Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

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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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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Recon-all: skip initial inhomogeneity correction
by Miguel Ángel Rivas Fernández 25 Feb '25

25 Feb '25

External Email - Use Caution Dear FreeSurfer developers, I am currently working with a T1-weighted MRI dataset that has already undergone intensity inhomogeneity correction. Since I would like to run recon-all on this data, is it possible to include a flag in recon-all to skip this step? If so, could you please specify the correct flag to use in order to run recon-all properly? Thank you very much for your assistance. Best -- *Miguel Ángel Rivas Fernández*

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dt_recon and corregistration (2)...
by Gonzalo Rojas Costa 24 Feb '25

24 Feb '25

External Email - Use Caution Hi: The error is in a misalignment between the FA and CC_Anterior section. Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University

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Re: [Freesurfer] Inquiry Regarding FreeSurfer Usage in Clinical Trials
by fsbuild 24 Feb '25

24 Feb '25

External Email - Use Caution  If you have not looked at the Freesurfer license terms (which you agreed to when you downloaded the software),https://secure-web.cisco.com/1TLtJ8aYiTR8TmbT0XIgGWuiazFxBl5kXBTS… - then you should note the following in Part B, section (e), number 4, 4. The Software has been designed for research purposes only and has   not been reviewed or approved by the Food and Drug Administration   or by any other agency. YOU ACKNOWLEDGE AND AGREE THAT CLINICAL   APPLICATIONS ARE NEITHER RECOMMENDED NOR ADVISED. Any   commercialization of the Software is at the sole risk of the party   or parties engaged in such commercialization. You further agree to   use, reproduce, make derivative works of, display and distribute   the Software in compliance with all applicable governmental laws,   regulations and orders, including without limitation those relating   to export and import control.. I am not aware of any reviews by the FDA (or from other government agencies) that have approved freesurfer for clinical use. Although the MGH license is essentially open source allowing use/re-distribution of the software, it is however subject to the license restrictions of the included 3rd party code as noted in Part B, section (e), number 3, 3. This Software License does not grant any rights with respect to   third party software, except those rights that MGH has been   authorized by a third party to grant to you, and accordingly you   are solely responsible for (i) obtaining any permissions from third   parties that you need to use, reproduce, make derivative works of,   display and distribute the Software, and (ii) informing your   sublicensees, including without limitation your end-users, of their   obligations to secure any such required permissions. Those 3rd party licenses can be found under ,https://secure-web.cisco.com/1q3oL4x5gqV_bdyKyRolyR9hw97oWH5oVRLzSotDPItR5GWo823uPbDV-qbLIcPZi8yiKAsU1U_3qYiRT_Va1aCW8kYvMGtM3jewxPEYAM_OWt6LJ-nf7BYt9279pXEW5w6ytY_kai534Hlz3AmWimuXTGoeTBrXfSLAHmF9u_X_s1HVaqVNZMFp3LrusDh5D07g0HMxg3IzGAXQNfjdpgMxjgAU4f6sXQ_BCAEs-woKvihQrDATyl4a3t594Z5EmrefAzESjgEm9sh1_CJAPyXgNXA73iOlV_qAB4a6m25Xtk_i1XZjaHMZTkmVmBhoYtkHO21npxrKPN1jdUtQtKQ/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Ftree%2Fdev%2Fdistribution%2Fdocs Some of those licenses may stipulate that once their 3rd party code in freesurfer is used in a commercial/for profit setting, then a paid for commercial license would need to be negotiated with the copyright holder. Freesurfer 6 is about ~7 years old now.  Freesurfer 7 releases were made available from 2020 thru 2023 with the last release as 7.4.1 in June of 2023.  Freesurfer 8.0.0 is about to be released (February 2025).   You can see the current releases here,https://secure-web.cisco.com/18FWAuTV9mgC0-k8_UudIcvI2UfmRMWvQDPOWoIWh… It would not surprise me if there was no point now in trying to get Freesurfer 6 approved for clinical trials because it will not run on recent versions of Linux OS’s. - R. On Feb 19, 2025, at 04:58, Yeh Shang Ming <yeh(a)micron-kobe.com> wrote:        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:Clinical Trial Usage: - Has FreeSurfer been utilized in any clinical trials? - If so, have any of these trials been submitted for regulatory approval? 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_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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dt_recon and corregistration...
by Gonzalo Rojas Costa 24 Feb '25

24 Feb '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 major error with the FA in CC_Anterior section (see attached image)? Sincerely Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University

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