2005 FBIRN Meeting

WelcomeFBIRN 2005

Housekeeping

Coffee breaks at 10:30 and 3 pm• Please keep these to 15 minutes

Lunch down the hall and on the patio at noon Wireless connection instructions

Wiki page: http://www.na-mic.org/Wiki/index.php/FBIRN:retreat2005

Please set cell phones and pagers to silence

Goals for this meeting

NO PINK SHEETS

Goals for this meeting

Review current progress • Identify current obstacles

• Set action plan to achieve specific aims

Do good science & have fun!

FIRST BIRN Specific Aims (2002-2005)

Aim 1 Develop, standardize, and cross-validate common activation tasks, acquisition methods, and data analysis (consortium test bed protocol).• Aim 1.1 Identify, measure, and minimize inter-site variability

when performing cross-site fMRI studies of healthy controls and patients with schizophrenia using the consortium test bed protocol.

Develop methods to compare functional imaging data set using different magnet strengths and acquisition strategies.

Develop methods to compare functional imaging data set using similar but not identical experimental designs (e.g., Sternberg versus N-back paradigm).

Aim 1.2Facilitate comparison of unique site-specific cognitive activation paradigms, imaging acquisition methods, and data analysis strategies to the consortium test bed protocol. Develop methods to correlate multiple functional imaging data sets collected in the same subjects and across subject populations.

FIRST BIRN Specific Aims (2002-2005)

Aim 1 Develop, standardize, and cross-validate common activation tasks, acquisition methods, and data analysis (consortium test bed protocol).• Aim 1.1 Identify, measure, and minimize inter-site variability

when performing cross-site fMRI studies of healthy controls and patients with schizophrenia using the consortium test bed protocol.

Develop methods to compare functional imaging data set using different magnet strengths and acquisition strategies.

Develop methods to compare functional imaging data set using similar but not identical experimental designs (e.g., Sternberg versus N-back paradigm).

Aim 1.2Facilitate comparison of unique site-specific cognitive activation paradigms, imaging acquisition methods, and data analysis strategies to the consortium test bed protocol. Develop methods to correlate multiple functional imaging data sets collected in the same subjects and across subject populations.

FIRST BIRN Specific Aims 2002-2005

Aim 2 Integrate morphometric methods developed by the Morphometry BIRN into fMRI studies (ie the time domain). Modify and extend into the time domain the Morphometry BIRN common set of database tools and computational resources used across partner sites.

Aim 2.1 Develop common open-source libraries and conversion utilities to enable reading and writing of raw and analyzed data, including image volumes, statistical parametric maps, surface geometries, segmentation/parcellation results, ROIs, and deformation/warping parameters.

Aim 2.2Make necessary modifications and extensions to the existing software tools to interface with the SDSC Storage Resource Broker Architecture, and take advantage of the computational resources that will be available through the National Partnership for Advanced Computational Infrastructure and Internet2.

Aim 2.3 Develop data models such that results of analysis and other forms of derived data can be queried, and integrated amongst the fMRI BIRN and morphometry BIRN sites.

FIRST BIRN Specific Aims 2002-2005

Clinical Aims Aim 3. To study brain functioning in schizophrenia with

standardized cognitive tasks and fMRI procedures (consortium test bed paradigm) with demonstrated inter-site and test-retest reliability.

Aim 4. To investigate specific regional brain dysfunction in schizophrenia.• Aim 4.1 To determine whether cognitive impairments in

schizophrenia involve both working memory / executive dysfunction and early auditory cortical processing.

• Aim 4.2To determine whether the same set of cognitive functions (e.g. working memory/executive functioning and early cortical auditory processing) are similarly altered in groups of schizophrenic patients differing in symptoms and illness course.

FBIRN Goals: Federated Database System, circa 2005

fMRI

Are chronic, but not first-onset patients, associated with Are chronic, but not first-onset patients, associated with superior temporal gyrus dysfunction?superior temporal gyrus dysfunction?

