Hi Mark,
you're on your own I'm afraid, this is not implemented (yet?) in FSL!... But I'm sure some FSLers will have some good recommendations.
Cheers,
Gwenaëlle
--- En date de : Mer 14.4.10, Walterfang, Mark <[log in to unmask]> a écrit :
> De: Walterfang, Mark <[log in to unmask]>
> Objet: Re: [FSL] FSLVBM GLM Setup
> À: [log in to unmask]
> Date: Mercredi 14 avril 2010, 0h13
> Hi again Gwenaelle
>
> Happy to do a multivariate analysis - what's the best way
> to approach this?
>
> Rgds
>
> Mark
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
> On Behalf Of Gwenaëlle DOUAUD
> Sent: Wednesday, 14 April, 2010 12:25 AM
> To: [log in to unmask]
> Subject: Re: [FSL] FSLVBM GLM Setup
>
> Hi Mark,
>
> I'd be happy with just the three two-way comparisons :-).
>
> However if you have the possibility, as univariate test
> between illness 1 and 2 does not yield significant results
> despite you having the feeling that illness2 is more severe,
> you might want to do a multivariate (type SVM) analysis on
> the processed GM images to maybe increase your sensitivity
> and obtain some way of distinguishing illness 1 from 2...
>
> Cheers,
> Gwenaelle
>
> --- En date de : Mar 13.4.10, Mark Walterfang <[log in to unmask]>
> a écrit :
>
> > De: Mark Walterfang <[log in to unmask]>
> > Objet: Re: [FSL] FSLVBM GLM Setup
> > À: [log in to unmask]
> > Date: Mardi 13 avril 2010, 13h58
> > Hi again Gwenaëlle
> >
> > Many thanks, that's most helpful. Just finally - if
> you were a
> > reviewer and saw just the three two-way comparisons,
> would you ask for
> > the three-group analysis and post-hoc t-tests, or
> would you be happy
> > with the three two-way analyses?
> >
> > Rgds
> >
> > Mark
> >
> >
> > On 13/4/10 9:01 PM, "Gwenaëlle DOUAUD" <[log in to unmask]>
> > wrote:
> >
> > > Hi Mark,
> >
> >
> > > Thanks for your response - I guess I am
> interested in
> > the
> > >
> > > result of an
> > > F-test across the three samples so it sounds like
> it
> > will
> > > be
> > > worth a try.
> >
> > Sure, but bear in mind that it will only tell you
> where are the
> > > significant changes across the 3 groups, so you
> will
> > still need to run the
> > > post-hoc t-tests on each pair of groups to
> determine
> > what's "driving" these
> > > results.
> >
> > > With regards to what my question is: it's
> partially answered by my
> > > results from the three 2-way analyses. I see that
> illness1 vs
> > > controls shows some key reductions; illness2 vs
> controls shows more
> > widespread
> > >
> > > reductions and in
> > > larger clusters; illness1 vs illness2 shows no
> differences in either
> > > direction. I'm interested in whether illness1 vs
> > > illness2
> > > really differ, as
> > > the separate comparisons against controls implies
> that they should,
> > > but a direct comparison between them suggests
> that they don't.
> >
> > Yes, it can happen, this means that though illness2
> seems
> > > more severe, this is not a significant effect.
> >
> > > (My numbers are
> > > 20-30 in
> > > each group). Does method II assist in this?
> >
> > There is no way of knowing for
> > > sure, and if it does when you'll do the post-hoc
> > t-test between illness1 and
> > > 2, this would be just because you have increased
> your
> > DoFs, not because you
> > > would have asked a different question...
> >
> > Cheers,
> > Gwenaelle
> >
> >
> >
> >
> > > Rgds
> > >
> > >
> > > Mark
> > >
> > >
> > > On 13/4/10 4:20 AM, "Gwenaëlle DOUAUD"
> > > <[log in to unmask]>
> > > wrote:
> > >
> > > > Hi Mark and Jay,
> > >
> > > there is no
> > > good answer to this question I'm afraid.
> > >
> > > Say
> > > > you've got two subjects
> > > in group A, 3 in B and 4 in C,
> > > then both approaches
> > > > are valid:
> > >
> > >
> > > Method I
> > >
> > > A B
> > >
> > > 1 0
> > > 1 0
> > > 0 1
> > > 0 1
> > > 0 1
> > > for the design.mat of the
> > > first
> > > > A and B groups with
> > >
> > > 1 -1 (A-B)
> > > -1 1 (B-A)
> > > for the
> > > design.con
> > > and then repeat
> > > > for groups B and C, then groups A and C
> > > (which is what
> > > you did Mark).
