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- | === Browser JAVA Requirements === | + | ==== Browser JAVA Requirements |
- | Your browser must have JAVA enabled to work with the xnat service. | + | For some functions on the XNAT server, your browser must have Java enabled to work with the xnat service. However since Java support is being phased out in major browsers, functionality is being transferred to desktop tools by the XNAT team. |
- | === Data Access outside of XNAT === | + | ==== Documentation ==== |
- | The XNAT data archive is stored on the /data/tesla-data volume, and is directly accessible with read-only permissions on the cluster at /data/XNAT. This allows direct processing from the cluster of data stored within XNAT. | + | The [[https://wiki.xnat.org/documentation|XNAT Wiki has documentation]] |
- | Individual project directories readable only by members of the project' | + | ==== Direct Data Access from the Cluster ==== |
- | === Pipelines === | + | The XNAT data archive is stored on the ''/ |
- | XNAT can also be setup to run 'pipelines', which are collections | + | Users who need to read this data must be added to the '' |
- | === Accounts === | + | ==== Pipelines ==== |
+ | |||
+ | XNAT can also be setup to run ' | ||
+ | |||
+ | ==== Accounts | ||
User logins are separate from CfN cluster logins. Please connect the admins for more information. | User logins are separate from CfN cluster logins. Please connect the admins for more information. | ||
- | === Uploading Data === | + | ==== Projects ==== |
- | To manually upload data, use the [[https:// | + | 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 ==== | ||
+ | |||
+ | === " | ||
+ | |||
+ | When data is "in Prearchive", | ||
+ | |||
+ | When data is "moved to Archive" | ||
+ | |||
+ | When data is uploaded/ | ||
+ | |||
+ | === Manual Uploads === | ||
+ | To manually upload data, use the desktop tool [[https:// | ||
For the Upload Assistant setup: | For the Upload Assistant setup: | ||
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username: your XNAT username (probably the same as you cluster username, but may not be)\\ | username: your XNAT username (probably the same as you cluster username, but may not be)\\ | ||
password: you XNAT password\\ | password: you XNAT password\\ | ||
+ | |||
+ | See below for handling anonymization. | ||
+ | |||
+ | === Pushing Data from PACS/Sectra or a Scanner === | ||
+ | |||
+ | XNAT can receive data directly from PACS/ | ||
+ | |||
+ | == 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/ | ||
+ | |||
+ | __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 === | ||
+ | |||
+ | Anonymization refers to the removal of personally identifying information in medical data (Protected Health Information - PHI) | ||
+ | |||
+ | == Site-wide Anonymization == | ||
+ | |||
+ | When data is uploaded to XNAT, a site-wide anonymization script is run as the data first goes to Prearchive. | ||
+ | [[https:// | ||
+ | |||
+ | == Project-specific Anonymization == | ||
+ | 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. | ||
+ | |||
+ | == ' | ||
+ | **IMPORTANT** The site-wide anon script **does not remove** these fields: | ||
+ | |||
+ | **Non-Anonymized (NA) Fields** | ||
+ | ^DICOM Tag ^ DICOM Tag Name ^ XNAT Field ^ | ||
+ | |(0008, | ||
+ | |(0008, | ||
+ | |(0010, | ||
+ | |(0010, | ||
+ | |||
+ | __Note on Accession Number__: XNAT generates its own Accession Numbers ('Expt ID') in the format '' | ||
+ | |||
+ | The above ' | ||
+ | |||
+ | __It's up to the user to change these 'NA Fields' | ||
+ | |||
+ | == Modifying NA Fields on the Research Scanner == | ||
+ | |||
+ | When pushing data from the research scanner (which allows the user to modify the DICOM ' | ||
+ | |||
+ | == Modifying NA Fields During Move to Archive == | ||
+ | |||
+ | If the user moves data manually from Prearchive to Archive (recommended), | ||
+ | |||
+ | 1) ' | ||
+ | |||
+ | 2) ' | ||
+ | |||
+ | == 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 Prearchive, the user is prompted to change the Subject and Session fields before it's moved to Archive. | ||
+ | |||