Dear Jesper,

Thank you for your clarification. About the first question. As far as I understand, sometimes we can find that some regions in the lesioned area have little activity whereas another ones not....depending on the time you are assessing the subject with MRI...so, in the case you skip lesioned area, (regressing out timeseries in this area)...would not we be inducing a bias...since we are "stating" that in this area there is no activity? Or...maybe it should be better taking a decision depending on we want to probe? In any case, it is quite complicated skipping the lesioned region based on presumed biological theory...that not always works for all subjects at different times...

Yours sincerely,
Rosalia.

2013/4/15 Jesper Andersson <[log in to unmask]>
Dear Janet and Rosalia,

> Based on your comment, I will skip entering the timeseries of the lesioned area as a nuisance covariate.

I didn't say you should necessarily skip it ;-) I remarked that one needs to be a little careful, especially if the lesioned area is one that in a healthy brain ones task would elicit activation.

> For the affine transform, can I use one of the .mat files that is produced in the original feat? If so, I assume this would be "highres2standard.mat"?

Yes, that is the one you want.

Jesper