Thank you Stam for the reply!

But I still have a doubt in using this method:-

Using the map that I obtain by using the procedure suggested by you, will I be getting lengths of individual fibers? I mean what if there are more than 1 fiber that reach voxel A in the target ROI that start from different voxels in the seed ROI, in this case the value in the voxel A will be sum/combination of the expected lengths of these fibers right? If the waytotal value is for example 389087, is there a way to obtain length of these individual 389087 fibers?

Thanks and regards,

Madhura

On Thu, Jun 5, 2014 at 2:31 AM, Stamatios Sotiropoulos <[log in to unmask]> wrote:

Hi Madhura

You can obtain a map that in each voxel A gives the expected length of paths that reach A, starting from the seed. In order to do that run probtrackx twice, with and without the option –pd. Then divide the respective fdt_paths_pd/fdt_paths.

Hope this helps

Stam

On 4 Jun 2014, at 21:57, Madhura Baxi <[log in to unmask]> wrote:

Hi FSL,

I wish to calculate fiber density between two ROIs. I have run probtrackx and obtained the fdt_paths. In order to calculate fiber density I need :-

1. Total number of fibers/tracks - which I can get using waytotal.

2. Size of ROIs - which is known

3. Length of each fiber - I don't know how to get this from the probtrackx results.

Is there a way to calculate this? Could you please guide me on how to proceed on this ?

I would greatly appreciate your help on this!

Thanks and regards,

Madhura