xnat project intake

XNAT Project IntakeJune 25, 2012

Jenny [email protected]

SEA-XNAT @ WashU• Central Neuroimaging Data Archive• Created by a group of neuroimaging

researchers from a Wash U local neuroimaging database called the “CAP”

• In 2004 Dan Marcus and his team released a version of generalized SEA-XNAT source code as “XNAT” an open source neuroimaging archive tool.

SEA-XNAT Vital Stats• Currently running on XNAT 1.5.3• 800 Projects• 16,000 Subjects• 20,000 Imaging Sessions• 200 Active Users• 100 New Experiments/Week

SEA-XNAT Team • 1 Operations Lead: Jenny Gurney• 3 Java/Web Developers– Lauren Wallace– Joel Balestra– James Ransford

• 1 Pipeline Developer: Mohana Ramaratnam (NRG India)

• 1 Dedicated Help Desk Associate: Jeanette Cline• 1 SEA-XNAT Intern: Shamima Walton

SEA-XNAT Tools• SEA-XNAT Help Desk Tickets: FogBugz• SEA-XNAT Help Wiki: SEA-XNAThelp.wikispaces.org• Wire Frames: ProtoShare• Flow Charts: LucidChart• Code Repository: Mercurial (bitbucket.org)

repositories– nrg/SEA-XNAT_xnat_prod (projects directory)– nrg/SEA-XNAT_scripts (various scripts used for SEA-XNAT

operations)• Development Environment: Eclipse• Collaboration: GoogleTalk, Google Hangouts, and

Webex

SEA-XNAT XNAT Customizations• Data Types, Forms and Uploaders: Lauren, Joel,

Mohana, Jenny• Reports: Lauren, Joel, Mohana, Jenny• Pipelines: Mohana, Lauren• Notification tools: Lauren, Mohana, Joel• Project sharing script: Joel, Jenny• Bulk image upload/download script: Jeanette,

Jenny• Bulk anonymization scripts (DICOM and Siemens

IMA): James• XNAT Modules: James, Mohana

Welcome to SEA-XNATCongratulations! 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.

BOGUS StudyThe BOGUS study will be doing a lot of imaging and is interested in storing their data in the SEA-XNAT. You are meeting with the primary investigator (PI) of the BOGUS study to gather requirements for their intake into SEA-XNAT.

The BOGUS Study• Big Open Group Unified Study • Studies Freud’s ego, super-ego, and id

through brain imaging• Draws its hypotheses from a 2012 study of

24 male teenage subjects, 17 of whom were removed from the study for not following instructions or falling asleep in the scanner.(Fisher, Steven Z. and Student, Steven T (2012), “A Triple Dissociation of Neural Systems Supporting ID, EGO, and SUPEREGO.” Psyence, 335, 1669.)

But seriously…• Have fun (this is meant to be an

icebreaker)• Participate!• Ask questions

BREAK INTO GROUPS• Meet the PIs, check the back of your

name tag for your number• Amenities• Meet back here at 11:15am to

discuss the results.

Which institutions will be collecting data?Oceanic University, Atlantis (BOGUS_OUA)University College Valhalla (BOGUS_UCV)Gotham State University (BOGUS_GSU)

Which institutions will be collecting data?Why do we ask this?• To gauge how many projects we might want to

create in our XNAT for the study. Multiple sites collection data often means multiple projects.

• To determine appropriate methods for uploading DICOM. – XNAT 1.6 Feature: Anonymization through all DICOM

upload methods + site wide anonymization Will be covered Day 2, Session 2: Data Upload and Entry (Lead: Kevin)– Direct DICOM send from scanner convenient, but for

security reasons, DICOM sends should only be done within an institution.

What modalities of imaging data will you be collecting?

• 3T MR• PET with FDG tracer

What modalities of imaging data will you be collecting?

• Confirm that base XNAT has all required imaging data types

• Determine whether the same data type will need to be used for two different types of scans– ie. PET with different tracers is pretty common

If same data type is used will cause complications in reporting, may require custom queries for search Will be covered Day 3, Session 2: Reporting and Analysis (Speaker: Jenny)

What kind of QC will you do on the imaging?

