Freesurfer January 2025

freesurfer@nmr.mgh.harvard.edu

44 participants
67 discussions

Re: [Freesurfer] Question on using thalseg_1.1.h5
by Georgios Argyropoulos 23 May '25

23 May '25

External Email - Use Caution Many thanks and apologies, Henry - I figured it out... I stupidly replaced your improved segmentation script in both the scripts and the bin directory instead of only replacing the former. many thanks for your time, much appreciated g

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Importing surface meshes from 3rd party cortical surface reconstruction tools for analysis in fsaverage template space
by James Hengenius 03 Apr '25

03 Apr '25

External Email - Use Caution Hi, I'm working with infant (0-30 month) MR data, and iBEAT ( https://secure-web.cisco.com/1T2WKIelhUu8n_wuNR_5gb37RydVg1xrWEVvlUOdcz2UFW…) is currently doing a better job than Infant FreeSurfer ( https://secure-web.cisco.com/1M3VIitCZu3azJ0yMsnC2UvSxSyhcRAkbfTg_v1IUkOJOb…) at cortical surface recon in this age range. However, I have custom surface ROI atlases on the fsaverage template and would very much like to leverage FreeSurfer's stats tools to map iBEAT subject surfaces to the template and extract stats from my custom ROIs. To do so, I need to - Bring my iBEAT VTK surfaces (~47K vertices per hemisphere) into FreeSurfer (mris_convert?) - Resample the meshes to FS surface resolution (~12.5K vertices per hemi) - Compute curvature stats on the iBEAT surfaces - Use mris_surf2surf (or equivalent) to map the resampled iBEAT surface to the fsaverage template using curvature - Compute/extract anatomical stats from the regions equivalent to the ROIs in my template space atlas. All of the above are presenting challenges. So far, I tried using mris_convert to bring the VTK into FS format, but when I tried using mris_anatomical_stats, I get errors. Note that I also ran InfantFS on the data, and that I copied the converted (but not downsampled) VTK pial surface from iBEAT to $SUBJECTS_DIR/$subjid/surf/lh.ibeat.pial > mris_anatomical_stats -log test.ibeat.log sub-0001 lh ibeat.pial outputting results to test.ibeat.log... reading volume /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/mri/wm.mgz... reading input surface /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.ibeat.pial... Using TH3 vertex volume calc Total face volume 58098.7 Total vertex volume 57390.1 (mask=0) reading input pial surface /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.pial... error: mrisReadTriangleFile opened /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.pial okay but surface doesn't match /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.ibeat.pial. nvertices:46854 != mris->nvertices:12240 || nfaces:93704 != mris->nfaces:24476 error: mrisReadTriangleFile failed. error: mris_anatomical_stats: could not read surface file /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.pial It appears this approach is failing due to a difference in meshes (the iBEAT mesh is at a different resolution, with more elements, than the lh.pial from InfantFS). Any tips for this and the other steps would be a big help! Thanks, Jim H. -- Jim Hengenius Research Associate Paus Research Group CHU Sainte-Justine Research Centre My Google Calendar <http://secure-web.cisco.com/1NyYdK1uBklqcDSsFMhBiedpJnPC-H6m83iYBtfLt-c-oKz…>

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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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fixing/editing white matter surface
by Eszter Boros 12 Feb '25

12 Feb '25

External Email - Use Caution Dear FreeSurfer Team, We are editing some longitudinal data using FreeSurfer 7.4.1. I am not sure how to fix the following issue (see the attached pictures). The white surface (blue line) almost touches the pial surface because some of the voxels are "too bright" at the edge, so they were misidentified as white matter. [image: Screenshot 2025-01-21 at 1.21.23 PM.png] [image: Screenshot 2025-01-21 at 1.21.32 PM.png] Which volume should I edit to fix this? I was thinking about deleting these voxels from the brainmask but that might lead to excluding/deleting gray matter incorrectly. Or maybe I could delete these voxels from the white matter. I was also considering cloning some of the surrounding voxels somehow to make this area less bright. Thank you, Eszter

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Error in loading wmparc2diff.mgz
by Ramesh Babu 04 Feb '25

04 Feb '25

External Email - Use Caution Dear Expert, I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is; $ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green -viewport coronal error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz Please see the attached file and give your suggestions. Regards Ramesh

