SPM/Batch

Batch Scripts

See this Powerpoint presentation for an overview.

See the relevant chapter in the SPM manual.

For general comments on scripting with MATLAB and SPM see the programming intro.

Batch Script for SPM12

Any batch script should follow the template:

spm('defaults','fmri');
spm_jobman('initcfg');

matlabbatch{1}.spm... = ...;

spm_jobman('run',matlabbatch);

Batch Script for SPM8

SPM12's advices also apply to SPM8.

The Batch Scripts for SPM5 below can also be used in SPM8.

Batch Script for SPM5

Examples of script (for SPM5 and compatible with SPM8) are provided with the SPM Data Sets, for example:

• First Level block fMRI data analysis
• First Level event-related fMRI data analysis
• Second Level fMRI data analysis
• DCM/PPI
• Multi-Subject PET data analysis

See also:

• http://www.icn.ucl.ac.uk/courses/MATLAB-Tutorials/Sessions2008_09/sessions2008_09.htm#S13 for a generic multi-subject preprocessing script.
• http://www.mrc-cbu.cam.ac.uk/people/rik.henson/personal/analysis.html
• http://imaging.mrc-cbu.cam.ac.uk/imaging/SpmBatch5

Batch Script for SPM2

There is an example batch script written by Rik Henson, for a single subject fMRI data set (preprocessing and statistics).