Resources for reporting talk

Task: Add Manual QC assessor to MR Session.

Go to Admin > Data Types
Select MR Session (not Manual QC!)
Scroll down to Available Report Actions
At the first empty row, enter:
- Name (of the vm you're linking to): XDATScreen_edit_xnat_qcManualAssessorData
- Display Name: Add Manual QC
- Secure Access (defines permissions needed to see/use link): edit
Scroll down and Submit

Task: Create a Manual QC for an imaging session

Go to an MR Session Page
Select "Add Manual QC"
An entry must be made for each scan to represent pass or fail. "1" = pass, "0" = fail.

BOGUS PI Report Definition

COLUMN HEADER	Gender	Handedness	MR QC	Stroke Scale Total	Self-Rated Awesome	Awesomeness	Solipsism
SCHEMA	xnat.xsd	xnat.xsd	xnat.xsd	nihss.xsd	egomaster.xsd	egomaster.xsd	egomaster.xsd
NAMESPACE	xnat	xnat	xnat	nihSS	bogus	bogus	bogus
DATATYPE	demographicData	demographicData	qcmanualAssessorData	nihStrokeScaleData	egoMaster	egoMaster	egoMaster
RAW/UNBOUNDED/DERIVED	RAW	RAW	DERIVED	DERIVED	DERIVED	RAW	RAW
COLUMN ID	GENDER	HANDEDNESS	PASS_TEXT	TotalScore	AWESOME	AWESOMENESS	SOLIPSISM
UNBOUNDED/DERIVED: SQL QUERY	n/a	n/a	tbd	DONE in display document	Would follow same pattern as MR QC	n/a	n/a
SAMPLE VALUE	female	left	pass	14	TRUE	2	8

Task: Create QC Worklist

1. cp /var/lib/tomcat6/webapps/xnat/schemas/xnat/display/mrSessionData_display.xml /var/lib/tomcat6/webapps/xnat/schemas/xnat/display/mrSessionData_display.xml.bak
2. vi /var/lib/tomcat6/webapps/xnat/schemas/xnat/display/mrSessionData_display.xml
3. Paste in:
<DisplayField id="MR_QC_COUNT" header="QC_COUNT" visible="true" searchable="true" data-type="integer">
<DisplayFieldElement name="Field1" schema-element="xnat:qcManualAssessorData" xdat-type="COUNT"/>
<Content type="sql">COALESCE(@Field1,0)</Content>
</DisplayField>

Task: Run an XNAT Report Tool

1. cd
2. vi .xnatPass
3. Paste:
admin@localhost:8080/xnat=admin
4. cd /opt/xnat/workshop2012
5. hg pull -u
6. cd d3s2-reportandnotifcation/user-report
7. chmod +x *.sh
8. ./user-report.sh --days 1 -j BOGUS_OUA,BOGUS_UCV,BOGUS_GSU --experimentsOnly -t xnat:mrSessionData -h "BOGUS MR QC" -f ./qc_report.html

9. firefox ./qc_report.html

Reference Materials

XNAT Documentation:

Data visualization javascript tool: gRaphael

XNAT Discussion Group: Gabriele's presentation of Advanced Image QC