Hi,

After trawling some more thorough the archives I was able to figure out that the solution to my problem (re. Index exceeds matrix dimensions.error) was that I needed to select "First functional volume as reference" in "functional Direct Segmentation and Normalization".

With regards the scrubbing covariate, the issue was that the values of FD were very high because they were being calculated from the motion parameters in fsl, which are swapped with respect to spm. So the last 3 parameters in fsl need to be the first 3 parameters in spm. 

Juan