Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30071 discussions

Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
by Hana McMahon 26 Sep '25

26 Sep '25

External Email - Use Caution Hi, I’ve processed the same set of T1‐weighted scans with both FreeSurfer v7.2.0 and the newer v8.0.0. When I compare the regional stats (aseg + subfield tables), the absolute proportional differences are surprisingly large (anywhere from ~1 % up to nearly 200 %, depending on the structure). I first noticed the issue while running ANCOVAs: with the v8 outputs, estimated total intracranial volume (eTIV) is highly significant in every model, whereas the v7 results (using identical R code and covariates) show a very different pattern. I am wondering: * Are these version‐to‐version shifts expected, given the changes in v8? * Have others reported similar magnitude differences, particularly for eTIV and subcortical/hippocampal measures? * Are large shifts expected from run-to-run as well? * Any insight would be greatly appreciated, as I am concerned by the magnitude of the differences I am seeing between versions, which are significantly changing my results. Thanks for your time. Kindest, Hana Confidential communication - This email and any files transmitted with it are confidential and are intended solely for the addressee. If you are not the intended recipient, please be advised that you have received this email in error and that any use, dissemination, forwarding, printing, or copying of this email and any file attachments is strictly prohibited. If you have received this email in error, please notify me immediately by return email and destroy this email.

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Request to Post Job Position on Freesurfer listserv
by Otero Ospina, Andrea 25 Sep '25

25 Sep '25

External Email - Use Caution [A close up of a logo Description automatically generated][UGWqtuoMAAAAASUVORK5CYII=] Department of Psychiatry and Behavioral Sciences Postdoctoral Associate Position in Human Neuroimaging University of Miami Miller School of Medicine, Miami, Florida, USA The Gabbay 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 fMRI and proton MR spectroscopydata 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. Proficiencies with at least one major neuroimaging software suite (e.g. FSL, AFNI, SPM, Freesurfer, Caret, Connectome Workbench, etc.) and Unix/Linux environment are expected. Familiarity with Matlab, Python, and/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 high-risk adult (e.g. HIV+) populations using innovative neuroimaging and immunological methodologies. The neuroimaging program features high-resolution data acquisition and analysis techniques modeled on the Human Connectome Project (HCP) and is committed to the highest standards for magnetic resonance imaging and spectroscopy. The lab is funded by four ongoing NIH R01 neuroimaging studies (R01MH120601, R01DA054885, R01MH128878, and R01MH131207) and several smaller grants, providing unparalleled funding 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 accelerated and multi-echo fMRI sequences, 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 PI’s 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 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][signature_4161372267]

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Question about using FreeSurfer license on another computer
by Andy Junghyun Kim 23 Sep '25

23 Sep '25

External Email - Use Caution Hi, I am currently using FreeSurfer on my local laptop and have a license.txt file. I will also need to run FreeSurfer on our lab server. Can I simply copy my existing license.txt file to the lab server, or do I need to request a new license for each computer? Kind regards, Andy Kim

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Freeview questions
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 22 Sep '25

22 Sep '25

External Email - Use Caution Hi freeview developers - Still trying to make a rough transition from tkmedit to freeview. I have two questions: *I want to the recon brush to paint the main volume voxels from a secondary volume. Is there a possible way to do that in freeview without doing it one voxel at a time? Ex. I want to draw back voxels from the brainmask.mgz from the T1.mgz. *What are waypoints? I don't see any instructions on the wiki on how to take advantage of them - are they designed to supersede control points? Thanks. Victor Zeng Beth Israel Deaconess Medical Center Vial of Victory LLC -- ---------------------------------------------------------------------- PLEASE NOTE: This message is intended for the use of the person to whom it is addressed. It may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. See our web page at http://secure-web.cisco.com/1an1yVo6v6mmRxVNWBlv4yPHWVxCUoCso9_-8NIHwNomwWY… for a full directory of Beth Israel Lahey Health sites, staff, services and career opportunities.

