Freesurfer August 2026

freesurfer@nmr.mgh.harvard.edu

23 participants
20 discussions

FreeSurfer 8.1 longitudinal masking consistency - recommendation request
by Kimmig, Ann-Christin Sophie 24 Aug '26

24 Aug '26

Dear FreeSurfer experts, I'm running longitudinal recon-all (2 timepoints/subject) in FreeSurfer 8.1 on pooled adult MPRAGE and MP2RAGE (MPRAGEised UNI) data, and would appreciate your recommendation on a few points. 1. Custom masking (-xmask) is overwritten by SynthStrip's internal call in FS8.1, so I inject a custom brainmask.mgz manually after -autorecon1 at the cross-sectional stage - this works. At the base stage, mri_robust_template correctly combines both sessions' brainmasks into brainmask_template.mgz (confirmed visually), but recon-all then runs SynthStrip fresh on the template and uses that instead. Is brainmask_template.mgz meant to propagate forward as the template's brainmask.mgz but gets overrun by the automated SynthStrip call? And is global-expert-options.txt the recommended way to enforce consistent SynthStrip settings across cross, base, and long, as an alternative to manual injection at each stage? 2. Default SynthStrip is sometimes overinclusive around the eye/optic nerve on our MPRAGEised UNI images. We're considering --no-csf (with -b 2 to offset its known underinclusiveness in MPRAGE images) to address this. Are there downsides to --no-csf we should be aware of for FreeSurfer's own downstream processing specifically - e.g., anything in intensity normalization, Talairach registration, or pial surface placement (mris_make_surfaces) that relies on some CSF margin being present in the mask? 3. For the MP2RAGE/MPRAGEised data: is it preferable to submit the full (non-skull-stripped) MPRAGEised UNI image as input, letting recon-all handle stripping (or interject with custom mask), or to submit a pre-stripped image plus mask (as presurfer-style pipelines recommend)? The recommendations I'm aware of for this are based on older FreeSurfer versions, so I'm wondering whether the same guidance still holds for 8.1, or whether its updated components (e.g. SynthStrip/SynthMorph) change that recommendation. The full image's non-brain regions have atypical, non-anatomical UNI intensities, and I'm unsure whether that helps or hinders FreeSurfer's intensity normalization versus supplying an already-stripped image. Thank you very much for your time. All the best, Ann-Christin -- Ann-Christin Kimmig, Ph.D. Visiting Postdoctoral Research Fellow Psychiatry Neuroimaging Laboratory Department of Psychiatry Brigham and Women's Hospital Harvard Medical School

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Reply - apply mri_synthmorph transform to a set of coordinates
by Ezequiel Mikulan 21 Aug '26

21 Aug '26

External Email - Use Caution Dear Malte, thanks for your reply. I need to apply a deformable transform. I've been using ANTs (antsRegistrationSyN and ApplyTransformsToPoints) and I would like to update that part of the pipeline with mri_synthmorph. Do you think it will be possible in the near future? Best, Ezequiel ________________________________________ Hi Ezequiel, Yes, this is supported by mri_label2label if you save the coordinates in a .label file with vox2ras=3Dscanner in the header. These are simple text fil es; you can find examples in the label subfolder of a FreeSurfer-processed subject. However, this currently only works for rigid or affine transforms, that is, LTA files. What kind of transform are you looking to apply? Best wishes, Malte ________________________________________ From: Ezequiel Mikulan <emikulan(a)yahoo.com> Sent: Monday, June 22, 2026 07:40 To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] apply mri_synthmorph transform to a set of coordinates External Email - Use Caution Hi, I would like to know whether it is possible to apply a transform estima ted with mri_synthmorph to a set of coordinates (i have them in RAS space). These are SEEG electrode positions, and the transform maps between a subje ct's native space and the MNI152 template. If this is not currently supported, is this something that might be added i= n the future? Thanks a lot for your tools. Best, Ezequiel

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来自杨浩宇的邮件
by 杨浩宇 19 Aug '26

19 Aug '26

External Email - Use Caution help

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Question Regarding Synth Tools for Quantitative Atrophy Analysis
by John Anderson 18 Aug '26

18 Aug '26

External Email - Use Caution Hello, Could an expert in the Synth collection of tools please confirm whether these tools are intended for reliable use in patient populations, or primarily in healthy brains? Specifically, we would like to understand whether the Synth tools can preserve and reproduce cortical atrophy measurements in a manner comparable to the full recon-all pipeline. Practically, it appears that recon-all and the Synth tools may produce different measurements for the same brains, so we would like to clarify the expected use case. For example, if we have a pooled MRI dataset from patients with different neurological pathologies, including Alzheimer’s disease, amyotrophic lateral sclerosis, and other disorders, each condition may have a distinct cortical atrophy pattern. Are the Synth tools able to perform segmentation while preserving these disease-specific pathological patterns, or should they not be used for quantitative atrophy analysis? Any advice would be appreciated. Thank you. John

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Unable to obtain FreeSurfer licence due to repeated reCAPTCHA failure
by Shriya Sai 17 Aug '26

17 Aug '26

External Email - Use Caution Hello, I am a student attempting to obtain the free FreeSurfer licence through the official registration form. The form repeatedly returns “reCAPTCHA challenge failed,” including after trying another browser/private window and disabling blockers. Could you please advise how I can obtain a license.txt file through an alternative registration route? Thank you, Shriya Sai

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segmentation fault
by Emmanuelle Renauld 12 Aug '26

