Freesurfer June 2025

freesurfer@nmr.mgh.harvard.edu

48 participants
57 discussions

Re: any updates on installing on Ubuntu 24?
by fsbuild 12 Jun '25

12 Jun '25

External Email - Use Caution  Recent freesurfer releases list the supported OS’s on the web page,https://secure-web.cisco.com/1-84lS_-Js-6g7gOAWL8t--PWCh83WInKO14q7DSc… While Ubuntu24 is not listed for 8.0.0, it is on the list to support for future releases. Recent changes in Linux OS’s can prevent binary backwards compatibility when upgrading to Rocky9, CentOS9, Ubuntu 24. - R. On Jun 11, 2025, at 22:07, William Graves <william.graves(a)rutgers.edu> wrote:        External Email - Use Caution        Dear FreeSurfer experts, In searching your email list archive, I saw a message from Feb 5 of this year about known issues with installing FreeSurfer on Ubuntu 24. Any updates on whether those issues have been resolved? I ask because when I download and try to install the .deb package for freesurfer 8.0, I get this: Unpacking freesurfer (8.0.0) ...dpkg: dependency problems prevent configuration of freesurfer: freesurfer depends on libncurses5; however:  Package libncurses5 is not installed. freesurfer depends on libc6 (<< 2.36); however:  Version of libc6:amd64 on system is 2.39-0ubuntu8.4. freesurfer depends on libicu70 (>= 70.1-1~); however:  Package libicu70 is not installed. dpkg: error processing package freesurfer (--install): dependency problems - leaving unconfiguredProcessing triggers for libc-bin (2.39-0ubuntu8.4) ...Errors were encountered while processing: freesurfer I’d appreciate any insight you could give! Best,Will --- William W. Graves, Ph.D. Associate Professor, Department of Psychology Rutgers, The State University of New Jersey Smith Hall, Room 337 101 Warren Street, Newark, NJ  07102 http://secure-web.cisco.com/1cXCzSOEdcDFawBCD5-AuANnnfi-8MvW9k8OYOzjwZVMCeL… _______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1vhVZTW4j8zk-aMIqGXiHh8iT6iUL5_5VaC_XGhTwDRfLw…

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Query related to controlling for ICV in the models for surface area and thickness
by Muskan Khetan 11 Jun '25

11 Jun '25

External Email - Use Caution Dear Team members, I have a question regarding vertex-wise analysis using FreeSurfer. In my current analysis, I’m looking at the effects of an independent variable on cortical thickness and surface area across the brain. I understand that for ROI-based surface area analyses, it is typically recommended to control for total brain volume (TBV) or intracranial volume (ICV), as surface area is correlated with these global brain size measures. However, I’m unsure whether this recommendation applies to vertex-wise analyses as well or whether any underlying preprocessing steps in FreeSurfer account for brain size differences automatically. Could you please advise on whether TBV or ICV should be included as covariates in vertex-wise surface area models? And more broadly, under what circumstances is it advisable to control for global brain size in vertex-wise analysis? Any insights would be greatly appreciated. Best, Muskan

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any updates on installing on Ubuntu 24?
by William Graves 11 Jun '25

11 Jun '25

External Email - Use Caution Dear FreeSurfer experts, In searching your email list archive, I saw a message from Feb 5 of this year about known issues with installing FreeSurfer on Ubuntu 24. Any updates on whether those issues have been resolved? I ask because when I download and try to install the .deb package for freesurfer 8.0, I get this: Unpacking freesurfer (8.0.0) ... dpkg: dependency problems prevent configuration of freesurfer: freesurfer depends on libncurses5; however: Package libncurses5 is not installed. freesurfer depends on libc6 (<< 2.36); however: Version of libc6:amd64 on system is 2.39-0ubuntu8.4. freesurfer depends on libicu70 (>= 70.1-1~); however: Package libicu70 is not installed. dpkg: error processing package freesurfer (--install): dependency problems - leaving unconfigured Processing triggers for libc-bin (2.39-0ubuntu8.4) ... Errors were encountered while processing: freesurfer I’d appreciate any insight you could give! Best, Will --- William W. Graves, Ph.D. Associate Professor, Department of Psychology Rutgers, The State University of New Jersey Smith Hall, Room 337 101 Warren Street, Newark, NJ 07102 http://secure-web.cisco.com/1I8rZLdj2YzaE8W0250oQF0RSuzgFcJPMFJR_VuHfSNlOQ6…

