Actually, I asked a similar question this week. If you look back in
the achieves for this week, it should have the answer.
What I was advised was to draw your mask in fslview. Then run this
command line, which generates just the skeleton within your region of
interest (if you're only interested in the white matter tracts within
fslmaths myregion_mask -mas mean_FA_skeleton_mask myfinal_mask
Then run randomise as usual with your myfinal_mask, and it should
generate the statistical maps for the white matter tracts within your
region of interest.
If you are not interested in the white matter tracts, but the FA
within all tissue types within your region (i.e. the mean FA within
Brod 4), then running the following command line outputs the mean
scaled FA for each subject (you need to divide by 10000 to get the
fslmeants -i all_FA -m myregion_mask -o output_filename.txt
I think this should help you.
On 23 Feb 2008, at 17:00, S. Groppa wrote:
> Dear list,
> I can not find a good way to generate masks for skeletonised data.
> So my direct question is how to generate a mask of for i.e Brod 4 that
> can be included in randomise for all_FA_skeletonised.
> thanks a lot and sorry for this trivial question.
> best wishes