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fBIRN Image Processing Stream (FIPS). Overview. Goals First Level Analysis Steps FLAC Higher/Group Level Analysis Near-term Workflow. Long-Range Goals. Queryable Highly flexible Multi-site Calibration Custom software plug-ins Prepackaged analysis software plug-ins

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Overview

  • Goals

  • First Level Analysis Steps

  • FLAC

  • Higher/Group Level Analysis

  • Near-term Workflow


Long-Range Goals

  • Queryable

  • Highly flexible

  • Multi-site Calibration

  • Custom software plug-ins

  • Prepackaged analysis software plug-ins

  • Portalized


Short-RangeGoals

  • Limited flexibility

  • FSL-only

  • Publishable

  • Start to solve data management problems


First Level (Run) Analysis

  • Slice-timing Correction (?)

  • Motion Correction

  • Spatial Smoothing

  • Intensity Normalization (Grand Mean)

  • Fit General Linear Model (GLM)

    • Regression Coefficients

    • Residual Variance

    • Contrasts of Regression Coefficients (Var)

    • t, F, z maps of contrasts

    • Clusters (GRF)

    • Spaces: Native, Talairach (FSL-MNI152)

  • ROI analysis/export



Flac first level analysis configuration
FLAC – First-Level Analysis Configuration

  • All pre-processing options (MC, slice timing, smoothing)

  • Hemodynamic model (SPM HRF, delay, dispersion, derivative)

  • Stimulus identity and timing (“Event Lumping”)

  • Nuisance regressors

  • Contrasts (would be better to do this later)

  • Data set independent!

  • Define ONCE!


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)


Short-term Workflow

  • “Local” Data Management Model

    • Uses (Evolving) Hierarchy

    • All data on SRB

    • All data mirrored locally

    • All analyses computed locally


First Level Analysis Workflow

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

For each session:

  • Collect data for a session

  • Upload to session to SRB/HID

  • Synchronize LocalDB to SRB

  • Create stimulus timing files from E-Prime

  • Analyze (First Level) locally

  • Synchronize SRB to LocalDB (Upload)

}Hierararchy

Group Level Analysis Workflow -- TBD


Analyzing data fips fla
Analyzing Data: fips-fla

USAGE: fips-fla

 --flac FLACName : name of the FLAC as created with flac-checkin

 --subj SubjId : BIRN Subject ID (eg, 00900000103)

--site SiteID : BIRN Site ID (eg, 006)

--visit VisitNo : Visit number (eg, 1)

--study StudyId : Study Id or number (eg, 1)

--exp ExpId : Name of experiment (eg, sm)

 --db database : BIRN database: (eg, Human. Default from RC)

--proj ProjectName : BIRN project (eg, fBIRNHumanPhantom. Default from RC)

--projid ProjectID : BIRN project ID (eg, 000005 . Default from RC)

 --overwrite : overwrite previously analyzed results

--help : a short story about a Spanish boy named ‘Manual’

Processes all runs in experiment


Phase I Data

  • Analyzed and on SRB

  • Motion Correction

  • Smoothing with FWHM=5mm

  • Intensity Normalized

  • BH, SM, and Rest – 15s ON, 15s OFF

  • SIRP and MMN

  • http://www.nmr.mgh.harvard.edu/~greve/fbirn/phase1


Database

Analysis

Parameters

(FLAC)

Site Data

--Scanning protocol

--Slice order

--Skip

Session1 Data

--Raw Pixel Data

--Stimulus Id and Timing

--Analyzed Data

Session2 Data

--Raw Pixel Data

--Stimulus Id and Timing

--Analyzed Data


Create Analysis (FLAC)

Database

Analysis

Parameters

(FLAC)

Site Data

--Scanning protocol

--Slice order

--Skip

Session1 Data

--Raw Pixel Data

--Stimulus Id and Timing

--Analyzed Data

Session2 Data

--Raw Pixel Data

--Stimulus Id and Timing

--Analyzed Data






Flac first level analysis configuration1
FLAC – First-Level Analysis Configuration

  • Save to create the configuration file

  • Import/upload

  • Data set independent!

  • Define ONCE!


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

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 timing1
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


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


Database

Analysis

Parameters

(FLAC)

Site Data

--Scanning protocol

--Slice order

--Skip

Session Data

--Raw Pixel Data

--Stimulus Id and Timing

--Analyzed Data

Session Data

--Raw Pixel Data

--Stimulus Id and Timing

--Analyzed Data

Analyze

  • Specify FLAC and Session

  • Session indicates:

    • where the data are

    • site (slice order, skip, …)

  • FLAC indicates:

    • relative names of raw data, timing files, etc

  • FLAC customized (full paths resolved, etc)

  • Design matrix created

  • GLM Estimation

  • Inference (contrasts, z, t)

  • Resample to Talairach space

  • Local: Upload/Synch with SRB


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


Where we are now:

  • Local Analysis (ie, not on the SRB/Portal)

  • Scripts to define FLAC and analyze data

  • Data must be in proper hierarch – but no way to achieve this easily (need upload script)


Immediate Goals:

  • Finalize session hierarchy

  • Add XML to FSL output directory

  • Resolve stimulus ID and timing specification

  • Resolve site-dependent parameters

  • Update FIPS scripts

  • Local Analysis with SRB synch (?)


