# data-steps

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. <mark style="color:red;">**Search**</mark> variables specify how to find data in a database, and <mark style="color:green;">**Export**</mark> variables specify how the data is exported.

<figure><img src="https://mermaid.ink/img/pako:eNptklFrwyAQx79KsBQsNKOM7MVBn7aXMTZY30ZervHSuCYqaraG0u8-TWrWZs1D_J_3O_-eeiSF4kgY2RnQVfL6kcvEf0YpR18272-9WqTpmoMDGn6Lxz_Ez2so9rBDeh6nWaGxFhItHdWEwINGIxqUztILPaGCccpF4YSSYDo6iRcD3M-m651RrQYJdWeFpX2UxDCue0Ztu_3CwltHEfMxDoxrufAdnMcbhNpaNN8QNmPpZXCDFdL5tG-xh6-ikR6MgrU_juDcD__TY4_T7ubzoSS9CxdkoLGlqMMdBRmh8UYCFc7DOtR2ONpeRjDadjUmI5f4FWs2K0t8WK2WPmvUHlMOtgJjoGP34076utHsum4oY7Msy846_RHcVSzTB7IkDZoGBPfP8xiWy4mrsMGcMC85ltDWLie5PHm01X5r-MyFU4awEmqLSwKtU5tOFoQ502KEngT4196MlH8rn0rF-PQL6OkObw?type=png" alt=""><figcaption></figcaption></figure>

### JSON variables

:blue\_circle: Primary key\
:red\_circle: Required

<table data-full-width="true"><thead><tr><th width="298" align="right">Variable</th><th width="114">Type</th><th width="91">Default</th><th>Description</th></tr></thead><tbody><tr><td align="right"><code>AssociationType</code></td><td>string</td><td><span data-gb-custom-inline data-tag="emoji" data-code="1f534">🔴</span></td><td>[<mark style="color:red;"><strong>Search</strong></mark>] <code>study</code>, or <code>subject</code>.</td></tr><tr><td align="right"><code>BehavioralDirectory</code></td><td>string</td><td></td><td>[<mark style="color:green;"><strong>Export</strong></mark>] if <code>BehFormat</code> writes data to a sub directory, the directory should be named this.</td></tr><tr><td align="right"><code>BehavioralDirectoryFormat</code></td><td>string</td><td></td><td>[<mark style="color:green;"><strong>Export</strong></mark>] <code>nobeh</code>, <code>behroot</code>, <code>behseries</code>, <code>behseriesdir</code></td></tr><tr><td align="right"><code>DataFormat</code></td><td>string</td><td><span data-gb-custom-inline data-tag="emoji" data-code="1f534">🔴</span></td><td>[<mark style="color:green;"><strong>Export</strong></mark>] <code>native</code>, <code>dicom</code>, <code>nifti3d</code>, <code>nifti4d</code>, <code>analyze3d</code>, <code>analyze4d</code>, <code>bids</code>.</td></tr><tr><td align="right"><code>Enabled</code></td><td>bool</td><td><span data-gb-custom-inline data-tag="emoji" data-code="1f534">🔴</span></td><td>[<mark style="color:red;"><strong>Search</strong></mark>] <code>true</code> if the step is enabled, <code>false</code> otherwise</td></tr><tr><td align="right"><code>Gzip</code></td><td>bool</td><td></td><td>[<mark style="color:green;"><strong>Export</strong></mark>] <code>true</code> if converted Nift data should be g-zipped, <code>false</code> otherwise.</td></tr><tr><td align="right"><code>ImageType</code></td><td>string</td><td></td><td>[<mark style="color:red;"><strong>Search</strong></mark>] Comma separated list of image types, often derived from the DICOM ImageType tag, (0008:0008).</td></tr><tr><td align="right"><code>DataLevel</code></td><td>string</td><td><span data-gb-custom-inline data-tag="emoji" data-code="1f534">🔴</span></td><td>[<mark style="color:red;"><strong>Search</strong></mark>] <code>nearestintime</code>, <code>samestudy</code>. Where is the data coming from.</td></tr><tr><td align="right"><code>Location</code></td><td>string</td><td></td><td>[<mark style="color:green;"><strong>Export</strong></mark>] Directory, relative to the <code>analysisroot</code>, where this data item will be written.</td></tr><tr><td align="right"><code>Modality</code></td><td>string</td><td><span data-gb-custom-inline data-tag="emoji" data-code="1f534">🔴</span></td><td>[<mark style="color:red;"><strong>Search</strong></mark>] Modality to search for.</td></tr><tr><td align="right"><code>NumberBOLDreps</code></td><td>string</td><td></td><td>[<mark style="color:red;"><strong>Search</strong></mark>] If <code>SeriesCriteria</code> is set to <code>usecriteria</code>, then search based on this option.</td></tr><tr><td align="right"><code>NumberImagesCriteria</code></td><td>string</td><td></td><td>[<mark style="color:red;"><strong>Search</strong></mark>] </td></tr><tr><td align="right"><code>Optional</code></td><td>bool</td><td><span data-gb-custom-inline data-tag="emoji" data-code="1f534">🔴</span></td><td>[<mark style="color:red;"><strong>Search</strong></mark>] <code>true</code> if this data step is option. <code>false</code> if this step is required and the analysis will not run if the data step is not found.</td></tr><tr><td align="right"><code>Order</code></td><td>number</td><td><span data-gb-custom-inline data-tag="emoji" data-code="1f534">🔴</span></td><td>The numerical order of this data step.</td></tr><tr><td align="right"><code>PreserveSeries</code></td><td>bool</td><td></td><td>[<mark style="color:green;"><strong>Export</strong></mark>] <code>true</code> to preserve series numbers or <code>false</code> to assign new ordinal numbers.</td></tr><tr><td align="right"><code>PrimaryProtocol</code></td><td>bool</td><td></td><td>[<mark style="color:red;"><strong>Search</strong></mark>] <code>true</code> if this data step determines the primary study, from which subsequent analyses are run.</td></tr><tr><td align="right"><code>Protocol</code></td><td>string</td><td><span data-gb-custom-inline data-tag="emoji" data-code="1f534">🔴</span></td><td>[<mark style="color:red;"><strong>Search</strong></mark>] Comma separated list of protocol name(s).</td></tr><tr><td align="right"><code>SeriesCriteria</code></td><td>string</td><td><span data-gb-custom-inline data-tag="emoji" data-code="1f534">🔴</span></td><td>[<mark style="color:red;"><strong>Search</strong></mark>] Criteria for which series are downloaded if more than one matches criteria: <code>all</code>, <code>first</code>, <code>last</code>, <code>largest</code>, <code>smallest</code>, <code>usecriteria</code>.</td></tr><tr><td align="right"><code>UsePhaseDirectory</code></td><td>bool</td><td></td><td>[<mark style="color:green;"><strong>Export</strong></mark>] <code>true</code> to write data to a sub directory based on the phase encoding direction.</td></tr><tr><td align="right"><code>UseSeriesDirectory</code></td><td>bool</td><td></td><td>[<mark style="color:green;"><strong>Export</strong></mark>] <code>true</code> to write each series to its own directory, <code>false</code> to write data to the root export directory.</td></tr></tbody></table>