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:
- https://flywheelio.atlassian.net/wiki/spaces/XNAT/pages/2507810313
- Codex: https://flywheelio.atlassian.net/wiki/spaces/XNAT/pages/2507810217
Data visualization javascript tool: gRaphael
XNAT Discussion Group: Gabriele's presentation of Advanced Image QC