I hadn't thought about it from a dof perspective, so given that, the
approach I'm actually using seems to be more conservative (I am
actually fitting each contrast's highest level in a separate model).
Seems like I could be committing a grave error with the one-big-model
approach and at best missing out on a much smaller correction.
Certainly, it is not easy to find anything on the forums, and I
couldn't find anything on this. The docs essentially never treat the
issue of multiple contrasts.
Thanks David!
Dav
On Nov 10, 2009, at 8:29 AM, David V. Smith wrote:
> OK -- I think I see your concern now, but I don't think you really
> have to worry about that (just dig through the forums a bit more,
> and I know you'll find a post where this has come up before). As far
> as I know, this is a fairly standard way of doing the subject-level
> analysis that isn't just specific to FSL...
>
> With your way, it seems like you're giving yourself free DFs (since
> the number of inputs you'd have would be subjects*copes). I guess
> that may not be a concern, but it still seems like an odd way build
> a model for a specific prediction. One of the FSL folks will have to
> respond with a more detailed information if you can't find what
> you're looking for on the forums... Sorry.
>
> Cheers,
> David
>
>
>
> On Nov 10, 2009, at 2:08 AM, Dav Clark wrote:
>
>> 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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