On Thu, Sep 5, 2013 at 2:46 PM, fMRI <[log in to unmask]> wrote:
Hello all,

I have not used one way anova before but I believe it is used for more than two groups.

A a one-way between group ANOVA would be for 2 or more groups.
A repeated measures ANOVA would be for 2 or more conditions.
A mixed 2-way ANOVA would be for 2 or more conditions and 2 or more groups.

 

My experiment involves five conditions, A, B, C, D, and E.

You want a repeated measures ANOVA. 

My aim is to see the relation between the five conditions and whether this increases the activations.

I have specified each condition in a separate regerssor for each subject. Then I contrast each condition versus rest, for example 1 0 0 0 0 0. So I created five contrasts in the first level.

This is correct 

Then, I took the contrast images of the first level from each condition and each subject and entered them into a one way anova. So I had five cells representing the five conditions. Here, I added an F tests like this:
1
0 1
0 0 1
0 0 0 1
0 0 0 0 1

Your ANOVA is missing a subject term and the contrast is invalid.
When you have a repeated-measures ANOVA (in SPM/FSL/etc.), you must compare the levels against each other. You cannot compare a level against 0. The reason for this is that the error term for the model is the within-subject error term and comparing an individual condition (level) against 0 is a between-subject effect and requires the between-subject error term, which is not available in SPM/FSL GLMs.
 

This allows me to investigate the contrast estimate for all of the five conditions.

No. It only allows comparisons of conditions and only if you add a subject factor. 


Questions:

1)is this correct?


See comments above for the changes needed.
 
2) if I would like to investigate a linear or non linear relations between the five conditions, for example acceleration rate - very slow, slow, mid, fast, very fast, and the contrast estimate at a voxel, can test the correlation outside spm and report it OR is there anyway of adding these five condition into spm, for example representing them by 1 2 3 4 5, and then see the relation.

Linear(T-test): -2 -1 0 1 2

Non-linear: custom defined change over level
Non-linear (F-test): 1 -1 0 0 0; 0 1 -1 0 0; 0 0 1 -1 0; 0  0 0 1 -1 



I hope I have explained it clearly:-).

Thank you in advance,
,

Aser