Hi Anderson,
I am so grateful for your prompt response. I am new to FSL and in particular to PALM. So, sorry for any stupid questions.
Let me explain more about the experiment and the hypothesis. My time points are:
t1: pre-intervention
t2: mid-intervention
t3: post-intervention
t4: follow-up (8 weeks after stopping intervention to see whether effect is persisting or not)
And my three groups are:
G1: control (no effect hypothesized within time points)
G2: intervention1 (small effect hypothesized within t1-t2-t3 + NO persisting effect on t4)
G3: intervention2 (greater effect hypothesized within t1-t2-t3 + persisting effect on t4)
So according to my hypothesis, it seems I should follow your advice on using PALM and -ISE (without the assumption of compound symmetry).
So now a couple of questions arose in my mind:
1) Can I still use semi-autonomous FSLVBM process (i.e., fslvbm_1_bet - fslvbm_2_template - fslvbm_3_proc) and later use PALM?
2) I know that in the longitudinal VBM analysis with two time-points, I should treat each time point as an individual subject, and later before randomize subtract GM_mod_merg_s* files between two time-points. I wonder in my case should I compute all pairwise differences and do PALM for each? (i.e., t1-t2, t1-t3, t1-t4, t2-t3, t2-t4, t3-t4). Does the following command seem right?
palm -i diff_t1_t2_GM_mod_merg_s3.nii -d design.mat -t design.con -m GM_mask.nii -f design.fts -eb eb_file.csv -vg vg_file.csv -T -C 3.1 -n 5000 -save1-p -corrcon -o myresults -ise
3) Should I use [Pset, VG] = palm_quickperms(M, EB, P, ISE) or can I make my own vg.csv file (likewise attachment). If this command is necessary can I use design.mat for M?
4) Can I still use FSL GLM command for making the design matrix? Please see attached design matrix. Is it right matrix in my case?
5) Should I run PALM separately for permuting within-block (using -eb -vg and -within options) and permuting whole-block (using -eb -vg and -whole options)?
Best regards,
Kavous