It is 3 (condition) by 2 (group) analysis. I have one sig LV explaining ~50% of variance and a second LV explaining ~25% of the variance but only p=0.15. The first LV provides novel evidence for shared neural activity between the groups and two of the conditions. The second LV nicely separates two of the conditions for one of the groups but not the other and reveals activation in regions consistent with previous research.

Thanks - the info you gave is fine.  What I would suggest is presenting both the p-values and the confidence intervals around the brain scores for both LVs to give an idea of the effect size.  You should also run the two groups separately as a sort of test for simple effects that one would do in an ANOVA type analysis.  You can map these separate analyses to the full analysis by correlating the brainLVs, which you will need to do at the command-line level.  It will be helpful however to show, that for example, in group 1, their dominant effects is split between two LVs for the full group analysis.

You can do this by: (assume Fbrainlv is from the full analysis and g1brainlv and g2brainlv are from the separate group)

Fbrainlv'*g1brainlv

Fbrainlv'*g2brainlv

the products of these will be the cosine (correlation) between analyses, where the rows will be the Full analysis LVs and the columns will be for the separate groups.

Hi,

Just returned from overseas and returning to this analysis. I thought I would show you the brain scores for LV2 and get your opinion. Is this reportable, even though the LV is non-sig? The effect seems to be quite large. I have tried running the groups separately but this doesn't "improve" things.

Thanks for your help.