Freesurfer

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30070 discussions

volumes and surfaces misalignment in freeview
by Paola Di Filippo 20 Feb '25

20 Feb '25

External Email - Use Caution Hi again everyone. I am using freesurfer 7.4.1. on ubuntu 22 with a virtual machine. I performed my first recon-all, without hard failures as the .log ended with "recon-all completed with no errors". Then, I have tried to launch freeview to visualize both volumes and surfaces for my subject, with the following command: freeview -v angcher.02.04.91.12.09.22/mri/T1.mgz angcher.02.04.91.12.09.22/mri/wm.mgz angcher.02.04.91.12.09.22/mri/brainmask.mgz angcher.02.04.91.12.09.22/mri/aseg.mgz:colormap=lut:opacity=0.2 -f angcher.02.04.91.12.09.22/surf/lh.white:edgecolor=blue angcher.02.04.91.12.09.22/surf/lh.pial:edgecolor=red angcher.02.04.91.12.09.22/surf/rh.white:edgecolor=blue angcher.02.04.91.12.09.22/surf/rh.pial:edgecolor=red but in freeview, surfaces are completely misaligned with volumes. This is an image to give you an idea of the problem (sorry for the quality, i'm controlling the computer on which i work remotely from home): [image: image.png] this is what i see in the terminal after launching the command: Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info when i first tried freeview after downloading the program, i had the same problem with bert; when i launch this command: freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red this is what I get: [image: image.png] again, this is what I see in the terminal: Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info The only time when i didn't experience this problem is after downloading tutorial data and trying this command: freeview -v good_output/mri/T1.mgz good_output/mri/wm.mgz good_output/mri/brainmask.mgz good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 -f good_output/surf/lh.white:edgecolor=blue good_output/surf/lh.pial:edgecolor=red good_output/surf/rh.white:edgecolor=blue good_output/surf/rh.pial:edgecolor=red that gave me this outoput in freeview: [image: image.png] but still I get this in the terminal: Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info. any ideas on how could I fix this problem? many thanks in advance. --

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Unable to download version 8.0.0
by Ziming Cui-MSBA23A 20 Feb '25

20 Feb '25

External Email - Use Caution Hello all, I'm trying to download version 8.0.0 of the “macOS X darwin_arm64 (64b) PKG installer”, but it says “Not Found” no matter what I try. Is there anything I can do? Best, By Ziming Cui

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*** buffer overflow detected ***
by Brunno M. de Campos 20 Feb '25

20 Feb '25

External Email - Use Caution Dear all, I run my script for longitudinal processing based on: individual processing (recon-all -i) + base image creation (recon-all -base) and longitudinal processing (recon-all -long). In some cases (not always), the process terminates with errors, apparently at the same stage. The log states, among other things, "Reading texture...*** buffer overflow detected ***: terminated Command terminated by signal 6". 1 - I assume that I have exceeded my memory capacity. Am I correct? I have, in fact, written a script that parallelizes these processes, but I might be distributing the workload poorly if that is the case. 2 - If this is indeed the issue, do you know the peak memory required for such a process? Thank you! Brunno M Campos University of Campinas

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Clarification on co-registration using bbregister
by Gabriella Monopoli 20 Feb '25

20 Feb '25

External Email - Use Caution Dears, I'm Gabriella, a PhD student in Neuroscience and Imaging. I am currently working on coregistering anatomical scans with DTI scans (FA and MD maps) using bbregister. However, there are some details in the pipeline that I find unclear. First, is it correct to use the DTI scan file directly as the --mov input? I came across discussions in the mailing list mentioning an intermediate step involving the lowb volume—specifically, performing bbregister first with the anatomical scans and the lowb volume, and then using mri_vol2vol to apply the registration matrix to the DTI map. I am unsure whether this step is always necessary or if it should only be performed when the direct coregistration (bbregister between the anatomical scan and the DTI map) is inaccurate. Additionally, regarding the initial registration parameter (--init-coreg), what criteria should be used to decide between the default option and alternatives such as --init-fsl? Thank you in advance for your time and assistance. I look forward to your response. Best regards, Gabriella

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Inquiry Regarding FreeSurfer Usage in Clinical Trials
by Yeh Shang Ming 19 Feb '25

19 Feb '25

External Email - Use Caution Dear Sir/Madam, My name is Shang-Ming (Tony) Yeh, and I work at an imaging CRO based in Japan. We are currently using FreeSurfer version 6.0.0 and are considering its use in a potential project. To support our evaluation, we would appreciate your insights on the following: 1. Clinical Trial Usage: - Has FreeSurfer been utilized in any clinical trials? - If so, have any of these trials been submitted for regulatory approval? 2. Comparative Studies: - Are there any publications that compare FreeSurfer with other similar software? If you have any relevant information or publications, we would greatly appreciate it if you could share them with us. Thank you for your time and support. We look forward to your response. Sincerely, Shang-Ming (Tony) Yeh

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CSF Volume difference between recon-all-clinical and SAMSEG
by Taghizadeh Mortezaei, Nima 18 Feb '25

