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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
ZURICH SPM COURSE 2011
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)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
FMRI DATA ANALYSIS
Overview
3Computational 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)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
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)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
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
5Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
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
6Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
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)
7Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
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)
8Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
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
9Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
FMRI DATA ANALYSIS
Overview
10Computational 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)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
FMRI DATA ANALYSIS
Spatial Preprocessing – Realign
sd
11Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)
FORMAT P = spm_realign
(P,flags)
GUIGUI Batch EditorBatch Editor Batch FileBatch File
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
FMRI DATA ANALYSIS
Spatial Preprocessing – Unwarp
12Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)
uw_params=spm_uw_estimate(P,uw_est_flags);
spm_uw_apply(uw_params,uw_write_flags);
GUIGUI Batch EditorBatch Editor Batch FileBatch File
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
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
13Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
FMRI DATA ANALYSIS
Overview
14Computational 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)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
FMRI DATA ANALYSIS
General Workflow for the batch interface
15Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)
Top-down approachSpecify subject-independent data/analysis stepsSpecify subject-independent file-dependencies (data flow)Specify subject-related data (e.g. event-timing)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
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
16Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
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
17Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
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
18Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
FMRI DATA ANALYSIS
Overview
19Computational 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)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
FMRI DATA ANALYSIS
Between-Subject-Batching (Multiple Subject)
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)
20Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
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
21Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
FMRI DATA ANALYSIS
Many, many thanks to
Klaas Enno Stephan The SPM developers (FIL methods group)
22Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
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
23Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)
ZURICH SPM COURSE 2011
BATCH PROGRAMMING OF
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
24Computational Neuroeconomics (Prof. Stephan, USZ) / MR-Technology (Prof. Prüssmann, IBT)
Kasper/Mathys (18-Feb-11)