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fBIRN Image Processing Stream (FIPS). Overview. Goals Hierarchy and Local Upload FIPS Database Stimulus Schedule Files First-Level Analysis Configuration. Design Goals. } Conflict. Automated Analysis Highly flexible Multi-site Calibration Data Sharing Query-Driven

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slide2

Overview

  • Goals
  • Hierarchy and Local Upload
  • FIPS Database
  • Stimulus Schedule Files
  • First-Level Analysis Configuration
slide3

Design Goals

} Conflict

  • Automated Analysis
  • Highly flexible
  • Multi-site Calibration
  • Data Sharing
  • Query-Driven
  • Portalized
  • Assure same analysis
slide4

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.

Disk Space

Management

slide5

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
slide6

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)

slide7

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)
slide9

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.

slide10

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.

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
slide12

Stimulus Schedule Issues

  • Automatically? fips-process.xml
  • On-upload?
  • Predefined analysis?
  • Post Hoc Event Definitions?
  • Keep in SRB Hierarchy or save in DB?
  • SIRP and MM schedules for Phase II in fips/etc (thanks Bryon!)
slide13

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
  • Smoothness

Lower-level, Hidden, Nuisance.

Handled at upload.

Higher-level, Share, Save in DB,

Queryable.

slide14

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
slide15

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!
slide16

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

slide19

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.

slide20

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”)
slide21

First-Level Analysis Visualization

  • FSL-created HTML File
  • fips-view
    • AFNI
    • FreeSurfer (tkmedit)
    • Slicer
slide22

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
slide23

Configure

First-Level

Analysis

Stimulus

Timing

Scanner

Human

Upload

FLAC Library

Import

First-Level

Analysis

Hierarchy

(Local SRB)

FIPS

Database

PixelData

ImageWrapper.xml

fips-process.xml

Stimulus Schedules

FIPS Overview

slide24

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?
slide26

Data Hierarchy and Local Disk Managment

  • $LOCAL_SRB_HOME_BIRN/
  • ProjectName_ProjectId
  • SubjectID/
  • Visit__SiteId_VisitNo/
  • Study__StudyId/
  • ExperimentSeries/
  • Native/
  • Original__0001/
  • Analyze_7.5/
slide28

Higher/Group Level Analysis

  • Select First Level Analysis (FLAC)
  • Select Contrast from First Level
  • Select Subjects (Query)
  • Group Model and Group Contrasts (GLM)
  • Talairach Space (FSL-MNI152)
  • Fit GLM
    • Regression Coefficients
    • Residual Variance
    • Contrasts of Regression Coefficients
    • t, z maps of contrasts
    • Clusters (GRF)
slide29

Group Analysis

  • Group Level Analysis Configuration (GLAC?)
  • Specify:
    • FLAC as input
    • FLAC contrast
    • Group model (eg, Age, IQ, diagnosis, etc)
    • Group contrasts
    • Can be done within FSL
fips rc file fipsrc
FIPS RC File (~/.fipsrc)

setenv LOCAL_SRB_HOME_BIRN /space/birn/26/users/greve/srb-mirror

setenv FIPS_FLAC_DIR ~/flac

setenv FIPS_DEFAULT_DATABASE Human

setenv FIPS_DEFAULT_PROJECT_NAME fBIRNHumanPhantom

setenv FIPS_DEFAULT_PROJECT_ID 000005

stimulus identification and timing1
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

Example: Happy and

Sad Faces as defined by

the experimenter.

Sad.stf:

3.0 2 1

13.0 2 1

15.0 2 1

37.1 2 1

  • Columns:
  • Onset Time
  • Duration
  • Weight

Happy.stf:

10.0 2 1

30.0 2 1

28.7 6 1

43.1 2 1

stimulus identification and timing2
Stimulus Identification and Timing

1

2

3

4

5

6

7

8

Experimenter

1

2

3

4

5

6

7

8

Subject

Experimenter

Subject

SAD

HAPPY

SAD

HAPPY

Sad.stf:

3.0 2 1

13.0 2 1

15.0 2 1

37.1 2 1

SadSubj.stf:

3.0 2 1

13.0 2 1

28.7 6 1

37.1 2 1

Happy.stf:

10.0 2 1

30.0 2 1

28.7 6 1

43.1 2 1

HappySubj.stf:

10.0 2 1

15.0 2 1

30.0 2 1

43.1 2 1

slide33

1

2

3

4

5

6

7

8

1

2

3

4

5

6

7

8

1

2

3

4

5

6

7

8

Subject

SS.stf:

3.0 2 1

13.0 2 1

37.1 2 1

HH.stf:

10.0 2 1

28.7 6 1

43.1 2 1

HS.stf:

28.7 6 1

SH.stf:

15.0 2 1

H

S

H

HH

HS

Experimenter

S

SH

SS

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