freesurfer command running from shell but not from script

Question

I want to convert a transformation matrix with freesurfer's lta-convert. If I run the following command in my bash-shell (echo $0 shows -bash)

lta_convert -inlta input.lta --outfsl output.mat

it runs without problem:

$Id: lta_convert.cpp,v 1.9.2.1 2016/08/09 02:33:22 zkaufman Exp $

--inlta: input.lta input LTA transform.
--outfsl: output.mat output FSL matrix.
 LTA read, type : 1
 0.93123   0.02020   0.00726  -12.56508;
-0.00133   0.92407   0.00102  -2.41168;
 0.00007   0.02780   1.00388   21.38016;
 0.00000   0.00000   0.00000   1.00000;
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = 8, ref det = 1
INFO: FSL2FreeSurfer: Mov volume is NIFTI with positive det,
  applying LR flip to registration matrix.
INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det,
  applying LR flip to registration matrix.
lta_convert successful.`

But if I try to run the same command in a shell script containing the following two lines:

#!/bin/bash

lta_convert -inlta input.lta --outfsl output.mat

it throws me an error.

$Id: lta_convert.cpp,v 1.9.2.1 2016/08/09 02:33:22 zkaufman Exp $

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

dyld: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

./test.sh: line 3: 91440 Abort trap: 6           lta_convert -inlta input.lta --outfsl output.mat

Why does this happen and how can I resolve this? Other freesurfer commands like mri_robust_register run from the shell without problems. I am running the script on Mac OS 10.12.4.

Answer 1

The issue you're having probably has to do with the environment variable DYLD_LIBRARY_PATH not being propagated because of System Integrity protection. The work around in your case is checking what is the value of DYLD_LIBRARY_PATH and LD_LIBRARY_PATH when freesurfer works and setting those variables in your bash script before running it.

There is more info in the following question: Why Isn't DYLD_LIBRARY_PATH being propagated here?

Answer 2

Found the solution. Add a line to the script so that it shows:

#!/bin/bash

source $FREESURFER_HOME/SetUpFreeSurfer.sh
lta_convert -inlta input.lta --outfsl output.mat