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Hi Amanda, Please see below: On 25 January 2017 at 15:34, Amanda Rodrigue <[log in to unmask]> wrote: > Thank you so much for the response. So just to clarify, does that mean by > using only the contrast provided say in the first line I am not testing if > there are any regions that are larger in group B than group A. And if I am > interested in both directions I would have to add additional contrasts to > the originals like below: > > 1 -1 0 > 1 0 -1 > 0 1 -1 > -1 1 0 > -1 0 1 > 0 -1 1 > > Exactly. > > Also on an unrelated issue, if I wanted to dump the volume values from > individual subjects, which file would I get that from? Is it the > *GM_to_template_mod.nii.gz? > To give some context I have genotype information for some subjects and > want to see if the regions that are significant in my group comparisons > differ by genotype within and across groups. I don't have enough power to > put the genotypes in the initial analysis so this is more of a pilot thing. > You'd use the same input image that is given to randomise. If using the FSL-VBM pipeline, that would be the file GM_mod_merg_s3. All the best, Anderson > > Thank you! > amanda > > > > On Sat, Jan 21, 2017 at 8:54 AM, Anderson M. Winkler < > [log in to unmask]> wrote: > >> Hi Amanda, >> >> It depends on how the regressors were coded in the design. Take your >> first contrast for instance: [1 -1 0]. It tests if the regression >> coefficient for the first regressor is larger than the second, and ignores >> the third. >> >> Say the coefficients are for group A, group B, and group C. Then another >> way of saying is that the first contrast is the same as testing: >> >> +1*groupA -1*groupB + 0*groupC > 0 >> >> that is the same as: >> >> groupA > groupB. >> >> The same principle goes for the other contrasts. >> >> All the best, >> >> Anderson >> >> >> On 20 January 2017 at 15:51, Amanda Rodrigue <[log in to unmask]> >> wrote: >> >>> Beginner question here. I've run TFCE based analysis on my VBM and have >>> clusters that differ between my groups. Can someone confirm how you figure >>> out what the direction of the difference is since the final output is a >>> p-map? For example how do you know whether group 1 > group2 or the other >>> way around. My design.con file looks like this: >>> >>> 1 -1 0 >>> 1 0 -1 >>> 0 1 -1 >>> >>> I can see the values on the t map but still not sure which group is >>> first when comparing the means (group1-group2 or group2-group1). Is >>> whatever group that is denoted by the positive 1 the first? This seems to >>> make the most logical sense but just want to check if this is correct. >>> Thanks! >>> Amanda >>> >> >> > > > -- > Amanda Rodrigue > Doctoral Candidate > Franklin Foundation Neuroimaging Fellow > Psychology: Brain and Behavior Sciences > University of Georgia >