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 which describe how to find the data for the step, and Export variables which describe how the data is exported on disk to the pipeline.

Variable	Type	Default	Description
StepNumber	number	🔴	The numerical order of this data step. (formerly Order)
IsEnabled	bool	🔴	true if the step is enabled, false otherwise
IsOptional	bool	🔴	true if this data step is optional. false if this step is required and the analysis will not run if the data step is not found.
IsPrimaryProtocol	bool		true if this data step determines the primary study, from which subsequent analyses are run. false otherwise.
SearchAssociationType	string	🔴	study, or subject.
SearchDataLevel	string	🔴	Where is the data coming from. nearestintime, samestudy.
SearchImageType	string		Comma separated list of image types, often derived from the DICOM ImageType tag, (0008:0008).
SearchModality	string	🔴	Modality to search for.
SearchNumberBOLDreps	string		If SearchSeriesCriteria is set to usecriteria, then search based on this option.
SearchProtocol	string	🔴	Comma separated list of protocol name(s). Protocol names with spaces must be "quoted".
SearchSeriesCriteria	string	🔴	Criteria for which series are downloaded if more than one matches criteria: all, first, last, largest, smallest, usecriteria.
ExportBehavioralDirectoryName	string		If BehFormat writes data to a sub-directory, the directory should be named this.
ExportBehavioralDirectoryFormat	string		nobeh, behroot, behseries, behseriesdir
ExportDataFormat	string	🔴	native, dicom, nifti3d, nifti4d, analyze3d, analyze4d, bids.
ExportGzip	bool		true if Nifti data should be gzipped, false otherwise.
ExportPreserveSeriesNumber	bool		true to preserve series numbers in directory names or false to assign new ordinal numbers.
ExportSubDirectoryName	string		Directory, relative to the analysisroot, where this data item will be written. (formerly Location)
ExportWritePhaseDirectory	bool		true to write data to a sub directory based on the phase encoding direction.
ExportWriteSeriesDirectory	bool		true to write each series to its own numbered directory, false to write all series data to the root export directory.