XNAT Workshop 2012 - Project Intake

Goal

To explore in depth the process of gathering requirements to successfully board a multi-site study into an existing deployment of XNAT.  Everyone will get a chance to meet with a primary investigator (PI) of the BOGUS study to extract the information necessary to complete the configuration, customization, data entry, and reporting tasks scheduled for the rest of the XNAT Workshop Admin Track.

The BOGUS project data is what we will use as a basis for all the talks in the Admin track.  We encourage people to participate as much as possible in this exercise. 

Video

Welcome to SEA-XNAT! Introduction to the BOGUS Project.

Project Intake Process: A Walkthrough. Contains the questions and answers from our "PI Interviews" for the BOGUS project in the XNAT Workshop.

Avoiding Common Pitfalls with the Project Intake process.

Resources

Tasks

Participate in a real life (well, sort of) scenario to add a new multi-site study's data to your XNAT instance.  We break into groups and interview the PI for the BOGUS Study.  Although this session is meant to be fun and a good way to meet other folks at the workshop, it is also intended to be a thorough examination of the details and pitfalls of project intake in a large multi-project XNAT environment.

I.  Welcome to SEA-XNAT

Congratulations!  You now work for SEA-XNAT, a deployment of XNAT at Oceanic University, Atlantis.  The SEA-XNAT is a brand new vanilla deployment of XNAT’s fantastic new 1.6 release. 

SEA-XNAT includes all the great features you have come to know and love in XNAT plus the additional features from releases 1.5 and 1.6 listed below:

XNAT 1.5

• Multiframe DICOM data:  Ability to archive and access in XNAT.  We are still fine tuning how some of the specific headers should be persisted, but this will be an ongoing process.
• Uploader Applet:  Refactored to send DICOM data over HTTP (rather than the DICOM protocol). It uploads data scan by scan as zips to improve reliability.
• Prearchive:  The Prearchive UI has been completely rewritten to support sorting, filtering and bulk actions.  Also, now accessible and manageable via the REST API.
• Image session merging:  Merge new content into existing sessions.  Users should be able to upload additional data to existing sessions, without eliminating pre-existing data. This includes adding new scans to existing sessions, and new files to existing scan id.
• DICOM server:  Incorporated into XNAT itself.  The XNAT server should support the receipt and storage of DICOM data sent via DICOM C-STORE.
• User cache space:  Add a user cache space for temporary storage of user files (via REST).  Users can now upload data into a user specific cache space via REST, for usage later on.
• New in XNAT 1.5.4:  Secured XNAT against cross-site request forgery (CSRF) attacks.

XNAT 1.6

• Modules!  Allows overriding and extending XNAT's functionality through the use of packaged modules.  Also, announcing XNAT Marketplace https://marketplace.xnat.org where XNAT admins can download XNAT modules and XNAT tools.
• Multiple DICOM SCP receivers:  Different scanners can send to different DICOM ports.
• Security and authentication enhancements:  Includes local database and multiple LDAP authentication, password complexity and expiration, and better protections against various security exploits
• Email support:  Support for SMTP credentials and encrypted transport for mail transfer (including pipelines)
• Anonymization:  UI support for anonymization scripts
• Upload Applet:  Streamlined upload applet functionality
• User session timeout:  A time-out counter and warning
• Audit trail:  Enhanced data lifecycle tracking/reporting

II.  PI Interview with the BOGUS Study

Below is the basic information which was distributed during the PI project intake sessions.

A.  Institutions

Oceanic University, Atlantis (OUA)

Project Abbreviation/ID:  BOGUS_OUA

Project Running Title:  OUA BOGUS Study

Project Title:  BOGUS Study at Oceanic University, Atlantis

Project Description:  The  Oceanic University, Atlantis site data for the Big Open Group Unified Study.

Keywords:  SUPEREGO, psychoneurobabble, Oceanic, Atlantis

Alias:  7048

Site PI:  Lucille Ostero

• MR:  Siemens, DICOM
• PET:  Siemens, ECAT

University College Valhalla (UCV)

Project Abbreviation/ID:  BOGUS_UCV

Site PI:  Bob Loblaw

Project Running Title:  UCV Bogus Study

Project Title:  BOGUS Study at University College Valhalla

Project Description:  The University College Valhalla site data for the Big Open Group Unified Study.

