fbirn image processing stream (fips)

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• Portalized

Short-Range Goals• 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

First-Level Analysis Results

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

1. Collect data for a session2. Upload to session to SRB/HID3. Synchronize LocalDB to SRB4. Create stimulus timing files from E-Prime5. Analyze (First Level) locally6. Synchronize SRB to LocalDB (Upload)

}Hierararchy

Group Level Analysis Workflow -- TBD

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

For each session:

Analyzing Data: fips-flaUSAGE: 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

DatabaseAnalysis

Parameters(FLAC)

Session1 Data--Raw Pixel Data--Stimulus Id and Timing--Analyzed Data

Session2 Data--Raw Pixel Data--Stimulus Id and Timing--Analyzed Data

Site Data--Scanning protocol--Slice order--Skip

DatabaseAnalysis

Parameters(FLAC)

Session1 Data--Raw Pixel Data--Stimulus Id and Timing--Analyzed Data

Session2 Data--Raw Pixel Data--Stimulus Id and Timing--Analyzed Data

Site Data--Scanning protocol--Slice order--Skip

Create Analysis (FLAC)

Configuring the First-Level Analysis using FSL-FEAT

Configuring the First-Level Analysis using FSL-FEAT

Configuring the First-Level Analysis using FSL-FEAT

Configuring the First-Level Analysis using FSL-FEAT

FLAC – First-Level Analysis Configuration

• Save to create the configuration file

• Import/upload

• Data set independent!

• Define ONCE!

Stimulus Identification and Timing

1 73 42 5 6 8

HAPPYSAD

Happy.stf:

10.0 2 1

30.0 2 1

28.7 6 1

43.1 2 1

Sad.stf:

3.0 2 1

13.0 2 1

15.0 2 1

37.1 2 1

Time

t=0 t=3.0 t=10.0

t=13.0

t=15.0 t=30.0 t=28.7 t=37.1 t=43.1

Columns:1. Onset Time2. Duration3. Weight

Example: Happy andSad Faces as defined by the experimenter.

Stimulus Identification and Timing

1 73 42 5 6 8

HAPPYSAD

Happy.stf:

10.0 2 1

30.0 2 1

28.7 6 1

43.1 2 1

Sad.stf:

3.0 2 1

13.0 2 1

15.0 2 1

37.1 2 1

Subject1 73 42 5 6 8

Experimenter

HAPPYSAD

HappySubj.stf:

10.0 2 1

15.0 2 1

30.0 2 1

43.1 2 1

SadSubj.stf:

3.0 2 1

13.0 2 1

28.7 6 1

37.1 2 1

Experimenter Subject

1 73 42 5 6 8

1 73 42 5 6 8

1 73 42 5 6 8

HH HS

SH SS

Subject

H S

H

S

Exp

erim

ente

r

SH.stf:

15.0 2 1

HH.stf:

10.0 2 1

28.7 6 1

43.1 2 1

HS.stf:

28.7 6 1

SS.stf:

3.0 2 1

13.0 2 1

37.1 2 1

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

DatabaseAnalysis

Parameters(FLAC)

Session Data--Raw Pixel Data--Stimulus Id and Timing--Analyzed Data

Session Data--Raw Pixel Data--Stimulus Id and Timing--Analyzed Data

Site Data--Scanning protocol--Slice order--Skip

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_ProjectIdSubjectID/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/

----RCRCRCCLCLCLCL------

RC = ~/.fipsrcCL = Command-line

In Analyze/: f0001.img, f0002.img, …

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-flaUSAGE: 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_ProjectIdSubjectID/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/

----RCRCRCCLCLCLCL------

RC = ~/.fipsrcCL = Command-line

In TaskData/ sensorimotor.stf

Creating a FLAC

1. Create temporary dir2. Copy one run of raw data (in analyze4d) - template3. Copy timing files (if using) – name important4. Run FSL Feat GUI (specify processing options) – do not

actually analyze data.5. flac-checkin (FIPS_FLAC_DIR)6. Delete temporary dir7. Do this once for each parameter set8. Analyze all data with this FLAC

flac-checkin --help

To Analyze Data1. Copy data into local SRB mirror2. 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.

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

4. View with html browser or AFNI

Data Hierarchy: Timing Files

VARIABLE NAMES------------------------------------LOCAL_SRB_HOME_BIRN/DataBase/ProjectName_ProjectIdSubjectID/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/

----RCRCRCCLCLCLCL------

RC = ~/.fipsrcCL = Command-line

In TaskData/ sensorimotor.stf

Timing Files (FSL: 3-column custom)

15 15 145 15 175 15 1105 15 1135 15 1165 15 1195 15 1225 15 1 

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

One timing file for each event type.

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

• 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

1. Collect data for a session2. Upload to session to SRB/HID3. Synchronize LocalDB to SRB4. Create stimulus timing files from E-Prime5. Analyze (First Level) locally6. Synchronize SRB to LocalDB (Upload)

• “Local” Data Management Model• All data on SRB• All data mirrored locally• All analyses computed locally

}Hierararchy