Freesurfer February 2025

freesurfer@nmr.mgh.harvard.edu

48 participants
82 discussions

FreeSurfer coordinates
by Yang Yifan 14 Feb '25

14 Feb '25

External Email - Use Caution Hi FreeSurfer Developers, I’m conducting manual ROI labelling on each participant’s inflated surface (after going through the ‘recon-all’ command), but I wasn’t very sure if the coordinates in the corresponding .label files are in MNI 305 space. At the top of the plain text files it’s showing ‘vox2ras=TkReg’. If they are not in MNI 305, could you please explain a bit about what coordinate system is used here and how I could convert that into MNI 305? Thank you very much! Best wishes, Vivian

3 3

Issue with Voxel Size Mismatch in Samseg-Long Pipeline
by Taghizadeh Mortezaei, Nima 14 Feb '25

14 Feb '25

Dear FreeSurfer Team, I am working with two timepoints for a subject and attempting to create a template for samseg-long using mri_robust_template. However, I encountered an error related to voxel size mismatch between the input images. Both timepoint images are T1W. The command I ran is: mri_robust_template --mov subject1_preRT.nii subject1_postRT.nii --template mean.mgz --satit --mapmov subject1_preRT_reg.mgz subject1_postRT_reg.mgz I received the following error: ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.428571, 0.428571, 4.4 size(0) = 0.449219, 0.449219, 5 error: Operation not permitted error: MultiRegistration::loadMovables: voxel size is different subject1_postRT.nii. >From what I understand, mri_robust_template does not support different voxel sizes between input images. Would the recommended approach be to first resample the images to the same voxel size using mri_convert --conform or another method before running mri_robust_template? Additionally, would this resampling introduce any potential biases that I should be aware of in a longitudinal analysis? If there is a better way to handle this issue, I would greatly appreciate your guidance. Best regards, Nima

1 1

Re: [Freesurfer] freeview runtime error...
by fsbuild 14 Feb '25

14 Feb '25

External Email - Use Caution  Try running the bash shell i.e., exec a new bash shell in the terminal window,$ bash I assume you installed the .deb file,https://secure-web.cisco.com/1vpMI_roAst1mdZTXwOe7ZmxVcxxk_NPabzpPTF6Z… from where you downloaded it to with the command ...$ sudo apt install ./freesurfer_ubuntu18-7.4.1_amd64.deb But if you did not run that command, then please do so. Make sure this package is installed. If it is already installed, the system should report there is nothing to do.$ sudo apt install mesa-utils If these 2 environment variables are not already set in your environment, i.e., there is no output listed for them using the echo command,$ echo $XDG_RUNTIME_DIR$ echo $DISPLAY …. then I would try setting them to be ...$ export XDG_RUNTIME_DIR=$HOME/.xdg$ export DISPLAY=:0 Then try running glxgears,$ glxgears If glxgeaqrs does not display rotating gears then there is something still not right with your graphics, display, system settings. If glxgears worked, then setup the freersurfer environment,$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh<output deleted> $ which freeview/usr/local/freesurfer/7.4.1/bin/freeview … then try opening an empty window with freeview …$ freeview If that worked, close the freeview window and try opening one of the provided volumes,$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz If that worked, then try opening one of your own files with freeview. If opening the bert volume file did not work, try setting this environment variable and re-run that command to open that volume,$ export QT_DEBUG_PLUGINS=1$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz … you will see quite a bit of output.  Look towards the end of the output and try to identify what it says is missing or what was not found on the system. - R. On Feb 13, 2025, at 22:55, Gonzalo Rojas Costa <gonzalo.rojas.costa(a)gmail.com> wrote:        External Email - Use Caution        Hi: it is freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460, under Ubuntu 18.04.4 LTS. In a real physical ubuntu. Sincerely, Gonzalo M. Rojas-CostaAdjunct Assistant Professor School of Medicine Finis Terrae University_______________________________________________ Freesurfer mailing list Freesurfer@nmr..mgh.harvard.edu https://secure-web.cisco.com/1VgXhN-f_Nad83y_Z7cLJL7GA2ENYdx-E6OK2zMWYbLOYL…

1 0

Re: [Freesurfer] freeview runtime error...
by Gonzalo Rojas Costa 13 Feb '25

13 Feb '25

External Email - Use Caution Hi: it is freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460, under Ubuntu 18.04.4 LTS. In a real physical ubuntu. Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University

1 0

Inquiry on Cortex and White Matter Volume Ratios in FreeSurfer
by Pamela González Méndez 13 Feb '25

13 Feb '25

External Email - Use Caution Dear FreeSurfer Team, I have been analyzing brain volumes using FreeSurfer and noticed that cortical volume is consistently larger than cerebral white matter volume, which seems counterintuitive. This pattern remains even after QA, where absolute values change but the ratio stays the same. The most striking case is in the cerebellum, where cortex volume is much greater than white matter. I wanted to ask if this is an expected outcome in FreeSurfer’s segmentation or if it could indicate a systematic bias. I was analyzing the following volumes: Cerebellar: Right-Cerebellum-White-Matter, Right-Cerebellum-Cortex, Left-Cerebellum-White-Matter, Left-Cerebellum-Cortex Global Brain: BrainSegVol, BrainSegVolNotVent, CerebralWhiteMatterVol, SubCortGrayVol, TotalGrayVol, SupraTentorialVol, SupraTentorialVolNotVent, CortexVol, rhCortexVol, lhCortexVol, lhCerebralWhiteMatterVol, rhCerebralWhiteMatterVol As part of QA, I manually checked the segmentation and made the following corrections: Checked skull and dura to prevent cortex invasion Reviewed sagittal and transverse sinuses to avoid misclassification Inspected orbits and middle cerebral arteries for segmentation accuracy Examined WM for extent and lesions to prevent miscalculations I have attached aseg_stats.txt for reference. I would greatly appreciate any insights on whether these volume relationships are expected. Best regards, Pamela González

