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fBIRN Image Processing Stream (FIPS) Douglas N. Greve MGH Martinos Center. FIPS Design Goals. Massive fMRI Analysis All Levels Query-Driven Facilitate Collaboration Calibration. A work in progress …. BIRN Data Hierarchy. Root (SRB). Directory Structure Naming Convention XML

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slide2

FIPS Design Goals

  • Massive fMRI Analysis
  • All Levels
  • Query-Driven
  • Facilitate Collaboration
  • Calibration

A work in progress …

slide3

BIRN Data Hierarchy

Root (SRB)

  • Directory Structure
  • Naming Convention
  • XML
  • Human Upload Script
  • SRB
  • FIPS “Database”
  • Well-Defined Rules

Project

Subject/BIRNId

Study

Visit

Series/Run

Analysis

K-Reconstruction

PixelData/XML

slide4

Analysis Levels

  • Preprocessing – MC, STC, B0, Smoothing, Brain Extraction, Registration
  • First Level – Estimate amplitude of HDR, Significance
  • Higher Levels
    • Visit, Subject, Group, Cross-Group, …
    • Fixed, Random, Mixed Effects
  • Stimulus Schedule – EPrime
  • FIPS Database and Web page
  • QA – All Levels (nothing in FIPS yet)
  • Mostly FSL-based
slide5

Analysis Configuration

Centralized vs Customized

  • Centralized/Global
    • Preprocessing and First-Level
    • High-Level Instructions
    • Do a few times
    • Assures same analysis
slide6

Automatic Analysis Customization

  • Low-Level Sources of Variance
    • Run, Visit, Subject, Site
    • Intended – Stimulus Schedule
    • Unintended, Known – Slice Timing
    • Unintended, Unknown – Smoothness, HDR, B0
  • Remove or Account for Automatically
    • Insulate the user
    • Starts with data upload – STC, EPrime; GIGO
    • Global Analysis Configuration (FLAC, PPC)
    • Customize – Schedules, STC, Smoothing-To
slide7

Query-Driven Analysis

Cross-Group

  • Specify Match Criteria
    • Eg, All subjects from Minn
    • Male, Left Handed, Schz
    • Hypothesis
  • Automatic Level Traversal

Group1

Subj1

Visit1

Run1

First-Level

PreProc

Raw

slide8

Facilitate Collaboration

  • Sharing of:
    • Raw Data
    • Analysis
    • Storage
    • Computation
  • Global Configurations (Centralized)
    • Stimulus Schedules
    • PPC
    • FLAC
    • Done a few times – bring all expertise to bear
slide9

Status …

  • Software Exists! www.nmr.mgh.harvard.edu/~greve/fbirn/fips
  • And people are using it.
  • Tue, 830-930AM, Laguna Room
  • Mostly wrappers around FSL
  • EPrime  Stimulus Schedules
  • PreProc –
    • FSL: MC, STC, Smooth
    • Smoothing-To
    • Some Modularization
  • First Level – FSL
slide10

… Status

  • Visit Level – FSL Fixed Effects
  • Subject Level – Not Yet
  • Group Level (Talairach Space)
    • OSGM FSL RFx, FFx, MFx
    • Where? DB?
  • XGroup Level – Not Yet. Where? DB?
  • Queryability
    • FIPS DB (need real DB)
    • Automatic Traversal
  • Local Processing Only
  • ROI – Some FreeSurfer Integration
slide11

Current Issues

  • Databasing – extracting info for designs
  • QA and Repair
  • Modularization
  • Centralized Configurations
  • Provenance/Distribution/Testing
  • Multi-Stage Registration
  • Format – currently Analyze, want NIFTI
  • Computational Power/Cluster
slide13

Configure

First-Level

Analysis

Stimulus

Timing

Scanner

Human

Upload

FLAC Library

EPrime

First-Level

Analysis

Hierarchy

(Local SRB)

