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Hi Sharmili,

Do you really have just 2 subjects, or is this only an example? If there are just 2 subjects, then there isn't enough data I'm afraid, and trying to analyse will likely violate assumptions. To see why, let's forget for a minute that you have 7 measurements per subject and consider just 2: baseline and post-intervention. Then to test the effect of intervention, you could subtract the baseline from the post-intervention scan, leaving 1 image (difference) per subject. WIth 2 subjects, you'd have just 2 images to analyse. With just 2 images, there's just one (!) degree of freedom, and nothing serious can be inferred.

Now, you have 7 images per subject, with 14 images overall. It may seem better, but actually, it's the same situation as above. Although your design has more degrees of freedom (14-8 = 6), not only this isn't much, but it also requires that all observations are pooled to estimate the error, which needs same variances (probably a fair assumption), but also requires compound symmetry, something hard to assume with 7 observations along time.

Perhaps an alternative option, for a different analysis, could be if you had a hypothesis about the response to the intervention (say, that the response would follow a certain curve). Then that curve could be modelled in the GLM, akin to a 1st level fMRI analysis. Still, this would produce one result per subject (fixed effects) but a group inference with just 2 won't be really possible.

Irrespective to the above, the design and contrasts that you show are correct. For randomise, however, you'd set the "group" column as one such "group" per subject, and use it with the option "-e design.grp" (but only if compound symmetry could be assumed).

All the best,

Anderson



On 20 October 2014 16:25, Sharmili <[log in to unmask]> wrote:
Dear all,

in my study i want to analyze the effect of a pharmacological intervention on resting state connectivity. Now I'm trying to analyze the data with melodic. I'm not sure if I'm doing right and I would appreciate any help!

This is a multisubject, multisession study. According to the FSL glm instructions I thought of the following model.

2 subjects,
1 Baseline scan before medical intervention
6 Scans at different time points after interventions

In the first step I want to to compare each postinterventional scan with the baseline scan within subjects.
The first two input images are baseline scans of both subjects, the second two inputs are postintervention scans obtained at
timepoint 1, the third two scans are obtained at timepoint two after intervention and so on. EV7 and EV8 estimate the subjects' mean.

  group   EV1      EV2  EV3   EV4   EV5   EV6  EV7   EV8
     1        -1       -1     -1     -1     -1      -1     1      0
     1        -1       -1     -1     -1     -1      -1     0      1
     1         1        0       0      0      0       0      1      0
     1         1        0       0      0      0       0      0      1
     1         0        1       0      0      0       0      1      0
     1         0        1       0      0      0       0      0      1
     1         0        0      1       0      0       0      1      0
     1         0        0      1       0      0       0      0      1
     1         0        0       0      1      0       0      1      0
     1         0        0       0      1      0       0      0      1
     1         0        0       0      0      1       0      1      0
     1         0        0       0      0      1       0      0      1
     1         0        0       0      0      0       1      1      0
     1         0        0       0      0      0       1      0      1


Baseline=-a-b-c-d-e-f
PI1=a
PI2=b
PI3=c
PI4=d
PI5=e
PI6=f

Contrasts:

PI1-Baseline=a-(-a-b-c-d-e-f)=2a+b+c+d+e+f
PI2-Baseline=a+2b+c+d+e+f
PI3-Baseline=a+b+2c+d+e+f
PI4-Baseline=a+b+c+2d+e+f
PI5-Baseline=a+b+c+d+2e+f
PI6-Baseline=a+b+c+d+e+2f

-->
                         EV1  EV2  EV3  EV4  EV5  EV6  EV7  EV8
PI1-Baseline         2      1     1       1    1       1     0      0
PI2-Baseline         1      2     1       1    1       1     0      0
PI3-Baseline         1      1     2       1    1       1     0      0
PI4-Baseline         1      1     1       2    1       1     0      0
PI5-Baseline         1      1     1       1    2       1     0      0
PI6-Baseline         1      1     1       1    1       2     0      0

Is that correct?

Best
Sharmili