Dear fellow ynic-users,

You may notice some difficulty removing non-brain tissue from structural MR images obtained at YNiC when using the brain extraction tool (bet - a part of FSL) with its default parameters. Symptoms are that tissue around the brainstem, mouth and throat is not removed. This might adversely affect coregistration.

One workaround I know some people have used is to coregister the "unstripped" brain to the "unstripped" reference volume (which seems to work quite well). However, the FSL help strongly recommends removing non-brain tissue, so this might not be the best solution.

Bet uses an estimate of the centre of the image to begin the process of finding the inner and outer scalp and brain boundaries. The default estimate doesn't seem to be right for out structural scans. I have had more success using the following from the command line:

bet myinfileroot myoutfileroot -c 87 108 165

Where you replace myinfileroot and myoutfileroot with the names of your input and output files (without .hdr or .img on the end).

The coordinates 87 108 165 may not be quite right for the centre of your image but the bet algorithm seems to work much better with these values.

Best wishes,

Tom Hartley =================================== Dr Tom Hartley Dept. of Psychology, University of York Heslington, YO10 5DD UK.

t.hartley@psychology.york.ac.uk http://www-users.york.ac.uk/~th512 tel: +44 (0)1904 432903