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Patlak PET/MRI
by Andrade Rey René 03 Feb '25

03 Feb '25

External Email - Use Caution Dear community, I have tried the tutorial for PETsurfer. I would like to ask some questions. 1) I have seen in the tutorial when you do PVC correction it is done on PET dynamic raw data. Is this correct? Because I have seen some tutorial where it is suggested on the motion corrected by AFNI image so called pet.mc.nii.gz 2) I also would like to compute hypometabolism on epileptic patients based on a dynamic PET so called Patlak Kinetic modeling. Is that possible with Freesurfer? I know there is Qmodeling toolbox in SPM but I cannot get access to their toolbox (some issue about the download) and I don’t know if there is another workaround. If not possible to do Patlak with FreeSurfer is it correct to assume the mean of the dynamic PET will provide epileptogenic zone for epileptic patients based on FDG-PET as hypo metabolic regions? Sincerely, Rene Andrade.

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Automated extraction of dural/meningeal ROI
by Sneha Pandya 03 Feb '25

03 Feb '25

External Email - Use Caution Dear Doug, We are working on PET images and our tracer has a lot of non-specific binding close to meninges. To do so we want to be able to mask out meninges and other areas outside the brain. Following up on your suggestion as in https://secure-web.cisco.com/1Ae5FkdxMKpYB4bvu5-OiOws53J6bGdKfXI6vjilmtNuqX… thread we are planning to extract meninges ROI and mask it out from our PET image. What labels should we include from the aseg.mgz and gtmseg.mgz file to be classified as "brain". We want to compare our regional PET uptake with PVC'ed PET data as well hence gtmseg.mgz. Thank you, Sneha

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[WARNING: ATTACHMENT UNSCANNED]Issue with mris_make_surfaces generating Incorrect pial surface
by 韦亚辉 31 Jan '25

31 Jan '25

External Email - Use Caution Dear FreeSurfer, I have modified some processing steps in NHPPipeline, but I am encountering an issue with the mris_make_surfaces command. Specifically, the pial surface generated appears correct in one half but incorrect in the other half. I have checked the required input files (aseg, filled, wm, T1, white surface), and they all seem fine. However, the issue persists. Here is the command I used: VARIABLESIGMA="12" MAXTHICKNESS="-max 15" PSIGMA="-psigma 7" NSIGMA_ABOVE="-nsigma_above 12" NSIGMA_BELOW="-nsigma_below 12" MINGRAY="-min_gray_at_csf_border 10" MAXGRAY="-max_gray_at_csf_border 20" mris_make_surfaces -variablesigma $VARIABLESIGMA $PSIGMA $MAXTHICKNESS $MINGRAY $MAXGRAY \ -white NOWRITE -aseg aseg -orig white.deformed -filled filled -wm wm \ -sdir $SubjectDIR -T1 $T1wHires $SubjectID lh -hires I have attached the necessary input files and results for your reference. Could you please help me identify the possible cause of this issue? Best regards, yahui

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Re: [Freesurfer] infantFS: expected outputs
by Zoellner, Frank 31 Jan '25

