Function BIRN Science

FBIRN Goals

Develop multi-site functional neuroimaging tools.

Develop the capability to analyze, as a single data set, data acquired from multiple sites using tools developed from multiple sites.

Implications for clinical applications and FDA approvals in addition to research.

The FBIRN Aims

Calibration: – Assess and correct for the major sources of multi-site variation

Cognitive Tasks: – Develop robust protocols for multi-site fMRI studies

Analysis: – Develop methods to analyze multi-site fMRI data

Tools: – Develop a scalable IT application toolkit to support multi-site fMRI

studies

Dissemination: – Make the tools, procedures, and collected datasets widely available

Research Plan 2005: Series B/CSeries B+C Year 1 Year 2 Year 3 Year 4 Year 5

Calibration Steps 1 & 2 BH and ASL development

Steps 2 & 3 Improved & Optimized BH ASL

Steps 2&3 on FHRF Evaluation Evaluation and Dissemination

Cognition Steps 1 & 2 Cognitive Task Development

Steps 2 & 3 Improvement & Optimization

Evaluation Evaluation and Dissemination

Step 3: Normals on the East Coast

Step 3 Normals on the East Coast

Traveling Subjects

Normals and Sz on the West Coast:

Normals and Sz on the West Coast:

Six Site Data Collection: IA, NM, Yale, Duke, UCI, UCLA

Step 4

Stats Analysis Phase 2 (Series A) analysis

Step 3 analysis Step 4 Analysis

Tool Development

HID usability improvements; FIPS inclusion; XML extensions and initial ontology building

HID query optimizations; Integrating Calibration requirements

LONI; Workflow queries; AFNI extensions to FIPS; etc.

Optimize query and analysis indexing; improved queries for machine learning; etc.

Evaluation and Dissemination

You Are Here

March 2008: 3rd year Progress Report due!!

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FBIRN IT - We’re Up and We’re Mediated!

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•Last year

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FBIRN IT - We’re Up and We’re Populated

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Duke: 67BWH: 22MGH: 12UCLA: 54UCSD: 6UCI: 71UNM: 57UI: 64UMN: 57Yale: 66

Duke: 67BWH: 22MGH: 12UCLA: 54UCSD: 6UCI: 71UNM: 57UI: 64UMN: 57Yale: 66

419 Subject 419 Subject VisitsVisits

419 Subject 419 Subject VisitsVisits

3174 Subject 3174 Subject AssessmentsAssessments

3174 Subject 3174 Subject AssessmentsAssessments

•This year

What have we learned from Phase II?What have we learned from Phase II?

QC of uploaded datasetsQC of uploaded datasets– Differences between formal protocol and what was Differences between formal protocol and what was

actually doneactually done

Importance of interoperability of datasets with Importance of interoperability of datasets with analysis toolsanalysis tools

Keeping track of what you have done- data Keeping track of what you have done- data provenanceprovenance

Keeping terms straight- database semantic markupKeeping terms straight- database semantic markup

Neuroinformatics progress

Last fall’s milestone: Wrap and query BrainMap (non HID and not BIRN); GCRC

This fall: BrainMap wrapped and registered. Mediated queries underway!

Neuroinformatics progress

Programmers Week, May in Iowa

•See also the posters later today

•HID Interface HID Interface improvementsimprovements•HID, CALM code HID, CALM code walkthroughswalkthroughs•Protocols added to Protocols added to database schemedatabase scheme•XCEDE 2.0XCEDE 2.0

•Integration of Integration of Freesurfer Freesurfer derived ROIsderived ROIs

•Webservices/portlets Webservices/portlets trainingtraining

The FBIRN Aims

Calibration: – Assess and correct for the major sources of multi-site variation

Cognitive Tasks: – Develop robust protocols for multi-site fMRI studies

Analysis: – Develop methods to analyze multi-site fMRI data

Tools: – Develop a scalable IT application toolkit to support multi-site fMRI

studies

Dissemination: – Make the tools, procedures, and collected datasets widely available

User Query

FIPS Results

FMRI ImagesAutomated Image Upload to SRB/HID for sharing •FIPS: FSL Image

•Processing Scripts

FBIRN Neuroinformatics VisionFBIRN Neuroinformatics Vision

HIDB

SRB/Local

fMRI Scanner

•Clinical Data•Computer Aided Scale Input(CALM/GAME)•Clinical Data Entry Interface

