Daniel,
You can't do these types of statistics on 2 subjects. It looks like #1
is correct, but #2 is odd as S3 is the first scan collected and S4 is
the last scan collected. If the scans go from S1 to S6, then you will
want the covariate to go in the same direction across all scans. [-2.5
-1.5 -.5 .5 1.5 2.5]
Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Mon, Feb 25, 2013 at 1:20 PM, Daniel Cole <[log in to unmask]> wrote:
> Hello FSLers,
> I'll start by explaining my experiment. We have 2 monkey subjects who have
> been receiving training on an identical test over the period of months. I
> currently have 6 structural scans (6 test sessions) and would like to 1) see
> if any one session is different from the last (6th) scan and 2) see if there
> is a linear growth or shrinking of grey matter over the 6 sessions.
>
>
> 1) ANOVA 1 Factor 4-Levels (Repeated Measures)
> From looking at the FEAT Manual
> (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT/UserGuide#FEAT_Basics) I've
> created the following design matrix and contrasts. The first two EVs are
> separate mean EVs for each subject and the rest model each session (except
> the 6th) across both subjects.
>
> Matrix
> 1.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> 0.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> 0.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> 0.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> 0.000000e+00 1.000000e+00
> 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> 0.000000e+00 0.000000e+00
> 0.000000e+00 1.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> 0.000000e+00 0.000000e+00
> 0.000000e+00 1.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> 0.000000e+00 0.000000e+00
> 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> 0.000000e+00 0.000000e+00
> 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00
> 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> 0.000000e+00 1.000000e+00
> 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> 0.000000e+00 0.000000e+00
>
> Contrasts
> C1:1-6 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> 0.000000e+00 0.000000e+00 *
> C2:2-6 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> 0.000000e+00 0.000000e+00 *
> C3:3-6 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> 0.000000e+00 0.000000e+00 *
> C4:4-6 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00 *
> C5:5-6 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> 0.000000e+00 1.000000e+00 *
> C6:6-1 0.000000e+00 0.000000e+00 -1.000000e+00 0.000000e+00 0.000000e+00
> 0.000000e+00 0.000000e+00 **
> C7:6-2 0.000000e+00 0.000000e+00 0.000000e+00 -1.000000e+00 0.000000e+00
> 0.000000e+00 0.000000e+00 **
> C8:6-3 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 -1.000000e+00
> 0.000000e+00 0.000000e+00 **
> C9:6-4 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> -1.000000e+00 0.000000e+00 **
> C10:6-5 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> 0.000000e+00 -1.000000e+00 **
> * and ** denote F-Tests
>
> My questions for the ANOVA are a) Is this the correct setup for the question
> I posed (looking for any difference effect with N scan and the 6th scan)?
> and b) What exactly would the -1 contrasts be showing? The activation for
> corresponding contrasts (C1 and C6) have no overlap, which might be
> expected, but I'm still unsure "what question" this contrast is asking.
>
>
> 2) Linear Trend
>
> Matrix
> 1.000000e+00 0.000000e+00 -2.500000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00 -1.500000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00 -5.000000e-01 0.000000e+00
> 1.000000e+00 0.000000e+00 5.000000e-01 0.000000e+00
> 1.000000e+00 0.000000e+00 1.500000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00 2.500000e+00 0.000000e+00
> 0.000000e+00 1.000000e+00 0.000000e+00 -2.500000e+00
> 0.000000e+00 1.000000e+00 0.000000e+00 -1.500000e+00
> 0.000000e+00 1.000000e+00 0.000000e+00 -5.000000e-01
> 0.000000e+00 1.000000e+00 0.000000e+00 5.000000e-01
> 0.000000e+00 1.000000e+00 0.000000e+00 1.500000e+00
> 0.000000e+00 1.000000e+00 0.000000e+00 2.500000e+00
>
> Contrasts
> C1: Sub1 Mean 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> C2: Sub2 Mean 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> C3: Sub1 Linear+ 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> C4: Sub2 Linear+ 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> C5: Sub1 Linear- 0.000000e+00 0.000000e+00 -1.000000e+00 0.000000e+00
> C6: Sub2 Linear- 0.000000e+00 0.000000e+00 0.000000e+00 -1.000000e+00
>
> Does this design look appropriate for the question- 'Where is grey matter
> increasing linearly across sessions and where is it decreasing?'
>
>
> Thank you very much for your time and help in teaching me to understand this
> program.
>
> Daniel
> --
> Daniel Cole
> University of Rochester
> Brain and Cognitive Sciences
> [log in to unmask]
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