Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30051 discussions

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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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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Trouble finding recent archives
by Dierker, Donna 26 Feb '26

26 Feb '26

External Email - Use Caution I'm having trouble finding the mailing list archives. This exists, but I can't find more recent messages: https://secure-web.cisco.com/1_AzCMVLSYPWXrEp1K-AJyCtXx9QQ9JDRC8EUf3bu9E09G… The archives link here says Forbidden: https://secure-web.cisco.com/1t7pgqdKCNN4T1zl63JGJU0ZpokAYt_RliqFTp2CWPt9AG… Thanks, Donna ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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recon-all in severe atrophy
by Andrea Müller 25 Feb '26

25 Feb '26

External Email - Use Caution Hello, I am running both longitudinal and cross-sectional FreeSurfer (version 7.4.1) on a dataset which includes participants with significant levels of atrophy.If I run the 'default' versions, I see many errors in segmentation and cortical surfaces during QC afterwards (mostly related to undersegmentation of gyri). We want to avoid having to add manual corrections. Therefore, I wanted to ask what the recommended settings are for running FreeSurfer on these populations (eg adding the -bigventricles or -seg-wlo flags?) Thanks!

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glm, longitudnal analysis
by Eszter Boros 24 Feb '26

24 Feb '26

External Email - Use Caution Dear FreeSurfer Team, We are trying to run some longitudinal data using FreeSurfer 7.4.1. We have one group and 3 scans. We would like to see the changes between these timepoints. I am not sure how to proceed with the GLM because I found two tutorials. One here is saying I should create a longitudinal qdec table including fsid-base column and years/timepoints then run mri_glmfit --osgm https://secure-web.cisco.com/12qS0acHTgwXhZDIytchwCnsXkPJ57shyJ2uQEuf0WkwB9… The other one is saying to do a paired analysis. This one does not include the base and years data. https://secure-web.cisco.com/1voT6D0EOLTXJrVgGSmPK-onn8JIxg74dwxqLG9An8DuCh… How should I proceed? Thank you! Best regards, Eszter

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FreeSurfer Longitudinal Pipeline Exits with Errors - Prior to Sphere registration?
by Peter Najdzionek 24 Feb '26

24 Feb '26

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Query on use of FreeSurfer with Clinical Epilepsy MRI Protocols (Anisotropic Voxel Size)
by Uttara Bakshi 23 Feb '26

23 Feb '26

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Instensity normalisation issues - how to fix bias field correction?
by Chanelle Hendrikse 23 Feb '26

23 Feb '26

External Email - Use Caution Dear FreeSurfer developers I am processing longitudinal 3T T1-weighted data (Freesurfer 7.1.1) from the same scanner and protocol at 3 timepoints across childhood. The first two waves processed without major issues, but in the current pre-adolescent wave I am seeing consistent segmentation failures, mainly in occipital regions (sometimes frontal/parietal). Recon-all “misses” these regions, which were also excluded from the brain mask. I managed to correct the brain masks by fixing skull stripping (using ms_watershed) and rerunning recon-all, but the segmentation issues persisted. Inspection of norm.mgz suggests residual intensity inhomogeneity as posterior white matter intensity is substantially higher than expected (up to ~140–150). The brain mask also appears brighter here. Could this be causing recon-all to “miss” these regions? From what I’ve read, a potential solution is running N4BiasFieldCorrection on the raw T1 prior to recon-all (then processing from scratch), and only using control points if needed afterward. Would this be an acceptable approach, particularly in a longitudinal developmental dataset? Any alternative suggestions are also welcome! Many thanks in advance for your advice. Kind regards, Chanelle Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at https://secure-web.cisco.com/1xGpoPcjPQtqGoQemnEYmTxxk01Cml8DAbleqc_se8czt_… or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://secure-web.cisco.com/12QWH4f3q4K3n4d15-z-1Z4Ye2973t6xEKRh2n4qKT28F1…

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