Hi Kasia,
> 1. what is the average number of particles that you
> analyzed?
> "we counted for each subject the average number of
> particles within the
> crossing fiblre ROI which "belonged" to ..."
> is it the product of: fslstats -M * fslstats -V or maybe
> the waytotal?
I think I've used the seed_to_target count using fslstats -m -k seed_mask instead of the fslstats -M as sometimes one or two voxels would have no particles reaching the targets and I thought they should count as zero (i.e. not be excluded), but I remember it not changing the results at all anyway...
As I performed the tractography using both fibre orientations crossing in my seed region as an initialisation, I then took the mean over the two tractography results (so if you want, seed_to_target_f1 and seed_to_target_f2).
> 2. did you threshold each subjects tractography (if so what
> was the
> threshold that you used)?
No I didn't for the calculation above. I did simply for the rendering in the figure.
Cheers,
Gwenaelle
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Gwenaëlle Douaud, PhD
FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington OX3 9DU Oxford UK
Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717
www.fmrib.ox.ac.uk/~douaud
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