Freesurfer December 2025

freesurfer@nmr.mgh.harvard.edu

26 participants
32 discussions

Request to Post Job Position on Freesurfer listserv
by Otero Ospina, Andrea 05 Mar '26

05 Mar '26

External Email - Use Caution [A close up of a logo Description automatically generated][cid:91EF027C-9846-4FE1-B2F9-8AA9ABA8FEE6] 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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Query on use of FreeSurfer with Clinical Epilepsy MRI Protocols (Anisotropic Voxel Size)
by Uttara Bakshi 02 Mar '26

02 Mar '26

External Email - Use Caution Dear FreeSurfer Support Team, Season's Greetings! I hope this email finds you well. May I take this opportunity to seek your support regarding the use of FreeSurfer for structural MRI data acquired using clinical epilepsy imaging protocols with non-isotropic voxel sizes in our hospital setting. To date, I have processed MRI data from over 90 epilepsy patients using *FreeSurfer v 6.0* (3T scanner 64-channel head coil, TA: 3:49 min; Voxel Size: 1.0 × 1.0 × 0.5 mm³; Acceleration factor: 2; Relative SNR: 1.00). The complete recon-all pipeline ran successfully for all subjects, generating cortical and subcortical segmentations as well as quantitative statistics files without any processing errors. However, I learnt that 1 mm³ isotropic resolution is recommended for optimal performance, although voxel sizes up to *1.3 × 1 × 1.3 mm³* are considered acceptable to reduce scan time or improve signal-to-noise ratio, as per FreeSurfer Wiki. Therefore recently, I have acquired one additional patient data using an isotropic protocol (1.0 × 1.0 × 1.0 mm³) and compared to epilepsy protocol mentioned above. To conclude , I got two different quantitative values. For example, in Left Hippocampus - Anisotropic : 3640.2 mm³ vs Isotropic : 3876.2 mm³ , Total intracranial volume- Anisotropic : 1504943.411530 mm³ vs Isotropic : 1529703.225834 mm3 , Mean cortical thickness – Anisotropic : 2.18512 mm vs Isotropic: 2.28844 mm. In this context, I would greatly appreciate your guidance on the following: 1. Would you recommend resampling 1 × 1 × 0.5 mm³ images to 1 mm³ isotropic resolution prior to running recon-all, or is it fine to process the native anisotropic resolution data? 2. Are there any appropriate FreeSurfer steps or commands to convert my already acquired 1 × 1 × 0.5 mm³ MRI data to isotropic resolution before running the FreeSurfer recon-all pipeline? 3. Are there any known limitations, biases, or segmentation inaccuracies, particularly affecting hippocampal volumetry or cortical thickness estimates, when FreeSurfer is applied to anisotropic voxel data in epilepsy research like I did? I am attaching the recon-all log files of both the protocols here. Thank you very much for your time and guidance. I would greatly appreciate your recommendations. -- Warm regards, *Uttara Bakshi* *Doctoral Fellow* *Institute Of Neurosciences Kolkata, India.*

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Postdoc position at MGH: Brainstem neuroimaging in Alzheimer's disease
by Jacobs, Heidi I.,PHD 20 Jan '26

