Preconfigured Files

Working With Preconfigured Files

We provide preconfigured versions of two files, data_config.yml (used to define file structure templates when generating subject lists) and scan_parameters.csv (used when running Slice Timing Correction) for use with key INDI data releases. While the preconfigured scan_parameters.csv files can be used unmodified, it is necessary to slightly edit the file structure templates in data_config.yml before they can be used.

For multiscan sites like the Enhanced NKI-Rockland Sample dataset, the multiscan parameters template is used. These must be modified with a path to the slice timing parameters which also available below. See Slice Timing Correction for further detail.

File structure templates in preconfigured copies of data_config.yml will be prefixed with the text /path/to/data. This is because though we are able to pre-define the folder structure of INDI releases, there is no way for us to know where exactly the data will be located on your specific system. You must replace /path/to/data with the path to the data files downloaded from INDI. For example, if you have downloaded the ABIDE data set and placed the files in an /ABIDE directory loaded in your /home/science/ folder, you would replace /path/to/data with /home/science/ABIDE.

We also include several files configured to work with datasets stored in Amazon’s Simple Storage Service (S3) as well, to demonstrate how C-PAC can integrate with the cloud. These files end with the suffix _s3.yaml.