Thanks for your response.  What I am more confused about is that adding only an exclusion mask caused a drop of 76 in the waytotal; adding only a waypoint mask caused a drop of 30474; but adding both caused a drop of 40118.  Why is the drop in waytotal greater when using both an exclusion and waypoint mask compared to the sum of the drops when adding each separately (i.e. 76 + 30474 < 40118)?   


On Tue, Aug 11, 2009 at 12:52 AM, Matt Glasser <[log in to unmask]> wrote:
It is perfectly expectable to have a drop in the waytotal when you are
placing a constraint on where the pathway must go (waypoint mask) or where
it cannot go (exclusion mask).  In either of these cases, samples will be
rejected because they either don't pass through the waypoint mask or do pass
through the exclusion mask.  --usef does not do quite what you think it
does, and is probably not what you want.  If you want to restrict your
pathways to be within regions of a certain FA value, you should threshold
the FA map, binarize it, and then subtract 1 and multiply by -1 to get the
inverse map, and use this map as a stop mask.

Be aware that FA drops significantly in areas of crossing fibers, so you
might be better off summing the mean_f1 and mean_f2 samples from bedpostx,
and thresholding this to reduce the effects of crossing fibers on your
diffusion anisotropy constraint.



-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Rachel Hawe
Sent: Monday, August 10, 2009 5:09 PM
To: [log in to unmask]
Subject: [FSL] waytotal results


I am trying to track the corticospinal tract, with a seed in the cerebral
peduncle.  I was interested in seeing how adding different combinations of
exclusion and waypoint masks would effect the outcome, and am confused by
the waytotal results:

with no exclusion or waypoint mask: waytotal = 95000
exclusion mask at corpus collosum: waytotal = 94924
waypoint mask in internal capsule: waytotal = 64526
waypoint in internal capsule AND exclusion mask at corpus collosum: waytotal
= 54882
same as above AND using FA to constrain tracking: waytotal = 61374

I am confused why the waytotal drops by so much when using both an exclusion
mask and waypoint mask.  Shouldn't the difference between the waypoint mask
with and without the exclusion mask be the same as the difference when just
the exclusion mask was used compared to no additional masks (i.e.
95000-94924)?  It also seemed strange that adding an additional constraint
(the FA constraint) resulted in a larger waytotal than without this
additional constraint.

Any insight would be greatly appreciated.

Thank you,