URL links

fMRI Scanner

Demographic Information

Diagnostic GroupSchizophrenia Healthy Volunteers

N with images 53 60

Female/Male 21/27 27/29

Age (years) 36.6 + 10.8 34.8 + 10.8

Significant Main Effect of Diagnosis: AudOdd with Smooth To

Significant Main Effect of Diagnosis: AudOdd with Smooth To

Site effects minimized

MAGH

ICA of Phase I Data

Novel analysis developments: fMRI Activation Pattern

• Spatial correlation of activation across voxels

– bell shapes in local regions • location of the activation centers

• size of peak activations

• area of the local activation cluster

Beta C

oefficien

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Whole brain 2D slide of β-map

(Sensorimotor task)

Thresholded results (incomplete)

Surface results

QA Tool Summary into HID

Summary of Analysis Achievements

• Implementation and testing of a NIfTI compatible fBIRN image analysis pipeline (FIPS)

• Completion of a multicenter image upload and processing cycle using SRB, BIRN upload and download tools, fBIRN data base, fBIRN file structures, and fBIRN processing tools

• Significant progress in completing quality assurance analyses of Phase II images

• Initiation of multicenter analyses aimed at testing clinical hypotheses about abnormal brain function in schizophrenia.

The FBIRN Aims

Calibration: – Assess and correct for the major sources of multi-site variation

Cognitive Tasks: – Develop robust protocols for multi-site fMRI studies

Analysis: – Develop methods to analyze multi-site fMRI data

Tools: – Develop a scalable IT application toolkit to support multi-site fMRI

studies

Dissemination: – Make the tools, procedures, and collected datasets widely available

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Scrambled images

Negative distracters

Neutral distracters

Memoranda

Forced Choice

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Working Memory for Words Design

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SCZ - Neutral

The FBIRN Aims

Calibration: – Assess and correct for the major sources of multi-site variation

Cognitive Tasks: – Develop robust protocols for multi-site fMRI studies

Analysis: – Develop methods to analyze multi-site fMRI data

Tools: – Develop a scalable IT application toolkit to support multi-site fMRI

studies

Dissemination: – Make the tools, procedures, and collected datasets widely available

Reduction in Site and Subject Variance After Adjusting for Smoothness

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The Effect of Adjusting for Site Differences inSignal-to-Noise-Ratio (Temporal)

Friedman, Glover & The FBIRN Consortium, 2006 (Nov), NeuroImage

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3.5 ≤ t ≤ 10

vol = 1.24 @ p .001 vol = 1.0

BH Calibration: Group Activation

M. Thomason et al. 2006

BH Calibration: Inspiration control

no control

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CBF can effect the amplitude & shape of the BOLD signal

ASL- quantitative rCBF maps

Selected Highlights Only

Be sure to see the posters in the Hall

The FBIRN Aims

Calibration: – Assess and correct for the major sources of multi-site variation

Cognitive Tasks: – Develop robust protocols for multi-site fMRI studies

Analysis: – Develop methods to analyze multi-site fMRI data

Tools: – Develop a scalable IT application toolkit to support multi-site fMRI

studies

Dissemination: – Make the tools, procedures, and collected datasets widely available

Dissemination

Web tutorials available: www.fbirntutorials.com

More tools and data available for download:

FBIRN Traveling Subjects Dataset (Phase I): Deidentified versions of the imaging and demographic datasets, now

with behavioral data of all subjects from many sites E-prime Programs used in data collection (Phase I and Phase II):

– The SIRP, MMN, Rest, Breathhold, Sensorimotor tasks, the Auditory Calibration and Reaction Time tasks for both Phase I and Phase II

Dissemination

FIPS 1.0 available with documentation and a training dataset

Updated BXH/XCEDE tools suite

External Collaborations:US: TURNSInternational: Phase 2 tools and paradigms to Italy, Norway and China

Invited presentations and abstracts this yearCalhoun, V.D., "Independent Component Analysis of BOLD fMRI Data" for ISMRM Educational Course on "Multi-Modal fMRI:

Physiology, Acquisition, and Analysis", May 2006.

Turner, J.A. (2006). Calibration strategies to improve data comparability. Optimizing fMRI approaches to Adolescent Mental Disorders, NIMH Workshop, August 17-18, 2006

Potkin, S.G. (2006). The Integration of Brain Imaging and Genetics: A Strategy to Study Neuropsychiatric Disease. University of Utah, Grand Rounds, September 5, 2006.

Yendiki, A., Wallace, S, Vangel, M., Clark, V., Lim, K.O., Andreasen, N., Greve, D., Manoach, D.S., Gollub, R.L. (2006). Multi-site characterization of an fMRI working memory paradigm: Reliability of activation indices. Annual Meeting of the Organization for Human Brain Mapping, Florence, Italy, June 11-15, 2006.