1 0

Re: [Freesurfer] freeview runtime error...
by fsbuild 12 Feb '25

12 Feb '25

External Email - Use Caution  Please provide the following information:- if your host is a virtual machine (VM, WSL) or on a real physical Linux or Mac system- what OS you are running- what freesurfer package you installed from under https://secure-web.cisco.com/13Sxt1nGEBeuhE82PO-puwa08Oje37_ApeR… R. - R. On Feb 12, 2025, at 23:31, Gonzalo Rojas Costa <gonzalo.rojas.costa(a)gmail.com> wrote:        External Email - Use Caution        Hi:   I tried to run freeview, but I got the following error: "This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb. Abortado (`core' generado)"    How can I fix this problem?     Sincerely, Gonzalo M. Rojas-CostaAdjunct Assistant Professor School of Medicine Finis Terrae University MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1PhbLODEY_JRVE2_Yjewd2-dkAapGrf55YcAT0… MailScanner has detected a possible fraud attempt from "secure-web.cisco..com" claiming to be https://secure-web.cisco.com/1zkp55G634Raq0-sMIl6BCjtiwKtvs-fB-3g6h… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1_nRLgk4n--iT0_ncqBzzY9dB_MMk_IRhPCQ9c… Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1A_j5gFVN0nOOJK4N8a3jsRdswCpKHIyHhHC3nDsEoKT0R…

1 0

freeview runtime error...
by Gonzalo Rojas Costa 12 Feb '25

12 Feb '25

External Email - Use Caution Hi: I tried to run freeview, but I got the following error: "This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb. Abortado (`core' generado)" How can I fix this problem? Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University https://secure-web.cisco.com/1Rn1LmM19mhz6YEJumHlVeHt-leun2RXhw8yGBqHnm1KFg… https://secure-web.cisco.com/1tbjGzI7OmnaJFc1C29spqeePgw4pYsCXFTy-_OytEpJNf… https://secure-web.cisco.com/1I9IUzaP_XD8mNkU0DDLYncj-OsztyMLcvFS0slF_u3ZmL…

1 0

Subcortical under segmentations
by Jeong Yeon Kang 12 Feb '25

12 Feb '25

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to run recon-all on a group of nifti T1’s (parameters listed below). All the T1’s look good (no noticeable artifacts) and the cortical parcellations work well, and log files say completed without error. However, when looking at the subcortical segmentations, the thalamus, caudate and hippocampus appear consistently under segmented (screenshots below). T1 MRI: 1.5 Tesla GE Signa HDxt scanner with an 8-channel head coil, using a three-dimensional fast spoiled gradient echo (3D-FSPGR) imaging sequence, with 188 sagittal slices scanned using the following parameters: repetition time (TR) = 11.70 ms, echo time (TE) = 5.12 ms, inversion time = 500 ms, flip angle = 8°, matrix size = 256×256, slice thickness = 1 mm, in-plane resolution = 1 mm^2. We have tried a number of preprocessing steps on the T1 images but none of them appear to significantly improve the subcortical segmentations: 1. Normalizing the intensity of T1 voxels 2. Running FreeSurfer versions 5.3, 6, and 7 3. FastSurfer 4. DeNoising using ANTS 5. Bias field correction using ANTS We did not find anyone with similar issues in the archive so any insights or guidance would be much appreciated. Sincerely, Melody -- *Melody Jeong Yeon Kang* Ph.D. Student Imaging Genetics Center *USC* Stevens Neuroimaging and Informatics Institute Keck School of Medicine of *USC* University of Southern California Email: jkang395(a)usc.edu

2 2

Inquiry About Longitudinal Analysis Using recon-all-clinical.sh
by Taghizadeh Mortezaei, Nima 12 Feb '25

12 Feb '25

Dear FreeSurfer Community, I want to work on a longitudinal analysis with two time points (pre-treatment and post-treatment) and would like to follow the recommended longitudinal pipeline. However, I want to use recon-all-clinical.sh and I want to ask whether the commands and steps for recon-all-clinical.sh are the same as the standard recon-all longitudinal pipeline? Are there any modifications or additional considerations required when using this script for longitudinal processing? I appreciate any guidance or documentation references that could help with this analysis. Thank you for your time and support! Nima

2 2

ROI analysis in the MNI305 space
by neda afzalian 12 Feb '25

12 Feb '25

External Email - Use Caution To whome it may concern I want to do a volume based analysis in the MNI305 space. Specifically i want to use the specified subcortical segments which are exteracted and labeled in the aseg.nii.gz file The problem is that the dimension of two space are not the same. How can i transform the indices of subcortical segments from aseg.nii.gz to mni305 space? Best Neda >

2 1

← Newer
1
2
3
4
5
6
7
8
9
Older →

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer February 2025