Automatic Analysis Recipes
These apply to the development version, soon to be released (Sep 2006).
== Issues
Order of slice timing and motion correction
Slice timing correction involves resampling through time but not moving images, while motion correction involves moving images relative to each other. There is no simple answer to which should be done first. If slice timing is done first, then if there are abrupt movements between scans, the interpolation across time will be blurring across voxels from different parts of the brain in its correction. If motion correction is done first, then the slices in the image no longer always correspond to order of acquisition of the slices.
If you use an interleaved slice order during acqusition (no longer the default at the CBU - see [http://imaging.mrc-cbu.cam.ac.uk/imaging/TipsForDataAcquisition#head-050cc11391e60b6442119a9e05cb0936e1659bf1 discussion of slice order] then you will probably want to apply slice timing before motion correction. Because all of the odd-numbered slices are acquired first, and the all the even ones, adjacent slices are acquired apart in time (0.5 * TR = around a second). A shift in the image by motion correction of 1 slice (4 mm) will cause a substantial shift in acqusition time for a particular slice, and slice timing will not be at all appropriately applied.
If you use a sequential slice order during acquisition, many people prefer to apply motion correction before slice timing. I do not know if this has been evaluated in any thorough way.
Slice timing or not?
Some people prefer to not use slice timing, and instead, to put temporal derivatives and