FIPS

Database

PixelData

ImageWrapper.xml

fips-process.xml

Stimulus Schedules

FIPS Overview

slide14

Local Human Upload and Data Hierarchy

  • $LOCAL_SRB_HOME_BIRN/
  • ProjectName_ProjectId
  • SubjectID/
  • Visit__SiteId_VisitNo/
  • Study__StudyId/
  • ExperimentSeries/
  • Native/
  • Original__0001/
  • Analyze_7.5/

/space/BIRN/

fBIRNPhaseII__000010/

00900000103/

Visit__009_0001/

Study__0001/

sm3/

Native/

Original__0001/

Analyze_7.5/

In Analyze_7.5/:

Pixel Data: f0001.img, f0002.img, … (analyze format + .mat)

ImageWrapper.xml – geometry, voxel size, slice order

fips-process.xml – paradigm, run, site, BIRN Id, etc (redundant)

XML files contain data-specific information.

slide15

fips-process.xml

  • paradigm – eg, SIRP
  • run number within paradigm
  • All hierarchy information (BIRNID, etc)
  • Analysis Level (none, FirstLevel)
  • Stored with Raw and Analyzed data
slide16

FIPS Resource File: ~/.fipsrc

setenv LOCAL_SRB_HOME_BIRN /space/mojave/1/users/swallace/SRB

setenv MY_FIPS_DIR /birn/users/share/fips/db

setenv FIPS_FLAC_DIR /birn/users/share/fips/flac

LOCAL_SRB_HOME_BIRN: root of Local SRB

MY_FIPS_DIR: Local FIPS Database (low storage)

FIPS_FLAC_DIR: Place were FLACs are saved (low storage)

slide17

FIPS Database

  • fips-build-db
  • Finds all fips-process.xml files 9 levels down
  • Creates a table in $MY_FIPS_DIR
  • Creates html in $MY_FIPS_DIR
  • $MY_FIPS_DIR not in the hierarchy (~/.fipsrc)
slide19

Analysis Parameters

Data-Independent

Data-Specific

  • Event Definitions
  • HRF
  • Smoothing Level
  • Use Slice Timing or not
  • Contrasts
  • Slice Timing (XML)
  • Discarded Acqs (XML)
  • Stimulus Schedules

Lower-level, Hidden, Nuisance.

Handled at upload, within-hierarchy.

ImageWrapper.xml, fips-process.xml

Higher-level, Share, Save in DB,

Queryable, extra-hierarchy. FLAC.

slide20

Stimulus Schedules and Data Hierarchy

  • $LOCAL_SRB_HOME_BIRN/
  • ProjectName_ProjectId
  • SubjectID/
  • Visit__SiteId_VisitNo/
  • Study__StudyId/
  • ExperimentSeries/
  • Native/
  • Original__0001/
  • StimulusSchedules/

/space/BIRN/

fBIRNPhaseII__000010/

00900000103/

Visit__009_0001/

Study__0001/

sm3/

Native/

Original__0001/

StimulusSchedules/

In StimulusSchedules/: Happy.stf, Sad.stf, …

fips-import-sched – program to copy stimulus schedules for a data set into the correct place in the hierarchy.

slide21

Stimulus Schedule Issues

  • More automation needed.
  • Combine with upload?
  • Predefined within analysis?
  • Flexible enough for post hoc event definitions?
  • Keep in SRB Hierarchy or save in DB?
  • Note: SIRP and MM schedules for Phase II in fips/etc (thanks Bryon!)
slide22

Analysis Parameters

Data-Independent

Data-Specific

  • Event Definitions
  • HRF
  • Smoothing Level
  • Use Slice Timing or not
  • Contrasts
  • Slice Timing (XML)
  • Discarded Acqs (XML)
  • Stimulus Schedules

Lower-level, Hidden, Nuisance.

Handled at upload.

