On 11 Dec 2015, at 21:42, Kabilar Gunalan <[log in to unmask]> wrote:

Hi Saad,

Thanks for the response!  Just to clarify, do the diffusion directions need to be uniformly distributed in the spherical or Cartesian coordinate system?  I chose phi and theta so that when transformed to Cartesian coordinates, the direction vectors were uniformly distributed.  That is, theta = arccos(2v-1) and phi = [0,2i), where v is randomly sampled from (0,1).

Thanks!

-Kabi

On Thu, Dec 10, 2015 at 6:08 AM, Saad Jbabdi <[log in to unmask]> wrote:

Hi

Yes, you can generate random theta/phi using uniform distribution on the sphere, then set all the volume fractions to 1 (not zero).

cheers

Saad

On 9 Dec 2015, at 20:55, Kabilar Gunalan <[log in to unmask]> wrote:

Hi all,

How do I run probtrackx(2) with an isotropic fiber orientation distribution?  Do I set all volume fractions (i.e., in merged_f*samples.nii.gz) to zero, or do I also need to modify merged_ph*... and merged_th* so that the sampled diffusion directions are uniformly distributed around the unit sphere?

Based on some preliminary runs, it appears merged_ph*... and merged_th*... must be modified, along with setting all volume fractions to zero.  I chose phi and theta so that when transformed to Cartesian coordinates, the direction vectors were uniformly distributed.  That is, theta = acos(2v-1) and phi = [0,2i), where v is randomly sampled from (0,1).

Thanks for all of your help!!

-Kabi

------------------------------------------------------------------

Saad Jbabdi, PhD

Associate Professor

MRC Career Development Fellow

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