Hi Javier, you don't want to use the gammarvar for Cohen's D. Gammavar is like the standard error (square of the std error). Instead, use rstd.mgh located in the main glmfit folder. Otherwise, I think your equation is right. I don't think you can do this with one call to fscalc. I think you'd need at least two.

doug

ps. Please post questions to the list and not directly to me. Thanks!

On 01/24/2013 07:55 AM, Javier Navas wrote:

Hi Doug,

I´m very new in Freesurfer and I cannot obtain a Cohen´s d Map as a Effect Size measure. Is it possible to generate surface maps for the Cohen´s d in cortical thickness between 2 groups within with Freesurfer. I have the mean thickness for each group; after obtained these gamma.mgh I tried with fscalc but I do not know how to do it: | MeanGroup1 sub MeanGroup2 | /sqrt((Std12add Std22)/2) ... it is right???

Is the gammavar.mgh the Standard Deviation (Std) ???

Thank you in advance

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