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.

JSON variables

*required

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