Step-by-step Protocol for the Pipeline-XNAT Interface
Anonymize Subject data
Open Pipeline Client and type anonymize at the search window.
Choose the module. Connect a data source with all the dicom directories that needs to be anonymized and save it the required location. Run the workflow to anonymize the dicom files. One could also change the .das file that is used here as the default and based on the user requirement a new new .das file can be generated.
Anonymize Subject Data
Uploading files to XNAT central
Go to
XNAT server (
http://central.xnat.org/app/template/Index.vm) and login if you have a username if not click on register to create one.
XNAT server
Once you login, click on New and choose Project.
New Project
Enter the information on the project form and also choose the accessibility option and submit.
accessibility option 
Also you could create new subjects under the project, by clicking on new Subject and filling out the information that is required.
new subjects
To upload images, click on Upload and choose Images,
Upload images
Choose Option1: Choose the project to which you want to upload the data. Select the .zip file and upload the images.
Choose Project
new subjects
Once the uploading is done, follow the instructions to review and archive the uploaded data.
Now go to Pre archived images and submit the sessions so it is achived in the specific project. For eg, Under Upload option choose “ Go to pre-archive” section.
new subjects
Here on this page you will see a list of all the images that are uploaded.
new subjects
Click on each session and select the Project, Subject and session option and click on submit to archive the sessions.
new subjects
Once the subject/sessions are submitted, you can view them under the main Project page.
Downloading archived files using Pipeline
Choose the Project that you are interested in. Go to MR sessions. Click on Options and select Download.
new subjects
This will open another window as shown below. Choose sessions and data type, and select Option 2 (XML) as download format.
new subjects
Click on submit and an XML file opens.
new subjects
Right click on this file and save it to you local computer.
Open the Pipeline client (PL 5.1). Go to Tools and select Database (IDA/XNAT).
new subjects
Under XNAT tab, browse and select the xml file that was downloaded from the XNAT central website. Fill in the username and password information and connect.
new subjects
Also one could download the data in different formats. Choose one. The data can also be saved on a remote server or on the local machine.
new subjects
Click on Create Module and connect a LONI viewer to view the data that is being downloaded, or module with appropriate input to process the data, or a data sink with specified download file location path to save the data.
new subjects
Run the workflow, XNATGet module will download the data.
new subjects
