Thanks Donald.

Ah! I thought the contrast is the effect size or at least maybe some papers refer to it. It is also mentioned in this link : http://www.fil.ion.ucl.ac.uk/spm/doc/manual/results.htm

You mentioned that it does plot the amplitude. So I am confused now between the contrast estimate, effect size and the amplitude ? What do them mean and represent?

Also from a practical point of view, If I enter the SPMT_0001.nii (or the t value maps) in imcalc and use this expression to calculate:

The effect size = (i1*2)/(sqrt(degree of freedom-1))

Then If I want to calculate the standard error I would enter both the t map and the con image and use the following expression : i1/i2

Are these practical steps correct to reach and calculate a map of the effect size and the standard error?

Many thanks

Aser

On Thu, Jun 11, 2015 at 6:57 PM, MCLAREN, Donald <[log in to unmask]> wrote:

Aser,

SPM does not plot, at least to my knowledge, the effect size (http://en.wikipedia.org/wiki/Effect_size). It does plot the amplitude, but amplitude is not the effect size.

The amplitude is just the value of the contrast image.

The standard error is the value of the T-image divided by the value of the contrast image. Alternatively, you could use: sqrt(diag(SPM.xCon(Ic).c'*ResMS*SPM.xX.Bcov*SPM.xCon(Ic).c)).

You can also compute the effect size directly from the T-map, the following link has come common formulas for computing the effect size from statistical values:
http://www.soph.uab.edu/Statgenetics/People/MBeasley/Courses/EffectSizeConversion.pdf

Hope this helps.

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 Thu, Jun 11, 2015 at 1:05 PM, fMRI <[log in to unmask]> wrote:
Thanks

I am still lost. Is the images that you are talking about the con images. Or in other words, using SPM plot contrast estimate, it plots the size effect with the standard error at this selected voxel and also creates and a mat called contrast which bas the values at this coordinates. All what I want to do is to try to find a way , e.g using imcalc, to generate this for list of coordinates. I am still not sure how I can do it.

Regards,

A

Regards,

AS

> On 11 Jun 2015, at 15:31, "H. Nebl" <[log in to unmask]> wrote:
>
> With Imcalc you can conduct operations like mean(X), std(X) based on a series of volumes, resulting in a 3D volume with corresponding values on a voxel-by-voxel basis. You have to go with "Yes - read images into data matrix".
>
> Best
>
> Helmut