Freesurfer tutorial module

This is the Pipeline module for the recon-all script in the Freesurfer tutorial.

Screenshots

Usage

Some caveats:

• This requires Freesurfer distribution after 12 September 2005
• This requires the latest Pipeline release
• This has only been tested on Mac OSX 10.4
• The data directory variable needs to be changed to reflect the location of your tutorial data
• The freesurfer modules need to be changed to reflect the location of your freesurfer location
• The nu_correct modules need to be changed to reflect the location of your nu_correct location
• mri_watershed may possibly output a lot of stuff to stdout and crash the Java virtual machine. To fix this, enable the ad-hoc quiet option (ie, >& /dev/null). However, this causes problems on Mac OSX 10.4 (and possibly other systems) because the JVM will think that it has aborted.

Files