Hi Steve -
OK, sorry for my misunderstanding!
But then, what I don't understand is that I'll have 4 thresholded zstrats maps at the output of the 3rd level analysis averaging the effect of each condition across subjects... So, what should I use as a mask for the differential testing? Should I create a single mask with the areas activated in each of the 4 conditions, or is there a more simple way?
Thank you very much
Stephane
On Thu, 30 Nov 2006 07:54:57 +0000, Steve Smith <[log in to unmask]> wrote:
> Right - so I'm suggesting that you take these mean effects (which
> will be stronger than the differential contrasts between the
> conditions that you were discussing before) and use them (see the
> post-stats tab in FEAT) as a pre-threshold mask when running the
> differential contrasts between conditions; this cuts down the search
> space for the differentials and a) helps interpretation of them and
> b) increases sensitivity.
>
> Cheers, Steve.
>
>
> On 29 Nov 2006, at 18:29, Stephane Jacobs wrote:
>
> > Thanks again for the clarification, Steve.
> > I am just a little bit confused by you last point:
> >
> >> Case 1 would be fine. This is a good idea, as you can use the output
> >> from the group-mean non-differential testing as a pre-threshold mask
> >> for the differential testing, which will reduce the multiple-
> >> comparison-correction.
> >
> > What exactly do you call "differential testing"? Here I just want
> > to have the mean affect for each condition at the group level, not
> > compare them with one another...
> >
> >
> > Thanks, your help is really appreciated!
> >
> > Best,
> >
> > Stephane
> >
> >
> >
> >
> >
> >>> On Wed, 29 Nov 2006 11:08:33 +0000, Steve Smith
> >>> <[log in to unmask]> wrote:
> >>>> Hi - this is pretty much right, though it does include cross-
> >>>> session
> >>>> and cross-subject variance within one analysis, which means that if
> >>>> you intend this to be a cross-subject mixed-effects analysis (which
> >>>> you probably do) then you are overestimating the degrees-of-freedom
> >>>> in this analysis and your results will be over-liberal. Ideall, you
> >>>> should move the cross-session analyses into a second-level
> >>>> analysis,
> >>>> and bring single image summaries for each condition of each subject
> >>>> up into the quadrupled-t-test-across-subjects for a third-level
> >>>> analysis (ie a combination of what you have here and the three-
> >>>> level
> >>>> example in the manual).
> >>>>
> >>>> Cheers, Steve.
> >>>>
> >>>>
> >>>> On 28 Nov 2006, at 19:05, Stephane Jacobs wrote:
> >>>>
> >>>>> Hello everyone,
> >>>>>
> >>>>>
> >>>>> Sorry to bug you with the details of my analysis, but I would need
> >>>>> to check
> >>>>> that what I'm doing is correct... I have of course looked up the
> >>>>> archives,
> >>>>> but did not find the answers to ALL my questions.
> >>>>>
> >>>>> I have 16 subjects, each scanned under 4 conditions, 2 or 3
> >>>>> runs per
> >>>>> condition (depending on the subject). I would like to contrast
> >>>>> these
> >>>>> conditions with each other. I therefore used an extended
> >>>>> version of
> >>>>> the
> >>>>> Tripled T-test described in the FEAT manual, with a design as
> >>>>> follows (with
> >>>>> only 2 subjects, 3 runs per condition, for the sake of clarity):
> >>>>>
> >>>>> EV1 EV2 EV3 EV4 EV5
> >>>>> S1 – Ar1 1 1 1 1 0
> >>>>> S1 – Ar2 1 1 1 1 0
> >>>>> S1 – Ar3 1 1 1 1 0
> >>>>> S1 – Br1 -1 0 0 1 0
> >>>>> S1 – Br2 -1 0 0 1 0
> >>>>> S1 – Br3 -1 0 0 1 0
> >>>>> S1 – Cr1 0 -1 0 1 0
> >>>>> S1 – Cr2 0 -1 0 1 0
> >>>>> S1 – Cr3 0 -1 0 1 0
> >>>>> S1 – Dr1 0 0 -1 1 0
> >>>>> S1 – Dr2 0 0 -1 1 0
> >>>>> S1 – Dr3 0 0 -1 1 0
> >>>>> S2 – Ar1 1 1 1 0 1
> >>>>> S2 – Ar2 1 1 1 0 1
> >>>>> S2 – Ar3 1 1 1 0 1
> >>>>> S2 – Br1 -1 0 0 0 1
> >>>>> S2 – Br2 -1 0 0 0 1
> >>>>> S2 – Br3 -1 0 0 0 1
> >>>>> S2 – Cr1 0 -1 0 0 1
> >>>>> S2 – Cr2 0 -1 0 0 1
> >>>>> S2 – Cr3 0 -1 0 0 1
> >>>>> S2 – Dr1 0 0 -1 0 1
> >>>>> S2 – Dr2 0 0 -1 0 1
> >>>>> S2 – DR3 0 0 -1 0 1
> >>>>>
> >>>>>
> >>>>> And I have set the contrasts as following, assuming that the
> >>>>> weight
> >>>>> for each
> >>>>> contrasts would be A = a + b + c; B = -a; C = -b; D = -c (a for
> >>>>> Ev1, b for
> >>>>> EV2 and c for EV3).
> >>>>>
> >>>>>
> >>>>> EV1 EV2 EV3 EV4 EV5
> >>>>> A – D 1 1 2 0 0
> >>>>> D – A -1 -1 -2 0 0
> >>>>> B – C -1 1 0 0 0
> >>>>> C – B 1 -1 0 0 0
> >>>>> A – B 2 1 1 0 0
> >>>>> B – A -2 -1 -1 0 0
> >>>>> D – C 0 1 -1 0 0
> >>>>> C – D 0 -1 1 0 0
> >>>>> AB – CD 0 2 2 0 0
> >>>>> CD - AB 0 -2 -2 0 0
> >>>>>
> >>>>>
> >>>>> So, basically my question is simple: is this correct? :-)
> >>>>>
> >>>>> I think it is, if I understood the Tripled T-test example, but
> >>>>> it's
> >>>>> counter-intuitive enough for me to still doubt... Especially since
> >>>>> I average
> >>>>> across sessions within each subject.
> >>>>>
> >>>>>
> >>>>> Also, I will run a separate second level analysis to get the mean
> >>>>> group
> >>>>> effect for each condition, with an EV per condition, and an input
> >>>>> per run
> >>>>> within each subject. Still correct?
> >>>>>
> >>>>>
> >>>>> Thanks a lot for all your help!
> >>>>>
> >>>>> Best regards,
> >>>>>
> >>>>> Stephane
> >>>>
> >>>>
> >>>> -------------------------------------------------------------------
> >>>> --
> >>>> ---
> >>>> ---
> >>>> 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
> >>>> -------------------------------------------------------------------
> >>>> --
> >>>> ---
> >>>> ---
> >>>>
> >>
> >>
> >> ---------------------------------------------------------------------
> >> ---
> >> ---
> >> 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
> >> ---------------------------------------------------------------------
> >> ---
> >> ---
> >>
>
>
> ------------------------------------------------------------------------
> ---
> 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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