Hi Annie,
It looks like you are using an older release - freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.
See compatibility issues discussed in this post:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg74552.html
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Annie Cooper Sent: Friday, March 17, 2023 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error When Running Recon-all- "Segmentation Fault"
External Email - Use Caution Hi there, I am currently trying to run recon-all using a supercomputer at my university and am running into more errors than usual. When trying to run recon-all from my terminal, I ran into this error message:
[asurite@agave1:~/Desktop/T1_IMAGE]$ recon-all -s ATN001v1 -i T1-MPRAGE-8min_Series0301_T1-MPRAGE-8min_20211223085844_301.nii.gz -all
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
INFO: SUBJECTS_DIR is /home/asurite/Desktop/subjects
Actual FREESURFER_HOME /packages/freesurfer-5.0.0
Linux agave1.agave.rc.asu.eduhttp://secure-web.cisco.com/1FrozpCwrrnwrFWtILL33jRuXDhw04fuiqoZmajZRZw0K2wLzkBjon4F8F2-1v6pwPbI0PwDt8xObVXQg_6kHQwZqC50jGlFiqWS-0PtX-Ts4IG847WQuGHFUG5GJH46UdiJzkxQHWswnjJSxyjHfz0MN9PVMgzeaszz8C33A-KxeBkPUAsDz4XdN--SgABPpCVoquv6G8ru-uFIGL4-QfX28nhLvciU2DUCxPpBsQYuSi7s9HhJfpbSot3cYkxpDA6Kv9B7NF3mIN14qfbvcE63EkfQ84_5V9irHCbqw5Y9ZiYIN-dstAkFGIzgE3Rbm7-iqwV2ZlHx8aELlUCIHvQ/http%3A%2F%2Fagave1.agave.rc.asu.edu 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
/home/asurite/Desktop/subjects/ATN001v1
mri_convert /home/asurite/Desktop/T1_IMAGE/T1-MPRAGE-8min_Series0301_T1-MPRAGE-8min_20211223085844_301.nii.gz /home/asurite/Desktop/subjects/ATN001v1/mri/orig/001.mgz
mri_convert /home/asurite/Desktop/T1_IMAGE/T1-MPRAGE-8min_Series0301_T1-MPRAGE-8min_20211223085844_301.nii.gz /home/asurite/Desktop/subjects/ATN001v1/mri/orig/001.mgz
Segmentation fault
Linux agave1.agave.rc.asu.eduhttp://secure-web.cisco.com/1FrozpCwrrnwrFWtILL33jRuXDhw04fuiqoZmajZRZw0K2wLzkBjon4F8F2-1v6pwPbI0PwDt8xObVXQg_6kHQwZqC50jGlFiqWS-0PtX-Ts4IG847WQuGHFUG5GJH46UdiJzkxQHWswnjJSxyjHfz0MN9PVMgzeaszz8C33A-KxeBkPUAsDz4XdN--SgABPpCVoquv6G8ru-uFIGL4-QfX28nhLvciU2DUCxPpBsQYuSi7s9HhJfpbSot3cYkxpDA6Kv9B7NF3mIN14qfbvcE63EkfQ84_5V9irHCbqw5Y9ZiYIN-dstAkFGIzgE3Rbm7-iqwV2ZlHx8aELlUCIHvQ/http%3A%2F%2Fagave1.agave.rc.asu.edu 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ATN001v1 exited with ERRORS at Fri Mar 17 10:44:47 MST 2023
Any tips on why I might be receiving a "Segmentation fault" when trying to run recon-all? I've tried utilizing the mail archive to find an answer and haven't found anything that helped. Thank you!
Best, Annie