This document contains code to initialize SPM and ANTs registration software, set default parameters, and run an image registration workflow that includes affine and SyN transformations using Mattes metric on two input images. The workflow is set to run using either the SGE or MultiProc plugin.

11. if isempty(which('spm')),
throw(MException('SPMCheck:NotFound',
'SPM not in matlab path'));
end
[name, version] = spm('ver');
fprintf('SPM version: %s Release:
%sn',name, version);
fprintf('SPM path: %sn', which('spm'));
spm('Defaults','fMRI');
if strcmp(name, 'SPM8') ||
strcmp(name(1:5), 'SPM12'),
spm_jobman('initcfg');
spm_get_defaults('cmdline', 1);
end

12. antsRegistration --collapse-output-transforms 1 --dimensionality 3 --initial-
moving-transform [ trans.mat, 1 ] --initialize-transforms-per-stage 1 --
interpolation Linear --output [ output_, output_warped_image.nii.gz ] --
restore-state trans.mat --save-state trans.mat --transform Affine[ 2.0 ]
--metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] --convergence [
1500x200, 1e-08, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-
estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.25,
3.0, 0.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] --convergence [
100x50x30, 1e-09, 20 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1
--use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-
image-intensities [ 0.0, 1.0 ] --write-composite-transform 1

32. workflow.run(plugin=“SGE”)
Workflow.run(plugin=“MultiProc”)