Hi Melissa,
If the command runs fine in the terminal but not from python, it’s most likely
because python is messing with aspects of your env before running commands in a
subshell. The easiest solution is to upgrade to FS v7, where this problem no
longer exists, but if you’re stuck at v6, you should verify that the
DYLD_LIBRARY_PATH env var in the python subshell is the same as in the terminal
environment.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Melissa Marie Rundle
<mrun...@wakehealth.edu>
Date: Friday, May 7, 2021 at 2:59 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_label2vol error
External Email - Use Caution
Hi,
I get the following error message when I run mri_label2vol (freesurfer v 6.0)
in a jupyter notebook(6.1.4) with python (v3.8.5):
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
However, when I run mri_label2vol directly in a terminal window, the command
runs just fine. Nor do I have trouble
running similar commands such as mri_vol2vol or mri_convert using the jupyter
notebook.
I tried running "sudo -E fs_update" as suggested in MailScanner has detected a
possible fraud attempt from "secure-web.cisco.com" claiming to be
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes<https://secure-web.cisco.com/1fu8uZTsG4VqEpMIJBtTitHsB5L2G2xXvyt_Drs1gEwm3WuwHgMyeZLPO0D6ectQaNT83w2L83fwdAZ6dYL11VWxEwXs3t7OTsq60LNmxv3IKg-k-8A1J4kV6FpsbelpABw2UvAQgIz0JG79TY4e9FQR-JkqvNpcIFcM7XVjkHSizly6NFyu_1UyxbP9qmgFTUfggygUMj1e16vSTcPUtpFqJ-kh031bD-RQUC_wQMgEskqymXyKIXeIdXo0-pRhNdonAws6hMhVrI-RVmU28hw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes>
but that didn't solve the problem.
Any suggestions would be greatly appreciated.
Sincerely,
Melissa Rundle
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