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30070 discussions

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

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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…

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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…

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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

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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

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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 >

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windows-based software to read freesurfer images...
by Gonzalo Rojas Costa 12 Feb '25

12 Feb '25

External Email - Use Caution Hi: Is there any software for microsoft windows (and/or ubuntu) that allows you to read mgz file format images, and transformations in lta format? Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University https://secure-web.cisco.com/19vM4DwV78b-sl3y_ZfZ3YTKhc_SBUVHiu8YDsEcieF_DJ… https://secure-web.cisco.com/1Xa-i1VwHCpv0bCwsPpt414POmWcFkEkwSJgY1b1DrHuGZ… https://secure-web.cisco.com/1zf2kHGSJ1-fpXe_XrU6IZqjV_bG212ekW83HqWiN6xqsb…

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recon-all: aparc+aseg.mgz missing labels
by tomjandrews＠sky.com 12 Feb '25

12 Feb '25

External Email - Use Caution Hello, I have run recon-all on ~1600 participants and will use the aparc+aseg.mgz parcellation to extract structural connectomes.Across the dataset, the number of labels in each parcellations ranges from 109 to 115. Where can I find a complete list of labels in aparc+aseg.mgz?The distribution of missing labels is as follows: Label Region Name Missing Count72 5th-Ventricle 155280 non-WM-hypointensities 14903 Left-Cerebral-Cortex 97042 Right-Cerebral-Cortex 64230 Left-vessel 6662 Right-vessel 541006 ctx-lh-entorhinal 21016 ctx-lh-parahippocampal 22016 ctx-rh-parahippocampal 1 Among these, which missing labels are problematic? I assume the absence of the 5th ventricle and non-WM-hypointensities is expected, but I am uncertain about the others.I am only interested in the regions defined in the linked grey matter parcellations(https://secure-web.cisco.com/10fM6Wa2LmQzTYhwuqFhYwNe8hfPJWj9… and will restrict my structural connectome extraction to those labels. However, do these missing labels above suggest segmentation issues? Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96uname -a: Linux login-d 4.18.0-348.20.1.el8_5.x86_64 #1 SMP Tue Mar 8 12:56:54 EST 2022 x86_64 x86_64 x86_64 GNU/Linux Best,Tom

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Compute Cortical Thickness for grouped ROIs
by Rohitkumar DATCHANAMOURTY 12 Feb '25

12 Feb '25

External Email - Use Caution Hello, I am working on obtaining cortical thickness values for customized groups of ROIs. Currently, I extract thickness values for the standard set of ROIs using the following command: aparcstats2table --subjects [SUBJECT_ID] --hemi lh --meas thickness --tablefile lh_thickness.csv However, I would like to compute the mean thickness for a specific anatomical region, such as the right cingulate lobe, which consists of the following ROIs: - ctx-rh-caudalanteriorcingulate - ctx-rh-rostralanteriorcingulate - ctx-rh-isthmuscingulate - ctx-rh-posteriorcingulate Does FreeSurfer provide a built-in feature to compute mean thickness for such grouped regions? If not, what would be the most methodologically sound approach? I considered computing a volume-weighted average thickness, but I would appreciate your insights on the best way to proceed. Looking forward to your guidance. Thanks, Rohit

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Vertex Correspondences in Icosahedral Mesh Downsampling
by Samuel D Anderson 12 Feb '25

12 Feb '25

External Email - Use Caution Hello, I am working on generating a vertex mapping file that identifies corresponding vertices across different levels of an icosahedral mesh. Specifically, for ico6, I want to determine which vertices contribute to each vertex in ico5 when downsampling is performed. Currently, I approximate this mapping using Euclidean distance: for each vertex in ico5, I find the n closest vertices in ico6 based on their (x, y, z) coordinates, then average across these. However, I’m wondering if there is a more formal or standard approach to defining these vertex correspondences—perhaps one based on the hierarchical structure of icosahedral refinement. Would you have any suggestions for a more principled method to determine vertex equivalence across levels? Thanks, Sam

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