1. Introduction to SPM Batching
from acquisition to publication…
Guillaume Flandin
Wellcome Trust Centre for Neuroimaging
University College London
MATLAB for Cognitive Neuroscience
ICN, May 2009

2. Statistical Inference
Image time-series
Spatial filter
Design matrix
Statistical Parametric Map
Realignment
Smoothing
General Linear Model
Statistical Inference
RFT
Normalisation
p <0.05
Anatomical reference
Parameter estimates

3. Installing SPM using SVN
FIL & ICN only
SPM repository
your SPM working copy
SPM
Install Subversion:
on Windows
Online instructions:
Repository URLs:
SPM5: svn://bread.fil.ion.ucl.ac.uk/spm/branches/spm5
SPM8: svn://bread.fil.ion.ucl.ac.uk/spm/trunk
TBR: svn://bread.fil.ion.ucl.ac.uk/tools/TBR/trunk
Import_Archive: svn://bread.fil.ion.ucl.ac.uk/tools/Import_Archive

4. TortoiseSVN: Checkout

5. TortoiseSVN: Update Case 1: your SPM files needed to be updated.
Case 2: your SPM files are up-to-date.

6. Remove older SPM versions from the path (or use spm_rmpath)
MATLAB path
Add Folder (and not with Subfolders)
Remove older SPM versions from the path (or use spm_rmpath)

7. Batching SPM{2,5,8} SPM Extensions webpage:
SPM99, SPM2
[1] [2]
Call SPM functions directly [1,2]:
spm_realign
spm_slice_timing
spm_normalise
spm_write_sn
spm_smooth
spm_fmri_spm_ui
spm_spm
spm_FcUtil
spm_contrasts
Requires knowledge about input/output arguments of main SPM functions and about the SPM.mat structure.
SPM5
Job Manager:
“jobs” structure.
Virtual files.
SPM8
Batch Editor:
“matlabbatch” structure.
Dependencies.

8. SPM “jobs”
Batch mode:
(“matlabbatch” for SPM8)
Goal: create a .mat file containing a Matlab structure ‘jobs’ similar to the one created using the GUI.
Tip: you only need to specify parameters that you would enter in the interface, the others will be automatically imported when executed.  The jobs structure will mimic the interface.

9. Useful SPM functions:
Select files: spm_select.m [files,dirs] = spm_select(‘FPList',dir,filt) ex.: f = spm_select(‘FPList',‘C:\data\exp’,‘^fM.*\.img$’);
Job manager: spm_jobman.m spm_jobman(‘initcfg’); % initialise SPM batch mode spm_jobman(‘run’,jobs); % execute a job spm_jobman(‘interactive’,jobs); % display a job in the GUI % jobs can be a Matlab variable or .mat/.m filename
Overall structure of a batch script: spm(‘defaults’,‘fmri’); spm_jobman(‘initcfg’); clear jobs % fill in jobs structure save(‘My_Batch.mat’,‘jobs’); spm_jobman(‘run’,jobs);
See also:
fullfile
cellstr
editfilenames*

10. Data organisation
Should be as generic as possible to ease batch script writing.

11. A potention pipeline for preprocessing with SPM:
Anatomical image
Realign
Coregister
Segment
Raw functional images
Update *.hdr mean.{img,hdr}
rp_*.txt
Update *.hdr
m*/c1*/c2*.{img,hdr}
*_seg_sn.mat
*_seg_inv_sn.mat
Normalize:
Write
Group mean
wm*. {img,hdr}
Smooth
Normalize:
Write …
sw*.{img,hdr}
w*.{img,hdr}

12. Workflow for SPM8 Batch Editor
Subject directory
Subject directory
Functional data
Functional data
Structural data
Structural data
Experimental design
Experimental design
Change directory
Realignment
Coregistration
Segmentation
Normalisation
Normalisation
Smoothing
Make directory
Model Specification
1. Subject-independent data/analysis steps
2. Data flow (dependencies)
Model Estimation
3. Subject-specific data

14. For more information…
SPM5/8 script examples:
SPM8 manual chapter 34:
L. Kasper’s slides for SPM8: