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If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1Ia6Ud55puWRILt2_mnFiSQklsfT7C9EDW3db8NhTcmq7VbUNFHhEauxIQeMm-CPARqu5fUazLdidH69ZTkYUwAFLbEMht1KzsDyGOsmXUzeH2uWHwh7nICotUCRaBkYbIK05Vt3041mvIVm6AKEobB9f9rXmIU432t04jKzBXKETm0qRA1PgQzJ1U0-Nu0aPsxTvpFrGhjDuDzxZjNE38r3s5CeBa3TFhdCOmNyjm6N7lIGRtXEtV8DoTJNSfEkgnFG4eCPE0Gov2QyKD1MSrrJHYIOqYp-n_jDxxkXOPcSvGuCOVBAv92lae8MptNPXaFeWX3ItCGYaLBjYo6CPHA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline < https://secure-web.cisco.com/1Ia6Ud55puWRILt2_mnFiSQklsfT7C9EDW3db8NhTcmq7VbUNFHhEauxIQeMm-CPARqu5fUazLdidH69ZTkYUwAFLbEMht1KzsDyGOsmXUzeH2uWHwh7nICotUCRaBkYbIK05Vt3041mvIVm6AKEobB9f9rXmIU432t04jKzBXKETm0qRA1PgQzJ1U0-Nu0aPsxTvpFrGhjDuDzxZjNE38r3s5CeBa3TFhdCOmNyjm6N7lIGRtXEtV8DoTJNSfEkgnFG4eCPE0Gov2QyKD1MSrrJHYIOqYp-n_jDxxkXOPcSvGuCOVBAv92lae8MptNPXaFeWX3ItCGYaLBjYo6CPHA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. ---------- Forwarded message ---------- From: Rob Kudyba <rk3...@columbia.edu> To: freesurfer-requ...@nmr.mgh.harvard.edu Cc: Bcc: Date: Fri, 26 May 2023 11:24:40 -0400 Subject: FS in a HPC cluster via module file: ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer External Email - Use Caution In. HPC cluster where Freesurfer is loaded ad hoc as a module. Running module avail results in the following warnings: /path/to/anaconda3-2021.11/bin/mpicc: line 285: x86_64-conda_cos6-linux-gnu-cc: command not found ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer. /path/to/anaconda3-2021.11/bin/mpicc: line 285: x86_64-conda_cos6-linux-gnu-cc: command not found ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer. In my .bashrc file: >>> conda initialize >>> !! Contents within this block are managed by 'conda init' !! __conda_setup="$('/path/to/anaconda3-2021.11/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" if [ $? -eq 0 ]; then eval "$__conda_setup" else if [ -f "/path/to/anaconda3-2021.11/etc/profile.d/conda.sh" ]; then . "/path/to/anaconda3-2021.11/etc/profile.d/conda.sh" else export PATH="/path/to/anaconda3-2021.11/bin:$PATH" fi fi unset __conda_setup The modulefile for Freesurfer contains: module-whatis "adds freesurfer to your environment variables" set root /path/to/freesurfer setenv "FREESURFER_HOME" "/path/to/freesurfer" setenv "SUBJECTS_DIR" "/path/to/freesurfer/subjects" prepend-path PATH $root/bin if { [ module-info mode load ] } { system "source /path/to/freesurfer/SetUpFreeSurfer.sh" } I see that SetUpFreeSurfer.sh has this: # Call configuration script: source $FREESURFER_HOME/FreeSurferEnv.sh After running module unload freesurfer several directories remain in $PATH: echo $PATH /path/to/freesurfer/fsfast/bin:/path/to/freesurfer/tktools:/path/to/freesurfer/mni/bin:/path/to/freesurfer/fsfast/bin:/path/to/freesurfer/tktools:/path/to/freesurfer/mni/bin So $FREESURFER_HOME and $SUBJECTS_DIR are being unset but all of the other env vars are not. Is there a way to unset the vars from FreeSurferEnv.sh? A thread on SO <https://secure-web.cisco.com/1r8-C-he2TdIjGUEFvriv0MeCNYVOFUUqm9zHSNCvE844JRdcDiH-zTozS1MK4YmLYbWW5owRn1_jG2pI7aRGML1VxZ6MwPyyX-l68SVs8CLh_OgXbNvqqbbKxc6H2wJOrR2lFw88J7e0uHHoheCpWptWc1c6Th6ZC3Whenq1oL2p0WFqeZ8Q4D1fzn1lVV4VcGrJifg3mWJAVj2aOc99MSR3rTJ_uaL_2kGcfPb8Ise9by7L3ccksmUQnGpVqZLXUOa2yx1QgokGaSQX04nJSeEbll11q-KQNwuX3qrnk2rbjZTPaJsLJ-dHCFItgVc6Ey2edjW1j1ABISrh-M2IAA/https%3A%2F%2Fstackoverflow.com%2Fquestions%2F69274347%2Foverwrite-and-restore-environment-variables-in-bash-with-environment-modules> mentions using unsetenv but perhaps there's an elseif that can be added to the modulefile?
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
