Hi John,
I think it does not really matter (or no one can tell;) but you should be consistent (i.e. use a predefined percentage). For clinical purposes, I often felt comfortable with 0.1% if (!) I wanted to threshold.
Similarily, normalizing fdt_paths to the waytotal does not alter the spatial extent of the original output. It just "scales" the values (to interpretable probabilities if you know that the tract you were after exists). Thresholding will change the spatial extent of the tract. So if you threshold at 0.1%. for example, you will exclude those voxels that have only a chance of 1 in a thousand that they belong to the tract of interest (given you have good reason that the tract must be there).
Hope that helps,
Cheers-
Andreas
________________________________
Von: FSL - FMRIB's Software Library im Auftrag von John D. Griffiths
Gesendet: Do 27.11.2008 16:17
An: [log in to unmask]
Betreff: [FSL] waytotal thresholding
Hi Tim + Matt +all.
With regard to this notion of thresholding as a
consistent % of the waytotal number: Roughly what kind of numbers have
people been using to do this? I know you need to choose one that looks best,
etc., but I'm wary of being too 'liberal'...
In Matt & Tim's nature neuroscience paper (Rilling et al. 2008), they
threshold to include only those voxels that received 'at least 0.000038% of
the total streamlines sent out from the ROI masks'. Now, given that the
analogy has been made several times on this mailing list between
thresholding as a proportion of the number of seed voxels and thresholding
as a proportion of the number of streamlines passing between two seeds (i.e.
the waytotal number) - would it be ok to threshold my results at values as
low as 0.000038% of the waytotal?
Could anyone point me to some papers that have used this thresholding as a
proprtion of the waytotal approach?
Finally (and sorry if this is a really dumb question...) - One suggestion on
this list has been to normalize probtrackx results by diving by the waytotal
number (which I read as 'fdt_paths -div (waytotal)'), whilst others have
been to threshold as a consistent % of the waytotal number (which I read as
'only include intensities greater than or equal to [(waytotal / 100)*(e.g.)
10]'). Are there any important differences between these?
Thanks,
John
