CVRG XNAT-CVI User Guide
From CVRG Wiki
Contents |
Overview
Welcome to the installation guide for the CVRG XNAT-CVI, a Web and XML based system for managing cardiovascular imaging data and associated analytical results. This system is based on the open source project eXtensible Neuroimaging Archive Tool (XNAT) developed by the team at Washington University St. Louis lead by Dr. Dan Marcus. The XNAT-CVI extends the original XNAT system with additional functions and data elements to enable cardiovascular imaging (CVI) research.
Using the XNAT-CVI Live Demo
There is a live demo available at http://portal.cvrgrid.org:8080/web/guest/xnat1.
Since administrator privileges cannot be granted to every user on the live demo, the VM User Guide below will not be able to be performed on the live demo. To use the live demo follow the live demo video tutorials available in the portal http://portal.cvrgrid.org:8080/web/guest/tutorials.
To request a user account with member privileges (able to upload and edit data), you can use the Register link in the login page, it will create an account with read only permissions and notify an XNAT administrator who will grant the appropriate permissions as soon as possible. You can also email Ricardo Peral (rperal@wfubmc.edu) with login requests.
XNAT-CVI Virtual Machine User Guide
Running the Virtual Machine:
This release of CVRG XNAT-CVI runs on a virtual machine(VM) and its purpose is to demonstrate basic functionality. Future releases of the VM will contain additional features.
To install and run the VM follow the instructions in CVRG XNAT-CVI Installation Guide.
The guest OS is CentOS 6.0. The VM has two users:
Username: root Password: password
Username: xnatuser Password: password
It is not necessary to be root to run the XNAT application. The users' passwords can be changed without any effect on the XNAT application.
Log in to the OS as xnatuser.
XNAT-CVI runs on a Tomcat server and uses a Postgres database for data storage.
The XNAT-CVI application is already running. To view the user interface open firefox and enter the following address:
http://localhost:8080/xnat14
If networking is not working in the VM, please refer to the networking sections in the XNAT-CVI Installation Guide: CVRG_XNAT-CVI_Installation_Guide#Networking_in_VirtualBox and CVRG_XNAT-CVI_Installation_Guide#Networking_in_VMware_Player.
CVI analytical data elements
Cardiovascular imaging research employs various commercial and research systems for image analysis. This release of XNAT-CVI includes data elements for importing analytical results from a number of systems.
Data elements available in this release:
HARP version 1.11 (http://www.diagnosoft.com): Cardiac MRI strain and function analysis
CIM version 6.2f (http://www.mri.auckland.ac.nz): Cardiac Image Modeler
QMASS version 7.1 (http://www.medis.nl): Cardiac MRI function and volume analysis
MIPAV version 4.1.1(http://mipav.cit.nih.gov): Customized to measure fat volume using CT and MRI
TeraRecon Aquarius Workstation version 3.1.11 (http://www.terarecon.com) : Calcium scoring of blood vessels
CAAS MRV version 3.2 (http://www.piemedicalimaging.com) : Cardiac MRI functional analysis
MIMP version 1.099 (http://www.wakehealth.edu) : Cardiac MRI analysis of pulse wave velocity and wall thickness
Future releases will expand this collection to enable more analysis platforms and imaging modalities.
Login and UI overview
There is currently one user in XNAT-CVI.
Username: admin Password: admin
The main user interface features in XNAT-CVI's home page are: a menu bar at the top for performing actions, a list of projects and data activity on the body of the page, and set of menus on the left that are shortcuts for easier access to data.
XNAT-CVI notifies the administrator when important events occur. To enter your email information into XNAT-CVI click on Administer -> Default Settings on the top menu bar.
On the settings page enter your email address and your institution's mail server.
Creating a new user
Create a new user by clicking on Administer -> Users on the upper menu.
Click on the Add User link.
Fill in the user’s information. Click Submit.
Under Step 1, click on Enabled so the user can login. Click Submit.
Under Step 2, add to project hstudy as member. Click Add.
Repeat for project kheart.
Click Submit.
There are 3 types of users in XNAT-CVI projects:
- Owners have read, write and administrative priviledges.
- Members can read and write.
- Collaborators can view but cannot change any project information.
The user has been created. Close the window.
Projects
Click on hstudy, on the project list.
XNAT-CVI will display general project information on the top of the screen of the window, and details about imaging sessions and analyses on the bottom.
The bottom area will display a list of subjects, click on the drop down menu and select CT Sessions.
XNAT-CVI now displays a list of CT scans belonging to the H Study project.
Click on the link to the first CT session (550001), and XNAT will display that session’s page.
The page contains some general information at the top. A list of scans (series) belonging to that session, and a list of assessments (imaging analyses) performed on the session’s images. On the right there is a list of actions that can be performed on that session.
Click on the project link at the top to get back to the project’s page.
Viewing analysis results
Click on the drop down menu and this time select Abdominal Mipavs. XNAT-CVI will now display a list of abdominal fat analysis results.
Click on the link to the analysis results for subject 550001.
XNAT-CVI now displays the complete results of the abdominal mipav analysis on that scan.
Click on the project link at the top to get back to the project’s page.
Uploading analysis results
To navigate to the 55002 CT session page, click on the CT Sessions tab and click the 550002 link.
Abdominal Mipav results have not yet been uploaded to XNAT-CVI for this session. On the right side of the page there is an Actions Menu. To upload abdominal fat results click on the Upload Abd MIPAV link.
XNAT-CVI expects to find results files in a specific folder, depending on analysis type, subject name and id, and scan date. Mipav results files for 550002 can be found in:
/imdata/hstudy/results/H0002_550002/20110927/mipav/
XNAT-CVI will display a form containing the contents of the abdominal fat results file for the current session. Click on the Submit at the bottom of the page and the data will be stored in XNAT-CVI’s database.
The Experiment details page containing the result data is now displayed.
Manual uploading of images
Although XNAT-CVI has the ability to receive images using the DICOM protocol this VM release can only receive images through manual uploading.
To manually upload images zip (.zip or .tar.gz) a folder containing one DICOM imaging session. Internal folder structure and file names are not important.
On the XNAT page, click on Upload --> Images
XANT-CVI will display the Compressed upload form.
Select the project where the images belong. Select Archive no quarantine for the images to go straight to the selected project. Click on Choose File and use the file browser to select the zipped file containing the images. Click on Upload.
XNAT-CVI will display an upload progress window. And will notify the user of a successful upload. The patient ID in the success notification is a link to the uploaded imaging session.
XNAT-CVI additional documentation and questions
For a complete set of documents visit XNAT’s official site:
http://docs14.xnat.org Note that the version of XNAT running on this VM is 1.4.
For questions and issues please contact Ricardo Peral (rperal@wfubmc.edu)
