Freesurfer August 2026

freesurfer@nmr.mgh.harvard.edu

24 participants
22 discussions

Re: Misidentification of the central sulcus in fsaverage registration
by Glasser, Matthew 26 Aug '26

26 Aug '26

External Email - Use Caution Was the rigid alignment derived from mris_register? Matt. From: Li, Jian,PhD <JLI112(a)mgh.harvard.edu> Date: Wednesday, August 5, 2026 at 11:13 AM To: Glasser, Matthew <glasserm(a)wustl.edu>; Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Re: Misidentification of the central sulcus in fsaverage registration Hi Matt, Yes, JOSA has been available for quite a while since FreeSurfer 8.0.0 through a simple “-josareg” flag in the recon-all command. Right side shows the functional improvement relative to the rigid rotation. Although FreeSurfer (mris_register) did not substantially outperform rigid in terms of functional alignment, it is more stable than others. Left panel, in contrast, shows the performance in alignment of folding patterns, where JOSA performs significantly better and should help quite a bit in various downstream tasks. Best, Andrew From: Glasser, Matthew <glasserm(a)wustl.edu> Date: Wednesday, August 5, 2026 at 11:40 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>; Li, Jian,PhD <JLI112(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Re: Misidentification of the central sulcus in fsaverage registration External Email - Use Caution Hi Bruce, It’s great that you have JOSA available in FreeSurfer now! I agree that it is an important upgrade over mris_register. One thing that is a little weird about your graph—why is FreeSurfer so tightly clustered relative to the other tools in the right-hand panel or FreeSurfer the left-hand panel? That is not something that I would expect to see based on my experience with the algorithm. Matt. From: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu> Date: Wednesday, August 5, 2026 at 10:30 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>; Li, Jian,PhD <JLI112(a)mgh.harvard.edu> Subject: [Freesurfer] Re: Misidentification of the central sulcus in fsaverage registration Hi Matt Yes, about 15% of the population has a folding variant that our old code struggled with. JOSA resolves many/most of those and also significantly outperforms other spherical registration in terms of both folding alignment and functional alignment. This is the bio archives link: https://secure-web.cisco.com/17fHBKO6TPIzygWDHkuO9-ifV7APDgsfp-mDBV0Wjz9gQr…<https://secure-web.cisco.com/1OryQNAwG92qEYESR5HSsFuF_QZUgNDNjQmM9AnN7YJShv…> and the Med. Image Analysis published link: https://secure-web.cisco.com/1KIRhAMIGpdTsba3q6GKAt_orVD_1ZK6nMERDNXghUbcbo…<https://secure-web.cisco.com/1OcBMbyd4SI030xJGOci4aomk92uDXm2qf_3Fi_v8OrNvM…> here is the relevant figure (4): [cid:image002.png@01DD24CD.C2FF9BD0] So in my opinion better to fix this using the high-resolution registration up front rather than let it be blurred out downstream Cheers Bruce From: Glasser, Matthew <glasserm(a)wustl.edu> Sent: Tuesday, August 4, 2026 9:08 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>; Li, Jian,PhD <JLI112(a)mgh.harvard.edu> Subject: [Freesurfer] Re: Misidentification of the central sulcus in fsaverage registration External Email - Use Caution Hi Donna, We have a few HCP individuals with this behavior as well. I have one of these cases in a talk I give to neuroradiology trainees. Most of them get it wrong too—it isn’t the easiest problem to solve with folding alone, though it would be interesting if folding registrations trained with multi-modal features like JOSA are better equipped to handle this. As I see in your ppt. we don’t really worry about this in the HCP Pipelines context because it always gets corrected when we run multi-modal registration. Matt. From: Dierker, Donna <donna(a)wustl.edu<mailto:donna@wustl.edu>> Date: Tuesday, August 4, 2026 at 3:12 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>; Li, Jian,PhD <JLI112(a)mgh.harvard.edu<mailto:JLI112@mgh.harvard.edu>> Subject: [Freesurfer] Re: Misidentification of the central sulcus in fsaverage registration Hi Madison, Bruce, and Andrew, I also have been looking at this issue, since most of the labs I work for use Freesurfer parcels as features in machine learning models. I'm adding to these slides as I learn more about the issue: https://secure-web.cisco.com/102EtLV9UnpQ9nx1CCw1q69d2SPnEvNC4goGHiEnyzXSfV…<https://secure-web.cisco.com/1KhR48Qvp4KsN3QfBMwFogNHJ4HrbBdH0dka_i8wA3EYk_…> We greatly appreciate your help. Donna ________________________________ From: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Sent: Tuesday, August 4, 2026 10:47 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>; Li, Jian,PhD <JLI112(a)mgh.harvard.edu<mailto:JLI112@mgh.harvard.edu>> Subject: [Freesurfer] Re: Misidentification of the central sulcus in fsaverage registration Hi Mackenzie This is almost certainly an error in the spherical registration. You can try Andrew Li’s JOSA algorithm, which is likely to fix this. Andrew: can you provide directions on how to run JOSA in the current recon-all? Cheers Bruce From: Mitchell, Mackenzie <macmitch(a)illinois.edu<mailto:macmitch@illinois.edu>> Sent: Tuesday, August 4, 2026 8:35 AM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Misidentification of the central sulcus in fsaverage registration External Email - Use Caution Hello, We are seeing that in some cases (13/167 subjects) FreeSurfer v7.3.2 incorrectly labeled the central sulcus in at least one hemisphere (see example below). In all cases, FreeSurfer is labeling the postcentral sulcus as the central sulcus. In one case, this is happening twice for the same subject who participated in two independent projects (i.e., we find this issue with different T1s and Freesurfer runs). See example below. [HUBS05_RH_looksincorrect.png] We have checked the segmentations and alignments for all subjects and they all look correct. We think this may be happening at the stage of normalization to fsaverage. Most critically for us, it looks like this error is displacing the mapping of our functional data to the surface, as the motor network functional connectivity maps are shifted forward, as would be expected from the mislabeling. See example below. [Bilateral motor FC.png] In an attempt to resolve this issue, we have run FreeSurfer v8.2.0 on these 13 subjects. This resulted in the central sulcus being correctly identified in only 4/13 subjects. Searching through past posts to this mailing list, we found this thread (https://secure-web.cisco.com/1MCbUy65pwm-NyzUw2VdWOwwFTfzvaBGo0cPTbRPvMr-20…<https://secure-web.cisco.com/1Av_o2jbMOBK2-QCYkM8TireDselI79riAZBd39wr1qcda…>) which suggested to rotate the spherical registration (e.g., z+15 degrees). We found that with various rotation parameters we could improve the cortical parcellation in a handful of subjects. However, we do not currently use the cortical parcellations for our work and our primary concern is being able to accurately map functional data to the surface. We are not sure if spherical rotation is the right point/method to intervene. All insight on how to intervene to improve fsaverage normalization would be greatly appreciated. Thank you, Mackenzie ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. 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/1M0ElAlahSpcuCZn1cFCsBylflYiq9noxxPE23GHynfMe0… . ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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PhD Position in Ultra-High-Field Layer fMRI of Cognitive Control and Interoception @ MPI Tübingen
by Romy Lorenz 26 Aug '26