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Question Regarding Longitudinal vs. Cross-Sectional FreeSurfer Analysis
by Keller, Lara 11 Jun '25

11 Jun '25

External Email - Use Caution Dear FreeSurfer Community, I am currently analyzing structural MRI data using FreeSurfer 8 and have a specific question regarding the longitudinal pipeline. My dataset consists of two groups: * One group has 3 follow-up timepoints * The other group has 2 follow-up timepoints I have processed the data using both the cross-sectional and longitudinal recon-all pipelines, and I am now wondering whether it is appropriate to proceed with the longitudinal output, despite the unequal number of timepoints between groups. Key Concerns: 1. Since FreeSurfer creates subject-specific within-subject templates, could the differing number of sessions lead to relevant systematic differences between the groups? Specifically, will the segmentation accuracy or signal-to-noise ratio be noticeably different between the groups due to these variations? 2. Would it be valid to continue using the longitudinal output but statistically account for the unequal number of sessions (e.g., via Linear Mixed Models)? 3. Alternatively, would it be preferable to use cross-sectional outputs to avoid potential biases introduced by differing template quality? 4. If I analyze only one specific timepoint for certain research questions, should I still use the longitudinal output, or would cross-sectional data be more appropriate? I find myself torn between the improved segmentation accuracy of the longitudinal approach and the potential systematic differences introduced by the varying number of timepoints. Would a viable solution be to proceed with the longitudinal output while ensuring robustness by replicating key findings using cross-sectional data? I would greatly appreciate your insights on whether it is methodologically sound to proceed with the longitudinal pipeline in this case and, if so, how best to control for the unequal timepoints in statistical analysis. Thank you very much for your time and guidance! Best regards, Lara

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WMH-SynthSeg: program "killed" while Pushing data through the CNN
by Nithin Thanissery 10 Jun '25

10 Jun '25

External Email - Use Caution Dear FreeSurfer experts, I am trying to use WMH-SynthSeg on FLAIR images to segment and quantify WMH. However, this error keeps popping up: The code I ran: mri_WMHsynthseg --i flair.nii --o output_dir/output.nii.gz --csv_vols volumes.csv --save_lesion_probabilities Message I got: Arguments seem correct; loading Python packages... Using cpu Using 1 thread(s) Preparing model and loading weights Working on image 1 of 1: flair.nii Loading input volume and normalizing to [0,1] Upscaling to target resolution Pushing data through the CNN Killed I am using Ubuntu 18.04 and using the FreeSurfer 8.0.0 installed using the .deb file. I have 32GB RAM. The nifti file is 100.7 MB (I am hoping that's not the problem). I checked my RAM utilization during the process. I could see it going upto 28GB before the process was killed. Read similar problems on the freesurfer mail list that were dated at least a year ago. But, I was not able to find any solution. Would you have any suggestions/solutions or recommendations to make this work? Thanks and regards

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NextBrain Cortical Segmentation Errors
by Boa Sorte Silva, Narlon 10 Jun '25

10 Jun '25

Hi there I am testing NextBrain in a dataset of older adults with MCI and evidence of cerebrovascular disease. In reviewing the outputs from NextBrain, I noticed that the cortical regions are not very well segmented, especially in comparison to SynthSeg. I have attached screenshots to illusive the differences. Of note, the T1w are generally of good quality with high signal-to-noise ratio. I am wondering if there is anything that can be done to try and improve the NextBrain cortical segmentation OR would you suggest using the cortical volumes from SynthSeg instead? We’re more interested in the subcortical regions anyway. Thanks so much for the help ! Narlon External Email - Use Caution

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Re: WMH-SynthSeg: program "killed" while Pushing data through the CNN
by fsbuild 10 Jun '25

