Freesurfer July 2022

freesurfer@nmr.mgh.harvard.edu

90 participants
122 discussions

infant freesurfer crash
by Knut J Bjuland 02 Jul '22

02 Jul '22

External Email - Use Caution I am able to run infant freesurfer on my local pc but when I run on a cluster I get segmentation error when running sscn_skullstrip. Segment error in $ sscnn_skullstrip -i /cluster/projects/nn9208k/007_fs/work/mprage.nu.conf.nii.gz -o /cluster/projects/nn9208k/007_fs/work/sscnn -c t1w Segmentation fault (core dumped) How can I provide more information, I have enable 24 Giga byte of ram. Knut Jørgen Bjuland

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help troubleshooting lta_convert error
by Megan Schendel 01 Jul '22

01 Jul '22

External Email - Use Caution Hi all, I had a working distribution on an old system a few weeks ago, but now I'm getting an error. Can anyone offer any troubleshooting ideas? I am working on a shared server with a freesurfer distribution that I own. Here is some system info: [mschendel@earth scripts]$ lsb_release -a LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch Distributor ID: CentOS Description: CentOS release 6.7 (Final) Release: 6.7 Codename: Final On the command line, the error looks like this: lta_convert: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by lta_convert) lta_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by lta_convert) lta_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.19' not found (required by lta_convert) lta_convert: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by lta_convert) The recon-all.log file contains the following: Fri Jul 1 11:08:24 MDT 2022 cd /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/M87124539 setenv SUBJECTS_DIR /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis /export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer//bin/recon-all -all -i /export/research/archive/human/dicom/prisma/dquinn/navigate_20673//M87124539/Study20210623at161830/mprage_5e_32ch_RMS_0003/SerieMR-0003-0001-1.dcm -s /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis//M87124539 -openmp 8 subjid M87124539 setenv SUBJECTS_DIR /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis FREESURFER_HOME /export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer/ Actual FREESURFER_HOME /export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Linux earth.mind.unm.edu 2.6.32-573.26.1.el6.x86_64 #1 SMP Wed May 4 00:57:44 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited ######################################## program versions used 7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b) ERROR: Executable 'lta_convert -all-info failed! Is it missing from the distribution?' MEG Technician Pronouns: she/her The Mind Research Network 1101 Yale Blvd. NE Albuquerque, New Mexico 87106

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Freesurfer July 2022