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Creating aparc+aseg files
by Chen Goldstein 22 Sep '25

22 Sep '25

External Email - Use Caution Hello, I’m working with data created using freesurfer, specifically aparc+aseg.mgz files (I’m using nii.gz). I was wandering if you can tell me what is the minimal way to create this file? I don’t want to run the whole Recon-All process and was wandering if there is a shorter way to create them, and if yes how long creating one scan might take? Thank you in advance.

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Questions for analyzing pediatric data
by Yoonho Hwang 22 Sep '25

22 Sep '25

External Email - Use Caution Dear FreeSurfer experts, Hello, I hope this message finds you well. I am planning to perform FreeSurfer analyses across a range of pediatric age groups. It is recommended to use the adult FreeSurfer pipeline for individuals aged 5 and older, and the infant FreeSurfer pipeline for those up to 2 years of age. Which pipeline should be used for analyzing pediatric subjects between the ages of 2 and 5? Additionally, could you recommend any papers that provide guidelines or age criteria for pipeline selection? Thank you very much! Sincerely, Yoonho

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Question about combining data from cohorts processed with different Freesurfer versions
by Stacey Schaefer 21 Sep '25

21 Sep '25

External Email - Use Caution Hello Freesurfer gurus, We have two samples of approximately n~125-150 whose T1s were collected on the same scanner with the same acquisiton, except for a difference in head coil (8 vs 32 channel) and processed with different Freesurfer versions (v5.3.0 and v. 6.0.0). Both also had the FreeSurfer segmentation of hippocampal subfields v 6.0.0 applied. We would like your guidance about combining their data if possible to maximize sample size. What would your suggestion be for hypothesis testing? Can we combine the samples - for example to test moderators of hippocampal x age relationships, using simply a covariate to account for the differences in acquisition/Freesurfer processing (in addition to the usual sociodemographic and estimated intracranial volume covariates)? OR is that problematic and would you instead suggest keeping them separate and using one as a replication sample? Thank you for your guidance! Stacey Stacey M. Schaefer, Ph.D. Leader of the MIDUS Neuroscience Project & Co-Leader of the MIDUS Admin Core MIDUS NEURO Keystone House 901 University Bay Dr Madison WI 53705

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Re: recon-all: expert options not applied to mris_inflate
by Su, Weizhong 21 Sep '25

21 Sep '25

External Email - Use Caution Hi Yahia, I faced same issue when using mris_inflate expert option. Do not use this option for Freesurfer v8.1.0 until FS developer team fixes this problem. Best, Wayne From: "Mokli, Yahia" <yahia.mokli(a)psychiat.med.uni-giessen.de> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, September 4, 2025 at 8:53 AM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] recon-all: expert options not applied to mris_inflate [CAUTION: Non-UBC Email] External Email - Use Caution Hello FreeSurfer Team, What I am trying to accomplish: I am running a full recon-all (-all) and trying to control the number of inflation iterations via an expert options file containing: "mris_inflate -n 30" FreeSurfer version and platform: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed Running inside Docker based on Ubuntu 22.04 Command I ran: recon-all -i /data/test/sub-0113_t1_axisAlign.nii.gz -s sub-0113 -all -hires -parallel -openmp 16 -expert /data/test/expert_inflate30.opts Error/output seen: During the Inflation1 stage, the log shows mris_inflate being invoked without the -n flag and with a bare “30” argument: mris_inflate -no-save-sulc 30 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Shortly after, recon-all exits with ERRORS. The recon-all.log file have these lines at the end: #@# Inflation1 lh Thu Sep 4 13:54:46 UTC 2025 /data/subjects/sub-0113/scripts mris_inflate -no-save-sulc 30 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #----------------------------------- #@# Inflation1 rh Thu Sep 4 13:54:46 UTC 2025 /data/subjects/sub-0113/scripts mris_inflate -no-save-sulc 30 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 4083 of (4083 4086) to complete... Waiting for PID 4086 of (4083 4086) to complete... mris_inflate -no-save-sulc 30 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading 30 ** failed to open GIFTI XML file '30.gii' mrisReadGIFTIdanum: ERROR reading gifti 30.gii [INFO] read, cannot find 30, trying 30.gii ... error: No such file or directory error: mris_inflate: could not read surface file 30 mris_inflate -no-save-sulc 30 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading 30 ** failed to open GIFTI XML file '30.gii' mrisReadGIFTIdanum: ERROR reading gifti 30.gii [INFO] read, cannot find 30, trying 30.gii ... error: No such file or directory error: mris_inflate: could not read surface file 30 PIDs (4083 4086) completed and logs appended. Linux 4fa29909686b 6.8.0-78-generic #78-Ubuntu SMP PREEMPT_DYNAMIC Tue Aug 12 11:34:18 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-0113 exited with ERRORS at Thu Sep 4 13:54:46 UTC 2025 Troubleshooting already tried: - Recreated the expert file to ensure ASCII hyphen and LF newline: printf 'mris_inflate -n 30\n' > /data/test/expert_inflate30.opts - Resumed with overwrite -xopts-overwrite -expert /data/test/expert_inflate30.opts - Verified that mris_inflate accepts -n 30 manually:: /usr/local/freesurfer/8.1.0/bin/mris_inflate -no-save-sulc -n 30 in.surf out.surf - Other expert options (e.g., “mris_smooth -seed 9999”) are honored and appear correctly in the log Is there a known issue in FreeSurfer 8.1.0 on Ubuntu 22.04 where expert options for mris_inflate are not applied? What is the recommended way to ensure -n 30 is honored? Thank you for your help. Best regards, Yahia Mokli

