Sample Data

XNAT Schema Extension

A sample schema, ext.xsd, which extends the XNAT schema is available in XNAT_HOME/deployments/PROJECT_NAME/src/schemas/ext folder. This schema has three root elements viz. ClinicalAssessment, AtlasScalingFactor and SegmentationFast. ClinicalAssessment extends xnat:subjectAssessorData and AtlasScalingFactor, SegmentationFast extend xnat:mrAssessorData.

Sample Data

Sample data can be downloaded from here. The sample data is organized into subfolders arc, xml-base and xml-extenstion.

The arc folder contains image data of three MRI sessions identified by sample1_MR1, sample2_MR1 and sample3_MR1. All the image files have been anonymized and are in Analyze 7.5 format.

The xml-base folder contains xml files describing three participants (viz. sample1, sampl2 and sample3) and the three MRI sessions for which the data is in the arc subfolder.

The xml-extension folder contains xml files representing ClinicalAssessment, AtlasScalingFactor and SegmentationFast data for three participants. The root element for these xml files is defined in the XNAT schema extension

Storing Sample Data

ACTION

1. Extract the sample data file into a folder, say, SAMPLE_DATA_ROOT.
2. Follow Steps 8-11 in the Quick Tutorial , if you havent already done so.
3. At the command prompt in your XNAT deployment (XNAT_HOME/deployments/PROJECT_NAME) execute the statement ‘StoreXML -project PROJECT_NAME -dir SAMPLE_DATA_ROOT/xml-base -r true -u admin -p admin –allowDataDeletion true ’. 

   SUMMARY: This will insert all the sample data in the xml-base subfolder into XNAT. This information will be visible through the admin account via the MR Session and the Subjects link on the website.

4. Optional: If you have used ext.xsd schema and have followed the steps mentioned under Customizing XNAT, at the command prompt in your XNAT deployment, execute the statement ‘StoreXML -project PROJECT_NAME -dir SAMPLE_DATA_ROOT/xml-extension -u admin -p admin –allowDataDeletion true ’. 

   SUMMARY: This will insert all the sample data in the xml-extension subfolder into XNAT. This information will be visible to the users who have access to the data via the ClinicalAssessment, AtlasScalingFactor and the SegmentationFast link on the website.

Viewing Sample Data Images

The images can be viewed either using the Quick View button on the home page or by using the View Images link under the Actions of an MR Session report.

In order for the viewer to work, you should have performed all the steps mentioned above. The viewer needs a directory into which it can create the low resolution image files. The directory is specified using the xdat.project.image.lo_res.location property in the build.properties file.

ACTION

1. In the build.properties file, set

xdat.cache.location=CACHE_DIRECTORY

xdat.archive.location=SAMPLE_DATA_ROOT/arc

xdat.project.image.lo_res.location=LO_RES_DIRECTORY

Note: The xdat.archive.location property should be set to the top level directory within which all the sessions are archived. So, for the sample data which you have downloaded, this property is set to SAMPLE_DATA_ROOT/arc.

2. Optional: If you have used the sample schema which extends XNAT schema and you want to view the image files associated with the SegmentationFast data, uncomment the statements in the XNAT_HOME/projects/PROJECT_NAME/PlexiViewerSpec.xml file by removing the <!-- and --> comment markers
3. At the command prompt in the root directory of the XNAT package, run ‘bin/update.sh’ or 'bin\update.bat' (include the -Ddeploy=true tag to deploy the changes directly to the webapp). 

   SUMMARY:This will update the project which you specified in the build.properties file to reflect the changes above.

4. Deploy the webapp
5. Restart tomcat

More info about image viewer