Questions Regarding Intra-Subject Inter-Session Registration

Context: I have 6 scans taken from the same subject (3 different sessions). I am interested in inter-session registration.

The information below was helpful.

3dvolreg -twopass -clipit -zpad 4 -base S1+orig \
-prefix S2reg S2+orig

3dZeropad -z 4 -prefix E1pad E1+orig

3dvolreg -clipit -base ‘E1pad+orig[4]’ -prefix E1reg \

3dvolreg -clipit -base ‘E2+orig[4]’ \
-rotparent S2reg+orig \
-gridparent E1reg+orig \
-prefix E2reg E2reg+orig

Before I move forward there are four things I am trying to figure out.

  1. I might be missing something but where is the E1 being aligned with S1? 3dvolreg is not good for alignment of different types of scans so is this being done before or after what I have posted above?
  2. I might be misunderstanding the nature of rotparent but in the final step (shown above) it seems that you are aligning to the structural as well because you are using information from the alignment of the two structural scans to inform the rotation/shift of E2. If this is true is it assuming the E2 was already aligned with S2?
  3. If rotparent takes care of the epi to structural alignment then, if I am not mistaken, I can just align each of my structural scans to S1 and then for EX plug -rotparent SXreg+orig into the step that lines the epi scans to a base epi to make sure everything is aligned with the first scan as well?
  4. If I am wrong about rotparent then should I just feed everything into right into 3dAllineate?

I assume this is related to your more recent post today, but just in case… That was from a very old document, not the most current one. The most current recommendations are in the later documents and particularly in’s help for general pipeline recommendations and options.

It is related to the post from today and thanks again