Dear FSL-experts,
I would like make all zeros outside the head (but not inside the head) of the standard brain+skull image MNI152_T1_2mm zero so that I can make a screenshot of the image and later on simply make the background color (i.e. all pixels outside the head) of all screenshot pixels with exactly the color "black" (RGB 0,0,0) transparent (e.g. using the set transparant color tool in MS Office).
This will allow for creating nice pictures very easily. Any idea how to do this? Note that the MNI152_T1_2mm file by default has random "black" values ranging between values 0 and ~2000. Simply thresholding the image at > 2000 is not going to work because it will make also the space between brain and the borders of the head "black" (RGB 0,0,0) whereas these ones should not become transparent in the final pictures, so they should not get value RGB 0,0,0.
So what I actually need is a kind of "head" instead of a "brain" extraction tool. ;) Any ideas on how to proceed? Thanks for your help.
Best,
Henk van Steenbergen
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