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

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.