Hi Martin and Beatriz,

Thank you very much for the clear and helpful feedback. Everything is coming along smoothly!

I am now visualizing group differences in shape alterations (magnitude of differences) in ShapePopulationViewer. I see in your 2009 Insight Journal publication (http://www.insight-journal.org/browse/pu...) that the difference maps show negative values if group A has shrinkage relative to group B, and positive values if group A has expansion relative to group B.

My question is: how can I confirm which group is group A in my study, and which is group B?

I see that, in the terminal in which I'm running shapeAnalysisMANCOVA, there is a printout that reads:
"data in group_type 0 has been relabeled: 1 --> group A = -1 ; 0 --> group B = 1
#(A)= 142; #(B)= 64
data in group_type 1 has been relabeled: 0 --> group A = -1 ; 1 --> group B = 1
#(A)= 250; #(B)= 162"
...which offers some hints. But given my analysis setup, I'm a bit confused as to what this means. Recall that my inputfile.csv file has the following headers:

diagnosis,sex,diagnosis_sex_interaction,Scaling,File,tbv,tbv_dm,age,age_dm

...To inspect a main effect of sex, controlling for tbv_dm and age_dm, with sex, diagnosis and the interaction of sex and diagnosis in the model, my shape command is as follows:

shapeAnalysisMANCOVA inputfile.csv --infileColumn 4 --numGroupTypes 2 --numIndependent 2 --columnGroupTypes 0,1,2 --columnIndependent 6,8 --testColumn 1

From the printout in the terminal, I'm inferring that re: "diagnosis", group A = individuals with a "1" in the diagnosis column, and group B = individuals with a "0" in the diagnosis column. But what about sex? Is there a way I can tell whether individuals with a "1" in the sex column are in group A or group B? Likewise for the "diagnosis_sex_interaction" column.

Many thanks for the continued help!
Lara