HowTo_elastix.md

How to: elastix

Software for medical image registration: http://elastix.isi.uu.nl/index.php

Add elastix path to environment in OSX

In the terminal:

• Type: cd

• Type: ls -a (shows also hidden files)

• Open or create:

  • Mac:
    .bash_profile by typing: nano .bash_profile
  • Linux:
    .bashrc by typing: nano .bashrc

• Type:

  • Mac:

    export PATH=yourelastixdir:$PATH
    export DYLD_LIBRARY_PATH=yourelastixdir:$DYLD_LIBRARY_PATH
    

    where yourelastixdir is something similar to /anaconda3/lib/python3.7/site-packages/pykneer/elastix/Darwin/
  • Linux:

    export PATH=yourelastixdir:$PATH
    export LD_LIBRARY_PATH=yourelastixdir:$LD_LIBRARY_PATH
    

    where yourelastixdir is something similar to /anaconda3/lib/python3.7/site-packages/pykneer/elastix/Linux/

• Save changes by pressing: ctrl+o; return;

• Close file by pressing: ctrl+x

• Activate changes by typing:

  • Mac:
    source .bash_profile
  • Linux:
    source .bashrc