Print

Print


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)?

Thanks,
Rachel

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.
>
> Peace,
>
> Matt.
>
> -----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
>
> Hello,
>
> 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,
> Rachel
>