Functional MRI Processing Pipelines
There are many processing and analysis steps undertaken on functional MRI (fMRI) images after they are acquired by the MRI scanner.
Processing steps include: image format conversion, slice timing temporal interpolation, within-run image realignment, within-brain masking, spatial normalisation across subjects, spatial smoothing, response modelling, statistical inference and display of results. There are many optional processing steps, and indeed even in those steps listed above there are many choices of methods.
Optimal choices depend upon the type of study, scanner and hypotheses to be tested. Often the optimal choices will require use of multiple software packages. The neuroinformatics laboratory developed the iBrain Analysis Toolbox for SPM to address many of the challenges of automating neuroimaging analyses, ensuring analyses can be repeated and providing provenance of the resultant data (a detailed history of the steps undertaken). The toolbox is designed to work together with the SPM neuroimaging software package, however it also utilises other software packages for some steps when that is advantageous.
See also the iBrain Analysis Toolbox for SPM