[email protected] [email protected] Institute for Biomedical Engineering (ETH Zurich) &...

[email protected]

[email protected]

Institute for Biomedical Engineering (ETH Zurich)

& Computational Neuroeconomics Group (Univ. of

Zurich)

ZURICH SPM COURSE 2011

Batch Programming of fMRI Data Analysis

Lars Kasper & Christoph Mathys


BATCH PROGRAMMING OF

FMRI DATA ANALYSIS

Overview

2Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)

Kasper/Mathys (18-Feb-11)

Introduction & Example Dataset General fMRI Data Analysis Workflow with SPM

Quality Assessment of Raw Data Spatial Preprocessing Statistical Design: The General Linear Model Results: Analyzing Contrast & Reporting

Within-Subject Batching (Single Subject) Subject-independent Analysis Steps Subject-independent Data Flow (Dependencies) Subject-related data

Between-Subject-Batching (Multiple Subject)



FMRI DATA ANALYSIS

Overview









FMRI DATA ANALYSIS

RealignmentRealignment SmoothingSmoothing

NormalisationNormalisation

General linear modelGeneral linear model

Statistical parametric map Statistical parametric map (SPM)(SPM)Image time-seriesImage time-series

Parameter estimatesParameter estimates

Design matrixDesign matrix

TemplateTemplate

KernelKernel

Gaussian Gaussian field theoryfield theory

p <0.05p <0.05

StatisticalStatisticalinferenceinference

Overview of SPM

Kasper/Mathys (18-Feb-11) 4Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)



FMRI DATA ANALYSIS

What is batch processing?

Repeats same data analysis for many subjects (>=2) Not prone to human errors, reproducible what was done

e. g. jobs mat-files

Runs automatically, no supervision needed Researcher can concentrate on assessing the results

CAVEAT: Tempting to forget about all analysis steps in between which could lead to errors in your conclusions

Therefore: Always make sure, that meaningful results were created at each step Using Display/CheckReg to view raw data, preprocessed data Using spm_print to save reported supplementary data output If anything went wrong, use debugging





FMRI DATA ANALYSIS

3 flavors of batching – Goals of this tutorialAfter finishing this session, you will be able to

analyze fMRI datasets using

1. the Graphical User Interface (GUI) of SPM:

2. The Batch Editor of SPM

3. A template Matlab .m-script file to batch very flexibly





FMRI DATA ANALYSIS

Introducing the Dataset

Rik Henson‘s famous vs non-famous faces dataset

http://www.fil.ion.ucl.ac.uk/spm/data/face_rep/face_rep_SPM5.html

Includes a manual with step-by-step instruction for analysis (homework ;-))

Download from SPM homepage (available for SPM5, but works fine with SPM8)





FMRI DATA ANALYSIS

Introducing the Dataset

Factorial 2 x 2 design to investigate repetition suppression Question: Influence of repeated stimulus presentation on

brain activity (accomodation of response)? Each stimulus (pictures of faces) presented twice during a

session Condition Rep, Level: 1 or 2 lag between presentations randomized

26 Famous and 26 non-famous faces to differentiate between familiarity (long-term memory) and repetition Condition Fam, Level F(amous) and N(onfamous)

Task: Decision whether famous or nonfamous (button-press)





FMRI DATA ANALYSIS

Introducing the Dataset: Published Resultsa. Right Fusiform face area

Repetition suppression for familiar/famous faces

b. Left Occipital face area (posterior, occip. extrastriate) Repetition suppression for familiar AND unfamiliar faces

c. Posterior cingulate and bilateral parietal cortex Repetition enhancement





FMRI DATA ANALYSIS

Overview









FMRI DATA ANALYSIS

Spatial Preprocessing – Realign

sd



FORMAT P = spm_realign

(P,flags)

GUIGUI Batch EditorBatch Editor Batch FileBatch File



FMRI DATA ANALYSIS

Spatial Preprocessing – Unwarp



uw_params=spm_uw_estimate(P,uw_est_flags);

spm_uw_apply(uw_params,uw_write_flags);

GUIGUI Batch EditorBatch Editor Batch FileBatch File



FMRI DATA ANALYSIS

Uh…this takes ages…

Now you can probably value the benefits of batch processing. If you are still keen on doing all that by hand (good exercise!), refer to the following

The SPM manual Most current version in your spm8-folder, sub-folder man/manual.pdf

Rik Henson‘s famous vs non-famous faces dataset

http://www.fil.ion.ucl.ac.uk/spm/data/face_rep/face_rep_SPM5.html

Included in SPM manual, chapter 29, with step-by-step instruction for analysis

Available for SPM5, but works fine with SPM8





FMRI DATA ANALYSIS

Overview









FMRI DATA ANALYSIS

General Workflow for the batch interface



Top-down approachSpecify subject-independent data/analysis stepsSpecify subject-independent file-dependencies (data flow)Specify subject-related data (e.g. event-timing)



FMRI DATA ANALYSIS

1. The subject-independent analysis parts

Load all modules first (in right order!)

Then specify details (where Xs are found) which are subject independent TR Nslices model factors contrasts of interest





FMRI DATA ANALYSIS

2. Data-flow specification (subject-independent dependencies)

Specify, which results of which steps are input to another step (DEP-sign) e.g. smoothed images needed for model spec

Afterwards save this job as template .mat file





FMRI DATA ANALYSIS

3. Add subject-dependent data/information

Essentially go to all X‘s and fill in appropriate values e.g. the .mat-file of the conditions onsets/durations

Save this job as subject-batch file & Run





FMRI DATA ANALYSIS

Overview









FMRI DATA ANALYSIS


Make sure, parameters to be adjusted have an X (clear value) for the single subject template

Specify a meta-job with Run batchCreate one run for every subject and add missing parameter values (in right order)





FMRI DATA ANALYSIS

Resources and Useful Literature

All step-by-step instructions can be found in the SPM manual, chapter 40 Also multiple-session and multiple subjects processing

included

The SPM helpline/mailing list E.g. bug precluding the batch-file selector form working was

fixed here, but not in the updates yet https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1001&L=SPM&P=R39357

Batch templates are in your spm path: Configured subject-independent analysis steps<spm8>/man/batch/face_single_subject_template_nodeps.m

With dependencies included <spm8>/man/batch/face_single_subject_template.m

With multiple subjects <spm8>/man/batch/face_multi_subject_template.m





FMRI DATA ANALYSIS

Many, many thanks to

Klaas Enno Stephan The SPM developers (FIL methods group)





FMRI DATA ANALYSIS

Extending the batchfile with SPM GUI functions Debugging Generally a good idea to find out how things work in

SPM Crucial for batch-programming using a .m-file Here: debug spm.m by setting a breakpoint If called function found, use edit <functionname>.m to look at the %comments in the file





FMRI DATA ANALYSIS

Tuning the engine – Matlab workspace variables e.g. to manipulate SPM.mat or jobs by hand also important during debugging, how variables are

defined and changed



[email protected] [email protected] Institute for Biomedical Engineering (ETH Zurich) &...

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