Freesurfer

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30070 discussions

Freesurfer 7.4.0 not working in Ubuntu 24.04
by vittal korann 03 Apr '25

03 Apr '25

External Email - Use Caution Hi Freesurfers, I updated my Ubuntu OS to 24.04 and successfully installed Freesurfer 7.4.0 in it. I am saying it was successful because I was able to open 'freeview' through the terminal. However, the real problem started when I tried to execute the 'recon-all' command. Moreover, I have seen a couple of similar threads on this issue (compatibility problem between freesurfer and Ubuntu 24.04) and the same link is pasted below. 1. https://secure-web.cisco.com/1svOIRTM9dlafSNLq9cR4qAfhog04NdsJtmKkMTcE2_x-K… 2. https://secure-web.cisco.com/1rtmIG1MiBse1Az5BA_1jyetPI0e-B6Vp3n6Jqh-W2kgSO… So, I am wondering whether this Freesurfer version supports the latest linux version or not? If not, I would appreciate it if somebody let me know the alternative ways of using it. Thanks in advance for your help! Regards Vittal

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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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Freesurfer Question - Pediatric pathology
by Stefanie Bradley 02 Apr '25

02 Apr '25

External Email - Use Caution Hi there, I'm working with MRI scans from children aged 3-6 years old. I was wondering if there's a way to integrate pediatric atlases into the Freesurfer recon-all pipeline? I'm also wondering if it's possible to integrate a lesion mask into the pipeline in the case of brain pathology? Thanks, Stef STEFANIE BRADLEY PHD CANDIDATE Holland Bloorview Kids Rehab Hospital 150 Kilgour Rd, Toronto, ON M4G 1R8 stefanie.bradley(a)mail.utoronto.ca [https://secure-web.cisco.com/1kWf2c8NzM8OclMTRcmltfW5rxRU9SRJI50sUcXDGlWqWx…]<https://secure-web.cisco.com/1uQzm_CoDmutDkOsJunQufG19PQx4c0AZhVnSO28l9XE9i…>

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Re: [Freesurfer] freesurfer 8
by fsbuild 01 Apr '25

01 Apr '25

External Email - Use Caution  The freesurfer_ubuntu22-8.0.0_amd64.deb installer may work if you are running an early version of Debian 12.  The system may refuse to do the install on the current version of Debian 12 because of system library conflicts.  I don’t see a container is currently available.  Another option would be to run an Ubuntu22 VM on your machine via virtualbox and install freesurfer there.  The VM is likely easier to use compared to the the container if you want to run the freeview image viewer.   There is a write up about creating a VM here,https://secure-web.cisco.com/10QGcnXeGUXgLlHRQsXLCaaMo-QzMvcEz4dlf1RcA… - R. On Apr 1, 2025, at 16:51, Gregory Book <gregory.a.book(a)gmail.com> wrote:        External Email - Use Caution        I'm attempting to run freesurfer 8 on debian 12. Are there any tips on making the Ubuntu package work on debian?orIs there a freesurfer 8 docker container out there?_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1Sn85p_MmVtQE68pcKYNp-8_KLB5cTUWlYD87srp-as4za…

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freesurfer 8
by Gregory Book 01 Apr '25

01 Apr '25

External Email - Use Caution I'm attempting to run freesurfer 8 on debian 12. Are there any tips on making the Ubuntu package work on debian? or Is there a freesurfer 8 docker container out there?

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FS8.0 Patch - Next Step Clarification
by Carly McIntyre-Wood 01 Apr '25

01 Apr '25

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Re: [Freesurfer] Issue with recon-all
by fsbuild 01 Apr '25

01 Apr '25

External Email - Use Caution  Assuming that you have set SUBJECTS_DIR to a path where you have read/write permission, then I wonder if you have an alias defined in your shell such that the rm command contains “-I” (the interactive switch) which would force rm to ask you for permission every time it wants to remove something.   Type “alias” into your shell prompt and see if something shows up for the remove command.  If so then I would remove that alias from your environment with unalias. $ alias... look for output containing rm -i ... $ unalias rm -R On Mar 31, 2025, at 20:48, Bedard, Patrick (NIH/NINDS) [C] <patrick.bedard(a)nih.gov> wrote:        External Email - Use Caution        Hello all I’m running the recon-all tool :    recon-all -all -sd .   -subjid  FS    -i   ${subj}_T1_al.niiIt works fine, but at some point, the program stops and asks at the terminal: writing to orig_nu.mgz...rm: descend into write-protected directory './tmp.mri_nu_correct.mni.41843'? yrm: remove write-protected directory './tmp.mri_nu_correct.mni.41843'? y and I have to answer “y”,but if I’m not checking it just sits and waits and take so much time… do you have any idea what might case that?I have all the permissions on the directories. BestPatrick  ===================Patrick Bédard, PhD, [C]ScientistNational Institutes of HealthNational Institute of Neurological Disorders and Stroke _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Issue with recon-all
by Bedard, Patrick (NIH/NINDS) [C] 31 Mar '25

31 Mar '25

External Email - Use Caution Hello all I’m running the recon-all tool : recon-all -all -sd . -subjid FS -i ${subj}_T1_al.nii It works fine, but at some point, the program stops and asks at the terminal: writing to orig_nu.mgz... rm: descend into write-protected directory './tmp.mri_nu_correct.mni.41843'? y rm: remove write-protected directory './tmp.mri_nu_correct.mni.41843'? y and I have to answer “y”, but if I’m not checking it just sits and waits and take so much time… do you have any idea what might case that? I have all the permissions on the directories. Best Patrick =================== Patrick Bédard, PhD, [C] Scientist National Institutes of Health National Institute of Neurological Disorders and Stroke

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trac-all -bedpostx error
by Gabriella Monopoli 31 Mar '25

31 Mar '25

External Email - Use Caution Hello, I'm trying to run the second step of TRACULA processing (in bash), which is: trac-all -bedp -c /path/to/configuration/file I'm currently using the FreeSurfer version v7.1.4 and I get the following error: WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 -model 1 /home/gmonopoli//Prova_TRACULA/trc/sub-007_S_6341/dmri /usr/local/freesurfer/7.4.1//bin/bedpostx_mgh: 128: Syntax error: "(" unexpected Since I am not familiar with this, do you have any advice on how to overcome this problem? Thanks in advance, Gabriella

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Incorrect segmentation and surface offset
by Tommaso Mariani 28 Mar '25

28 Mar '25

External Email - Use Caution Hi everyone, I am experiencing a tricky situation in freesurfer. Due to hypo- and hyper-intensity problems I obtained a bad reconstruction and I've been working on it since. My first question is then: do I need to refresh the aseg file after the wm.mgz intensities modifications? However I also noticed that when I loaded the surface to verify the corrections they were all with a significant offset and this message was printed on the console: 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 Together with that, I was also unable to obtain the final parcellization, possibly due to the absence of correlation between the volumes and surfaces. I already tried to manually adjust the offset and relaunch the reconstruction, as suggested in the Freesurfer documentation for tailarach errors, but it looks like it did nothing to it. If you need any file or info to examine the situation further, feel free to contact me, I would really appreciate your help. Thanks in advance, Tommaso Mariani

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