Hi Bo, you can think of  the Ftest as a logical 'OR' between the t-test contrasts indicated in each row. Each row is a difference of differences, so

1. (A-B)om - (A-B)pm --> Does the difference between A and B differ between groups O and P for Males?
2. (A-B)om - (A-B)qm
3. (A-C)om - (A-C)pm
4. (A-C)om - (A-C)qm
5. (A-B)of - (A-B)pf --> Does the difference between A and B differ between groups O and P for Females?
6. (A-B)of - (A-B)qf
7. (A-C)of - (A-C)pf
8. (A-C)of - (A-C)pf

I've put together the first 9 columns of the first 4 rows. The last 9 columns are all 0s. For the last for rows, the 0s and below matrix are swapped to give you the same for the females

doug

 AOM  BOM  APM  BPM  AQM  BQM  COM  CPM  CQM                                 
--------------------------------------------------------------------------
 +AOM -BOM -APM -BPM    0    0    0    0    0                                 
 +AOM -BOM    0    0 -AQM +BQM    0    0    0                                 
 +AOM    0 -APM    0    0    0 -COM +CPM    0       &nb sp;                         
 +AOM    0    0    0 -AQM      -COM    0 +CQM                                 
 

On 11/17/12 9:21 PM, xiangbo_2010 wrote:

Hi Freesurfer experts,

I'm very sorry to bother you, but I am very confused with the following questions:

My experimental design includes three discrete factors:  factor 1 with three levels (A,B,C ); factor 2 with three levels (O,P,Q); gender (F, M), and one covariate.

So I can get 18 classes: FAO, FAP,FAQ,FBO,FBP,FBQ,FCO,FCP,FCQ,MAO, MAP,MAQ,MBO,MBP,MBQ,MCO,MCP,MCQ.  I want to perform the interaction between factor 1 and factor 2 regressing out the effect of gender and one covariate, but I don't know the rules for setting the contrasts for the F-test.  The contrast matrix I used is:

1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

1 0 -1 1 0 -1 1 0 -1  0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

0 0 0 0 0 0 0 0 0 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

is it correct?  

 

Any help will be very appreciated.

 

Best wishes,

 

Bo Xiang 

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