Hello to the SPM community
I have recently been using SPM's 'realign' tool to estimate motion parameters for image-navigators (in my case, FatNavs acquired using a fat-excitation) which are then used to retrospectively correct the 3D k-space of the structural host sequence to reduce motion artifacts in high resolution imaging (some more details available here: http://www.cibm.ch/page-117748-en.html ).
In attempting to find the 'optimal' parameters for my navigator (in terms of voxel size and parallel acceleration) I have discovered that the estimated motion parameters are quite dependent on the choice of the 'sep' and 'fwhm' parameters in realign. Would someone please be able to describe how I should choose the values for these parameters? - The SPM manual implies that 'sep' should be as small as possible - but for FWHM suggests only to use 7mm for PET and 5mm for MRI, and doesn't put this into perspective with respect to voxel size. I assume here 'MRI' refers to fMRI experiments with large EPI voxels...
The specific experiment which I have completed to test various navigator parameters involved acquiring data with several subjects making small head movements while 2mm images were acquired. I then downsampled these images to various resolutions and acceleration factors, and would like to see how far this can be done while still getting good motion estimation. Should I use the same 'sep' and 'fwhm' for all image resolutions?
A further consideration is that of the 'register to mean' option. This would seem to be a good idea in order to get the most robust motion estimates - but in this validation experiment comparing different navigator resolutions I suspect it may introduce a bias in the comparison if the 'zero-motion' case is not quite the same for each image resolution. Am I right to think this could be a problem?
Thanks for any help and suggestions you may have for this.