Hello,
I'm familiar with the FSL GUI interface for BET and FEAT analysis of
the data but since we're working with very large datasets, I'm trying
to learn how to use scripting to do these in FSL. While the FEAT
analysis seems to be running smoothly as a script based on the .fsf
design, my BET sript has most likely a problem because about one third
of the subjects fail the registration! (mostly because of brain cut
off in the frontal or occipital lobe) This does not happen when
working on the same dataset manually.
Could anybody please explain how to run BET as a script and how to do
the tuning so that it's able to incorporate individual differences in
the brain?
Here's the BET sript I'm using now for reference:
bet input.nii output.nii -f 0.5 -g 0
where
-f <f> fractional intensity threshold (0->1); default=0.5;
smaller values give larger brain outline estimates
-g <g> vertical gradient in fractional intensity threshold
(-1->1); default=0; positive values give larger brain outline at
bottom, smaller at top
Thanks a lot for any suggestions,
Klara
|