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Institute for
Biomedical Engineering (ETH Zurich)
and Empirical Research in Economics (Univ. of
Zurich)
ZURICH SPM COURSE 2009
fMRI Single Subject Analysis &
Batch ProgrammingLars Kasper
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
Overview
2Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
Quality Assessment of Raw Data Spatial Preprocessing
Realign and Unwarp Coregister
General Linear Model: The Design Matrix Estimating the Model Results: Defining and Analyzing Contrasts Reporting and Summarizing Outlook: What to do with a lot of single subject
results
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
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
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
Goals of this tutorial
After finishing this session, you should be able to
Analyze single subject fMRI datasets using
1. the Graphical User Interface (GUI) of SPM
2. The Batch Editor of SPM
3. A template Matlab .m-file to batch very flexibly
4Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
Batch processing of data
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, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
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 SPM8b)
6Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
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)
7Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
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
8Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
Overview
9Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
Quality Assessment of Raw Data Spatial Preprocessing
Realign and Unwarp Coregister
General Linear Model: The Design Matrix Estimating the Model Results: Defining and Analyzing Contrasts Reporting and Summarizing Outlook: What to do with a lot of single subject
results
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
Overview
10Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
Quality Assessment of Raw Data Spatial Preprocessing
Realign and Unwarp Coregister
General Linear Model: The Design Matrix Estimating the Model Results: Defining and Analyzing Contrasts Reporting and Summarizing Outlook: What to do with a lot of single subject
results
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
Spatial Preprocessing – Realign
sd
11Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
FORMAT P = spm_realign
(P,flags)
GUIGUI Batch EditorBatch Editor Batch FileBatch File
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
Spatial Preprocessing – Unwarp
12Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
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 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
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 spm8b-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 SPM8b
13Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
Overview
14Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
Quality Assessment of Raw Data Spatial Preprocessing
Realign and Unwarp Coregister
General Linear Model: The Design Matrix Estimating the Model Results: Defining and Analyzing Contrasts Reporting and Summarizing Outlook: What to do with a lot of single subject
results
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
Overview
15Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
Quality Assessment of Raw Data Spatial Preprocessing
Realign and Unwarp Coregister
General Linear Model: The Design Matrix Estimating the Model Results: Defining and Analyzing Contrasts Reporting and Summarizing Outlook: What to do with a lot of single subject
results
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
General Workflow for the batch interface
16Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
Top-down approach1. Specify subject-
independent data/analysis steps
2. Specify subject-independent file-dependencies (data flow)
3. Specify subject-related data (e.g. event-timing)
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
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
17Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
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
18Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
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
19Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
4. Making it multi-subject
1. Make sure, parameters to be adjusted have an X (clear value) for the single subject template
2. Specify a meta-job with Run batch3. Create one run for every subject and add
missing parameter values (in right order)20Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann,
IBT)Lars Kasper (11-Feb-09)
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
Resources and Useful Literature
All step-by-step instructions can be found in the SPM manual, chapter 35 Also multiple-session and multiple subjects processing
included
Batch templates are in your spm path: Configured subject-independent analysis steps<spm8b>/man/batch/face_single_subject_template_nodeps.m
With dependencies included
<spm8b>/man/batch/face_single_subject_template.m
With multiple subjects
<spm8b>/man/batch/face_multi_subject_template.m
21Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
Many, many thanks to
Klaas Enno Stephan The SPM developers (FIL methods group)
22Computational Neuroeconomics (Prof. Stephan, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
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, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)
ZURICH SPM COURSE 2009
SINGLE SUBJECT ANALYSIS
BATCH PROGRAMMING
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, IEW) / MR-Technology (Prof. Prüssmann, IBT)
Lars Kasper (11-Feb-09)