12 Aug '26

External Email - Use Caution Hi freesurfer, I have a segmentation fault error and I would like your help, either in fixing the issue or in running recon-all in another way. Here is what I tried: I decided to skullstrip my images first, and 1) use autorecon-1 with -noskullstrip, 2) place the brainmask myself. 3) run autorecon-2 and autorecon3. I am trying to do that on AllianceCanada's clusters. They have already installed Freesurfer for us, and I can do "module load freesurfer". I have access to version 8.2. I am launching tasks through sbatch, using environments with 32G memory. This fails nearly at the end of the process, with: mri_brainvol_stats --subject my_subj Segmentation fault (core dumped) Linux nc10227 5.14.0-611.49.1.el9_7.x86_64 #1 SMP PREEMPT_DYNAMIC Tue Apr 21 16:39:08 EDT 2026 x86_64 AMD EPYC 7532 32-Core Processor AuthenticAMD GNU/Linux Note that I also get many warnings along the way, with: "libtiff.so.5: no version information available, if this could be a clue." When testing manually this line only: >> mri_brainvol_stats --subject $SUBJECT_ID It works (most of the time. I have run into the same issue once, I don't know what was different). But if I run it through recon-all, it fails again. I thought I could use option -make all and continue from there, considering that I did run it manually, but make is not longer supported. Then I thought I could start at the next step. I saw from the log that mri_brainvol_stats happens during the step APas-to-ASeg, after it says "mri_surf2volseg done". I tried to run recon-all with option -noapas2aseg, but it still fails with the same error. Do you know what causes this? Can you help? Thank you, Emmanuelle Renauld

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recon_all or infant_recon_all for 4yo?
by Vladimir Vainer 09 Aug '26

09 Aug '26

External Email - Use Caution Hi, I'm trying to understand which recon is best for pediatric patients? Is there a guideline for which range to use infant_recon_all? Thanks -- If you can't explain it *simply*, you don't understand it well enough. - Albert Einstein

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Request FreeSurfer academic license
by 杜文杰 08 Aug '26

08 Aug '26

External Email - Use Caution Dear FreeSurfer Support Team, I am a postgraduate student majoring in medical imaging from University of Shanghai for Science and Technology. I need a free academic license.txt for FreeSurfer v7.4.0 to process T1-weighted MRI brain data for my research. Please send the license file to my email address: 251300255(a)st.usst.edu.cn Type of research: Non-profit academic research Thank you very much! Best regards, Wenjie Du 杜文杰 251300255(a)st.usst.edu.cn

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Re: siemens distortion correction?
by Glasser, Matthew 07 Aug '26

07 Aug '26

External Email - Use Caution 1. If you are using the HCP Pipelines, you can do the correction post-hoc easily as long as you have the gradient nonlinearity file for your scanner. It is just an extra flag to include. 2. I believe (and Mike CCed can confirm) that the gradient nonlinearity file is the same for each scanner of a given model and gradient set. 3. Depending on software version, on-scanner gradient nonlinearity may be required. Mike may remember these details. Also gradient nonlinearity interacts with pre-scan normalize (on Siemens) depending on software version. 4. I would use the 3D correction if you do on-scanner. 5. Historically we did the gradient correction offline when we could because then we controlled the interpolation used (preferring spline to trilinear to reduce blurring). 6. Newer software versions are now including b0 (AKA EPI, AKA susceptibility) distortion correction of fMRI data. We would still do this offline for a research study, but this is great for clinical data where the analysis software may not be able to do this correction. Matt. From: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Date: Friday, August 7, 2026 at 2:41 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Re: siemens distortion correction? No idea. Depending upon the scanner, it is not always perfect, but it is better than nothing. There is some inevitable resampling and so some blurring, so some people will analyze the uncorrected data then apply the correction to the analysis. For 2D scans, I think they will only do the correction in 2D, which is pretty useless. On 8/6/2026 1:01 PM, Jason Tourville wrote: External Email - Use Caution Hi Doug, Thanks for the reply. There's a good chance that the data will ultimately be used for a pooled analysis of data acquired across multiple sites at some point. In the relatively recent past, we've used the online-corrected scan without applying post hoc correction. When planning a new study, the staff here at BU warned against using that scan. Do you know why there is pushback on using the online corrected scan? Best, Jason On Mon, Aug 3, 2026 at 11:50 AM Douglas N. Greve <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> wrote: Hi Jason, it depends on what you are going to use it for. If you have a situation where distortion correction is going to be important at some point (eg, multi site study), then I would probably use the distortion corrected version. It is possible to apply it post hoc, but it is a pain. In the end, I don't think it will make much of a difference. On 7/28/2026 12:44 PM, Jason Tourville wrote: External Email - Use Caution Hi Freesurfer supporters, When collecting T1-weighted MEMPRAGE for input to FS recon, is it better to use the online distortion corrected RMS volume? Or the RMS volume without correction? Best, Jason _______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu<mailto:freesurfer-leave@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1MBSjH6W3xmW784x0vzUhGvSz9Qc3Zbtn4h3RsB5M0obiP…<https://secure-web.cisco.com/1kbpcV1aZXMxOcyREMG2eveFl58yGmCA6uwqHX5fhru38Q…> _______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu<mailto:freesurfer-leave@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1MBSjH6W3xmW784x0vzUhGvSz9Qc3Zbtn4h3RsB5M0obiP…<https://secure-web.cisco.com/1kbpcV1aZXMxOcyREMG2eveFl58yGmCA6uwqHX5fhru38Q…> The information in this e-mail is intended only for the person to whom it is addressed. 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siemens distortion correction?
by Jason Tourville 07 Aug '26

07 Aug '26

External Email - Use Caution Hi Freesurfer supporters, When collecting T1-weighted MEMPRAGE for input to FS recon, is it better to use the online distortion corrected RMS volume? Or the RMS volume without correction? Best, Jason

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Freesurfer August 2026