Fbirn image processing stream fips
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fBIRN Image Processing Stream (FIPS) PowerPoint PPT Presentation


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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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fBIRN Image Processing Stream (FIPS)

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Fbirn image processing stream fips

fBIRN Image Processing Stream(FIPS)


Fbirn image processing stream fips

Overview

  • Goals

  • Hierarchy and Local Upload

  • FIPS Database

  • Stimulus Schedule Files

  • First-Level Analysis Configuration


Fbirn image processing stream fips

Design Goals

} Conflict

  • Automated Analysis

  • Highly flexible

  • Multi-site Calibration

  • Data Sharing

  • Query-Driven

  • Portalized

  • Assure same analysis


Fbirn image processing stream fips

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


Fbirn image processing stream fips

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


Fbirn image processing stream fips

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)


Fbirn image processing stream fips

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)


Fbirn image processing stream fips

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.


Fbirn image processing stream fips

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


Fbirn image processing stream fips

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!)


Fbirn image processing stream fips

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.


Fbirn image processing stream fips

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


Fbirn image processing stream fips

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!


Fbirn image processing stream fips

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


Fbirn image processing stream fips

Configuring the First-Level Analysis using FSL-FEAT


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


Fbirn image processing stream fips

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.


Fbirn image processing stream fips

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”)


Fbirn image processing stream fips

First-Level Analysis Visualization

  • FSL-created HTML File

  • fips-view

    • AFNI

    • FreeSurfer (tkmedit)

    • Slicer


Fbirn image processing stream fips

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


Fbirn image processing stream fips

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


Fbirn image processing stream fips

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?


Fbirn image processing stream fips

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/


Fbirn image processing stream fips

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)


Fbirn image processing stream fips

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


Fbirn image processing stream fips

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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