This repository contains the code used to preprocess data from the NDAR database and upload the results/log files to tables in the database.

• act_interface.py - Nipype interface made to work with the ANTs cortical thickness extraction script found here
• ndar_act_cluster.py - Streamlined script to execute the nipype workflow from the interface defined in act_interface.py and then upload the results and log files to the NDAR database. This script is designed to be launched from a cluster of C-PAC AMI's on AWS using the Sun Grid Engine job scheduler.
• ndar_run.sge - Bash script to use to submit the ndar_act_cluster.py script in parallel over a cluster of nodes.
• ndar_unpack - Bash-executable Python script which will download and extract imaging data from the NDAR database. Originally cloned from here, but slightly modified to add untar-ing functionality.

The OASIS template data files can be acquired from Mindboggle using this link and this link.

• Note the fetch_creds module needed for this database is a custom-module which returns AWS and RDS Oracle DB sensitive information. One can replace the variables this module returns with their own keys and database log-in information to use this functionality.

Python depenencies:

• Boto - Python module for interacting with Amazon Web Services
• cx_Oracle - Python module for interacting with Oracle databases
• Nibabel - Python module for read/write access to various neuroimaging data formats
• Nipype - Python module for Neuroimaging data analysis pipelines
• Numpy - Python module for fast numerical computations
• PyYaml - Python module for parsing and emitting Yaml files