Freesurfer

freesurfer@nmr.mgh.harvard.edu

26 participants
30107 discussions

WM segmentation in tutorial Subj001
by Bélinda Boudi 28 Aug '26

28 Aug '26

External Email - Use Caution Hello Freesurfer team, I am working through the Freesurfer tutorial using the "Subj001" dataset. I ran recon-all using Freesurfer 8.2.0 on macOS. While looking through wm.mgz I noticed what appears to be a small region of white matter in an unusual location that is also included within the pial surface (see the attached pictures). Interestingly, it also does not appear in brainmask.mgz. I was wondering if you could help me understand what this represents and if it is something I should address. If it does need to be corrected, I am unsure which volume I should edit. I thought of deleting the relevant voxels from wm.mgz, but I would be concerned about affecting the surface reconstruction. I was wondering what you would recommend as the appropriate way to correct this, if any correction is needed. Thank you for your help. Best, Belinda Boudi

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Postdoc position in MRS/fMRS at MGH
by Jacobs, Heidi I.,PHD 28 Aug '26

28 Aug '26

Postdoctoral fellow position: Neurochemical changes in aging and neurodegeneration: MRS/fMRS/combined fMRS-fMRI at Massachusetts General Hospital The Athinoula A. Martinos Center for Biomedical Imaging, located within the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for a highly qualified postdoctoral individual to work with Dr. Heidi Jacobs. The Jacobs lab is focused on improving the early detection and early treatment of Alzheimer’s disease. The lab focuses on the neuromodulatory subcortical nuclei, in particular the locus coeruleus, using a variety of approaches, including 3T MRI, 7T MRI, PET imaging, pupil measurements, physiological recordings, blood-based markers, cognitive assessments and perturbational approaches, such as pharmacological manipulations and non-invasive vagus nerve stimulation. We are seeking a postdoctoral fellow with experience in magnetic resonance spectroscopy (MRS), functional MRS (fMRS), and/or combined time-resolved fMRI-fMRS to investigate neurochemical changes associated with aging and neurodegeneration. The successful candidate will have hands-on experience setting optimal sequence parameters, designing tasks, and analyzing (f)MRS data at 3T and 7T MRI, and will be able to accurately interpret neurochemical changes while critically acknowledging the methodological limitations of these techniques. This position is well-suited to candidates with a strong interest in aging and neurodegenerative disease who want to apply and further develop their (f)MRS expertise within a multimodal imaging environment. The candidate will work closely with the Jacobs lab team and will have the opportunity to integrate (f)MRS with other imaging modalities used in the lab, including structural and functional MRI and PET, as well as cognitive and physiological measures. The Jacobs Lab consists of a multidisciplinary team of two instructors, three postdocs, two PhD students, two clinical research coordinators, and one project manager. The work in this project will be performed at the Athinoula A. Martinos Center for Biomedical Imaging, Charlestown Navy Yard. The candidate will be part of ongoing collaborations and work in a stimulating and inspiring environment. Our research group values open communication, motivation, optimism, mutual respect, teamwork, and innovative thinking. Dr. Jacobs is highly committed to individualized mentoring to help trainees achieve the most out of their postdoctoral candidature and to move forward in their career. This is a one-year appointment. Extension beyond the first year will depend on funding and performance. Requirements: Candidates should hold a Ph.D. in Bio/medical Physics, Biomedical Engineering, Neuroimaging, Cognitive Neuroscience, or a related discipline. Essential qualifications include demonstrated hands-on experience with MRS, fMRS, and/or combined time-resolved fMRI-fMRS, including optimization of sequence parameters, task design optimized for fMRS, data analysis at 3T and/or 7T MRI. Advanced programming skills (e.g., Python, MATLAB) and a solid background in signal processing are required. The candidate should be highly motivated, a strong communicator (verbally and in scientific writing), have an internal drive to learn independently, and be comfortable working as part of a larger collaborative team. A real necessity is a passion for science and a positive attitude. Experience or a strong interest in aging and/or neurodegeneration research is required. Start date as soon as possible, but is negotiable. Apply: The successful candidate will have joint appointments at MGH and HMS. If interested, please send your CV, letter describing interests, background, major achievements, skills, goals and contact information for three professional references. Applications will be reviewed on a rolling basis until October 1st, 2026. Please send application materials to Dr. Heidi Jacobs, Associate Professor of Radiology at hjacobs(a)mgh.harvard.edu<mailto:hjacobs@mgh.harvard.edu> Center and lab websites: www.martinos.org<http://www.martinos.org> and www.heidijacobs.org<http://www.heidijacobs.org> ___________________________________________ Heidi Jacobs, PhD Associate Professor of Radiology Massachusetts General Hospital | Harvard Medical School Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging 149 13th Street Charlestown, MA 02129 hjacobs(a)mgh.harvard.edu www.heidijacobs.org<http://www.heidijacobs.org> Learn about what we do and why: https://shorturl.at/fEFa8 [A blue and black logo Description automatically generated] [signature_3581815700] Social media: Linkedin: https://www.linkedin.com/in/heidijacobs/ Bluesky: https://bsky.app/profile/heidijacobslab.bsky.social [Please note: I might send an email out of office hours, at weekends or during holidays. This suits me – but doesn’t mean I expect you to do the same]

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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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