Higher-level, Share, Save in DB,

Queryable.

slide23

First Level Analysis Configuration (FLAC)

  • Motion Correction
  • Slice-timing Correction
  • Spatial Smoothing
  • Intensity Normalization (Grand Mean)
  • Fit General Linear Model (GLM)
    • Event Types and Schedules
    • HRF Type and Parameters, Derivatives
    • Contrasts of Regression Coefficients
    • Register to Standard Space
    • Configure ONCE
slide24

Creating the FLAC

  • fips-fla-config – program that uses FSL’s FEAT GUI to configure
  • first-level analyses. Saves FLAC to FLAC “library”.
  • fips-fla-config --flac sirp-stc-smth5mm –paradigm SIRP
  • –projectname fBIRNPhaseII
  • --flac: name of the FLAC to be used in later calls
  • --paradigm: as specified during upload
  • --projectname: as specified during the upload
  • Creates: $MY_FLAC_DIR/fBIRNPhaseII/SIRP/sirp-stc-smth5mm
  • sirp-stc-smth5mm is a text file crated by FSL.
  • FLAC “Library” $MY_FLAC_DIRnot in the hierarchy (~/.fipsrc)
  • DO THIS ONCE!
slide25

What fips-fla-config is doing

  • Creates temporary staging directory
  • Copies the data and schedules from a template subject (confusing but required by FEAT)
  • Runs FSL’s FEAT GUI
  • User specifies the config (including schedules)
  • User saves to “design.fsf”
  • Renames design.fsf and copies to FLAC Library
analyzing data fips fla
Analyzing Data: fips-fla

USAGE: fips-fla

--projectname name : eg, fBIRNPhaseII

--paradigm name : eg, SIRP

--flac FLACName : eg, sirp-stc-smth5mm

Analyzes all matching data sets, unless:

--birnid id : eg, 00042105

--siteid id : eg, 0006

--visitid id : eg, L0001

--studyname name : eg, bay4-trio

--run nthrun

--visitname name

--studyid id

slide28

FLA and Data Hierarchy

  • $LOCAL_SRB_HOME_BIRN/
  • ProjectName_ProjectId
  • SubjectID/
  • Visit__SiteId_VisitNo/
  • Study__StudyId/
  • ExperimentSeries/
  • Analysis/
  • Original__0001/
  • FLACName.feat/

/space/BIRN/

fBIRNPhaseII__000010/

00900000103/

Visit__009_0001/

Study__0001/

sirp3/

Analysis/

Original__0001/

sirp-stc-smth5mm.feat/

In FLACName.feat/: FSL Analysis results, fips-process.xml.

Rebuild DB (fips-build-db) to see results in HTML.

slide29

What fips-fla is doing

  • Finds a matching data set
  • Copies FLAC file (FSL FEAT format)
  • Customizes for that data set (eg, slice order)
  • Runs FEAT scripts (does “everything”)
  • Runs a check to catch errors
  • Creates a new fips-process.xml (changes “Analysis Level” to “FirstLevel”)
slide30

First-Level Analysis Visualization

  • FSL-created HTML File
  • fips-view
    • AFNI
    • FreeSurfer (tkmedit)
    • Slicer
slide31

First Level Analysis Workflow

0.Define and upload FLAC (once for all sessions)

For each session:

  • Collect data for a session
  • Local Upload
  • (Re)Build FIPS DB
  • Upload stimulus timing files (if necessary)
  • Analyze (First Level)
  • Rebuild FIPS DB
  • Visualize
slide32

FIPS and MBIRN/FreeSurfer

  • Visualization
  • ROI Definition and Analysis
  • fips-fsreg – register functional to anatomical
  • fips-feat2surf – sample results on surface
  • fips-fsroi – maps ROIs to functional space
  • fips-fsroisum – summarizes ROIs
outstanding issues
Outstanding Issues
  • Higher-Level Analysis (where in hierarchy?)
  • Analyze on Upload (stimulus timing files)
  • Include FLAC in DB?
  • Portalize
  • Continue to use FEAT?
stimulus identification and timing
Stimulus Identification and Timing

1

2

3

4

5

6

7

8

Time

t=0

t=3.0

t=10.0

t=15.0

t=30.0

t=28.7

t=37.1

t=43.1

t=13.0

SAD

HAPPY

Sad.stf:

3.0 2 1

13.0 2 1

15.0 2 1

37.1 2 1

Happy.stf:

10.0 2 1

30.0 2 1

28.7 6 1

43.1 2 1

  • Columns:
  • Onset Time
  • Duration
  • Weight