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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

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