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xnat [2018/03/02 22:43] mgstauff |
xnat [2018/03/19 21:21] (current) mgstauff [Projects] |
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The [[https:// | The [[https:// | ||
- | ==== Data Access | + | ==== Direct |
The XNAT data archive is stored on the ''/ | The XNAT data archive is stored on the ''/ | ||
- | Individual project directories are readable only by members of a linux group for lab/project members. If you need to be added to the appropriate group, please tell the admins. | + | Users who need to read this data must be added to the '' |
==== Pipelines ==== | ==== Pipelines ==== | ||
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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 |
- | + | ||
- | === Projects | + | |
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 ==== | ||
=== " | === " | ||
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When data is "moved to Archive" | When data is "moved to Archive" | ||
+ | |||
+ | When data is uploaded/ | ||
=== Manual Uploads === | === Manual Uploads === | ||
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password: you XNAT password\\ | password: you XNAT password\\ | ||
- | === Pushing from PACS/Sectre or Research Scanner === | + | See below for handling anonymization. |
- | XNAT can receive data directly | + | === Pushing Data from PACS/Sectra or a Scanner === |
- | === Data Anonymization === | + | 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 | ||
Anonymization refers to the removal of personally identifying information in medical data (Protected Health Information - PHI) | 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. | When data is uploaded to XNAT, a site-wide anonymization script is run as the data first goes to Prearchive. | ||
[[https:// | [[https:// | ||
- | When moved from prearchive to archive, | + | == Project-specific Anonymization == |
+ | When data is moved from prearchive to archive, | ||
- | Data's final destination at the end of the push process from scanner or PACS, is either prearchive or archive. This depends on project-specific settings. Namely under ' | + | == 'NA' Fields That Are NOT Automatically Anonymized == |
+ | **IMPORTANT** The site-wide anon script **does not remove** these fields: | ||
- | When pushed from PACS/ | + | **Non-Anonymized (NA) Fields** |
+ | ^DICOM Tag ^ DICOM Tag Name ^ XNAT Field ^ | ||
+ | |(0008, | ||
+ | |(0008, | ||
+ | |(0010,0010) | | ||
+ | |(0010,0020) | Patient ID | Session Label | | ||
- | When pushed from a scanner | + | __Note on Accession Number__: XNAT generates its own Accession Numbers ('Expt ID') in the format '' |
- | https:// | + | |
+ | 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 | ||
+ | |||
+ | == 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 | ||