There are various steps required to convert the raw data once it has arrived at the CBU to images that SPM will apply preprocessing steps on. Initially, if the data have been acquired on the new standard EPI protocols (for instance, those with a 1.1s or 1.6s TR), then we also need to reconstruct the data ourselves. Following this, the reconstructed data need to be converted to Analyze format, so that SPM can read the images. Finally, the 4D Analyze images created need to be split into 3D images (without a time component per image).
Each of these stages can be accomplished by in house software at the command prompt (see below). However, there is a useful program that creates a batch file to automatically perform all the stages above (or a subset of these as the need arises), as well as a few other common steps carried out at this stage (writing appropriate directories out to place the different types of files, copy phase maps and structural images to useful locations, etc.). See Daniel Bor's MakefMRIBatch page for details about how to run this program and the batch file it generates.
Getting the data
If you have Bruker data from the Wolfson Brain Imaging Centre, see the Bruker data page. If you followed the steps in these pages, you should now have 4D (X,Y,Z, time) Analyze format images for the functional runs, and 3D images for the structural etc scans.
Making images for SPM
There are two steps needed before processing the data with SPM; you will need to convert the 4D functional images into a series 3D volumes, with one volume for each time point. Then you may need to discard a few dummy scans from the beginning of the time series. Deleting dummy scans is useful because there is a large signal change in the first few images in a functional dataset, as the tissue reaches a steady state of radiofrequency excitation. We usually discard 15 seconds of data (5 scans with a TR of 3, 8 scans with a TR of 2).You can make the 3D volumes and discard the dummies with the ana4dto3d program. If you do not use ana4dto3d to throw away the dummies, and you are going to discard the first few images, now would be a good time to move them out of the directory with the other images, or delete them if you are brave.
Diagnostics
If you have used ana4dto3d, you might have created a mean and variance image for the functional runs. It is a good idea to inspect these using SPM or MriCro, to look for reconstruction or data acquisition problems (funny brain shape, strange effects on lower image slices, high ghost variance, radiofrequency artefact). See the FMRI diagnostics page for details.
Now, you can start SPM 99 / SPM2...