31 Jan '25

External Email - Use Caution Hi, I have another question. I set ccseg option to get CC stats but they do not show in the final aseg.stats file though it seem that the CC segemntnation is performend ? Yours Frank ---------------- adj. Prof. Dr. Frank Zoellner Acting head Computer Assisted Clinical Medicine Mannheim Institute for Intelligent Systems in Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim Phone: +49 (0)621 3835117 Fax: +49 (0)621 3835123 Email: Frank.Zoellner(a)MedMa.Uni-Heidelberg.de<mailto:Frank.Zoellner@MedMa.Uni-Heidelberg.de> Web: https://secure-web.cisco.com/1m0Kj20FyM86PUSYrf0HbRKDAEbErELxTGijhcN-gjE85P… Von: <freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von "Zollei, Lilla,Ph.D." <LZOLLEI(a)MGH.HARVARD.EDU> Antworten an: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Datum: Donnerstag, 24. Oktober 2024 um 03:59 An: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] infantFS: expected outputs Dear Frank, You are correct. The list of segmentation labels is not 100% the same. For the infantFS segmentation labels you can refer to Table 1 in https://secure-web.cisco.com/1yiUa1Vk5ihTnaFGWa_rpomMezNViMShkgspNV0lMBe5DL… Best, Lilla ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Zoellner, Frank <Frank.Zoellner(a)medma.uni-heidelberg.de> Sent: Monday, September 23, 2024 4:31 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] infantFS: expected outputs External Email - Use Caution Dear Lilla, Besides the differences in the files, when looking at the segmentations we wondered why there are some labels zero in the aseg stats file. These are : Left-Inf-Lat-Vent CSF Right-Inf-Lat-Vent Brain-Stem Left-vessel Left-choroid-plexus Right-vessel Right-choroid-plexus 5th ventrikel WM-hypointensities We also did a cross check and had run the same subject with the normal freesurfer pipeline and here there have been segmentations for the above structures. Maybe you have an idea what is happening here ? or are these not included in the atlas? Thanks in advance Yours Frank ----------- adjunct Prof. Dr. Frank Zoellner Acting head Computer Assisted Clinical Medicine Mannheim Institute for Intelligent System in Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim Phone: +49 (0)621 3835121 Fax: +49 (0)621 3835123 Email: Frank.Zoellner(a)MedMa.Uni-Heidelberg.de<mailto:Frank.Zoellner@MedMa.Uni-Heidelberg.de> Web: https://secure-web.cisco.com/1m0Kj20FyM86PUSYrf0HbRKDAEbErELxTGijhcN-gjE85P… Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> Im Auftrag von Zollei, Lilla,Ph.D. Gesendet: Sonntag, 22. September 2024 16:12 An: freesurfer(a)nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] infantFS: expected outputs Hi Marlene, This is correct. Even though infant_recon_all is trying to mimic the output folder structure and follows the FreeSrufer naming convention, it does not generate all of the files that the adult version does. Lilla ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Marlene Staginnus <ms2290(a)bath.ac.uk<mailto:ms2290@bath.ac.uk>> Sent: Monday, September 16, 2024 9:57 AM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] infantFS: expected outputs External Email - Use Caution Dear FreeSurfer Team, Apologies in case I missed this elsewhere, but I was wondering whether there is any information on what the expected outputs of running infant_ recon_all are, similar to this (https://secure-web.cisco.com/1842_5uJLUmhL9zjqueT9IG-O2ijdmDUyVixpX5UWMvoZ6…) for the adult pipeline? I am asking as after testing the pipeline using the example participant provided on openneuro (https://secure-web.cisco.com/1ZFwVrUQPg9OdHj5xfWvCvA6li9k0cO4hetJ6og0O1nRrJ…, I’ve noticed that some of the output differs from the adult version and I wanted to ensure that everything is running correctly before applying it to our data. For example, there is no ‘orig’ subdirectory or orig.mgz file in the ~/mri folder. Similarly, fewer files are included in the ~/stats folder (only: brainvol.stats, lh.aparc.stats, rh.aparc.stats) although I was able to able to generate other files (e.g., aseg.stats) using mri_segstats. Overall, only the following folders are generated following recon-all without errors: label, log, mri, stats, and surf. Is this correct or might there be something going wrong on my end? 1) FreeSurfer version: infant-dev-4a14499-20210109-4a14499 2) Platform: CentOS release 7 3) uname -a: Linux fhpc-1840 6.8.0-40-generic #40~22.04.3-Ubuntu SMP PREEMPT_DYNAMIC Tue Jul 30 17:30:19 UTC 2 x86_64 x86_64 x86_64 GNU/Linux 4) infant_recon_all log: see attached Thank you in advance! Best wishes, Marlene

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Corpus Callosum Missing in SAMSEG Output
by Taghizadeh Mortezaei, Nima 30 Jan '25

30 Jan '25

Dear FreeSurfer Support Team, I am using FreeSurfer version 7.4.1 and recently ran SAMSEG on a subject’s MRI data. However, I noticed that the corpus callosum does not appear as a distinct label in the segmented structures. After reviewing the output files and label definitions, I was unable to find any explicit segmentation for the corpus callosum in the SAMSEG results. Could you please clarify if the corpus callosum is included as a distinct structure in the default SAMSEG atlas? If not, is there a recommended approach to extract or segment the corpus callosum using SAMSEG? Any guidance or suggestions would be greatly appreciated. Please let me know if additional details or files are needed for context. Thank you for your time and support. Best regards, Nima Taghizadeh

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Freesurfer January 2025