I'll try a different explanation:
1st level: Separate first-level analysis for each run, containing
multiple contrasts - e.g. subject1/scan1.feat
2nd level: FE analysis across run, separately for each subject (group
average) - e.g. subject1/scan1.feat + .../scan2.feat + ... ->
subject1/all_scans.gfeat
3rd level: ME analysis across all copes for a given contrast (group
average) - e.g. subject1/all_scans.gfeat/cope1.feat + subject2/<the
same> + etc.
I understand you could do it a slightly different way and end up with
cope images instead of cope feat directories. My way seems to work
(I'm fortunate in that I have a simple primary motor activation that's
guaranteed to come out in one of my contrasts). I'm just concerned
that I'm cheating in terms of family-wise error, etc. The alternative
I see is incorporating all copes into a single ME analysis, with a
separate contrast for each lower-level contrast (corresponding to a
single EV that picked out all contrasts of a particular type).
Cheers!
Dav
On Mon, Nov 9, 2009 at 7:08 PM, David V. Smith <[log in to unmask]> wrote:
> 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
>>>
>
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