The official website for SPM can be found here.
This page describes the processes used to analyse fMRI data using SPM in its GUI mode.
DICOM Conversion
COREGISTERING ANATOMICAL TO TEMPLATE
The concept of coregistration is discussed below. This step needs to be done once before any other pre-processing is done.
REALIGNMENT
The first step in statistical parametric mapping is realignment (aka motion correction). This step registers all the images of a specified run from one subject to each other, and gives us information regarding how much the subject moved their head during the scan. This information is later used to ensure that functional images are accurately mapped onto structural ones.
- On the SPM menu, click "Realign," and from the drop-down menu, select "Est and Res" (estimate and reslice).
- Under the "Data" heading, use the "Session" file selector to select all the converted DICOM files of the specified run for the subject.
- For "Estimation options," "Quality" controls the quality of the images generated, on a range of 0 to 1. The "Interpolation" option also increases quality of images, with higher degree B-Spline options producing higher quality images. This should be changed to a minimum of "4th Degree B-Spline." The rest of the "Estimation Options" can be left as they are.
- Under "Reslice Options," the "Resliced Images" option should be changed to "Mean Image only". The rest of the options can be left as they are.
COREGISTRATION
Coregistration refers to the spatial alignment of a series of images.