Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30055 discussions

Need to re-download for SAMSEG
by Sebastian Adolfo Rios Quintanilla 05 Mar '25

05 Mar '25

External Email - Use Caution Hello FreeSurfer Developers, I try using SAMSEG for my subjects' data. I acquired 3 subjects in 3 different months and everytime I wanted to use samseg for brain segmentation I encountered "zsh: command not found" and found myself in the need to re-do all the installation steps. At first, after going from subject 1 to subject 2 I thought It was a mistake I may have made in the installation. But now after around a month, trying to work on subject 3 I get the same error. I reach out to the dev team because I plan to scan more subjects in the coming months and having to reinstall everytime is not efficient and time consuming. Thank you very much for your time, help and support. -Sebastian Rios MSc. student at Polytechnique Montreal, MTL, CA

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"Re:" text in the Subject: is okay
by 叶贝宁 05 Mar '25

05 Mar '25

External Email - Use Caution confirm 8055d10f3553375c75c1fa2ec5094235bf27c2f5

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cortical thickness group analysis
by Maria Czarnecka 04 Mar '25

04 Mar '25

External Email - Use Caution Hello, I am trying to run a group analysis on cortical thickness (two groups, no covariates). I have been trying to follow the tutorial (FsTutorialGroupAnalysis) but I run into a problem with the mri_glmfit. My script looks like this: fspath="/dat/freesurfer" for hemi in lh rh; do echo $hemi cd $fspath mri_glmfit \ --y ${hemi}.norm_${hemi}_thickness.mgh \ --fsgd /dat2/maria/scripts/final/group.fsgd dods \ --C /dat2/maria/scripts/final/group.diff.mtx \ --surf fsaverage ${hemi} \ --cortex \ --glmdir ${hemi}.group.diff.glmdir done I think the function is searching for " --y ${hemi}.norm_${hemi}_thickness.mgh" in the main freesurfer directory instead of going into each participant's folder. What am I missing? The first error that i get is: " ... FSGD /dat2/maria/scripts/final/group.fsgd labelmask /dat/freesurfer/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.group.diff.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.group.diff.glmdir Loading y from /dat/freesurfer/lh.norm_lh_thickness.mgh *error: mghRead(/dat/freesurfer/lh.norm_lh_thickness.mgh, -1): could not open file ... done reading.ERROR: loading y /dat/freesurfer/lh.norm_lh_thickness.mgh* ..." Does it mean that something is wrong with my group.fsgd file? A sample of this file, just in case: " GroupDescriptorFile 1 Title ThickBlinds Class Class1 plus blue Class Class2 circle green Input sub-NW01W Class1 Input sub-NW02W Class1 ..." I will be grateful for your help. Best, Maria Czarnecka

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Using HCP-MMP1 (Glasser) atlas with freesurfer
by Blum, August 04 Mar '25

04 Mar '25

Hi there, I'm on a linux machine, and trying to use the HCP-MMP1 atlas. I tried adding the corresponding .annot file to a freesurfer folder on a /usr/local/freesurfer filepath. However, my computer stated that I don't have permission. Let me know what I can do and if there's any more information that you need! Thank you, August Blum Clinical Research Coordinator I Early Brain Development Initiative Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129

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News: subregion probabilistic atlases in MNI space available
by Iglesias Gonzalez, Juan E. 03 Mar '25

03 Mar '25

Hi everyone, People have asked me to do this multiple times, and I finally got down to it: I put the subregion atlases (hippocampal subfields, nuclei of the amygdala, brainstem subregions, thalamic nuclei) in MNI/ICBM152 space. Details here: https://surfer.nmr.mgh.harvard.edu/fswiki/SubfieldAtlasesICBMspace Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com

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illegal instruction - core dumped with samseg lesion
by Paola Di Filippo 03 Mar '25

03 Mar '25

External Email - Use Caution Hi everyone, I am using freesurfer v. 7.4.1 on a VM and I am trying to run samseg for an MS patient with the following command, but I get the following error: illegal instruction - core dumped. -------- freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1 FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects MNI_DIR /usr/local/freesurfer/7.4.1/mni paolasofia@Freesurfer-ub22:~$ run_samseg --input /home/paolasofia/DICOM.ANG.CHER.2.4.91/NIFTI/A.C.2.4.91.MRI.12.9.22.T1.nii /home/paolasofia/DICOM.ANG.CHER.2.4.91/NIFTI/A.C.2.4.91.MRI.12.9.22.FLAIR_reg.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/paolasofia/LESION.SEG/A.C.2.4.91.MRI.2.9.22.LESIONS/ Illegal instruction (core dumped) any ideas on how I could solve the problem? thanks in advance --

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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

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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

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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.

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