Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30127 discussions

extracting percent change values
by Victor Jenkins 11 Mar '26

11 Mar '26

External Email - Use Caution Hi everyone, I am using Fressurfer 7.4.1 for a longitudinal analysis with 4 timepoints. I followed this instruction below to see cortical thickness changes, and I found 3 significant clusters. https://secure-web.cisco.com/1zkw2d7WuvQHYpAKmrGwmY4HTHyJc1TV0m82jbLxopbfDf… -- Second Stage: Option QDEC This one from the website: long_mris_slopes --qdec long.testretest.qdec \ --meas thickness \ --hemi lh \ --sd $SUBJECTS_DIR \ --do-pc1 --do-label \ --generic-time \ --fwhm 15 \ --qcache fsaverage \ --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \ --isec-labels lh.testretest.fsaverage.cortex.label mri_glmfit --osgm \ --glmdir lh.testretest.thickness-pc1.fwhm15 \ --y lh.testretest.thickness-pc1.stack.fwhm15.mgh \ --label lh.testretest.fsaverage.cortex.label \ --surf fsaverage lh I also ran mri_glmfit-sim. (mri_glmfit-sim --glmdir lh.testretest.thickness.fwhm15 --cache 4 neg --cwp 0.05 --2spaces) I want to extract the percent change values/numbers (pc1, *pc1 = rate / thick1*) from the 3 significant clusters we found so I could visualize those values for every participant. I was not able to find how to do this step. Is there a way to do this? Thank you for the help! Best regards, Victor

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Difference between 7.3 and 7.4
by Aaron Tanenbaum 11 Mar '26

11 Mar '26

External Email - Use Caution Hello, I would like for our lab to move to freesurfer 7.4 from 7.3. Mainly because 7.4 can handle enhanced DICOMS. My lab will not move to 7.4 because of the potential difference between the recons. From my understanding there is no difference in the default recons. However we use the flag -3T. We finish using the segmentBS.sh command. With the -3T and segments.sh, will there be a difference in the results between 7.3 and 7.4? Thank you in advance.

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Using HCPex on Freesurfer Data
by Carly McIntyre-Wood 10 Mar '26

10 Mar '26

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Re: Missing vtk and qt dependencies in 8.1.0 compiled binaries
by fsbuild 10 Mar '26

10 Mar '26

External Email - Use Caution The Rocky8 8.1.0 release should run on Rocky9 and an installer can be found on the download page,https://secure-web.cisco.com/1Y-hgYUnsl39CGV1agic6tunpDoyDxITSoTLbdvGJ… There will be a Rocky9 installer in the forthcoming 8.2.0 release.  You could try the Rocky9 development build (which was previously announced on the Freesurfer mailing list), https://secure-web.cisco.com/1KnCLencGtvb2-jQPHIRiSpBXm1M0vkcx9… at this point,  I would wait for the 8.2.0 release to be announced on the mailing list in order to run a Rocky9 version of freesurfer because we do not recommend development builds for ongoing/long term work. I would check with your system administrator(s) about how they install of Linux .rpm packages and ask them to install and support freesurfer, e.g., the existing Rocky8 8.1.0 .rpm and the forthcoming Rocky9 8.2.0 .rpm.   Some sysadmins use a container to test (install) the .rpm, then take the list of dependencies and update their modules, Spack, etc.. configurations to provide the required system packages when freesurfer binaries run.   It’s not practical for us to support end users unarchiving a tar file and then try to diagnose what is missing on each remote system when the .rpm and .deb files should provide the dependency information. - R.

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Missing vtk and qt dependencies in 8.1.0 compiled binaries
by Tian Fang 10 Mar '26

10 Mar '26

External Email - Use Caution Dear FreeSurfer Developers, Our cluster runs Rockey 9 and we are trying to download the latest version (8.1.0) FreeSurfer, we did not find the installers for Rockey 9. However, we did find the compiled binaries for Rockey 9 (https://secure-web.cisco.com/1lRFVzFdsP_OaO91nqnuod4udTdF8XuYh52pE-EQsIqVyr…) We downloaded this version and try to launch freeview and encountered this error: "freeview: error while loading shared libraries: libvtkFiltersPoints.so.1: cannot open shared object file: No such file or directory" I compared the compiled binaries with that of previous version (e.g., 7.4.1) and find that the 8.1.0 version is missing lib/qt and lib/vtk. Is is possible for you to release a version with these? Thanks in advance for your help! 1) FreeSurfer version: freesurfer-linux-rocky9_x86_64-8.1.0.tar.gz 2) Platform: Rockey 9 Best regards, Tian Fang ________________________________ Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.

