Hi Erik

what is the dimensionality of sig.cluster.mgh? You can tell this with mri_info. It is problaby a surface overlay (so nvertices in one dimension), and can't be viewed in the volume but only on the surface.

cheers Bruce

On Mon, 25 Jan 2016, Erik Lindberg wrote:

Dear Douglas and Freesufers,

You suggested:

mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

I tried this and was expecting that I would get a three-dimensional mask in which the statistical significant part would be white and the rest black.

This seems not to be the case. While the program is telling me that it is creating a mask in which x-number of voxels are included I cannot see anything when I open the thresholded.mgh (in Freeview) Further when I look at the dimensions of the generated image it seems to have 27307 “slices” in one direction but only one and 6 slices in the other directions.

Is this the wrong approach for creating a 3-dimensional mask for the region with the significant clusters?

Best

Eric