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21 Sep '25

External Email - Use Caution Hi Freesurfer community, I am currently trying to project 3D density maps in individual diffusion space onto the cortical surface (within individual space). I'm not sure which registration function to use to obtain the register.dat file required for mri_vol2surf . Does bbregister work for this situation? If so, assuming I create a registration from diffusion space (RASmm/ACPC) to fsnative, would the --mov file as the T1w in diffusion space – same affine as that of the diffusion data, and same resolution as diffusion data– (obtained from qsiprep) work with the target being the T1 in fsnative space? Or should I use another type of function such as tkregister2 or something like this? My current code is the following: template_file = op.join(bids_path, 'derivatives', 'qsiprep', participant, 'anat',f"{participant}_space-ACPC_desc-preproc_T1w.nii.gz") registration_file = op.join(out_dir, 'ACPC2fsnative_register.dat') # 1) Generate registration file .dat cmd = ["bbregister", "--s", participant, "--sd", fs_path, "--mov", template_file, "--reg", registration_file, "--init-fsl", "--t1" ] print("Running:", " ".join(cmd)) subprocess.run(cmd, check=True, env={**os.environ, "SUBJECTS_DIR": fs_path}) #2) Apply ACPC2fsNative registration and project density map to surface hemisphere = ['L', 'R'] roi = ['LeftMTxWMxLGN', 'RightMTxWMxLGN'] for h, hemi in enumerate(hemisphere): mask = roi[h] density_map = op.join(analysis_path, 'tdi_maps', 'dipy_tdi_maps', participant, f"{participant}_ses-concat_desc-{mask}_tdi_map.nii.gz") # density_img = nib.load(density_map) # print(density_img.affine) # Output file name out_file = os.path.join(out_dir, f"{participant}_hemi-{hemi} _space-fsnative_label-{mask}_tdi_on_surf.mgh") if hemi == 'L': hm = 'lh' else: hm = 'rh' # Build mri_vol2surf command cmd = [ "mri_vol2surf", "--mov", density_map, "--regheader", participant, "--hemi", hm, "--reg", registration_file, "--surf", "white", "--projfrac", "0", "--sd", fs_path, "--out", out_file ] # Run the command print("Running:", " ".join(cmd)) subprocess.run(cmd, check=True, env={**os.environ, "SUBJECTS_DIR": fs_path}) Thanks, Best, -Loïc

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Zero Values for SegmentedTotalIntracranialVol
by Carly McIntyre-Wood 21 Sep '25

21 Sep '25

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