbDNb0…> <https://secure-web.cisco.com/1GjbFqGYeRYKxhsKBqhwWvb4IR-ThC-uehtArT0fuRKW4p…<https://secure-web.cisco.com/1LGU4CR67sZ5KdtF2pZUdbVJLT5XFwciQ4V1hEMiMbDNb0…>> . 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

Issue with TRACULA - failure Orient LAS
by Gabriella Monopoli 02 Jul '25

02 Jul '25

External Email - Use Caution Hi everyone, I hope this email finds you well. I'm trying to run TRACULA on a subject using FreeSurfer 8 (working on Ubuntu 22). However, when launching the first step of TRACULA (-prep), I encountered some issues with the creation of the dwi.bvecs file: after the LAS orientation, the dwi.bvecs file is empty. As a result, the symbolic links created afterward are incorrect, and the subsequent dtifit step produces empty files. After some attempts, I realized that the problem is caused by the fact that the orientLAS command fails, thus creating empty files. I wonder if anyone has ever encountered the same type of error and if they could help me solve it. I've attached the log file, the script, and the configuration file I used to this email. Best regards, Gabriella Monopoli

1 0

Re: Updates/bug fixes available for the 8.0.0 release
by fsbuild 01 Jul '25

01 Jul '25

External Email - Use Caution  The freesurfer 8.0.0 patch archive is back online with a new update, and the script to download and run is now called fs800_updates.sh instead of fs8_updates.sh.  Please delete any copy of the old fs8_updates.sh script and download and use the fs800_updates.sh script in all of the example commands previously listed in the thread. - R.

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer