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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 > ===================== > This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED > HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is > intended only for the use of the individual or entity named above. If the > reader of the e-mail is not the intended recipient or the employee or agent > responsible for delivering it to the intended recipient, you are hereby > notified that you are in possession of confidential and privileged > information. Any unauthorized use, disclosure, copying or the taking of any > action in reliance on the contents of this information is strictly > prohibited and may be unlawful. If you have received this e-mail > unintentionally, please immediately notify the sender via telephone at > (773) > 406-2464 or email. > > 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 >> > >