Hi Meredith,
Sorry not to answer your question directly - but I would just
recommend waiting for the new release of FSL, hopefully quite soon -
as this has proper multi-subject ICA - so this is probably the best
route forward for you - hope that's ok?
Cheers, Steve.
On 31 Jul 2007, at 01:29, Meredith Braskie wrote:
> Hi All,
> I’ve been reading through past threads about using melodic at a
> group level and just want to
> make sure I understand what needs to be done, as I am new to using
> melodic like this. We have a
> number of subjects, each of whom has 6 functional scans of the same
> task. We are interested in
> determining which areas on average co-activate with a single region
> of interest, and also want to
> investigate whether the ICAs associated with that ROI will vary
> with another continuous variable
> (such as age) across subjects. Based on past threads, I think we
> need to do the following:
> 1) Run melodic on each individual scan.
> 2) Select ICAs that include our region of interest (except for
> those that are obvious noise).
> 3) Do avwsplit and avwmerge to merge those ICAs of interest into a
> single 4D file for each scan.
> 4) Move all the functional data into common space using flirt to
> create the transformation
> matrix and applyxfm4D to apply it.
> 5) Run flame –cope=4Ddata –vc=4Ddata –mask=mask –ld=stats –
> dm=design.mat –
> cs=design.grp –tc=design.con –jols
>
> Is this correct so far?
>
> My questions are:
> 1) Since we obviously did not do a first level FEAT with the task
> paradigm outlined in the stats,
> what exactly will be the output of the flame? Will it find the
> average of the ICAs? Does it matter if
> there are different numbers of ICAs for each scan?
> 2) Once we have run that second level flame (one for each subject)
> as –jols, will the correct files
> (i.e. copes etc.) be created so that we will be able to perform the
> flame across subjects in the gui?
> If not, how would we proceed to the next step? Will we be able to
> see how certain ICAs are or are
> not present on average as a continuous variable changes across
> subjects?
> 3) I saw that some threads talk about using the Zstats images.
> Should we be using those
> instead of the 4D concatenated files to do what I want to do? If
> so, how?
> 4) In the command applyxfm4D that was suggested for bringing the 4D
> file into common space,
> what is the –singlematrix for?
>
> Sorry for the long email. I just want to make sure we get it right.
> Thank you for your help with this!
> Best,
> Meredith
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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