• Image Validation• Manual QC

What kind of QC will you do on the imaging?

• Image Validation XNAT 1.5.3 Feature: Pipeline for validation of imagesXNAT Day 1, Session 2: Project Configuration / Image Validation (Speaker: Mohana)

• Manual QC– XNAT has manual QC type– Implies possibly creating an additional

project for failed scans

Will you be collecting demographic data?

• Demographics– Gender– Handedness– Education– Race– Ethnicity– Year of Birth– Blood type

Will you be collecting data other than imaging?

Demographics• Determine whether the default XNAT

subject demographics fields will suffice.• If it’s just one or two fields we’re missing,

we can use project-specific custom variables to cheaply extend a data type.Custom variables will be covered in Day 1, Session 2: Project Configuration


• NIH Stroke Scale• EGO Master


NIH Stroke ScaleEGO Master

• Discover new data types which will need to be added to SEA-XNAT and work needed.

• Determine whether these data types are common and already exist in the Marketplace or if we’ll have to model them ourselves.

XNAT 1.6 Feature: Modules + XNAT Marketplace

Will be covered Day 2, Session 1: System Configuration and Customization (Lead: Rick)

How/Who do you envision uploading each data type into the SEA-XNAT?

• Scanner techs and clinicians/study coordinators should upload the imaging scans. However, they are only on the IRB for their own site. Must not see other sites’ data.

• Clinicians/study coordinators need forms to enter their demographics and the NIHSS.

• EGO Master online testing tool outputs a csv file. Would be nice to easily upload this.


Scanner techs and clinicians/study coordinators should upload the imaging scans. However, they are only on the IRB for their own site. Must not see other sites’ data.• Determine whether a project for each site

is required.• Determine users who will need access to

each project and at what level: Coordinator/Member/Owner


Clinicians/study coordinators need forms to enter their demographics and the NIHSS.

• Determine whether edit and report forms are required a new data type.Will be covered in Day 2, Session 1: System Configuration and Customization (Lead: Rick)


EGO Master online testing tool outputs a csv file. Would be nice to easily upload this.

• Determine whether the XNAT Spreadsheet Uploader tool could be used to input some of the data.Day 2, Session 2: Data Upload and Entry (Lead: Kevin)

Can we please get a sample of each type of data from each site?

• Imaging sessions (MR and PET) from each site

• Demographics• NIH Stroke Scale• EGO Master Spreadsheet


Imaging sessions (MR and PET) from each site• Determine scanner types: Siemens, Philips, GE. Occasionally

processing code needs to operate differently on data from different scanners.

• Determine whether there is PHI in private fields which will need to be scrubbed.Day 2, Session 2: Data Upload and Entry (Lead: Kevin)

• Derive correct values for Image Session Sequence Validation from DICOM.Day 1, Session 2: Project Configuration / Validation Schematrons (Mohana)

• Determine whether sessions are so large they could cause performance issues during upload.


Demographics

• Determine whether values for fields are compatible with current demographics data type and form.


NIH Stroke Scale• Determine whether the data actually

collected by the study will work in the data type available in Marketplace.Day 2, Session 1: System Configuration and Customization (Lead: Rick)


EGO Master Spreadsheet• Use values in spreadsheet to model new data

type and display document listings.Day 2, Session 1: System Configuration and Customization (Lead: Rick)

• Determine whether CSV Uploader is feasible with this data:– No unbounded types– One project at a timeDay 1, Session 2: Project Configuration (Lead: Tim)

What kind of processing will need to be done on your imaging data?

• Convert DICOM to NIFTI• DICOM dump to text file

What kind of processing will need to be done on your imaging data?

Why do we ask?• Determine whether pipelines exist already in

our deployment of XNAT• Determine source of processing tools:– Standard tools (eg. FSL, FreeSurfer)– Tools provided by study (eg. An in-house DTI

processing pipeline that they would like to be able to launch within XNAT)

– New tools written by the SEA-XNAT siteDay 3, Session 1: Pipelines (Lead: Mohana)

Do you have clearly defined visits or encounters in your study?