Intermediate Goals:

  • Portalize and/or incorporate into upload script

  • Group analysis

Long-Rang Goals:

  • Generalize FLAC (ie, not dependent upon FSL)

  • Incorporate other analysis packages

  • Incorporate Calibration Recommendations


Data Hierarchy: Image Data

VARIABLE NAMES

------------------------------------

LOCAL_SRB_HOME_BIRN/

DataBase/

ProjectName_ProjectId

SubjectID/

Visit__SiteId_VisitNo/

Study__StudyId/

Experiment__Series/

Native/

Original__0001/

Analyze/

EXAMPLE

--------------------------------------

/home/BIRN/

Human/

fBIRNHumanPhantom__000005/

00900000103/

Visit__009_0001/

Study__0001/

sm__0003/

Native/

Original__0001/

Analyze/

----

RC

RC

RC

CL

CL

CL

CL

--

--

--

In Analyze/: f0001.img, f0002.img, …

RC = ~/.fipsrc

CL = Command-line


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


Analyzing data fips fla1
Analyzing Data: fips-fla

USAGE: fips-fla

 --flac FLACName : name of the FLAC as created with flac-checkin

 --subj SubjId : BIRN Subject ID (eg, 00900000103)

--site SiteID : BIRN Site ID (eg, 006)

--visit VisitNo : Visit number (eg, 1)

--study StudyId : Study Id or number (eg, 1)

--exp ExpId : Name of experiment (eg, sm)

 --db database : BIRN database: (eg, Human. Default from RC)

--proj ProjectName : BIRN project (eg, fBIRNHumanPhantom. Default from RC)

--projid ProjectID : BIRN project ID (eg, 000005 . Default from RC)

 --overwrite : overwrite previously analyzed results

--help : a short story about a Spanish boy named ‘Manual’

Processes all runs in experiment


Data Hierarchy: FSL Output

VARIABLE NAMES

------------------------------------

LOCAL_SRB_HOME_BIRN/

DataBase/

ProjectName_ProjectId

SubjectID/

Visit__SiteId_VisitNo/

Study__StudyId/

Experiment__Series/

Analysis/

Original__0001/

FLACNAME.feat/

EXAMPLE

--------------------------------------

/home/BIRN/

Human/

fBIRNHumanPhantom__000005/

00900000103/

Visit__009_0001/

Study__0001/

sm__0003/

Analysis/

Original__0001/

sensorimotor.feat/

----

RC

RC

RC

CL

CL

CL

CL

--

--

--

In TaskData/ sensorimotor.stf

RC = ~/.fipsrc

CL = Command-line


Creating a flac
Creating a FLAC

  • Create temporary dir

  • Copy one run of raw data (in analyze4d) - template

  • Copy timing files (if using) – name important

  • Run FSL Feat GUI (specify processing options) – do not actually analyze data.

  • flac-checkin (FIPS_FLAC_DIR)

  • Delete temporary dir

  • Do this once for each parameter set

  • Analyze all data with this FLAC

flac-checkin --help


To analyze data
To Analyze Data

  • Copy data into local SRB mirror

  • Copy timing files into TaskData/ for each run. Use the same names as when defining the FLAC. Names stay the same across runs, subjects, etc.

  • Analyze with fips-fla, which will customize the FLAC for each data set

  • View with html browser or AFNI


Data Hierarchy: Timing Files

VARIABLE NAMES

------------------------------------

LOCAL_SRB_HOME_BIRN/

DataBase/

ProjectName_ProjectId

SubjectID/

Visit__SiteId_VisitNo/

Study__StudyId/

Experiment__Series/

Native/

Original__0001/

TaskData/

EXAMPLE

--------------------------------------

/home/BIRN/

Human/

fBIRNHumanPhantom__000005/

00900000103/

Visit__009_0001/

Study__0001/

sm__0003/

Native/

Original__0001/

TaskData/

----

RC

RC

RC

CL

CL

CL

CL

--

--

--

In TaskData/ sensorimotor.stf

RC = ~/.fipsrc

CL = Command-line


Timing files fsl 3 column custom
Timing Files (FSL: 3-column custom)

Onset Time (sec), Duration (sec), Weight

15 15 1

45 15 1

75 15 1

105 15 1

135 15 1

165 15 1

195 15 1

225 15 1

One timing file for each event type.


Outstanding issues
Outstanding Issues

  • How to upload timing files to SRB

  • How to upload FLAC to SRB

  • Adding XML files to FSL output

  • Synching output with SRB

  • Slice-timing correction – site dependent

  • Delete/Skip first few volumes – site dependent


Future
Future

  • FLAC creation without a template data set

  • All processing through portal – no need to have local mirror

  • Interface with group analysis

  • Generalize FLAC to other packages


First Level Analysis Workflow

  • “Local” Data Management Model

    • All data on SRB

    • All data mirrored locally

    • All analyses computed locally

  • Collect data for a session

  • Upload to session to SRB/HID

  • Synchronize LocalDB to SRB

  • Create stimulus timing files from E-Prime

  • Analyze (First Level) locally

  • Synchronize SRB to LocalDB (Upload)

}Hierararchy


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