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publicadmin 1.1 1 == Dataset Organization and Validation ==
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3 The VRE provides tools for organizing the files and folders within your Dataset, and for validating the structure against a supported* external specification standard.
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5 ~* Currently, the [[Brain Imaging Data Structure (BIDS)>>https://bids.neuroimaging.io/specification.html]] standard is supported.
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8 {{toc start="4"/}}
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13 ==== Organizing Dataset contents ====
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15 {{info}}
16 **Note: **Datasets contain //copies// of files from the VRE Core.  Moving, renaming, or deleting files and folders within a Dataset will not affect the original files stored in the VRE Core.
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19 To view, rearrange and edit the contents of your Dataset, open the Dataset from the Datasets landing page, then select the **Data **tab.
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21 1. **Explore**: Click the **Explorer **tab to view the files and folders in your Dataset
22 1. **Move**:** **To rearrange files or folders in your Dataset, check the box next to the item you wish to move, then click **Move to **and select a destination within the Dataset.
23 1. **Validate BIDS**: See "BIDS Validation" below for instructions on validating a Dataset against the BIDS standard.
24 1. **Actions**: Click the name of a file or folder in your Dataset to view the available actions.
25 1*. **Preview **- click the preview ("eye") icon to see a preview of csv or json files in the right panel of the **Explorer **tab.
26 1*. **Download **- click the download icon to save a copy of the file or folder to your local device.
27 1*. **Edit **- click the pencil edit icon to rename the file or folder.
28 1*. **Trash **- click the trash icon to remove the file or folder from your Dataset.
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30 [[image:VRE UI Diagrams for User Manual - Datasets - Dataset Explorer V2.png||height="426" width="528"]]
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35 ==== Validating Dataset structure to external specification standards ====
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38 ===== BIDS Validation =====
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40 [[image:BIDS_Logo.png||alt="BIDS_Logo" height="65" width="150"]]
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43 The VRE provides a native tool to validate that the structure of a Dataset conforms to the [[Brain Imaging Data Structure (BIDS)>>https://bids.neuroimaging.io/specification.html]] specification standard.
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45 {{info}}
46 **Note: **The VRE BIDS Validation tool uses the open-source [[bids-validator 1.8.4 Python Package>>https://pypi.org/project/bids-validator/#quickstart]]
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49 To check that your Dataset aligns with the [[BIDS specification>>https://bids.neuroimaging.io/]]
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51 1. Ensure that your //VRE Dataset Type//** **is set as **BIDS**.  This property can be viewed in the //Dataset Information// section of the Home tab or in the //VRE Essentials //schema of the [[Metadata>>doc:Main.user_guide.Working with Datasets.Metadata Schemas.WebHome]] tab of the [[Dataset Canvas>>doc:Main.user_guide.Working with Datasets.Navigating the Dataset Canvas.WebHome]].
52 1*. To set this property at the time of [[Dataset Creation>>Dataset Creation]], select the //Type// as **BIDS** in the //Define //Dataset page.
53 1*. To set this property after Dataset creation, navigate to the Metadata tab of the Dataset canvas, locate the Schemas pane and click the pencil icon to edit the Essential Schema, change the Dataset Type from **GENERAL **to **BIDS, **then click **Update **to save.
54 1. In the **Explorer** tab of the Dataset canvas, use the Explorer tools to organize the Dataset folders according to the BIDS standard.
55 1. When ready to validate, click **Validate BIDS** and allow some time for the validation to process. After validation, one of the following results will be displayed adjacent to the BIDS Validation icon:
56 1*. **Green - Validated, no warnings:** A valid BIDS Dataset, no further modifications needed.
57 1*. **Green - Validated + orange warning icon: **A valid BIDS Dataset with optional recommendations to make the Dataset more BIDS compliant. Click the warning icon to view the explanations.  If desired, make the recommended corrections to the Dataset and re-run the validation.
58 1*. **Red - Not Validated: **An invalid BIDS Dataset. Click the warning icon to view the errors. Make the necessary corrections to the folder structure and re-run the validation.
59 1. After validation, the status of //BIDS compliant// will be preserved in Data tab until next validation
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63 **See Also: **
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65 [[Dataset Creation>>doc:Main.user_guide.Working with Datasets.Dataset Creation.WebHome]]
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67 [[Annotations and Metadata Schemas>>doc:Main.user_guide.Working with Datasets.Metadata Schemas.WebHome]]
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69 [[Activity Stream>>doc:Main.user_guide.Working with Datasets.Data Explorer.WebHome]]
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75 image:https://i.creativecommons.org/l/by-sa/4.0/88x31.png
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78 Copyright © 2022, Indoc Research. This work is licensed under a [[Creative Commons Attribution-ShareAlike 4.0>>http://creativecommons.org/licenses/by-sa/4.0/ ||rel="noopener noreferrer" target="blank"]] International License.
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