> > >
> > > Method
> > > > II
> > >
> > > A B C
> > >
> > > 1 0 0
> > > 1 0
> > > 0
> > > 0 1 0
> > > 0 1 0
> > > 0 1 0
> > > 0 0 1
> > > 0 0 1
> > > 0 0 1
> > > 0 0 1
> > > for the
> > > >
> > > design.mat of the 3 groups with
> > >
> > > 1 -1 0 (A-B)
> > > -1 1 0 (B-A)
> > > 0 1 -1
> > > (B-C)
> > > 0 -1 1
> > > > (C-B)
> > > 1 0 -1 (A-C)
> > > -1 0 1 (C-A)
> > > for the design.con
> > > (t-tests)
> > > and
> > >
> > > 1 0 1 0 0
> > > > 0
> > > for the design.fts (F-test, as many
> > > columns as there are
> > > rows in your
> > > > design.con, you just need to click in
> > > "F-tests" in the
> > > Glm gui and then click
> > > > in front of the two relevant
> > > "Contrasts" you have
> > > already set up)
> > >
> > > So with
> > > > Method II, you can
> > > also ask the question of where are
> > > the changes *across the
> > > > 3 groups*
> > > (F-test with the design.fts). You also get an
> increase in DoF but,
> > > > as
> > > Tom Nichols said, if it happens that group C for
> instance has wildly
> > > >
> > > smaller variance, you can get inflated
> significances (or reduced
> > > power if it
> > > > has wildly larger variance).
> > >
> > > So it depends on what your main
> > > question is,
> > > > really.
> > >
> > > Hope this helps,
> > > Gwenaelle
> > >
> > >
> > > --- En date
> > > de : Lun 12.4.10, Mark
> > > > Walterfang <[log in to unmask]>
> > > a
> > > écrit :
> > >
> > > > De: Mark Walterfang
> > > > <[log in to unmask]>
> > > > Objet:
> > > Re: [FSL] FSLVBM GLM Setup
> > > > À:
> > > > [log in to unmask]
> > > > Date: Lundi 12
> > > avril 2010, 14h18
> > > > Hi all
> > > >
> > > > I'm in the
> > > > same situation as Jay. I
> > > have three groups
> > > > (illness1, illness2
> > > > and
> > > > controls), all matched
> > > to each other. I've run three
> > > > two-way analyses,
> > > >
> > > > which is pretty
> > > laborious and I'm pretty sure it's
> > > not
> > > > statistically
> > > > ideal.
> > > > What
> > > I can't work out is how to set up the design
> matrices
> > > > &
> > > > contrasts
> > > in
> > > > the way Jay describes, as the online manual
> for
> > > Randomise
> > > >
> > > >
> > > doesn't really
> > > > provide guidance here. Gwenaëlle, is this
> > something
> > > you
> > >
> > > > can
> > > > advise on?
> > > >
> > > > Thanks in advance,
> > > >
> > > > Mark Walterfang
> > > >
> > >
> > > >
> > > > On 10/4/10
> > > > 12:29 PM, "Jay Ives" <[log in to unmask]>
> > > > wrote:
> > > >
> > >
> > > > > I have 70 subjects in
> > > > 4 groups and would like to test
> > > > between
> > > individual
> > > > > groups and
> > > > combinations of the groups. Can someone
> > > >
> > > please advise me how to set
> > > > > up
> > > > the design.mat and design.con files
> > > to do this?
> > > > Thx
> > > >
> > > >
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> > >
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> > >
> > >
> > > Dr Mark Walterfang
> > > Consultant
> > > Neuropsychiatrist
> > > Neuropsychiatry Unit
> > > Level 2, John Cade Building
> > > ROYAL
> > > MELBOURNE HOSPITAL 3050 AUSTRALIA
> > > T +61-3-93428750
> > > F +61-3-93428483
> > > E
> > > [log in to unmask]
> > > W www.neuropsychiatry.org.au
> > >
> > > Research
> > > Fellow
> > > Melbourne Neuropsychiatry Centre
> > > University of Melbourne
> > > Level 2
> > > & 3, Allan Gilbert Building
> > > 161 Barry St
> > > CARLTON SOUTH 3023 AUSTRALIA
> > > T
> > > +61-3-83441800
> > > F +61-3-93480469
> > > E [log in to unmask]
> > > W
> > > www.psychiatry.unimelb.edu.au/mnc
> > >
> >
> >
> >
> >
> >
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> >
> >
> > --
> > Dr Mark Walterfang
> > Consultant Neuropsychiatrist
> > Neuropsychiatry Unit
> > Level 2, John Cade Building
> > ROYAL MELBOURNE HOSPITAL 3050 AUSTRALIA T
> +61-3-93428750 F
> > +61-3-93428483 E [log in to unmask]
> W
> > www.neuropsychiatry.org.au
> > --
> >
>
>
>
>
>
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