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Hi Matt, I used the non bias corrected myelin maps as you said in the HCP mailing list that they are better for calculating group comparisons. Best, Lisa On 22 August 2017 at 13:58, Matt Glasser <[log in to unmask]> wrote: > Which files did you use? > > Peace, > > Matt. > > From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of > Lisa Kramarenko <[log in to unmask]> > Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> > Date: Tuesday, August 22, 2017 at 5:34 AM > To: <[log in to unmask]> > Subject: [FSL] Help with PALM results > > Dear experts, > > I have performed PALM analysis on CIFTI files (myelin maps from HCP). I > used tail approximation and 500 permutations. I did it with the -logp > option so that when I visualise the results I set the threshhold with the > minimum at 1.3 (which corresponds to 0.05) and max to whatever max there is > in the picture. Now my results seem a bit peculiar and I wanted to ask your > advice. > > I have six contrasts (g1>g2, g2>g1 and positive and negative effects of > age and gender). In g1>g2 contrast literally almost whole brain is > significant, whereas in the g2>g1 I cannot even threshhold anything because > everything is zero. The positive effect of age, however, is also > significant almost everywhere. > Now I am a bit confused, a) if the positive effect of age is significant > in almost all regions, should the g1>g2 comparison be not as strong > (because it should be adjusted for the age effect?) Is it normal that g1>g2 > still shows so much significance everywhere (same regions as the positive > age effect)? and b) Even though it is line with my expectations I am a bit > wary to see significant differences covering the whole brain. Is there > maybe some error that might have led to that or something I have to double > check? So far I checked my GLM and input files and cannot find anything > weird/wrong there. > > Sorry for the probably basic question and thanks a lot for the help! > > Lisa >