IntegratedIntegrated ViewView

Receptor Density ERP

WebWeb

PubMed, Expasy;

Brain Map fMRIDC

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Structure

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Clinical

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MediatorMediator

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ARIP - 20MG ARIP - 30MG RISP - 06MG PLACEBOTreatment Group

Current State of the FBIRN

Phase I Data: • Processed using FSL Image Processing Pipeline (FIPS)• Uploaded for FBIRN sharing• Published in several reviewed papers, numerous conference

presentations Zou KH, Greve DN, Wang M, Pieper SD, et al. (2004). A prospective multi-institutional study

for the reproducibility of fMRI: a preliminary report from the Biomedical Informatics Research Network. Lecture Notes in Computer Science, Springer: Berlin, 2004, 3217: In Press.

Zou KH, Greve DN, Wang M, Pieper SD, et al. (2005). Factors Impacting the Reproducibility of Functional MR Imaging: Preliminary Results of a Prospective Multi-Institutional Study by the Biomedical Informatics Research Network. Radiology, In press.

Kim, S. et al. (2005) Parametric response surface models for analysis of multi-site fMRI data. Manuscript submitted.

33 conference posters, seminars, presentations, five conference proceedings published and four other papers submitted

• Scheduled for upload via standard scripts for public sharing

• FBIRN deliverable: Intersite calibration and corrections recommendations

Current State of the FBIRN

Phase II data collection underway• Cognitive tasks: Auditory Oddball and SIRP• Calibration tasks: Sensorimotor and breaththold• Continued agar phantom scans weekly• Clinical assessments:

SCID Non Patient Version and Patient Version Deficit Syndrome Scale Premorbid Adjustment Scale Socioeconomic Scale Fagerstrom Smoking Scale, Family History Scale FIGS, Edinburgh

Handedness Inventory CALGARY InterSePT Scale SANS and SAPS, and Modified PANSS Questionnaire Quick Mood Scale (used immediately before and after each scanning session) AIMS, BARNES SCALE. SIMPSON ANGUS

• Genetic samples: BDNF, COMT, D2DR, D1DR, etc. Number of subjects collected so far: 27, with ten from Iowa alone!!

Current state of the FBIRN

To be finalized: How to combine these Phase II datasets for analysis, visualization, and datamining

Infrastructure and tool development: • Clinical assessment layouts: The clinical HID has

been extended to include Phase II assessments

• Improved GUI for data input and missing data • Improved directory hierarchy on SRB for generic storage

and retrieval• Image processing pipelines for standardized analyses• XML-based event description for fMRI experiments• Slicer extended to include fMRI time-series

HIDB

SRB

FBIRN as a collaboratory

The effects of technology on scientific interaction:• Interactions with Cal-(IT)2

VTC use assessment: More input needed by 2 pm VTC usage and feedback survey is in your booklet

Demos of further collaborative VTC augmentations Tuesday at 1 pm

FBIRN External Collaborations

Morph BIRN• FBIRN adopting ADNI 3T protocols as much as possible• T1 scans from Phase II will help Morph BIRN test 3T

protocols for segmentation• So far, success!

T1 scan from MN 3T

FBIRN External Collaborations

BIRN GCRC interactions• BWH: Cardiac imaging and Slicer extensions

• BWH: Intersite variability assessment• Wisconsin: Agar Phantom Calibration• San Antonio (BrainMap): Experimental Design

Taxonomies

Cardiac Perfusion Study

Network for Translational Research Optical Imaging (NTROI)

A multi-site consortium developing optical imaging methods for breast cancer

• Comparing to CT, MRI, and the “gold standard” of biopsy results.

Optical imaging data from breast mammography on fifteen cancer subjects with multiple visits were input into the BIRN HID.

The data consisted of demographics, clinical assessments, and summary optical data on hemoglobin, oxygenated hemoglobin, oxygen saturation, fat fractions, among others.

These data are not at all similar in content to the clinical and behavioral assessments of the FBIRN, but the HID schema successfully incorporated them. The data were made available to researchers via the HID GUI and searchable by any criteria among the stored data.