18 Feb '25

Dear FreeSurfer Developers, I seek clarification regarding a discrepancy in cerebrospinal fluid (CSF) volume measurements obtained using different FreeSurfer tools. In my analysis, I measured CSF volume using both recon-all-clinical.sh and SAMSEG for the same subject. However, the results were significantly different: recon-all-clinical: 236,073.36 mm³ (~236 mL) SAMSEG: 471,854.76 mm³ (~472 mL) Additionally, I conducted SAMSEG on 10 neurologically healthy subjects, and in all cases, the CSF volume was at least twice the normal average CSF volume (~150 mL) reported in the literature. I would appreciate any insights into the following questions: Why is there such a large discrepancy between the two methods? Which method provides a more reliable estimate of total CSF volume? Why are the estimated CSF volumes significantly higher than the known physiological average? Thank you for your time and assistance! Best regards, Nima

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problem with autorecon-pial
by Yildirim, Irem 18 Feb '25

18 Feb '25

External Email - Use Caution Hello, I am trying to fix the freesurfer results after running recon-all with fmriprep. The problem is in the pial surface, wm, and brain masks because of some inhomogeneity in the 7T MPRAGE data. I am fixing the brain mask following the instructions here: https://secure-web.cisco.com/1yEIcMRf9tPPRvYNsf-fTOA8sAaKck250MhUSiZCJA7LZQ… . After I fix the brain mask, I am trying to run the code for surfaces to be updated based on the updated brain mask with "recon-all -autorecon-pial" command. Every time I tried with different subjects, it updated the surfaces but not in a corrected way. The results for surfaces never really changed, and the mri/brain.mgz file was never even updated. One solution is to run recon-all -all with the options I want for skullstripping but it is time consuming for me and I usually prefer the fmriprep's pipeline for freesurfer. Can you help me find a way to fix this without having to rerun all the analysis? You can find an example log file where you can see the skullstripping with different settings starting on Line 3959 and the calling of autorecon-pial starting on Line 4245. Thank you, Irem FsTutorial/SkullStripFix_freeview - Free Surfer Wiki<https://secure-web.cisco.com/1yEIcMRf9tPPRvYNsf-fTOA8sAaKck250MhUSiZCJA7LZQ…> top | previous. Fixing a bad skull strip. To follow this exercise exactly, be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names. surfer.nmr.mgh.harvard.edu

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hounsfield units based in some aseg.mgz labels
by Gonzalo Rojas Costa 17 Feb '25

17 Feb '25

External Email - Use Caution Hi: I completed the co-registration of CT images to a freesurfer processed MRI image using the command: mri_coreg --mov sub-OAS30001_sess-d3132_CT.nii.gz --reg reg.lta --s OAS30001_MR_d0757 How can I get the mean and SD Hounsfield units (from corregistered sub-OAS30001_sess-d3132_CT.nii.gz) using aseg.mgz labels (of freesurfered OAS30001_MR_d0757) ? Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University

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Re: [Freesurfer] ERC_bayesian_segmentation is not shipped in the nightly dev build
by fsbuild 17 Feb '25

17 Feb '25

External Email - Use Caution That set of files is too large to be included in some packages.   Not sure what info you are following about pulling the files from GitHub, but for now you could try, - R. $ cd $FREESURFER_HOME/python/packages/ERC_bayesian_segmentation$ sudo wget https://secure-web.cisco.com/16qOF4aueY_oOax52PDUZUC7cA… wait for download to finish …$ sudo rm -rf  atlas_full  atlas_simplified$ sudo tar zxpf ERC_bayesian_segmentation/atlas_subdirs_20250217.tgz$ sudo rm ERC_bayesian_segmentation/atlas_subdirs_20250217.tgz On Feb 17, 2025, at 11:27, Chourrout, Matthieu <m.chourrout(a)ucl.ac.uk> wrote:        External Email - Use Caution        Hi all, I was trying to run the dev version of FreeSurfer from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1gGb7gF2nKiypt4FLjrahIBuWyn147VH1mU3Ia… the content from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://github.com/freesurfer/freesurfer/tree/dev/mri_histo_util/ERC_baye… not present in ${FREESURFER_HOME}/python/packages/ As instructed, I've put atlas_full/ and atlas_simplified/ inside ${FREESURFER_HOME}/python/packages/ERC_bayesian_segmentation/ when trying to run mri_histo_atlas_segment_fireants but had to manually create the subdir. can't open file '/share/apps/freesurfer-dev/python/packages/ERC_bayesian_segmentation//scripts/segment_fireants.py': [Errno 2] No such file or directory Can the files from ERC_bayesian_segmentation/ in GitHub be manually pulled out into this directory? Which files are required? Best regards, Dr Matthieu Chourrout Research Fellow on Correlative X-ray Imaging for the Large-scale Imaging of Neural CircuitsUCL Mechanical EngineeringMaterials, Structure and Manufacturing at Harwell (MSMaH)Rm 4.17 Malet Place Eng. Building, Torrington Place, London, WC1E 7JEBloomsbury Campus, University College London_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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hounsfield units for some aseg.mgz labels
by Gonzalo Rojas Costa 17 Feb '25

17 Feb '25

External Email - Use Caution Hi: I completed the co-registration of CT to a freesurfer processed MRI image using the command: mri_coreg --mov sub-OAS30001_sess-d3132_CT.nii.gz --reg reg.lta --s OAS30001_MR_d0757 How can I get the mean and SD hounsfield units of some aseg.mgz labels? Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University

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