Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30127 discussions

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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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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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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Postdoc Associate Position at the University of Miami Miller School of Medicine
by Otero Ospina, Andrea 05 Aug '26

05 Aug '26

External Email - Use Caution [A close up of a logo Description automatically generated][cid:5EA7B1DB-1490-409A-91BB-DE9D4CF7359D] Department of Psychiatry and Behavioral Sciences Postdoctoral Associate Position in Human Neuroimaging University of Miami Miller School of Medicine, Miami, Florida, USA The IMPACT Mental Health Laboratory within the Department of Psychiatry at the University of Miami Miller School of Medicine is seeking highly motivated postdoctoral scholars in the field of human neuroimaging. Available positions will focus on analyzing proton magnetic resonance spectroscopy (MRS) data as well as acquiring or processing related MRI and biological measures. Candidates should either have completed or be near completing a PhD in neuroscience, psychology, cognitive neuroscience, radiology, engineering, biostatistics, or a related field, and should have a strong background in quantitative analysis. Experience with MRS data acquisition (e.g. MEGA-PRESS) and processing (e.g. LCModel) techniques as well as Unix/Linux scientific computing environments is expected. Familiarity with MATLAB, Python, or R programming languages is a plus. The primary responsibilities for this postdoctoral fellow will be to run scans, analyze neuroimaging data from multiple ongoing and recently concluded research projects, and write manuscripts. Under the mentorship of Vilma Gabbay, MD and Benjamin Ely, PhD, postdoctoral scholars will be expected to advance clinical and methodological knowledge through their postdoctoral training. Our lab is dedicated to the study and treatment of mood, anxiety, and substance use disorders in adolescent and adult populations using innovative neuroimaging and immunological methodologies. The neuroimaging program features high-resolution data acquisition and analysis techniques and is committed to the highest standards for magnetic resonance imaging and spectroscopy. The position is funded by five ongoing NIH R01 neuroimaging projects (R01MH120601, R01DA054885, R01MH128878, R01MH131207, and R01DA059527), providing unparalleled resources for active and exploratory studies. Major research topics include longitudinal studies of adolescent mood and anxiety disorders; comorbidity of depression, cannabis use, and HIV infection; and an intervention study aimed at improving well-being among healthcare workers with parental responsibilities during the COVID-19 pandemic. Project abstracts with further details can be found on NIH RePORTER. Resources available on-campus and through long-standing collaborations include multiple research-dedicated 3T MRI scanners (Siemens Skyra/Vida/Prisma) with cutting-edge sequences licensed from the University of Minnesota Center for Magnetic Resonance Research (CMRR), high-performance scientific computing clusters, and an extensive library of analytic and statistical software. The PIs are fully committed to fostering the trainee's research independence through publication of first-authored manuscripts in top journals and mentorship in grant applications. In addition to assisting with the PIs' proposals, the successful applicant will be highly encouraged to develop and pursue funding for their own research project through federal (e.g. NIH F32) or foundation grant programs by the end of their first year. Please send a CV, statement of interest, and contact information for three references to axo833(a)med.miami.edu<mailto:axo833@med.miami.edu>. All qualified candidates will be given equal consideration. Priority will be given to candidates available to start sooner. Compensation will be proportional to experience and will follow standard postdoctoral fellowship rates posted by the University of Miami. Andrea Otero, M.D. IMPACT Lab Research Supervisor Department of Psychiatry and Behavioral Sciences University of Miami — Miller School of Medicine Email: axo833(a)med.miami.edu Phone: 305-243-7086 [Image][cid:image002.png@01DC085F.16143290]

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Research Study Support
by Kasperek, Jessica 05 Aug '26

05 Aug '26

External Email - Use Caution Hello, One of my research studies, a retrospective Multiple Sclerosis (MS) study, is looking to conduct analyses on volumetric changes in brain MRI scans of MS patients during the course of their treatment. Specifically, it is looking for these items: * Overall brain volume change * Total lesion load * Cervical spine lesion * New MRI lesions * Asymmetrical atrophy between left and right hemispheres * Hippocampus * Thalamus * Basal ganglia * Prefrontal cortex * Cerebellum * Cortical GM Each patient has approx. 10 MRI scans or so. Is this a doable project for FreeSurfer? Any recommendations on how to approach this with the software? Any help is appreciated as there is no one at my institution that could direct me with the appropriate steps. Thanks, Jessica ******************* PLEASE NOTE ******************* This message and any documents accompanying this transmission may contain information that is privileged, confidential, and/or exempt from disclosure under applicable law and is intended solely for the addressee(s) named above. If you are not the intended addressee/recipient, you are hereby notified that any use of, disclosure, copying, distribution, or reliance on the contents of this message is strictly prohibited and may result in legal action against you. Please reply to the sender advising of the error in transmission and immediately delete/destroy the message and any accompanying documents. Thank you.

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Re: Misidentification of the central sulcus in fsaverage registration
by Glasser, Matthew 05 Aug '26

05 Aug '26

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/1aBm1vW4vLfCgH8tA8ut9N-zzjGzx9SpvUzHOYDCpFDS0-… and the Med. Image Analysis published link: https://secure-web.cisco.com/1ulKZlEJ6BztistS0A78t6NaH0o7kRP6VdGudvWo7jZn89… 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/1-n9tvb0yUExZTNk_ZNsDHUX7n6B3H4tzfFSRO0TPS5J3z…<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/1UVx9HLlUTTrl79FoQMCabwUMMqGLCrC0W9Gid_h3LeyZG…<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.

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Re: Misidentification of the central sulcus in fsaverage registration
by Glasser, Matthew 05 Aug '26

05 Aug '26

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> Date: Tuesday, August 4, 2026 at 3:12 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 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/1jq71lWjXpnK-Zw3St_xFo5laeuPEw4otvSFTOK5WtAK4x…<https://secure-web.cisco.com/1KhR48Qvp4KsN3QfBMwFogNHJ4HrbBdH0dka_i8wA3EYk_…> We greatly appreciate your help. Donna ________________________________ From: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu> Sent: Tuesday, August 4, 2026 10:47 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 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> Sent: Tuesday, August 4, 2026 8:35 AM To: freesurfer(a)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/13AoOSJF2KLOXJczpz8heqJi_LoQAmr9sjJOTF4riUuSaY…<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.

2 1

recon-all-clinical pediatric ventricle segmentation
by Betz, Anja Katharina 05 Aug '26

05 Aug '26

2 3

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