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xnat [2018/03/03 00:48] mgstauff |
xnat [2018/03/19 21:21] (current) mgstauff [Projects] |
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XNAT organizes data by Project. Each Project has private control of its data and a user must be granted access to a Project to view or edit data. | XNAT organizes data by Project. Each Project has private control of its data and a user must be granted access to a Project to view or edit data. | ||
+ | ==== User Roles and Permissions ==== | ||
+ | |||
+ | XNAT users can have different permissions within a Project: | ||
+ | |||
+ | **Project Owners**: If you define additional project owners, they will have all of the permissions on your project that you do. They can read, insert, modify, and delete anything (and everything) associated with your project. They can also add additional users to your project and modify the data types associated with your project. | ||
+ | |||
+ | **Project Members**: Members have the ability to manage the data in your project. They can read, insert, and modify subjects and experiments in your project. They cannot modify the project users and data types. | ||
+ | |||
+ | **Project Collaborators**: | ||
+ | |||
+ | [[https:// | ||
==== Uploading Data ==== | ==== Uploading Data ==== | ||
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password: you XNAT password\\ | password: you XNAT password\\ | ||
- | === Pushing Data from PACS/Sectre or Research Scanner === | + | See below for handling anonymization. |
- | XNAT can receive data directly from PACS/Sectre | + | === Pushing Data from PACS/Sectra or a Scanner === |
+ | |||
+ | XNAT can receive data directly from PACS/Sectra, from clinical scanners, | ||
== Prearchive or Archive as Final Destination == | == Prearchive or Archive as Final Destination == | ||
- | Data can end up in either Archive or Prearchive at the completion of the upload/push process from a scanner or PACS/Sectre. This depends on project-specific settings. Namely, within a project' | + | Data can end up in either Archive or Prearchive at the completion of the upload/push process from a scanner or PACS/Sectra. This depends on project-specific settings. Namely, within a project' |
+ | |||
+ | __We recommend__ setting this option to leave data in Prearchive, so your group knows it needs to be reviewed and probably have PHI removed before moving to Archive. The setting' | ||
+ | |||
+ | All image data should be placed in a temporary location (prearchive) before being manually transferred into the permanent archive. | ||
=== Data Anonymization - IMPORTANT === | === Data Anonymization - IMPORTANT === | ||
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When data is moved from prearchive to archive, a Project-specific anon script is run, if one is set. Each Project can define its own anonymization script if the site-wide script is insufficient. | When data is moved from prearchive to archive, a Project-specific anon script is run, if one is set. Each Project can define its own anonymization script if the site-wide script is insufficient. | ||
- | == Fields That Are NOT Automatically Anonymized | + | == ' |
- | **IMPORTANT** | + | **IMPORTANT** The site-wide anon script **does not remove** these fields: |
- | The site-wide anon script **does not remove** these fields: | + | |
**Non-Anonymized (NA) Fields** | **Non-Anonymized (NA) Fields** | ||
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__Note on Accession Number__: XNAT generates its own Accession Numbers ('Expt ID') in the format '' | __Note on Accession Number__: XNAT generates its own Accession Numbers ('Expt ID') in the format '' | ||
- | The above ' | + | The above ' |
__It's up to the user to change these 'NA Fields' | __It's up to the user to change these 'NA Fields' | ||
- | When pushed | + | == Modifying NA Fields on the Research Scanner == |
- | https:// | + | |
+ | When pushing data from the research | ||
+ | |||
+ | == Modifying NA Fields During Move to Archive == | ||
+ | |||
+ | If the user moves data manually from Prearchive to Archive (recommended), | ||
- | If the user moves data manually from prearchive to archive, they have two options: | ||
1) ' | 1) ' | ||
+ | |||
2) ' | 2) ' | ||
- | When using the XNAT Desktop Upload Assistant (client-side tool for manual uploading), data goes straight to project archive. However after the data first enters | + | == XNAT Upload Assistant and Anonymization == |
+ | When using the XNAT Desktop Upload Assistant (client-side tool for manual uploading), data goes straight to project archive. However after the data first enters | ||