Dear Alfonso,

I have a question regarding realigment and running ART.
In my preprocessing pipeline I started with slice time correction & motion correction. Several steps later, after distortion correction (performed outside of CONN), I found myself forced to do a (minimal) manual reorientation as images no longer alligned well enough with the SPM template T2 to do normalization. I expected this not to impact my realignment parameters. To test this I ran realignment in a single subject: one original scan, and one slightly reoriented (not motion corrected previously). It turns out that the parameters do differ.

My questions are
1) Why are the motion parameters affected by reorientation? I thought the images would just be realigned with the first image, hence it wouldn't matter how the images are oriented?
2) depending on the first question/answer: I want to use the motion parameters to run ART. How would the reorientation (and altered motion parameters) affect this processing step? 

Many thanks in advance.
Best regards,
Bram