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
>
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