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Hi-
only a minor addendum to what Tim just said: 
On the other hand, the more directions you acquire the longer the acquisition time and the more likely these data may get contaminated by physiological issues, such as movement.
Thus, you need to find a sensible trade-off between the number of directions, averages, and the patient / volunteer compliance. Anything above 25 or 30 collected directions will probably be sufficient for a probabilistic FDT solution, and you are not likely to gain anything beyond 60 - 72. Most scanners suitable for DTI should be able to acquire a 'minimal' data set of ~ 30 directions within roughly 5 min.
Cheers-
 
Andreas

	-----Ursprüngliche Nachricht----- 
	Von: Tim Behrens [mailto:[log in to unmask]] 
	Gesendet: Mi 03.11.2004 09:06 
	An: [log in to unmask] 
	Cc: 
	Betreff: Re: [FSL] dtifit and bad slices
	
	

	Erin - the short answer is no - there is no flag to ignore certain slices
	in certain orientations. If you did this you would have different biases
	on your estimates of (e.g.) anisotropy in different slices. How much of an
	affect this would have depends on how much data you collected originally.
	If you collected many directions, and/or many averages, there may be
	things you can do to replace dodgy data without messing up the estimates
	too much, but it very much depens on exactly what data you acquired.
	
	T
	
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	Tim Behrens
	Centre for Functional MRI of the Brain
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	On Mon, 1 Nov 2004, Erin Gibson wrote:
	
	> Is there anyway of having dtifit ignore particular image files (e.g. slice
	> 5, orientation 2) when calculating FA?  I'm wondering how best to deal with
	> the odd image file that is contaminated by artifact.
	>