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--- xnat [2018/03/02 22:46]
mgstauff [Uploading Data]
+++ xnat [2018/03/19 21:21] (current)
mgstauff [Projects]
@@ Line 32: / Line 32: @@
 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**: Collaborators have read-only access on all of the data in your project. They cannot insert or modify data owned by your project. They can download your data and use it within their projects.
+[[https://wiki.xnat.org/display/XNAT17/Understanding+User+Roles+and+Permissions|Full details are here.]]
 ==== Uploading Data ====
@@ Line 39: / Line 50: @@
 When data is "moved to Archive" in XNAT, it means the data has been fully integrated into the XNAT database as part of a Project. It is now viewable and actionable from the Project's page in the web interface.
+When data is uploaded/imported to XNAT, it always goes into Prearchive, even if only temporarily before it's moved to Archive.
 === Manual Uploads ===
@@ Line 49: / Line 62: @@
 password: you XNAT password\\
-=== Pushing from PACS/Sectre or Research Scanner ===
+See below for handling anonymization.
-XNAT can receive data directly from PACS/Sectre and from the Stellar-Chance research scanner. Please contact the admins for details.
+=== Pushing Data from PACS/Sectra or a Scanner ===
-=== Data Anonymization ===
+XNAT can receive data directly from PACS/Sectra, from clinical scanners, and from research scanners such as the Stellar-Chance scanner. This is typically called 'pushing' data to a 'DICOM (SCP) Receiver', or to an 'AE Title', or simply 'to XNAT'. Please contact the admins for details.
+== 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/Sectra. This depends on project-specific settings. Namely, within a project's 'Manage' tab, it's set under 'Define Prearchive Settings'. Data always 'goes through' Prearchive briefly even if its final destination is Archive.
+__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's label reads:
+  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://wiki.xnat.org/display/XNAT17/Where+Anonymization+Happens+in+XNAT|See here for details.]]
-When moved from prearchive to archive, the project-specific anon script is run, if one is set.
+== 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.
-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 'Define Prearchive Settings' within a project's 'Manage' tab.
+== 'NA' Fields That Are NOT Automatically Anonymized ==
+**IMPORTANT** The site-wide anon script **does not remove** these fields:
-When pushed from PACS/Sectre, the site-wide anon script does not remove DICOM 'Study Description', 'Patient Name', or 'Patient ID' ("SPP fields", for convenience). Thus it's up to the user to change these as needed to protect PHI.
+**Non-Anonymized (NA) Fields**
+^DICOM Tag ^ DICOM Tag Name ^ XNAT Field ^
+|(0008,0050)    | Accession Number | <No direct map to XNAT> |
+|(0008,1030)	| Study Description	| Project ID |
+|(0010,0010)	| Patient Name	| Subject Label |
+|(0010,0020)	| Patient ID	| Session Label |
-When pushed from a scanner that allows the user to modify the DICOM 'Patient Comments' or 'Study Comments' field before pushing the data, the user has the option to assign metadata that XNAT will use to new assign values to the SPP fields during import. Otherwise, the SPP fields be preserved as in a push from PACS.
+__Note on Accession Number__: XNAT generates its own Accession Numbers ('Expt ID') in the format ''PICSL_xnat_<xyz>''. These are generated for Subjects and for Sessions, and are shown in the XNAT database, but are not used to modify DICOM headers. Yes, it can be confusing.
-https://wiki.xnat.org/pages/viewpage.action?pageId=36373129
+The above 'NA' fields are not anonymized because they are used by users to identify data within XNAT before it can be given whatever kind of unique, anonymized identifiers that a research group's study protocol specifies. Before data is pushed from PACS/Sectra and clinical scanners, the DICOM header info cannot be modified, so this information must be preserved upon entry into XNAT.
+__It's up to the user to change these 'NA Fields' as needed to protect PHI.__
+== Modifying NA Fields on the Research Scanner ==
+When pushing data from the research scanner (which allows the user to modify the DICOM 'Patient Comments' or 'Study Comments' field before pushing the data), the user has the option to assign metadata that XNAT will use to new assign values to the some of the NA fields during import. Otherwise, the NA fields be preserved as in a push from PACS/Sectra. [[https://wiki.xnat.org/pages/viewpage.action?pageId=36373129|See here for details.]]
+== Modifying NA Fields During Move to Archive ==
+If the user moves data manually from Prearchive to Archive (recommended), they have two options:
-If the user moves data manually from prearchive to archive, they have two options:
 ) 'Review and Archive' - user is prompted to change the XNAT Subject (DICOM field 'Patient Name') and XNAT Session (DICOM field 'Patient ID') fields.
 ) 'Archive' - data is archived without prompting user to change anything
-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.
+== 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.

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