10 Jun '25

External Email - Use Caution If you have not already tried making sure no other applications, e.g., browsers, etc. are running on your machine before running that command, then I would do so.  The process was likely killed because the machine does not have the memory (and/or memory management) resources to run that python code.    It could be that newer versions of Ubuntu Linux will provide more efficient memory management and allow it to run, but that is not for certain.  However, Ubuntu 18 is end of life’d and future freesurfer releases will not be available for Ubuntu18.  At some point you should consider upgrading, e.g., to Ubuntu 22, which is more current.. - R. On Jun 10, 2025, at 09:32, Nithin Thanissery <nithin.cogsci(a)gmail.com> wrote:        External Email - Use Caution        Dear FreeSurfer experts,å I am trying to use WMH-SynthSeg on FLAIR images to segment and quantify WMH. However, this error keeps popping up: The code I ran: mri_WMHsynthseg   --i flair.nii   --o output_dir/output.nii.gz   --csv_vols volumes.csv --save_lesion_probabilitiesMessage I got: Arguments seem correct; loading Python packages... Using cpu Using 1 thread(s) Preparing model and loading weights Working on image 1 of 1: flair.nii      Loading input volume and normalizing to [0,1]      Upscaling to target resolution      Pushing data through the CNN Killed I am using Ubuntu 18.04 and using the FreeSurfer 8.0.0 installed using the .deb file. I have 32GB RAM. The nifti file is 100.7 MB (I am hoping that's not the problem).  I checked my RAM utilization during the process. I could see it going upto 28GB before the process was killed. Read similar problems on the freesurfer mail list that were dated at least a year ago. But, I was not able to find any solution. Would you have any suggestions/solutions or recommendations to make this work?  Thanks and regards_______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1iA1vIZjaXS6o9hokJaSMWEbIHxI1na9HQJehQQsC0WXZO…

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Call for Applications: 2025 Tsinghua University Global Summer School on Culture, Psychology & Brain Imaging
by YAN Chao-Gan 09 Jun '25

09 Jun '25

External Email - Use Caution Dear colleagues, Apologies for the cross-post. As a long-term member of the Freesurfer community, I would like to share an opportunity that may interest students and junior colleagues with broad interests in neuroscience, mental health, and interdisciplinary research. Tsinghua University has recently established the *Research Center for Culture and Psychology*, and I am honored to serve as the founding director. One of our first major initiatives is the *2025 Tsinghua University Global Summer School on “Advancing Global Mental Health: Cultural Commonalities and Differences”* (July 14–27, 2025, in Beijing). While the program’s core is in cultural and clinical psychology, it places strong emphasis on the integration of *brain imaging, cognitive neuroscience*, and *AI* for mental health research. Several sessions will focus on neuroimaging approaches to mental health, cross-cultural brain science, and the intersection of spontaneous thought, resting-state fMRI, and culture—topics that connect directly to the Freesurfer community’s expertise. *Program Highlights:* - Academic lectures by leading international faculty in psychology, psychiatry, neuroscience, brain imaging, and AI - Cross-cultural teamwork and project-based learning - Hands-on Chinese cultural activities - All-English program; open to senior undergraduates and graduate students (non-Chinese nationality) - *Full scholarships* covering tuition and program fees (students only need to pay for airfare, and likely accommodation is also covered) Please see the attached brochure for details and feel free to forward this to interested students, trainees, or colleagues. We would be grateful for your help in spreading the word, and are happy to answer any questions (please see the link in the brochure). Thank you very much for your attention! Best regards, Chao-Gan -- Chao-Gan YAN, Ph.D. Professor, Department of Psychological and Cognitive Sciences, Tsinghua University Director, Research Center for Culture and Psychology, Tsinghua University Lyu Dalong Building, Tsinghua University, Haidian District, Beijing, 100084, China - Initiator <http://secure-web.cisco.com/16FGWHeS2T8gsAfg5wEoNF08iO93zUiYiz8TLNkfi_i8ynF…>DPABI <http://secure-web.cisco.com/1GuFeg6MEDVAq9c6YrM8cPrfZ4wdTHRh4O35EmBc5hfs7SR…> <http://secure-web.cisco.com/16FGWHeS2T8gsAfg5wEoNF08iO93zUiYiz8TLNkfi_i8ynF…>, DPABISurf, DPABIFiber, DPABINet, <http://secure-web.cisco.com/1rSdWLBmbrfRwy3bk2KjGv5uwi02BgCvcO4Br1cx4jfMjcG…>DPARSF <http://secure-web.cisco.com/16FGWHeS2T8gsAfg5wEoNF08iO93zUiYiz8TLNkfi_i8ynF…>, and The R-fMRI Network <http://secure-web.cisco.com/1L8HWxeI2Dir7aZgbVobzCDZ2R35lMIf3wtNhxhPs2ju6HV…> (RFMRI.ORG <http://secure-web.cisco.com/1mxksQogxXHr-ncxRsJ652w4XZiRYlUvkSqYL3nbKEuqlIG…>) Depression Imaging REsearch ConsorTium (DIRECT) <https://secure-web.cisco.com/1A4cQt28EgEPSm372SCeMHC1a5gFnlzDUZ9IcI6KdwDrmV…> "Mind Flower" Depression Research and Intervention Initiative <http://secure-web.cisco.com/1OPPCGwXaLLZfxIV9vYcj-utp3rwjl66WuDzirS7lq5lVAC…> https://secure-web.cisco.com/1Md_ZcZyWlSTREZS939yU97qlHtahZuHErtgZvcC6vwHBV… http://secure-web.cisco.com/1XyKg5sw9ha0A9OQ9X-B-FxjwttZkVhabDhR3zu6bJis_OG…

