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

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.

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

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Amanda Rodrigue

Doctoral Candidate

Franklin Foundation Neuroimaging Fellow

Psychology: Brain and Behavior Sciences

University of Georgia