Keywords: SUPEREGO, psychoneurobabble, Valhalla

Alias:  7055

• MR:  Philips, DICOM
• PET:  Philips, DICOM

Gotham State University (GSU)

Project Abbreviation/ID:  BOGUS_GSU

Site PI:  Barry Zuckerkorn

Project Running Title:  GSU BOGUS Study

Project Title:  BOGUS Study at Gotham State University

Project Description:  The Gotham State University site data for the Big Open Group Unified Study.

Keywords: SUPEREGO, psychoneurobabble, Gotham

Alias:  6318

• MR:  GE, DICOM
• PET failed qualification, will be down all year, subjects currently being sent to OUA

B.  Visit Protocol

Baseline Visit

Baseline Visit Label:  v00

Data Protocol

• 3T MR
• PET-FDG
• Demographics
• EGO Master
• NIH Stroke Scale

One Year Follow-Up

One Year Visit Label:  v01

Data Protocol

• 3T MR
• EGO Master
• NIH Stroke Scale

C.  Data

Subject demographics

Data type:  xnat:subjectData

Exists already in XNAT:  yes

       Subject Label Format:  <site_abbrev>nnn

Subject Label Example:  OUA001

To be stored in the Subject data type:

• Gender
• Handedness
• Education
• Race
• Ethnicity
• Year of Birth
• Blood type – Will need to be a custom variable on xnat:subjectData

Imaging

MR

Data type:  xnat:mrSessionData

Exists already in XNAT:  yes

MR Label Format:  <subject_label>_<visit_label>_mr

MR Label Example:  OUA001_v00_mr

PET

Data type:  xnat:petSessionData

Exists already in XNAT:  yes

PET Label Format:  <subject_label>_<visit_label>_pet

PET Label Example:  OUA001_v00_pet

Tracer:  FDG

Only administered at first visit

Imaging QC

Manual QC

Data type:  xnat:qcManualAssessorData

Exists already in XNAT:  yes

Processed Imaging

DICOM to NIFTI

Pipeline to create nifti files from dicom files.  Files will be stored on file system under same directory as dicom and will be available for download through REST or GUI.  Other processing tools take only nifti files as input.  Files are only output.  No other data stored.

DICOM dump to text file

For a DICOM imaging session, dump contents of one file to text.  Store this file in the session directory to be available for download through REST or GUI. Aids in checking for PHI.  Files are only output.  No other data stored.

Clinical

EGO Master

Tests for the presence and significance of ego indicators in subjects.  Only used by the BOGUS study.  Online test, so results output into a spreadsheet.

EGO Master Label Format:  <subject_label>_<visit_label>_ego

EGO Master Label Example:  OUA001_v00_ego

Administered at each visit.

NIH Stroke Scale

Systematic assessment tool that provides a quantitative measure of stroke-related neurologic deficit. Very well known tool.  Coordinators will enter this data.

NIH Stroke Scale Label Format:  <subject_label>_<visit_label>_nihss

NIH Stroke Scale Label Example:  OUA001_v00_nihss

Administered at each visit.

D.  Planned Data Entry

Imaging

• Valhalla and Gotham sites use upload applet
• Atlantis does DICOM Send straight from scanners

Imaging QC

• External groups will be performing QC on MR and PET.  Groups will enter results directly into SEA-XNAT form.
  

Demographics 

• Coordinators will enter data into base XNAT online form

Clinical data 

• NIH Stroke Scale
  
  • Coordinators will enter information into online form in XNAT.
• EGO Master
  
  • Users take a test at computer terminal, results output into a .csv.
  • Use spreadsheet uploader 

E.  Notifications

1. Alert MR QC team that new imaging sessions have been uploaded on a nightly basis.

2. Report to PIs any new clinical assessments (NIH Stroke Scale, EgoMaster) on a weekly basis. 
   

F.  Reporting

1. Worklist for MR QC group.
2. Data freeze spreadsheet containing data across data types.  DataFreezeReport.xlsx
3. Visualization of EGO Master data points versus NIH Stroke Scale data points (graphs, charts, scatter plot).