I'm not sure I completely understand what you're asking. I typically  
do a 3rd level analysis for each cope using the cope image  
(subject.gfeat/cope1.feat/stats/cope1.nii.gz) as the input (i.e., one  
contrast at a time). I've never done it the way you suggest -- under a  
three level set up (runs/subjects/group), I thought we had to go one  
cope at a time. The only times I have multiple cope images in a 3rd  
level model is when I'm doing ANOVAs or paired t-tests -- never for  
simple main effects.



On Nov 9, 2009, at 7:04 PM, Dav Clark wrote:

> Yeah - I was pretty sure that was OK.
>
> One remaining question, though, one could do a single mixed effects  
> model with an EV for each contrast, and then contrasts picking out  
> each EV separately. OR, you can do a mixed effects model for just  
> contrast 1 (i.e. all cope1.feat directories), then another for each  
> remaining contrast.
>
> Does that have any effect on results?
>
> Thanks again!
> DC
>
> On Nov 9, 2009, at 3:57 PM, David V. Smith wrote:
>
>> I actually do a fixed effects analysis for each subject  
>> individually -- and that produces the output you say say you expect  
>> to see. But as long as it's FE, it shouldn't make a difference (cf. https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0908&L=FSL&P=R474 
>> ).
>>
>> The FSL folks will have to look into your request about clarifying  
>> the documentation here.
>>
>>
>>
>> On Nov 9, 2009, at 3:22 PM, Dav Clark wrote:
>>
>>> On Nov 9, 2009, at 6:19 AM, David V. Smith wrote:
>>>
>>>> Alternatively, are you just trying combine multiple sessions that  
>>>> all have the same conditions? If so, the solution is easy:http:// 
>>>> www.fmrib.ox.ac.uk/fsl/feat5/ 
>>>> detail.html#MultiSessionMultiSubject. You could also do this a  
>>>> bit differently by doing a second level fixed effects analysis  
>>>> for each subject.
>>>
>>> Actually, I am also struggling with the docs here right now.  
>>> Specifically, after running an FE analysis as suggested in the  
>>> docs there, you are supposed to:
>>>
>>> "select the 5 relevant directories created at second-level, named  
>>> something like subject_N.gfeat/cope1.feat"
>>>
>>> Thus I would expect something like:
>>>
>>> subject_1.gfeat/cope1.feat
>>> subject_2.gfeat/cope1.feat
>>> ...
>>>
>>> But this is not what happens. You instead get a single gfeat  
>>> directory (named whatever you said to call it) that contains a  
>>> cope directory for each subject. In your example, you'd get  
>>> something like
>>>
>>> fixed_eff.gfeat/cope1.feat
>>> ...
>>> fixed.dff.gfeat/cope5.feat
>>>
>>> (i.e. a copeN directory corresponding to each subject)
>>>
>>> Thus, a reasonable person might assume either the first part or  
>>> the second part of these instructions is misleading and assume  
>>> either:
>>>
>>> 1) I should do a fixed effect model separately for each subject's  
>>> set of runs (thus obtaining subject_N.gfeat directories for each  
>>> subject - 5 such in the example above with 3 copeN.feat  
>>> directories in each). Then, I simply select the cope1.feat from  
>>> each subject and do a flame model on that, then again for the  
>>> remaining two contrasts.
>>>
>>> 2) or perhaps I should do the first part according to the  
>>> instructions and then just select those 5 cope directories for  
>>> each subject in the fixed effects gfeat directory. (this is what I  
>>> did)
>>>
>>> It's not clear to me if there'd be any difference mathematically  
>>> in the above - perhaps some correction for multiple comparisons in  
>>> the latter?
>>>
>>> In any case, I think the wording there could be cleaned up just a  
>>> bit and it'd make the docs a lot nicer to use.
>>>
>>> Cheers,
>>> Dav
>>