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

VariableTypeDefaultDescription

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.

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