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nextbrain segmentation tool issue
by Vittorio Rispoli 06 Mar '26

06 Mar '26

External Email - Use Caution Dear all, I successfully downloaded the atlas, but when I try to run the segmentation tool, I have the following error. Could you help me please? Best regards Vittorio disordinimovimento2@Disordini-Movimento-2 ~ % mri_histo_atlas_segment_fireants --i/Users/disordinimovimento2/Documents/Vittorio/T1.nii.gz --o /Users/disordinimovimento2/Documents/Vittorio/prova_nextbrain --device cpu --side left --mode invivo Running command: fspython /Applications/freesurfer/dev/python/packages/ERC_bayesian_segmentation//scripts/segment_fireants.py --i/Users/disordinimovimento2/Documents/Vittorio/T1.nii.gz --o /Users/disordinimovimento2/Documents/Vittorio/prova_nextbrain --device cpu --side left --mode invivo --atlas_dir /Applications/freesurfer/dev/python/packages/ERC_bayesian_segmentation//atlas_simplified Traceback (most recent call last): File "/Applications/freesurfer/dev/python/packages/ERC_bayesian_segmentation//scripts/segment_fireants.py", line 9, in <module> import ext.my_functions as my File "/Applications/freesurfer/dev/python/packages/ERC_bayesian_segmentation/ext/my_functions.py", line 4, in <module> import cv2 ModuleNotFoundError: No module named 'cv2' disordinimovimento2@Disordini-Movimento-2 ~ %

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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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Truncated T1.mgz after recon-all
by Kim, Minhae 04 Mar '26

04 Mar '26

Hello FreeSurfer team, I encountered an error while running recon-all where T1.mgz files for two subjects appear to be cropped posteriorly along the Y dimension (RAS). The cortex is preserved, but portions of the skull and the scalp are removed. The input file ($subj/mri/orig/001.mgz) is intact, suggesting a possible issue during conversion (e.g., mri_convert). I didn’t find similar reports in the archive, and the problem reproduces identically across both versions of FreeSurfer below. recon-all.log files are attached. * FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 AND freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 * OS: Rocky 8.10 * uname -a: Linux r440-05.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux Any insight would be greatly appreciated. Thank you! Kindly, Ellie Ellie Minhae Kim (she/her/hers) Program Director | Pain and Neuroinflammation Imaging Lab Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 Thirteenth St, Suite 2316 Charlestown, MA 02129 Phone: (617) 643-0569 https://loggialab.mgh.harvard.edu/

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NextBrain segmentation tool not working
by Vittorio Rispoli 02 Mar '26

02 Mar '26

External Email - Use Caution Dear all, I unsuccessfully tried to run the NextBrain segmentation tool. Could you help me, please? My machine has freesurfer 8.0 installed - usually all look fine. After typing the command suggested in the nextbrain page, I have this error message vittorio@Disordini-Movimento-1 ~ % export FREESURFER_HOME=/Applications/freesurfer/8.0.0 source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/8.0.0 FSFAST_HOME /Applications/freesurfer/8.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/8.0.0/subjects MNI_DIR /Applications/freesurfer/8.0.0/mni vittorio@Disordini-Movimento-1 ~ % which mri_histo_atlas_segment_fireants /Applications/freesurfer/8.0.0/bin/mri_histo_atlas_segment_fireants vittorio@Disordini-Movimento-1 ~ % which mri_histo_atlas_segment_fireants /Applications/freesurfer/8.0.0/bin/mri_histo_atlas_segment_fireants vittorio@Disordini-Movimento-1 ~ % mri_histo_atlas_segment_fireants \ --i /Users/vittorio/Documents/Vittorio/prova_nextbrain/T1.nii.gz \ --o /Users/vittorio/Documents/Vittorio/prova_nextbrain/output_prova_nextbrain \ --device cpu \ --side left \ --mode invivo \ --threads 20 Incorrect number of arguments. Usage: mri_histo_atlas_segment_fireants INPUT_SCAN OUTPUT_DIRECTORY GPU THREADS [BF_MODE] Or, for help mri_histo_atlas_segment_fireants --help vittorio@Disordini-Movimento-1 ~ % --------------------------------------------------------- Do you have any suggestions to solve the issue? Best wishes Vittorio

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Freeview command line for "clear background" capability
by Jonathan Power 02 Mar '26

02 Mar '26

External Email - Use Caution In the Freeview 3.0 "Run Command" window, searching commands in the -h list, there are many ways to control image coloring. But I do not see anything for the "Clear background" capability. This capability is there in the GUI. If I load, say, a T1.mgz, and brainmask.mgz on top, for the brainmask.mgz volume, below the GUI color settings Color map / Window / Level / Min / Max sliders there are 3 buttons, the middle of which is "Clear background". Can this be switched on in a command line call? I ask because I would like to automate image generation where the within-mask tissue is normal grayscale, but the out-of-mask tissue is colored with a heat map, and this is nicely done when I can clear the brainmask background. Thanks, Jonathan

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