26 Aug '26

External Email - Use Caution My lab at the MPI for Biological Cybernetics in Tübingen, Germany is currently recruiting a new PhD student for an exciting cross-species collaborative project using layer fMRI to investigate how interoception shapes cognitive control. Please feel free to share with your colleagues! Application deadline is: 1.10.2026 Start: Jan 2027 More info: https://secure-web.cisco.com/1MRidUQnaErtf9Wrq1jYO9QxJkKcnZZk3aTg3WQGZlQ6-a… If you have questions about this position, please reach out! Best, Romy Dr. Romy Lorenz Max Planck Research Group Leader Research Group Cognitive Neuroscience & Neurotechnology Max Planck Institute for Biological Cybernetics Tübingen, Germany romy.lorenz(a)tuebingen.mpg.de http://secure-web.cisco.com/190tGFf9eK5wH_7NYMXzm0f2XxFdfZSi-5V5kKsTxJAxs0U…

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PhD Position in Ultra-High-Field Layer fMRI of Cognitive Control and Interoception @ MPI Tübingen
by Dr. Romy Lorenz 26 Aug '26

26 Aug '26

External Email - Use Caution My lab at the MPI for Biological Cybernetics in Tübingen,Germany, is currently recruiting a new PhD student for an exciting cross-species collaborative project using layer fMRI to investigate how interoception shapes cognitive control. Please feel free to share with your colleagues! Application deadline is: 1.10.2026 Start: Jan 2027 More info: https://secure-web.cisco.com/1wfT71VzpTsJ5EyWCLMHSWnIugy3HCaR1BYe9QpcL_JBIv… If you have questions about this position, please reach out! Best, Romy Dr. Romy Lorenz Max Planck Research Group Leader Research Group Cognitive Neuroscience & Neurotechnology Max Planck Institute for Biological Cybernetics Tübingen, Germany romy.lorenz(a)tuebingen.mpg.de http://secure-web.cisco.com/1jbgK2TWORjaL0PHGfhm0yGbxipe6TUadClOVqHwmCRXV3Q…

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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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Freesurfer August 2026