Freesurfer

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30070 discussions

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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Re: Freesurfer Digest, Vol 256, Issue 4
by Riheb Naili 07 Jun '25

07 Jun '25

External Email - Use Caution Dear FreeSurfer Support Team, I hope this message finds you well. I am currently in the process of installing FreeSurfer for my research work and would like to request a license file in order to complete the installation. Could you please provide me with the necessary license or let me know the steps to obtain it? Thank you very much for your support. Best regards, Le sam. 7 juin 2025 à 02:20, <freesurfer-request(a)nmr.mgh.harvard.edu> a écrit : > 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. Question Regarding Longitudinal vs. Cross-Sectional FreeSurfer > Analysis > (Keller, Lara) > 2. PetSurfer surface-based SUVR (Mia Anthony) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 6 Jun 2025 09:43:35 +0000 > From: "Keller, Lara" <Lara.Keller(a)lvr.de> > Subject: [Freesurfer] Question Regarding Longitudinal vs. > Cross-Sectional FreeSurfer Analysis > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <53e88a0d5d704d97b16fa0e14f362ce9(a)lvr.de> > Content-Type: multipart/alternative; > boundary="_000_53e88a0d5d704d97b16fa0e14f362ce9lvrde_" > > 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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Re: Freesurfer Digest, Vol 256, Issue 4
by fsbuild 07 Jun '25

07 Jun '25

External Email - Use Caution  You should download and install the latest 8.0.0 installer package matching your machines OS (unless you have previous work you need to continue and/or support that was processed using an older version of Freesurfer).  The table of download links for the 8.0.0 release is here:https://secure-web.cisco.com/1Fv5NKe-WJ3HEIvKFeah03WXMkmxek9CVftoYlMfL… There is a link on that page to “… setup and install notes for 8.X releases …”https://secure-web.cisco.com/14v3LUZSDxyxAotnogEMhXQVJQETg8F-blx28o4LAmRKX_q6CWk4U8-CWEeOdVDSC3laKwG0q6K4ipxWmt9dFiISrsUWdu45X_Aivw_6hQp5JCJ1Y3KRPE9je5X4YV3lig7LPW3NXXtt3Iw1RHwY5WF5sIkpNX0YBKf-0koOlsReokBGKxUSgSVX6L5H7raIwH6zIN8ltXImEp0FJrVSeyuS1grweSurWpnfggbdNk1_gAaBp-lCaHgtwQXxL12ecm21eCjFUBKJGCCUEcNdi7jRuQPaRbt2pCr-ncmF0ZN8-xaITHUEeXaxtb4z8Bn0F/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads%2Frel8notes You can read at the top of that page about where to route to to fill out the form to get a license file emailed to you.  Once you have received the license file, follow the above instructions about how to setup the license file on your machine. - R. On Jun 7, 2025, at 02:34, Riheb Naili <riheb.naili(a)isimg.tn> wrote:        External Email - Use Caution        Dear FreeSurfer Support Team, I hope this message finds you well. I am currently in the process of installing FreeSurfer for my research work and would like to request a license file in order to complete the installation. Could you please provide me with the necessary license or let me know the steps to obtain it? Thank you very much for your support. Best regards,

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Open slots at upcoming FreeSurfer course
by Sennott, Liam Ricker 04 Jun '25

04 Jun '25

Hello all, There are still spots open for the Virtual FreeSurfer course happening next week on June 9th, 10th, and 12th. Please visit our course page to learn more and sign up: https://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse We will be accepting new registrations up until the start of the class (Monday, June 9th at 9:00am EDT). However, we will not be providing technical support past 5:00pm EDT on Friday, June 6th. Afterwards, you will need to get the course software set up on your own if you wish to attend. Any question about the course can be sent to fscourse(a)mgb.org<mailto:fscourse@mgb.org>

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03 Jun '25

Dear Freesurfer experts, I would like to register surface data (an 'overlay' file) from fsaverage_sym space back to the subject's native rh.white surface. This seemed to work fine for the lh data using: mri_surf2surf --srcsubject fsaverage_sym --trgsubject fs8 --hemi lh --sval mysurfacedata_lh.gii --tval mysurfacedata_lh_native.mgh However, I am struggling to do this for the right hemisphere. Do you have any recommendations? Thank you in advance, Best, Felix

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Re: recon-all error: SynthStrip process killed on macOS Sequoia 15.5 for subject 100206
by fsbuild 02 Jun '25

02 Jun '25

External Email - Use Caution The path /Applications/Freesurfer/dev/bin in the log indicates a development build is running.  Since that could be unstable, you could try installing and running the 8.0.0 release, https://secure-web.cisco.com/1q_jK67tubl-gK663E2lJ1Cv-nNx2UB7fhRxZMVS2UCp5E… But with either the 8.0.0 release from 2/2025 or subsequent dev builds, the machine may not have the resources to run the new recon-all setup.  MacOS may kill any process that is too greedy for system resources - which is consistent with the message in the log.   The 8.0.0 release and subsequent dev builds requires at least 16G of RAM for recon-all on top of what MacOS plus any other programs are currently using for memory.   That could translate to a minimum of 24G of RAM ; the 8.0.0 release was tested on Macs with not less than 32G RAM with no other applications running. So you could also try reverting to the old recon-all behavior from the 7.X releases by setting the environment variable  FS_V8_XOPTS on the recon-all command line, e.g., $ export FS_V8_XOPTS=0 && recon-all -all -i I50 -s Subj001 - R. On Jun 2, 2025, at 04:53, nil ahmadi <naiaddiamond1998(a)gmail.com> wrote:        External Email - Use Caution        Hello FreeSurfer Developers, I am running FreeSurfer on my MacBook Air with macOS Sequoia Version 15.5 (ARM64 architecture). I am processing subject 100206 using the recon-all pipeline with T1w and T2w images from my data directory located on an external drive. However, during the process, the step involving mri_synthstrip fails with the following error message: mri_synthstrip --threads 1 -i /Volumes/MyDRIVE/freesurfer_output/100206/mri/orig.mgz -o /Volumes/MyDRIVE/freesurfer_output/100206/mri/synthstrip.mgz Configuring model on the CPU Running SynthStrip model version 1 Input image read from: /Volumes/MyDRIVE/freesurfer_output/100206/mri/orig.mgz Processing frame (of 1): 1 Killed After this, the recon-all command exits with errors at Thu May 29 09:27:14 CST 2025. Here are some details about my setup: FreeSurfer version: dev version built May 26 2025 (freesurfer-macOS-darwin_arm64-dev-20250526-d84643b) Platform: macOS Sequoia Version 15.5 running on Apple Silicon (ARM64) Hardware: MacBook Air (Apple M3) Data location: External drive mounted at /Volumes/MyDRIVE with sufficient free space (4.4 TiB available) Memory status: System has some paging/swapping activity (vm_stat output attached) I have attached the recon-all.log file from Could you please advise on how to resolve this SynthStrip “Killed” error?  Any suggestions on running FreeSurfer successfully on macOS 15.5 with Apple Silicon would be greatly appreciated. Thank you very much for your support. Best regards, Niloufar Ahmadi

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