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Dear all,

thanks for the replies.
Here is my recap of the last few points:

1. As most of you said, the FWER can be affected by this and it need not go down:
According to Gaussian RFT, FWER is proportional to the number of voxels in the volume divided by the product of the smoothness in the 3 directions (i.e. x, y and z).
What I am doing is reducing V (the numerator), but also changing the denominator.
So ... the effect could go either way. Furthermore using a GM mask can be motivated in cases where we are not interested in performing hypothesis testing in what I call irrelevant voxels anyways.

Also as Bruno pointed out this would not affect the non-parametric tests (e.g. using SnPM) and perhaps also FDR.

2. I agree with the last point that activations in irrelevant regions might be a hint towards poor pre-processing or GLM in some subjects at least.

3. I totally agree with the point about smoothing. 

Bests
Hamed





On Fri, Dec 2, 2016 at 2:37 PM, MRI More <[log in to unmask]> wrote:
Dear Hamed,

In case your functional volumes were smoothed I would smooth the GM files accordingly before applying a threshold to generate the mask (or alternatively, mask the functional volumes and only then apply smoothing). The decision should be based on where GM is present in the processed images, not where GM was present initially.

I wouldn't go with any such masks though (at least as long as you don't have acquired functional data with very high resolution). The unmasked maps provide some useful information. "Activations" in ventricles and/or WM might point to some problems with drift or head motion. Once you apply a mask only the boundary areas of the artefact might remain and look like "nice" activations in basal ganglia.

Best regards

Helmut