External Email - Use Caution        

Hello Megan,

The errors you list below usually result from running a version of Freesurfer that does not match the operating system you are using, i.e., it looks like you are trying to run the version built for Ubuntu linux,

7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b)

… on a CentOS6 system,

Description:    CentOS release 6.7 (Final)

If you have admin privileges on your system, then I would try installing the Freesurfer 7.2.0 CentOS6 rpm file on your CentOS6 system, which you can download from, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer-CentOS6-7.2.0-1.x86_64.rpm

If you do not have admin privs to install the RPM, then you can download and expand the tar archive from,
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer-linux-centos6_x86_64-7.2.0.tar.gz

The Freesurfer 7.2.0 distributions available for each operating system are currently listed on this page, https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads

- R.

On Jul 1, 2022, at 13:32, Megan Schendel <mschendel@mrn.org> wrote:

        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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