# SPM/Programming intro
## Aim

This page is intended to provide a quick-start guide to writing your own MATLAB scripts and functions using SPM as a library. SPM programming can mean simply writing batch scripts to automate common pipelines, writing short helper scripts or functions to accomplish useful tasks, writing your own SPM extensions, or even modifying your local installation of SPM.

## MATLAB

MATLAB is a programming language developed by MathWorks.
* MATLAB and MathWorks on Wikipedia
* MATLAB on WikiBooks
Many MATLAB tutorials are available online:
* MATLAB Tutorial
There are also useful books:
* MATLAB for Neuroscientists
* MATLAB for Psychologists
MATLAB courses:
* MATLAB for Psychology and Neuroscience short course in Nottingham
* MATLAB for Psychologists short course in London

## SPM functions
### Introduction

SPM has extensive developer documentation in the headers of the source files. To view the documentation of a function either open the corresponding source file or call help function from the MATLAB command line. Make sure that the SPM folder is in MATLABs search path.

### Reading image headers and data

* spm_vol – header information
* spm_read_vols – for reading entire volumes (see also: spm_vol)
* spm_slice_vol – for arbitrary planes
* spm_sample_vol – any voxels
* spm_get_data (spm_sample_vol) – any voxels from multiple volumes
* spm_bsplins (spm_bsplinc) – NB spm_slice_vol and spm_sample_vol offer polynomial or sinc interpolation; these functions provide b-spline interp as used in spm_reslice

### Writing data

* spm_write_vol (spm_vol)
* spm_create_vol
* spm_write_plane

### Reading and writing data with the alternative NIfTI class library

* nifti (@nifti/Contents, @nifti/create)
* file_array (@file_array/Contents)

### Geometry, voxel-world mappings

* spm_get_space – get the voxel-world mapping matrix (a rigid or affine transform, in homogeneous coordinates)
* spm_imatrix – convert above matrix to parametrised form
* spm_matrix – convert parameter vector to affine matrix
* spm_check_orientations

### Linear (rigid/affine) registration and reslicing

* spm_realign
* spm_coreg (spm_reslice)
* spm_affreg
* spm_reslice – needs reference image; see following for reslicing to specified geometry
* reorient (resize_img) – available from John's Gems 2 and 3

### Preprocessing, including segmentation and non-linear normalisation

* spm_preproc (spm_config_preproc, spm_prep2sn, spm_preproc_write) – SPM5's unified segmentation and normalisation
* spm_normalise – the old pre-SPM5 non-unified spatial normalisation
* spm_segment – the old pre-SPM5 non-unified tissue segmentation
* spm_smooth

### Processing

* spm_imcalc – perform arbitrary calculations on volumes (low level function)
* spm_imcalc_ui – high level convenience wrapper for spm_imcalc

### Statistics

* spm_ancova (spm_reml_ancova) – unused by SPM itself, but often useful for scripting or educational purposes

### Viewing data

* spm_check_registration (spm_image, spm_orthviews) – the ubiquitous three orthogonal views
* slover – slices through images, overlays of thresholded or raw statistics; see also slice_overlay
* spm_mip_ui (spm_mip) – maximum intensity projections or glass brain images

### Configuration

* spm_defaults
* spm_get_defaults

### Batch System

* spm_select
* spm_jobman

## Illustrative examples
### Reading and writing a volume (to replace NaNs with zeros)

A simpler (but more memory-hungry) version of an old Gem. See the SPM8 version of gem for an example of plane-wise reading and writing.

## External links

See also:
* John Ashburner's SPM Gems (SPM2, SPM5)
* Ged Ridgway's SPM8 scripts
* Chris Rorden's SPM8 scripts
* SPM Batch scripting
* SPM Extensions