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Re: Issues with mri_histo_atlas_segment_fast and mri_histo_atlas_segment_fireants
by fsbuild 09 Jun '25

09 Jun '25

External Email - Use Caution  Maybe you could let us know the details about what version of MacOS you are running,  how much memory your machine has and what the M1 processor has for efficiency and performance cores. - R. On Jun 8, 2025, at 21:25, Treeby, Bradley <b.treeby(a)ucl.ac.uk> wrote:       External Email - Use Caution         Dear FreeSurfer Developers and Community, I am trying to run Bayesian Segmentation with the Histological Atlas "NextBrain" in FreeSurfer on an M1 Mac on the CPU. I downloaded the 8.0.0 installer and followed the instructions, downloaded the atlas, etc. If I run mri_histo_atlas_segment_fast. It runs until “Reading in atlas” and then fails with a long error trace including "An attempt has been made to start a new process before the current process has finished its bootstrapping phase." If I run mri_histo_atlas_segment_fireants it quits almost immediately, complaining about missing modules (‘fireants.registration.deformation.geodesic’). My call in both cases follows: mri_histo_atlas_segment_xxx $SUBJECT_IM $SUBJECTS_DIR/$SUBJECT_ID/mri_histo_atlas_seg/ 0 $FS_THREADS Are there any pointers, or some setup steps that I’ve missed? If it’s helpful, other tools like recon-all are working correctly. I’m excited to try this out! Best, Bradley Treeby. _______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1LRJFj-q1whe_aJdjQvnpHmOonFsjyU1a_OJFlT1gMirGb…

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Issues with mri_histo_atlas_segment_fast and mri_histo_atlas_segment_fireants
by Treeby, Bradley 08 Jun '25

08 Jun '25

External Email - Use Caution Dear FreeSurfer Developers and Community, I am trying to run Bayesian Segmentation with the Histological Atlas "NextBrain" in FreeSurfer on an M1 Mac on the CPU. I downloaded the 8.0.0 installer and followed the instructions, downloaded the atlas, etc. If I run mri_histo_atlas_segment_fast. It runs until “Reading in atlas” and then fails with a long error trace including "An attempt has been made to start a new process before the current process has finished its bootstrapping phase." If I run mri_histo_atlas_segment_fireants it quits almost immediately, complaining about missing modules (‘fireants.registration.deformation.geodesic’). My call in both cases follows: mri_histo_atlas_segment_xxx $SUBJECT_IM $SUBJECTS_DIR/$SUBJECT_ID/mri_histo_atlas_seg/ 0 $FS_THREADS Are there any pointers, or some setup steps that I’ve missed? If it’s helpful, other tools like recon-all are working correctly. I’m excited to try this out! Best, Bradley Treeby.

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