1. Image Session Validation Before we begin, please open this link on your VM: https://wiki.xnat.org/display/Workshop2012Pub cd /opt/xnat/workshop2012 hg pull -u

2. Image Session Validation Mohana Ramaratnam mohanakannan9@gmail.com

3. What is validation? Checking that your study was acquired with all parameters as defined by the study protocol. Checking that your study was acquired with all parameters as defined by the study protocol. For example: For example: A subject must be scanned with 3 T1 acquisitions, atleast 1 T2 and 2 Resting state scans. A subject must be scanned with 3 T1 acquisitions, atleast 1 T2 and 2 Resting state scans. The inversion time (TI) of the T1 scan must be 1100ms and echo time (TE) must be between 3.17 and 3.47ms. The inversion time (TI) of the T1 scan must be 1100ms and echo time (TE) must be between 3.17 and 3.47ms.

4. Why validate? It’s a first pass at quality assurance. It’s a first pass at quality assurance. Automatically check for accuracy of acquisition parameters. Automatically check for accuracy of acquisition parameters. Very useful for multi-site projects. Very useful for multi-site projects.

5. How is it implemented? /catalog/validation_tools/V alidate.xml is the pipeline which enables validation. /catalog/validation_tools/V alidate.xml is the pipeline which enables validation. XPATH and XSLT based using Schematron rule file. XPATH and XSLT based using Schematron rule file. An assessor, val:ProtocolVal, specified in /plugin-resources/project- skeletons/xnat/validation/Validation.xsd, is created which contains the validation results. An assessor, val:ProtocolVal, specified in /plugin-resources/project- skeletons/xnat/validation/Validation.xsd, is created which contains the validation results.

6. What is Schematron? A rule-based validation language for making assertions about the presence or absence of patterns in XML trees A rule-based validation language for making assertions about the presence or absence of patterns in XML trees What does that mean: What does that mean: – We need to specify rules in a rule file – We need a XML document in which we are finding patterns Reference: www.schematron.com Reference: www.schematron.com

7. Schematron assertions T1 scan labelled as MPRAGE must have TR of 2400ms T1 scan labelled as MPRAGE must have TR of 2400ms ………..</iso:assert>

8. How do I add validation to my site? Perform Step 1 in the handout Perform Step 1 in the handout Site administrators would add the Validate pipeline to the site: Site administrators would add the Validate pipeline to the site: /catalog/validation_tools/V alidate.xml /catalog/validation_tools/V alidate.xml with the custom webpage PipelineScreen_protocolcheck.vm

9. How do I add validation to my project? Create a schematron rule file for the data- type Create a schematron rule file for the data- type Add the Validation pipeline to the project Add the Validation pipeline to the project Perform Step 3 in the handout Perform Step 3 in the handout

10. Steps to validation - I The rules are applicable to a data-type within a project The rules are applicable to a data-type within a project Create a schematron rule file for the project and the datatype Create a schematron rule file for the project and the datatype Associate the rule file to a project and the datatype Associate the rule file to a project and the datatype

11. Steps to Validate - II Perform Step 2 in the handout Perform Step 2 in the handout Create a resource called validation_XNAT_DATATYPE To the resource add the rule file by issuing a PUT to Create a resource called validation_XNAT_DATATYPE To the resource add the rule file by issuing a PUT to /data/archive/projects/YOUR_PROJECT/resou rces/validation_XNAT_DATATYPE_HERE/files ?content=CONTENT_HERE

12. How do I launch the pipeline? Automatically on archival - this is possible when the pipeline is setup to be invoked on archival automatically. Automatically on archival - this is possible when the pipeline is setup to be invoked on archival automatically. Launching using Actions -> Build -> ProtocolCheck Launching using Actions -> Build -> ProtocolCheck POSTing to REST URI -> /data/archive/projects/YOUR_PROJECT/pip elines/AUTO_ARCHIVE_PROTOCOLCHECK/ex periments/SESSION_ID_HERE POSTing to REST URI -> /data/archive/projects/YOUR_PROJECT/pip elines/AUTO_ARCHIVE_PROTOCOLCHECK/ex periments/SESSION_ID_HERE

13. Advanced rule file details One can create custom java functions for checking things like number of files, more details from the headers. One can create custom java functions for checking things like number of files, more details from the headers.

14. Questions?