Freesurfer

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30071 discussions

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

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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

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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

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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.

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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

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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.

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Measuring longitudinal changes in brain volume using SynthSeg
by Marco Ganzetti 01 Jul '25

01 Jul '25

External Email - Use Caution Does SynthSeg offer any functionality for estimating longitudinal changes in segmented brain volumes beyond simply subtracting values from two time points? Marco

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Re: freeview -ss orientation inconsistencies
by fsbuild 01 Jul '25

01 Jul '25

External Email - Use Caution We usually do not recommend using development builds instead of officially released builds with numbers, e.g., 8.0.0, because development builds can be unstable and may not entirely work - or work the same way - depending upon the day you happen to download a dev build.  However If you can try the latest development build from under,https://secure-web.cisco.com/1jq3XGGcHpTiWr_hdA87MKZEwqIqc5TaHaDuWhZ4… … which will echo a July 01 identifier (20250701) when you source the freesurfer environment,freesurfer-<os_arch>-dev-20250701-f62f34b … then that would help us to look at making a fix on top of the most recent code changes if your issue persists in that current dev build. - R.

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Re: freeview -ss orientation inconsistencies
by Ania Holubecki 01 Jul '25

01 Jul '25

External Email - Use Caution Hi, To clarify, I also tried a development build around the end of May when I first posted about this issue (freesurfer/dev-20250521-bad34cc). Does the development build that is currently there (dated today) contain an updated fix to this issue? *Ania Holubecki* On Tue, Jul 1, 2025 at 4:49 PM <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > 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: freeview -ss orientation inconsistencies (fsbuild) > 2. Recon-all clinical vs. FS version 8.0.0 (Stefanie Bradley) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 01 Jul 2025 20:23:36 +0200 > From: fsbuild <fsbuild(a)contbay.com> > Subject: [Freesurfer] Re: freeview -ss orientation inconsistencies > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <52b66d0818f14b6dbb070d0b4ba95965(a)trashmail.com> > Content-Type: multipart/alternative; > boundary="_=_swift_1751394216_db214b4c34d05cc9b5bbc04bb0801152_=_" > > External Email - Use Caution > > If you downloaded something labelled with 8.1, you should delete it and > either use the development builds from, > https://secure-web.cisco.com/15RxK9bSzU8k6FeMdNbLLEWxJ9eqC8NUcpIHgEEoSw3r4_… > OR use the 8.0.0 releases from, > https://secure-web.cisco.com/1uAi36bt4wpXbEOWQNu5DvWB0yjpPPP-Tgs_0dXQoN7JFc… > - R. > >

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Re: freeview -ss orientation inconsistencies
by fsbuild 01 Jul '25

01 Jul '25

External Email - Use Caution If you downloaded something labelled with 8.1, you should delete it and either use the development builds from,https://secure-web.cisco.com/15RxK9bSzU8k6FeMdNbLLEWxJ9eqC8NUcpIHgEEoS… OR use the 8.0.0 releases from,https://secure-web.cisco.com/1uAi36bt4wpXbEOWQNu5DvWB0yjpPPP-Tgs_0dXQo… - R.

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