• Baseline Visit Data Protocol (v00) 3T MR PET-FDG Demographics EGO Master 3.7 NIH Stroke Scale

• One Year Follow-Up Visit Data Protocol (v01) 3T MR EGO Master 3.7 NIH Stroke Scale

Do you have clearly defined visits or encounters in your study?

Why do we ask?• XNAT is about to release visit and protocol support.

Will help studies validate that visits are complete or track why items are missing.Day 1, Session 2: Project Configuration – Visits and Protocols Discussion (Jordan)

• Determine whether we have longitudinal reports. Must have a pivot data type that will always be present.Day 3, Session 2: Reporting and Analysis (Lead: Will)

• Consider incorporating visit label into experiment labels.

Can we define some standardized labels now for your subjects and data?• Subject Label Format: <site_abbrev>_nnn• Subject Label Example: OUA_001• MR Label Format: <subject_label>_<visit_label>_mr• MR Label Example: OUA_001_v00_mr• PET Label Format: <subject_label>_<visit_label>_pet• PET Label Example: OUA_001_v00_pet• EGO Master Label Format:

<subject_label>_<visit_label>_ego• EGO Master Label Example: OUA_001_v00_ego• NIH Stroke Scale Label Format:

<subject_label>_<visit_label>_nihss• NIH Stroke Scale Label Example: OUA_001_v00_nihss

Can we define some standardized labels now for your subjects and data?Why do we ask?• Data is better organized and “self-

documented”.• To prevent a lot of work later helping

site to relabel experiments or subjects. When you rename a session, XNAT must move files to a new directory, so there is a lot of potential for problems.Day 1, Session 2: Project Configuration (Lead: Tim)

Will you need to grant access to data to people outside your study? Will anyone at a site ever be allowed to see other sites’ data?• Outside investigators can request

access and be granted access to QC’ed data.

Will you need to grant access to data to people outside your study? Will anyone at a site ever be allowed to see other sites’ data?

Why do we ask?• Through XNAT sharing of resources,

we have the ability to display limited data sets to select groups of people.Day 1, Session 2: Project Configuration (Lead: Tim)

Does your team need any kind of notifications from SEA-XNAT.

• Our third party QC groups need to be notified immediately when new image sessions arrive in the SEA-XNAT.

• Our PIs would like to be notified of new EGO Master and NIH Stroke Scales in an email once a week.

Does your team need any kind of notifications upon upload of data into the SEA-XNAT.

Why do we ask?• Determine whether existing tools can

provided required notifications to users.Day 3, Session 2: Reporting and Analysis (Jenny will present)

What kind of reports or work lists would you like to see in the SEA-XNAT? Do you have any examples you can give us?• Data freeze spreadsheet containing

data across all data types, some columns are calculated from other columns

• Work list for QC people• Visualize EGO Master data versus

NIH Stroke Scale data

What kind of reports or work lists would you like to see in the SEA-XNAT? Do you have any samples you can give us?Why do we ask?• Determine whether heavy customization of

display documents will be necessary for derived or unbounded variables.

• Use samples to map out data types and columns to be used in the display of each report column.

• Determine whether XNAT needs to be customized for charts and graphics.Day 3, Session 2: Reporting and Analysis (Lead: Will)

Evaluating Cost Feasibility• Funding source• Data size and duration• New data types– Size– Reusability

• New processing pipelines– Additional tools and/or licenses required– Heterogeneity of scanner data

Common pitfallsPitfall Mitigation

Sites added after initial intake Stay in contact with study PIs

New untrained users after initial intake

Plan for ongoing user training at intake

Requirement flux Use wireframing to plan. Have PI sign-off on all designs

Heterogeneity of multi-site data

Obtain complete set of sample data for all sites.

Hard to find PHI in imaging sessions

Obtain complete set of sample data for all sites.

Thanks!

Jenny [email protected]

xnat project intake

Documents

seaxnat vital statscurrently

fogbugzseaxnat help

bogus studythe bogus

atlantis bogus

data upload

kevindirect dicom

oceanic university

multiple projects