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Hi Helmut - thanks for your response. Yes, the data has already been realigned and normalized (as well as low pass filtered) within FSL. And I have the motion realignment parameters - which are stored in a .par file (which is basically a .txt file). The format looks the same (ie 6 columns = 6 regressors, 700 rows = 700 time points in the ts) between SPM and FSL. I don't plan on doing any additional preprocessing within SPM or FSL. I think that I can just input the normalized and realigned 4D functional .nii file to SPM and start the first-level analysis. Thanks, Joelle On Tue, Jun 9, 2015 at 3:06 PM, H. Nebl <[log in to unmask]> wrote: > As far as I understand the original message the data has already been > realigned and normalised within FSL, it seems to be more about the rp text > file. There's nothing special about the rp file, it stores the necessary > translations/rotations needed to reorient the images relative to the first > volume of the series (or the mean volume depending on settings). If you > have preprocessed your data with a different software you will receive a > similar file, as realignment is really a fundamental step. There might be > different conventions though, maybe the realignment parameters are e.g. > based on a different origin, maybe it's not relative to the first or mean > volume but always relative to the subsequent one. However, as long as all > the subjects have been preprocessed the same way with the same package you > don't have to worry about that. The obtained parameters stored in a certain > format would be added during model specification (possibly the format has > to be adjusted though). > > But nonetheless you have to be careful when switching between different > packages. As far as I remember when realigning 4D nii files (just estimate, > no reslice) with SPM the realignment parameters are not stored in the > header of the individual nii files (as there's just one big file) but in an > extra mat file. These parameters are applied during the next module with a > reslice step within your preprocessing pipeline, usually this would be the > normalisation. If you switch between different packages and/or delete the > mat file too early then relevant information would be lost, meaning > although you ran realignment the parameters might actually not be applied > on the data. To avoid this you should stay within a certain package for > preprocessing purpose. > > Best > > Helmut > >