No - the thresholds from lower levels never affect the higher level
analyses. The only pieces information that passed up are the copes and
varcopes.
Tim
-------------------------------------------------------------------------------
Tim Behrens
Centre for Functional MRI of the Brain
The John Radcliffe Hospital
Headley Way Oxford OX3 9DU
Oxford University
Work 01865 222782
Mobile 07980 884537
-------------------------------------------------------------------------------
On Wed, 8 Sep 2004, Ongur, Dost,M.D. wrote:
> Thank you for your mail, this is very helpful.
>
> Another second level analysis question: Do the thresholds that we set at the
> second level have any bearing on the third level analyses? If I set more
> stringent thresholds at the second level, does that reduce my ability to look at
> the data with more liberal thresholds in the third level?
>
> Thanks,
> Dost
>
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of
> Tim Behrens
> Sent: Wednesday, September 08, 2004 4:18 AM
> To: [log in to unmask]
> Subject: Re: [FSL] second level analysis
>
>
> Hi -
> Unfortunately, as you only have two runs per subject, you will not be able to
> estimate a between-session variance separately for each subject.
>
> What we advise under these circumstances is to make the assumption that all
> subjects in a given group have the same between-session variance. Then you
> estimate a single between-session variance for each group, which will
> effectively be added onto the variance associated with the mean of the
> measurements, and be taken up to the third level.
>
> To do this, you could eaither have 1 big design matrix with 2 groups in it, or
> (easier) one design matrix for each group, each of which will look
> like:
>
> GP EV1 EV2 EV3 ....
> 1 1 0 0 ....
> 1 1 0 0 ....
> 1 0 1 0 ....
> 1 0 1 0 ....
> 1 0 0 1 ....
> 1 0 0 1 ....
> . . . . ....
> . . . . ....
>
> con: 1 0 0 ....
> 0 1 0 ....
> 0 0 1 ....
>
>
> If you take the two DM approach, then you can run the group without your new
> subject in, before you collect data from the new subject.
>
> Hope this is useful
>
> T
>
> -------------------------------------------------------------------------------
> Tim Behrens
> Centre for Functional MRI of the Brain
> The John Radcliffe Hospital
> Headley Way Oxford OX3 9DU
> Oxford University
> Work 01865 222782
> Mobile 07980 884537
> -------------------------------------------------------------------------------
>
> On Tue, 7 Sep 2004, Dost Ongur wrote:
>
> > Hello,
> >
> > We have a study with 34 subjects in 2 groups (patient and control).
> > Each subject had 2 identical runs.
> >
> > We are waiting to scan a final patient and have 35 subjects for the
> > ultimate analysis. In the meantime, we would like to go ahead and
> > finish the first and second level analyses for all existing data sets.
> >
> > Is it OK to do the second level analysis (across runs for each
> > subject) for the 34 existing subjects in one large batch and then run
> > the final subject's data when they become available on its own? Would
> > we have to repeat the second level analysis once we have all 35 scans?
> >
> > Thanks,
> > Dost Ongur
> >
>
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