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 courses:

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.

fnm = spm_select(1, 'image');
[pth, bnm, ext] = spm_fileparts(fnm);
VI = spm_vol(fnm);
VO = VI; % copy input info for output image
VO.fname = fullfile(pth, [bnm '_zn' ext]);
img = spm_read_vols(VI);
img(isnan(img)) = 0; % use ~isfinite instead of isnan to replace +/-inf with zero
spm_write_vol(VO,img);