The Desktop Client only supports uploading one image session at a time. If you have a large number of sessions to upload, consider using an upload script that uploads image sessions via the REST API. A new version of the application that support bulk upload of multiple sessions is in development.
With an authenticated XNAT connection, you can select image sessions to upload. Click "Upload Files" to get started.
The Desktop Client will display a list of projects that you have permission to upload image session files to. This permission is given to project owners and members, and potentially to other custom roles. If you need to upload to a project but do not see that project in this listing, contact that project owner or request access to that project through the XNAT UI.
Once you select a project, the Desktop Client will display a list of subjects in that project that you can upload your image session to. You can select one of these, or create a new subject.
After selecting a project and subject to upload to, you will be prompted to select a folder on your desktop that contains one or more DICOM image sessions. Select the folder that has your image session in it.
If you select a folder that contains more than one session, you will be prompted to pick one of those sessions before continuing.
This step may or may not be required depending on your XNAT's configuration, or the configuration of the project you are uploading to.
You may need to enter the visit date of the image session that you are uploading, before proceeding. This is an error-prevention measure, to ensure that users don't inadvertently upload the wrong session to a given project.
By default, all scans in the image session will be selected to upload. You can select a subset of these scans to upload if you like.
The Desktop Client will auto-generate a session label, based on the subject label and other variables. You can override this label if you like.
Uploading PET Sessions: Select PET Tracer
If the Desktop Client recognizes your image session as a PET session, the PET Tracer field will be added to the list of configurable inputs. You can set a list of default tracers in the Desktop Client's application settings, if you like. Click on the "Settings" gear icon in the upper right of the main navigation.
Setting Custom Values
The DICOM anonymization script specified by the XNAT site or the selected project may specify additional variables that will be included in the session's metadata. These will appear above the scan selection table.
The next step allows you to review the image data and look for PHI that might be burned into the pixels. See the screen captures below for Ultrasound images that have acquisition parameters included in the image data but not actual PHI. You start by clicking on the Select Area icon in the upper left part of the display. Draw as many rectangular regions as you need to remove unwanted pixels. As you draw these, they are highlighted with orange boxes, and you will also see an orange circle in the thumbnail view to indicate you have started the process. The rectangles that you draw are applied to all images in the current series. You can use the mouse to scroll through the series to ensure that all images are properly modified; right click and scroll through the image panel. When you are satisfied, you need to click on the "Save scan" icon. The application will turn the circle that appears on the thumbnail image to green to indicate confirmation. If there are other series, you can perform the same procedure. When you are done, select the "Finish and Upload" button at the bottom right of the screen.
You are not required to search for PHI, and you are not required to draw any rectangles on any scan. If your images do not contain PHI burned into the pixels, you can just select "Finish and Upload" when you see this screen and continue to the next step. In a similar manner, your session may have multiple scans. The application is designed to capture rectangular regions separately for each scan. This allows you to black out pixels in different regions of the image data on a per scan basis. Again, you might have data with PHI in some scans but not in others, and the tool gives you the flexibility to manage those scans separately.
Once you start the upload, you will be taken to the transfer manager screen. You can watch the progress of the upload, or start another workflow. As long as the application is running and you have an active network connection, the upload will proceed in the background. You can check on the progress of your data transfer at any time.
See: Managing Data Transfers