Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30128 discussions

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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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

2 3

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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Clarification on FreeSurfer recon-all Output and Preprocessing Steps
by Akanksha Upadhyay 23 Feb '26

23 Feb '26

External Email - Use Caution Hello FreeSurfer Developers, Greetings of the day. I am attempting to replicate a previously published work and have applied the recon-all pipeline on our structural MRI data (T1w.nii) using FreeSurfer. After segmentation and normalization, the output we are obtaining appears unusual to us. I would like to confirm whether these results are expected or if additional preprocessing steps are required prior to running recon-all . I have also attempted reorientation of the input image; however, I was only able to find GUI-based orientation options. I would appreciate your guidance on the following points: 1. Whether the observed segmentation and normalization outputs are expected, or if further preprocessing steps (such as reorientation, intensity correction, or format conversion) should be performed before running recon-all. 2. If manual reorientation is recommended, how should the orientation be determined (e.g., reference axes, alignment criteria, or specific angles)? 3. Any best practices for preparing T1w.nii files to ensure optimal processing with FreeSurfer. I am attaching screenshots of the normalization and segmentation results (aseg output) for your reference. Kindly guide me on how to proceed further. Thank you very much for your time and support. [image: Normalisation_results.jpg] [image: Segmentation_output_aseg.jpeg] -- *Regards* *Akanksha Upadhyay* *Department of Computer Science* *University of Delhi*

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Pineal Gland on v8
by Thakore, Radha 23 Feb '26

23 Feb '26

External Email - Use Caution Hello, I had a quick question about pineal gland segmentation. I heard that it would be possible to run pineal gland segmentation using FreeSurfer v.8. However, I am unsure about the Terminal input code with recon-all to specifically do that. Would you be able to help me with quantification of the pineal gland? Thank you! Sincerely, Radha Thakore M.D. Student | Class of 2028 Creighton University School of Medicine | Phoenix Campus

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License Registration Issue - 504 Gateway Timeout
by Alice Chen 18 Feb '26

18 Feb '26

External Email - Use Caution Dear FreeSurfer Team, I am writing to request a license file for FreeSurfer. I attempted to register via the online form (https://secure-web.cisco.com/177L6Jl_Bcj3JUMv1gTQIJ3dvJDC9gvlPAjizrI3y5crM0…) but I am repeatedly receiving a "504 Gateway Timeout" error. I am a researcher at the University of New South Wales (UNSW) and will be using FreeSurfer for non-profit research. Here are my registration details: Name: Alice Chen Title: Dr. (or your actual title) Institution: University of New South Wales (UNSW), Sydney, Australia Email: alice.chen3(a)unsw.edu.au<mailto:alice.chen3@unsw.edu.au> Operating System: Linux (HPC Cluster) Type of use: Non-profit education/research Could you please provide me with a license.txt file so I can proceed with my analysis? Thank you for your time and assistance. Best regards, Alice Ruiye Chen, PhD, MD Postdoctoral Research Fellow | School of Psychology, UNSW Sydney Visiting Postdoctoral Fellow | NeuRA W: http://secure-web.cisco.com/1jUJcMHl6XyXsg47bCeTsMPAF5dhUkWbQJBJXMFNDxi5WYh…<http://secure-web.cisco.com/1tEO6JgURwv0QF4P_BSmKpSw5o-_Epu524hdJjD2Ti66Zhf…> Google scholar<https://secure-web.cisco.com/1A5jBnt_pbS4abQ5DBdY56gImIMJcHn7zyR0Gct_3Qm4sz…> I pay my respects to Aboriginal and Torres Strait Islander peoples past and present, their cultures and traditions and acknowledge their continuing connection to land, sea and community. This email and any files transmitted with it may contain confidential information. If you believe you have received this email or any of its contents in error, please notify me immediately by return email and destroy this email. Do not use, disseminate, forward, print or copy any contents of an email received in error.

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