Freesurfer February 2025

freesurfer@nmr.mgh.harvard.edu

48 participants
82 discussions

longitudinal analysis on one subject
by Isabella Rossellini 13 Jul '25

13 Jul '25

External Email - Use Caution Hello Freesurfer users/experts, I am working with Freesurfer 7.4.1 on a MacStudio (macOS 15.2) and I would like to ask your opinion about the following. Basically, we had an anxiety treatment study and I would like to analyze one subject who has 5-time points (0, 3, 6, 9, 12) with a longitudinal pipeline, two-stage model. Is it possible to run this on one person only and see the changes between these time points? I have never done this before on one subject so I am not sure what the best approach would be to look at the changes. After running the longitudinal preprocessing (base, long), should I generate the tables of freesurfer parcellation/segmentation stats data (aparcstats2table, asegstats2table)? Or can I just follow the two stage model steps? Maybe glm only works on a group of subjects. https://secure-web.cisco.com/1iC7gpXrtEAUPrcmI22C302poe7thUhcUmsjgK95UydNOq… (We have 9 more subjects - 10 in total - so I was hoping to visualize the pattern of changes one by one, in each subject, since these patients showed different changes in anxiety based on self-reported questionnaires) Sincerely, Isa Rosselini

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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

2 5

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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Issues with FS 7.3 skull stripping but NOT mri_synthstrip
by Carly McIntyre-Wood 26 Mar '25

26 Mar '25

3 2

dt_recon, CC_Anterior (T1) and FA corregistration.
by Gonzalo Rojas Costa 26 Mar '25

26 Mar '25

External Email - Use Caution Hi: I used the following commands: dt_recon --i sub-OAS30003_ses-d1631_run-01_dwi.nii.gz --b sub-OAS30003_ses-d1631_run-01_dwi.bval sub-OAS30003_ses-d1631_run-01_dwi.bvec --s OAS30003_MR_d1631 --o dt_recon_result cd dt_recon_result mri_vol2vol --mov lowb.nii.gz --targ $SUBJECTS_DIR/OAS30003_MR_d1631/mri/aseg.mgz --inv --interp nearest --o $SUBJECTS_DIR/OAS30003_MR_d1631/mri/aseg2diff.mgz --reg register.dat --no-save-reg mri_segstats --seg $SUBJECTS_DIR/OAS30003_MR_d1631/mri/aseg2diff.mgz --ctab /home/gonzalorojascosta/freesurfer/FreeSurferColorLUT.txt --i fa.nii.gz --sum fa.stats And, to view the results, I used: freeview -v $SUBJECTS_DIR/OAS30001_MR_d0757/mri/brain.mgz $SUBJECTS_DIR/OAS30001_MR_d0757/mri/orig.mgz $SUBJECTS_DIR/OAS30001_MR_d0757/mri/aseg.mgz:colormap=lut:opacity=0.2 fa.nii.gz:reg=register.dat:colormap=heat -colorscale -viewport coronal Why is there a corregistration error between the FA and the CC_Anterior (T1) section ? Sincerely Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University

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Re: [Freesurfer] FS version 8.0.0 released
by fsbuild 27 Feb '25

27 Feb '25

External Email - Use Caution    Please also see the setup notes for 8.X which includes setting up a license, recon-all behavior/times, setting up Matlab, and enabling CUDA for use with the python distribution, https://secure-web.cisco.com/1xOPRpyj7uAiM4Z1ghuHP3ztBuZaaYUxLFfg5A_bzFAKmr… R. On 2/27/25 09:42, Douglas N. Greve (dgreve(a)mgh.harvard.edu) wrote: Hi Y'all, version 8.0.0 is officially released. You can download from here https://secure-web.cisco.com/1VUAphTO6aiMmKMj3lyh2LZx6LjriTaN_K9hUeaIV8DeAd… Release notes here https://secure-web.cisco.com/1Tg3ruxpEtN2GlKMbmWbEkKWUAA3-KjD0yTd9LtgVhsSRN… best doug

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Manual Segmentation Adjustments
by Asli Eroglu 27 Feb '25

