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> is there a good manual about the preprocessing procedures in spm? The manual is pretty comprehensive (256 pages), but we don't necessarily have all the answers. Everybody has different data and questions that they want to attempt to answer with that data. The choices you make in your analysis will depend on what works best, and empirical exploration is sometimes needed. Chapters 25 and 26 of the manual describe procedures that work well for data from the FIL. I would suggest using these procedures by default, but it is possible that a different strategy may be better for your particular data. Similarly, many of the tools have default settings. In most cases, I would suggest using these values. Just as there is no "canonical design matrix" for fitting any general linear model through time series data, there is also no single pre-processing strategy that works best for everything. There are many different imaging modalities, field strengths, sequences etc. Each of these has its own artifacts, image intensity distributions etc. Repeat times, fields of view etc are all very variable. Some people collect field maps for correcting distortions. Some scans have more or less distortion or dropout than others. All these things should influence the choices that are made. > - do i get better results in normalisation with coreg my epi on the t1 > image and normalize the latter with the t1 template (there is a mail > in the spm list archives, i think it was john ashburners, who prefers > normalization with the mean epi image, but it was according spm99)? This was applicable six years ago, but hopefully the software (and data??) are now rather better than they were back then. This strategy worked reasonably well for data from the FIL scanner, because the tissue intensities and artifacts in the data were similar to those in the templates. Back in the late 20th century, spatial normalization was done by warping the subject's images so that the intensity differences between the image and template were minimized. The relative intensities of the different tissue types had to be similar for the template and individual image for this to work. Things can be done slightly differently by SPM5. If you use the Segment button for estimating spatial normalization parameters, then no assumptions about the intensity of the different tissue types are made - other than grey matter is all about the same intensity, and that white matter and CSF also have fairly uniform intensities. The Segment procedure also models out intensity non-uniformity artifact. In the past, many of the spatial normalization procedures encountered problems because of this artifact - but the situation should be slightly improved by now. It is still possible that using the Segment button with your EPI data could produce more accurate spatial normalization than estimating the warps from your anatomical images, and applying them to your coregistered fMRI data. This will mostly depend on the amount of distortion in your fMRI. Because coregistration only estimates a rigid-body transformation, then it may not necessarily determine an accurate alignment between the functional and anatomical data. Even if your spatially normalized anatomical data are all in alignment with MNI space, if the anatomical and functional data are not in register, then the spatially normalized functional data may not be so accurately aligned with each other. This is something that is data dependant, and may need empirical exploration in order to figure out the best strategy. It is possible that distortions in fMRI data have not been taken seriously enough by us SPM authors. In fact, I'm not sure they are taken seriously enough by others either - especially in terms of the effects of such mis-registration on surface based analysis methods. > or - do i have to estimate & resclice images in the coreg step or is it > enough to just estimate (by the way, reslicing "blows" up my single epi > images to a size of the t1 image (160mb) and therefore it takes hours). As Simon points out, you don't need to do any reslicing at this stage (maybe I'll take out the Coregister and Reslice option from the next SPM release). Avoiding such un-necessary reslicing was my main motivation for introducing the .mat files that confused (and still confuse) so many people for so long. These .mat files are no longer used (except for 4D data). Image orientations are now written straight into the .hdr files. The Check reg button is useful for seeing if your images are considered by SPM to be in register with each other. > the spm5 manual is no real help, because it just describes the single > features, but gives no advise what do do. the typical related papers > are no real help either, because their are overloaded with mathematical > terms and procedures, i do not understand. > so anything around for a dummy who just want to drive a car without > being a mechanic? Currently, SPM can be thought of as a bunch of components - rather than a complete car, so you'll sometimes have to be a mechanic as well as a driver. Making it work in good driving conditions is generally fairly straightforward, but customization is sometimes needed for other situations. One of the features of SPM is that it is relatively easy to get at what is under the bonnet. Best regards, -John