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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 On Thu, Jun 1, 2017 at 11:07 AM, Anderson M. Winkler <[log in to unmask] > wrote: > PS: If you choose to use PALM, with the 4 timepoints, consider using the > "-ise" option. It doesn't require compound symmetry, but requires that the > errors themselves are symmetrical (i.e., have a symmetrical distribution > around zero). > > On 30 May 2017 at 23:23, Anderson M. Winkler <[log in to unmask]> > wrote: > >> Hi Kavous, >> >> What are the research hypotheses? If it's about changes over timepoints, >> and interaction group by timepoint, then this needs the assumption of >> compound symmetry, which is fine for 2 timepoints, but becomes harder with >> 4. If you want to make that assumption, then you can use PALM, defining one >> exchangeablity block per subject, and permuting within-block and also >> whole-block (for the interactions. >> >> If you can't make the compound symmetry assumption, consider Bryan >> Guillaume's toolbox called SwE. It seems the most recent version is on >> GitHub: https://github.com/BryanGuillaume/SwE-toolbox >> >> If, however, the hypothesis is about group differences regardless of >> changes in time, then randomise can be used directly, with the option >> --permuteBlocks. This is the Example 6 of the randomise paper: >> http://www.sciencedirect.com/science/article/pii/S1053811914000913 >> >> Hope this helps! >> >> All the best, >> >> Anderson >> >> >> On 30 May 2017 at 05:05, Kavous <[log in to unmask]> wrote: >> >>> Hi FSLers, >>> >>> I'm going to analyze a longitudinal VBM between 3 groups and within 4 >>> time-points. >>> >>> By reading following discussions, I know that in 2 time-points analysis >>> I have to use all my subjects' data to make a study-specific template and >>> subtract pre-post data after smoothing for randomise analysis. >>> >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;d6651f48.1008 >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;3dc8868b.1408 >>> >>> However, my question is that is there any way to consider all 4 >>> time-points in a single analysis? >>> >>> Thanks, >>> Kavous >>> >> >> >