National Alliance for Medical Image Computing (NAMIC)

Wiki page hosting NA-MIC in cooperation with mBIRN and fBIRN

modified Slicer for fMRI data NA-MIC will be made increasingly more stable for

post –processing Future DTI package for Slicer Example of leveraging different efforts that

contribute to one whole

Treatment Unit for Research on Neurocognition in Schizophrenia: TURNS

NIMH-funded network of seven sites Consortium for clinical studies of pharmacological

agents to enhance cognition in schizophrenia They wish to use fMRI as a biomarker

Calibration, intersite correction, data base and data sharing possibilities for collaboration

Discussion at 4 pm today

Agenda

Monday AM• 9:30-10:30 Statistics Working Group presentations

• 10:30 Coffee break! (and again at 3pm)Data Blitz: Please bring slides to computer up front

• 10:45 -11:30 IT Working Group presentations

• 11:30 -12:00 Data Blitz

Monday PM• 1 – 5 pm Clinical Working Group (BIRN offices)

• 1:30 – 5pm IT Working Group (Board Room)

• 2 – 4 pm Calibration/Statistics discussion: QA and calibration tools (Huntington)

• 4 – 5pm TURNS discussion (Huntington)

• 4 – 5pm Experimental Design Taxonomies (Atrium)

• 5 pm Plenary session (need title!)

Agenda

Tuesday AM• Breakfast 8 am• 8:45 One slide summaries of previous discussions: IT,

Calibration, Taxonomies

• 9-10 Clinical data and the HID: How-to’s

• 10-10:30 FSL Image Processing Pipeline: Imaging Data

• 10:30 Coffee break! (and again at 3 pm)

• 10:45 -11 FSL Image Processing Pipeline

• 11 -12 FBIRN Statistical Discussion for Phase II plans

Tuesday PM• 1 – 2 pm VTC: Demonstrations and review

• 2 – 5pm IT Working Group (Board Room)

• 2 – 5pm Continued Working Group discussions: How do we achieve our specific aims? (Huntington and Atrium)

• 3:30 pm TURNS teleconference (TBA)

• 5 pm Integrated review of milestones for the next few months

Statistical Goals from Oct 2004

Deliver a standard, preprocessed and fully processed Phase I dataset for FBIRN use immediately. • The IT Phase I re-upload using the Image Processing Pipeline will

provide a standard dataset also for public use.

Apply the reliability toolkit developed so far to the standard dataset to publish final reliability measures. • Variance components, STAPLE, generalizability and their

comparisons.• Make the toolkit available to the scientific community.

In conjunction with the Calibration group, use the full toolkit of reliability measures to compare the effects of differential pre-processing.• Smoothing effects as the top priority• Publish best practices

Cog Challenge Group Goals

Evaluate Phase II SIRP design• Did the inclusion of three working memory loads differentiate

schizophrenic and control samples? With and without intersite calibration

Evaluate Phase II Auditory Oddball task• Did temporal lobe activation differentiate schizophrenic and control

samples?

Cross-task generalizability for Phase II data• Were similar patterns of dorsolateral PFC activation observed in both

SIRP and Oddball tasks?

FBIRN Informatics MilestonesFBIRN Informatics Milestones

Database Schema• Insert functions for PostgreSQL instance• Official documentation (user manual, testing, etc) • Official release (HID 1.0) • CVS reorganization/integration of mBIRN/fBIRN

Graphical User Interface• Double entry assessment forms, conflict forms • Phase II assessment forms • Interface options for intentionally blank data items • Mediator integration

XML Schema• Packaged fMRI visit (images+assessments+behavioral data) • Packaging of SRB metadata

Upload Scripts• Raw data human upload script • Upload script + XML metadata integration• BIRNDUP integration into workflow with upload script

By 5 pm Tuesday

Each group delivers their action plan/milestones to achieve current goals• Phase I publication plan and public access• Phase II—Intersite calibrations on 5 normals and Sz• Calibration Toolkit release date• Best practices release date: Calibration corrections, Image processing

pipeline• IT developments

Phase I final uploads Phase II uploads and derived data storage Mediated queries on Phase I and Phase II data, and derived data

• External collaborations GCRCs: Wisconsin, BWH, San Antonio Experimental Taxonomy Development plan: San Antonio, fMRIDC, NLM TURNS

Fun

Reception at 6 pm Banquet here at 6:30 tonight Croquet!! All free time…

BRAINS/Slicer Workshop• Wednesday: 8:30 am to 5 pm • Social Sciences Tower Room 220B• Breakfast is not served but lunch is!