Kilpatrick, L.A., Fallon, J., Turner, J.A., Kennedy, J., Macciardi, F., Potkin, SG. (2006). Genetic Impact on Dorsolateral Prefrontal Functional Connectivity in Schizophrenics During a Working Memory Task. Annual Meeting of the Organization for Human Brain Mapping, Florence, Italy, June 11-15, 2006.

Turner, J.A., Stern, H., Friedman, L., Brown, G., Greve, D., Glover, G.H., Wible, C., Potkin, S.G., FBIRN. (2006) Variance reduction in multi-site functional imaging. Annual Meeting of the Organization for Human Brain Mapping, Florence, Italy, June 11-15, 2006.

Keator, D.B, Grethe, J., Ozyurt, B., Gadde, S., Wei, D., Turner, J.A., Potkin, S.G., Brown, G.G., McCarthy, G., Glover, G.H., Stern, H., Lauriello, J., Friedman, L., Belger, A., Lim, K.O., Pieper, S., Greve, D., FBIRN. (2006). Function Biomedical Informatics Research Network (FBIRN) Open Source FMRI Informatics, Calibration, and Data Tools Repository. Annual Meeting of the Organization for Human Brain Mapping, Florence, Italy, June 11-15, 2006.

Keator, D.B., Ozyurt, B., Wei, D., Gadde, S., Potkin, S.G., Brown, G., Morphometry BIRN, FBIRN., Grethe, J. (2006). A General and Extensible Multi-Site Database and XML based Informatics System for the Storage, Retrieval, Transport and Maintenance of Human Brain Imaging and Clinical Data. Annual Meeting of the Organization for Human Brain Mapping, Florence, Italy, June 11-15, 2006.

Polina Goland. Anatomically-Guided MRF Spatial Regularization Model for fMRI Detection. (Using FBIRN Phase I data) Annual Meeting of the Organization for Human Brain Mapping, Florence, Italy, June 11-15, 2006.

Manuscripts and Publications This YearThomason, M.E., Foland, L.C, and Glover, G.H. (2006) Calibration of BOLD fMRI using breath-holding reduces group

variance during a cognitive task. Human Brain Mapping, in press.

Friedman L, Glover GH (2006) Report on a Multicenter fMRI Quality Assurance Protocol. Journal of Magnetic Resonance in Imaging, 23:827-839.

Brown, GG and Eyler, LT. (2006) Methodological and conceptual issues in functional magnetic resonance imaging: Applications to schizophrenia research. Annual Review of Clinical Psychology, Vol. 2: 51-81

Friedman L., Glover GH, Krenz D, Magnotta V. FIRST BIRN. (2006). Reducing Scanner-to-Scanner Variability of Activation in a Multi-center fMRI Study: Role of Smoothness Equalization. Manuscript submitted.

Friedman, L., FBIRN. (2006). Intra-Scanner and Inter-Scanner Reliability in a Multicenter fMRI Study. Manuscript submitted.

Friedman L., Glover GH, FIRST BIRN. (2006). Reducing Scanner-to-Scanner Variability of Activation in a Multi-center fMRI Study: Controlling for Signal-to-Fluctuation-Noise-Ratio (SFNR) Differences. Neuroimage, in press.

Lee, C.P., Dourish, P., Mark, G. (2006). The Human Infrastructure of Cyberinfrastructure. Manuscript in press.

Kim, S, Smyth, P, Stern, H. (2006). A nonparametric Bayesian approach to detecting spatial activation patterns in fMRI data. Proceedings of the 9th International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), October 2006.

Kim, S, Smyth, P. Hierarchical Dirichlet processes with random effects. Advances in Neural Information Processing 19, in press.

Zou, KH, Bhagwat, JG, Wu, IY, Wells, WM, Jolesz, FA, Black, PM, Kikinis, R, Ohno-Machado, L, Talos, I. Statistical Designs of Neuroimaging Studies via Retrospective and Prospective Sample Size Calculations: An illustration on MR Guided Neurosurgery and Functional MR Imaging. Submitted to Academic Radiology special issue.

FBIRN Plans Continue

New and better multi-site Calibration methods– Using BH improvements– Using ASL

Broader multi-site Cognitive tasks– Efficient, combined tasks– Activating emotional and cognitive circuits, and

interactions

Improved multi-site Analysis methods and toolsPublicly available, mediated datasets for queries

and analysis