Help with thesis

Hai everyone..

I am now working on a project, which measures perfusion in a part of brain, before and after a therapeutic intervention. This procedure is done in one side of the brain, and hence the perfusion measurement in one side acts as a sort of control. So I have perfusion measurements in 'affected' side of the brain, and 'normal' side of the brain, before and after intervention (pre affected, pre not affected, post affected and post not affected).

So what i was thinking to do was,
1. check means of perfusion in affected and not affected side -- to show that in the affected side, it is actually less
2. measured increase in perfusion in the affected and not affected side -- to show that in affected side, it is increased more than the normal side

3. somehow, perfusion studies done in different times are not that comparable (limitation of the measurement process). so i used perfusion from a 'standard' area in each sample, which is very less likely to vary due to the intervention, and vary only due to the measurement process. I divided the perfusion values with the standard value, to get an unitless normalized perfusion value. Did step 1 and 2 again, for this value.

4. the other thing i did was, dividing the affected side perfusion by normal side perfusion and comparing with affected side by normal side perfusion after intervention. Theory is that, perfusion difference will be there on both sides bfore intervention and it sorts of become equal after intervention.

for eg, for a sample patient,
affected side pre - 40
affected side post - 70
not affected side pre - 60
not affected side post - 65
standard perfusion pre - 100
standard perfusion post - 80

1. 40 is actually less than 70
2. difference of 70-40 is more, compared with 65-60
3. normalized perfusion become 0.4, 0.75, 0.6 and 0.81 (aff pre, aff post, not aff pre, not aff post) respectively. Now the difference is 0.75-0.4 and 0.81-0.6 respectively.

Doubts are,

a. for 1. comparing affected and not affected side, for each patients, can i use paired t test? I was having doubt, if it could be used only for before and after intervention (for eg, affected side before and after)
b. for 2. again paired t test?
c. in 3, i dont actually expect a difference between the pre and post intervention in the non-affected side (0.81-0.6). This difference of 0.21 is actually process related and likely to happen in the affected side also. ie, out of 0.35 (0.75-0.4), some may be due to process and itself and some due to the intervention. is there any way to neutralize this? Obviously i cant use 0.21 as due to the process in the affected side also. How should i correct for this difference induced by the process itself. I was thinking, = (0.75-0.4)/1-(0.81-0.6) or (0.75-0.4)/(0.81/0.6).

Please help and thanks.