20 Jan '26

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 7T MRI, PET imaging, pupil measurements, physiological recording, blood-based markers, cognitive assessments and non-invasive vagus nerve stimulation. This project is focused on the functional balance between the brainstem and cortex in relation to pathological changes in preclinical Alzheimer’s disease. This project will require combining fMRI and PET-data from existing datasets with computational modeling approaches. The Jacobs Lab consists of a multidisciplinary team of two instructors, four 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. At a minimum, the training environment will include professional development, one-on-one meetings, group lab meetings, frequent seminars and journal clubs, opportunities to present their work at national and international scientific conferences (i.e. Human Amyloid Imaging, Alzheimer’s Association International Conference), collaborations with partners within and outside MGH, and manuscript preparation for publication in high-impact journals. In addition, Dr. Jacobs has a strong funding record and will strongly encourage and provide mentorship in grant applications. Requirements: Candidates should hold a Ph.D. in Cognitive Neuroscience, Computational Neuroscience, bio/medical physics, Neuroimaging, Psychology (Biological), or a related discipline. Strong analytical, quantitative, and programming skills, along with experience in complex fMRI modeling, are essential, as is the ability to relate neuroimaging findings within a pathobiological framework of neurodegenerative diseases. The candidate should be highly motivated, a strong communicator, possess internal drive to learn independently, but also be comfortable with working as part of a larger collaborative team. A real necessity is a passion for science, strong scientific writing and organizational skills, and a positive attitude. Experience in Alzheimer’s disease or aging research would be beneficial. 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. Please send application materials to Dr. Heidi Jacobs, Associate Professor of Radiology, at hjacobs(a)mgh.harvard.edu<mailto:hjacobs@mgh.harvard.edu> ___________________________________________ 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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Clarification on running -autorecon2-wm, -autorecon-pial, and -autorecon3 after manual white matter and pial edits
by Camilo Castelblanco Riveros 05 Jan '26

05 Jan '26

External Email - Use Caution Hello FreeSurfer Developers and Community, I am currently refining surface reconstructions for my subjects by performing manual edits on both the white matter segmentation and pial surfaces using FreeSurfer. According to the FreeSurfer documentation, after making white matter edits, the recommended command is: recon-all -autorecon2-wm -subjid <subject> and after pial surface edits, it is recommended to run: recon-all -autorecon-pial -subjid <subject> followed by: recon-all -autorecon3 -subjid <subject> My main goal is to ensure that both white matter and pial manual edits are correctly incorporated without losing either. However, I have seen in the FreeSurfer tutorial the combined command: recon-all -autorecon2-wm -autorecon3 -subjid <subject> which runs both stages sequentially. I have two related questions: 1. If I run `recon-all -autorecon2-wm -autorecon3` after both white matter and pial edits, will my manual pial edits be preserved, or will they be overwritten by the `-autorecon2-wm` step? 2. Is the recommended workflow to run `-autorecon2-wm` first, then `-autorecon-pial` as a separate command, and finally `-autorecon3`? Or can some of these stages be combined safely in a single command line? For reference, I am using: - FreeSurfer version: 7.4.1 - Platform: Red Hat Enterprise Linux With gratitude, Camilo =================================== *Camilo Castelblanco Riveros (He/His)* Neuroscience Ph.D. Candidate (G4) Robertson Lab <https://secure-web.cisco.com/1VGQeQdcjwLtBi3C9UBo55c7SqVai-UrjQm1lF9QaAVlL0…> & Bujarski Lab <https://secure-web.cisco.com/1y_9Zgr30ubJ5JlJFc0I6-yJcgPm8sSkph5TvzTpqhl6nv…> Student Interest Group in Neurology (SIGN <https://secure-web.cisco.com/1uGgfMp5acPV-NG-koj4ZIyk0_wqPKAvcoF_BCuwGLKcw_…>) Co-Leader Global Health Fellow e: ccastelblanco.gr(a)dartmouth.edu Zoom <https://secure-web.cisco.com/1i_IGOhLxqGYKgaY8rs_7Ga3801HHvx4C0j37X5CbmatR6…>

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Re: Freesurfer Digest, Vol 262, Issue 31
by Jerome Maller 30 Dec '25

