Hi Jeff

Inter-subject differences in fdt_paths can also be driven by:
- Differences in uncertainty in orientation across subjects (quantified with dyads_dispersion). 
- Differences in the precise definition of the seed region
- … and of course true differences in anatomy

You can also reduce inter-subject variability by jittering the streamline starting point (—sampvox option).

Re the parallel question: Increasing the number of samples helps you determine whether the algorithm has converged in building the spatial histogram of connections (you need to divide by the total number of sample streamlines if you want to compare different runs that use different number of samples).  

Cheers
Saad



On 17 Nov 2014, at 20:18, Jeff Waugh <[log in to unmask]> wrote:

Hello FSL,
  I have run FSL-based tractography on a cohort of 20+ healthy
volunteers. I visually inspected all of them for defects in
registration or FA extraction - all appear good, with no evident
errors. For any given seed ROI, I find that the peak amplitude for
tractography varies tremendously between subjects. My lowest-amplitude
subjects have values in the 100s, while my highest-amplitude subject
have peaks well above 100K. Looking back at the sizes of their seed
ROIs, the quality of their FA, the amount of motion (derived from BET
output), and a dozen other confounds I've imagined, I can't find a good
explanation for why there is such high variability in tractography.

  Is this degree of variability among healthy volunteers something that
others find?

  A parallel questions: if one uses a higher number of iterations for
probtrackx2 (say, 50,000 instead of the standard 5000), will that
change improve one's signal to noise ratio, or simply elevate all
output (my true tractography plus background, a problem in my
low-amplitude subjects) equally?


  Thank you for your insights.

 - Jeff



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Saad Jbabdi, PhD
MRC Career Development Fellow &
University Research Lecturer

FMRIB Centre, University of Oxford,
John Radcliffe Hospital, Oxford, OX3 9DU, UK. 
tel (+44)1865-222466  (fax 717)
www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi