data-steps

JSON array

dataSpec describes the criteria used to find data if searching a database (NiDB for example, since this pipeline is usually connected to a database). The dataSpec is a JSON array of the following variables. Search variables specify how to find data in a database, and Export variables specify how the data is exported.

JSON variables

🔵 Primary key 🔴 Required

Pipeline data steps are separated into Search variables and Export variables. Search describes how to find the data for this step, and Export describes how the data is exported on disk to the pipeline.

Variable	Type	Default	Description
AssociationType	string	🔴	[Search] study, or subject.
BehavioralDirectory	string		[Export] if BehFormat writes data to a sub directory, the directory should be named this.
BehavioralDirectoryFormat	string		[Export] nobeh, behroot, behseries, behseriesdir
DataFormat	string	🔴	[Export] native, dicom, nifti3d, nifti4d, analyze3d, analyze4d, bids.
Enabled	bool	🔴	[Search] true if the step is enabled, false otherwise
Gzip	bool		[Export] true if converted Nift data should be g-zipped, false otherwise.
ImageType	string		[Search] Comma separated list of image types, often derived from the DICOM ImageType tag, (0008:0008).
DataLevel	string	🔴	[Search] nearestintime, samestudy. Where is the data coming from.
Location	string		[Export] Directory, relative to the analysisroot, where this data item will be written.
Modality	string	🔴	[Search] Modality to search for.
NumberBOLDreps	string		[Search] If SeriesCriteria is set to usecriteria, then search based on this option.
NumberImagesCriteria	string		[Search]
Optional	bool	🔴	[Search] true if this data step is option. false if this step is required and the analysis will not run if the data step is not found.
Order	number	🔴	The numerical order of this data step.
PreserveSeries	bool		[Export] true to preserve series numbers or false to assign new ordinal numbers.
PrimaryProtocol	bool		[Search] true if this data step determines the primary study, from which subsequent analyses are run.
Protocol	string	🔴	[Search] Comma separated list of protocol name(s).
SeriesCriteria	string	🔴	[Search] Criteria for which series are downloaded if more than one matches criteria: all, first, last, largest, smallest, usecriteria.
UsePhaseDirectory	bool		[Export] true to write data to a sub directory based on the phase encoding direction.
UseSeriesDirectory	bool		[Export] true to write each series to its own directory, false to write data to the root export directory.