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
>>>>
>>
|