FreeSurfer is fairly easy to initiate, but there are lots of different types of edits that can be done within the pipeline, and no out-of-the-box way of tracking them. Setup FreeSurfer attempts to standardize all these things, creating standard scripts for running reprocessing commands, viewing commands, and tracking with a web-based spreadsheet.
Options:
Running the script with the -h option will output a help page, which lists the information below.
Usage:
setupfreesurfer.py [options] (--data_dir <dir> | -d <dir>) (--code_dir <dir> | -c <dir>) [(--freesurfer_home <dir> | -f <dir>)] [--host <host>]
Breaking this down, you must provide a data and code directory (if it does not exist it will be created), Additionally, there are options to indicate the --freesurfer_home (omitting will try to use an environmental variable), and host. If you specify --host as current, the current host is required. The -l command creates scripts for the longitudinal stream.
##Requirements:
- Python 2.7
- FreeSurfer
MIT