27 Feb '25

External Email - Use Caution Hi everyone, I hope you're all doing well! I'm running into a bit of trouble with some manual adjustments to our segmentation results and was wondering if anyone has encountered something similar. After running recon-all, I noticed that the white and pial surfaces aren’t aligning properly with the brain mask—especially around the motor areas where some white and gray matter seem to be missing. I went ahead and edited the white matter (wm.mgz) file and ran autorecon2-wm. Normally, this runs through the steps from -normalization2 to -curvstats, stated in this site: https://secure-web.cisco.com/1AUk84tBnT0XsxZ2iOt4m3Vg71XkMkCLnMtpqtMs1crG4W… However, it stopped after the -fix stage, so I had to run remaining commands one by one. That worked out fine for the white surface. Now, for the pial surfaces, I ran autorecon3, but I got this error: reading surface from ../surf/lh.white.preaparc... error: No such file or directory error: mrisReadTriangleFile opened ../surf/lh.sphere.reg okay but surface doesn't match ../surf/lh.white.preaparc. nvertices:246347 != mris->nvertices:135204 || nfaces:492690 != mris->nfaces:270404 error: No such file or directory error: mrisReadTriangleFile failed. error: No such file or directory error: mris_jacobian: could not read target surface ../surf/lh.sphere.reg Linux compute-11 4.18.0-513.18.1.el8_9.x86_64 #1 SMP Wed Feb 21 21:34:36 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux recon-all -s freesurfer exited with ERRORS at Thu Feb 20 17:32:52 CET 2025 Any advice or insights on how to move forward would be much appreciated. Thanks a lot! Best, Asli

1 0

FS version 8.0.0 released
by Douglas N. Greve 27 Feb '25

27 Feb '25

Hi Y'all, version 8.0.0 is officially released. You can download from here https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads Release notes here https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes best doug

1 0

Unknown error when running longitudinal analysis
by Quah, Bryan 27 Feb '25

27 Feb '25

External Email - Use Caution Hello FreeSurfer Enthusiasts, I'm attempting to run longitudinal analysis, as described here https://secure-web.cisco.com/1afGGFCyfveweaeVugpgH1DSg-Q9U8pxbe-yGl2q4FZoab… I am able to run the CROSS and BASE analyses without any errors logged, but running the LONG analysis produces an error message at the end of the process: "recon-all -s CID220_20211116.long.CID220 exited with ERRORS at Mon Feb 17 22:26:11 PST 2025" I ran this process with the command "recon-all -long CID220_20211116 CID220 -all -parallel -openmp 12". I have also looked through the recon-all.log file but could not find anything describing the error. I have attached the log file and hopefully you will be able to find it useful. Could anyone help troubleshoot the log file to see if there is an error during processing? Or is there a way I could verify if the longitudinal analysis process ran correctly based on produced output masks/metrics? More details: 1) FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b 2) Platform: Ubuntu 20.04.6 LTS 3) uname -a: Linux titan2 5.13.0-39-generic #44~20.04.1-Ubuntu SMP Thu Mar 24 16:43:35 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thanks, Bryan Quah IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is strictly prohibited. Thank you for your cooperation.

2 1

Convert 1D mgh back to 3D
by Melissa Thalhammer 26 Feb '25

26 Feb '25

External Email - Use Caution Dear everyone, I know that this might be not exactly the right place to ask, but I unfortunately did not reach the authors of the publication so far. I want to work with the evolutionary expansion map by Wei et al. published in Nat Comm (2019; https://secure-web.cisco.com/1EOa2cp_XKYtekyLUN3mqm-iZxVh0pAiE-j1_IvELbdew0…) On their website, they provide a download link leading to two mgh files (attached; https://secure-web.cisco.com/1wjBHK0nX5LW0U-Wy1w4rY2bystAnHOCIGlVB_T3xRlPwI…) I read them with the Matlab load_mgh.m function provided here (https://secure-web.cisco.com/1-0OpH0qgfeFpbCMfaVWHm-btTsT6A2ZX44WYfXtCEzjf9…) and it shows a 163842 x 1 vector (which probably corresponds to fsaverage6 I guess...). I now want to convertthe 1D vector back into 3D. I have come across save_mgh.m but don't know what should be put in as M (4x4 vox2ras transform). Any ideas what is the correct way to do that? Thank you! Best, Melissa

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Freesurfer February 2025