30 Dec '25

External Email - Use Caution Thanks Matt. However I am wondering why the -expert flag is not working? Regards, Jerome On Tue, 30 Dec 2025 at 11:23, <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. Problem using my own mask in recon-all (Jerome Maller) > 2. Re: Problem using my own mask in recon-all (Glasser, Matthew) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 30 Dec 2025 08:45:24 -0600 > From: Jerome Maller <jerome.maller(a)monash.edu> > Subject: [Freesurfer] Problem using my own mask in recon-all > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CAMsE-JKS3KGXtTFGqGfU0ysnCwn-C8= > ngZ5uf+3v-h-dZ4SHpA(a)mail.gmail.com> > Content-Type: multipart/alternative; > boundary="000000000000a7a85006472c69f9" > > External Email - Use Caution > > Hi Freesurfer experts. > > > > I am trying to process a T1-MPRAGE 7T scan with 0.5mm isotropic resolution > with the recon-all -highres flag. FS is struggling to make a good mask even > though I’ve tried various combinations in the recon-all command (e.g. > different -skullstrip -wsthresh numbers, -wsmore, different -watershed > atlases). I have tried with and without neck removal (using FSL’s > robustfov) as well as bias field correction (via SPM and also FSL’s FAST), > and feeding in with and without the scan already brain extracted (via > robex). I am now trying to feed in my pre-made mask using the -expert flag. > > > > * I have named my pre-made mask as brainmask.mgz and placed it in the > directory where my t1.nii.gz is located > > * I have made a text file (called expert.opts) that contains: > > > mri_mask brainmask.mgz > > > > My recon-all command calls the file using -expert expert.opts > > > > However, recon-all seems to ignore the calling of the expert.opts and so > tries to make its own mask… > > > > So my question is: am I correctly using the =expert flag and expert.opts to > use my pre-made brainmask.mgz? > > > > PS. I am using FS version 7.1 (as I am running Ubuntu 18.04 and can’t > upgrade due to lots of other software running on the computer) > > > > Thankyou! > > > > Jerome > -- >

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Problem using my own mask in recon-all
by Jerome Maller 30 Dec '25

30 Dec '25

External Email - Use Caution Hi Freesurfer experts. I am trying to process a T1-MPRAGE 7T scan with 0.5mm isotropic resolution with the recon-all -highres flag. FS is struggling to make a good mask even though I’ve tried various combinations in the recon-all command (e.g. different -skullstrip -wsthresh numbers, -wsmore, different -watershed atlases). I have tried with and without neck removal (using FSL’s robustfov) as well as bias field correction (via SPM and also FSL’s FAST), and feeding in with and without the scan already brain extracted (via robex). I am now trying to feed in my pre-made mask using the -expert flag. * I have named my pre-made mask as brainmask.mgz and placed it in the directory where my t1.nii.gz is located * I have made a text file (called expert.opts) that contains: mri_mask brainmask.mgz My recon-all command calls the file using -expert expert.opts However, recon-all seems to ignore the calling of the expert.opts and so tries to make its own mask… So my question is: am I correctly using the =expert flag and expert.opts to use my pre-made brainmask.mgz? PS. I am using FS version 7.1 (as I am running Ubuntu 18.04 and can’t upgrade due to lots of other software running on the computer) Thankyou! Jerome --

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localGI recon-all failure related to cerebellum/dura inclusion (multiple subjects)
by 효원 29 Dec '25

