Using Nipype to organize a non-default Freesurfer pipeline

I would like to use Nipype to automate (and parallelize) a non-default Freesurfer pipeline. Specifically, I would like to:

  • Submit skullstripped data to autorecon1 (with -noskullstrip)
  • Execute a simple non-Freesurfer command to make the necessary links when autorecon1 is complete (per
  • Continue Freesurfer with autorecon2 and autorecon3

I have tried this myself by running autorecon1 with nipype, manually linking the files, and then trying autorecon2 with nipype, but autorecon2 chokes with an error. Any advice would be very welcome.

Nipype already includes a custom workflow that does exactly that:

1 Like

That is amazingly convenient and probably not a coincidence. :smiley: Many thanks!

1 Like