29 Dec '25

External Email - Use Caution Hello FreeSurfer Developers, I am running recon-all with the -localGI option to compute local gyrification index (LGI). Across multiple subjects from the same dataset, the pipeline fails at different stages. Although the failure points differ, all errors appear to be related to *posterior fossa inclusion (cerebellum or dura)* in the filled or white matter volumes. Below I describe two distinct failure patterns observed in different subjects. *1) What I am trying to accomplish* I am running recon-all with -localGI to compute local gyrification index (LGI). The error occurs only in a specific subject. *2) Command I ran* recon-all -i {name of the nii files}.nii -s {name of the new file} -sd {directory of the new file} -all *3) Exact error output* *1) Failure pattern 1: filled volume stage* (*Subjects: SPR_023_gi, SPR_024_gi, SPR_025_gi, SPR_037_gi*) In these subjects, recon-all fails early at the mri_fill stage with the following error message: error: Please check filled volume. Cerebellum may be included. *2) Failure pattern 2: topology defect correction stage* *(1) Topology Abort* (*Subject: SPR_039_gi, SPR_052_gi, SPR_070_gi, SPR_071_gi, SPR_078_gi, ,SPR_082_gi, SPR_084_gi, SPR_085_gi, SPR_092_gi*) 1. SPR_039_gi An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. CORRECTING DEFECT 101 (vertices=11842, convex hull=2982, v0=103450) Abort The run terminates with: recon-all -s SPR_039_gi exited with ERRORS 2. SPR_052_gi In an additional subject (SPR_052_gi), recon-all also aborts during topological defect correction: CORRECTING DEFECT 26 (vertices=16843, convex hull=2967, v0=19098) Abort 3. SPR_070_gi CORRECTING DEFECT 11 (vertices=20829, convex hull=3275) Abort 4. SPR_071_gi CORRECTING DEFECT 83 (vertices=15893, convex hull=2782, v0=123875) Abort 5. SPR_078_gi CORRECTING DEFECT 0 (vertices=54094, convex hull=2051, v0=0) Abort 6. SPR_082_gi CORRECTING DEFECT 43 (vertices=13775, convex hull=2607, v0=41288) Abort 7. SPR_084_gi CORRECTING DEFECT 16 (vertices=14335, convex hull=4350, v0=21574) Abort 8. SPR_085_gi CORRECTING DEFECT 0 (vertices=18840, convex hull=3104, v0=591) Abort 9. SPR_092_gi CORRECTING DEFECT 19 (vertices=9080, convex hull=3587, v0=17615) Abort (2) Topology segfault(signal11) (*Subject: SPR_058_gi, SPR_063_gi,*) 1. SPR_058_gi An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. CORRECTING DEFECT 38 (vertices=15899, convex hull=3154) Command terminated by signal 11 2. SPR_063_gi CORRECTING DEFECT ... Command terminated by signal 11 *(3) LGI computation stopped due to topological defects* *(Subject: SPR_079_gi, SPR_136_gi)* 1. SPR_079_gi WARNING -- Problem for vertex iV = 20401, lGI value is aberrantly high (lGI=47.0556)... This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file 'rh.pial_lgi.asc' 2. SPR_136_gi ERROR: compute_lgi did not create output file 'lh.pial_lgi.asc' *4) FreeSurfer version* freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b *5) Platform* OS: Ubuntu 20.04.1 LTS uname -a: Linux climb 5.15.0-139-generic #149~20.04.1-Ubuntu SMP Wed Apr 16 08:29:56 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux *6) recon-all.log* all files are attached to this email. Thank you very much for your time and help. Best regards, Hyowon Ju.

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To unsubscribe from FreeSurfer Mailing List
by Khine, Win 27 Dec '25

27 Dec '25

External Email - Use Caution Hi, I want to unsubscribe from FreeSurfer Mailing list, please. I previously subscribed to FreeSurfer Mailing list to ask questions for support and I am getting enormous amounts of emails from the FreeSurfer Mailing list, hence I would like to unsubscribe as soon as possible please. Thank you. Warm regards, Win

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To unsubscribe from FreeSurfer Mailing List
by Khine, Win 27 Dec '25

27 Dec '25

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Expert option is not appropriately reflected in recon-all
by Ikko Kimura 23 Dec '25

23 Dec '25

External Email - Use Caution Dear FreeSurfer Developers, I'm trying to run recon-all using freesurfer 8.0.0. with the command "recon-all -s ${sub} -i ${sub}_T1w.nii.gz -T2 ${sub}_T2w.nii.gz -T2pial -all -qcache -hires -expert expert," and writing to you because I got the following error: ------------------ mris_inflate -no-save-sulc 25 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading 25 ** failed to open GIFTI XML file '25.gii' mrisReadGIFTIdanum: ERROR reading gifti 25.gii [INFO] read, cannot find 25, trying 25.gii ... error: No such file or directory error: mris_inflate: could not read surface file 25\00 Command exited with non-zero status 255 -------------------- I added "mris_inflate -n 25" as expert option, and, as far as I see, this error happened because recon-all does not reflect the expert option properly (should be "mris_inflate -no-save-sulc -n 25 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix" not "mris_inflate -no-save-sulc 25 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix"). I could run exactly the same recon-all command without error using freesurfer 7.4.1. Could anyone kindly guide me on how to solve this issue? Best regards, Ikko ------------------- Ikko Kimura ikkok(a)drcmr.dk Postdoctoral researcher Neurophysics Group DRCMR, Copenhagen University Hospital - Amager and Hvidovre

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