If you add the option “--ompl" to the probtrackx2 call, then there will be an extra output file that gives the average streamline length at each voxel. Then (e.g. in matlab) you can load that file together with an FA volume (needs to be in the same space) and plot FA against tract length. You can then bin the tract length if you want to summarise all that data in a nice easy plot.

Note that this approach only makes sense if you are seeding from the extremities of a tract - if your seed voxels are in the middle of the tract trajectory, then the distance travelled along the tract does not unambiguously distinguish e.g. the two halves of the tract.

On 11 Apr 2016, at 11:45, Alberto Stani <[log in to unmask]> wrote:

Hi FSLers,

I'm looking for a software to visualize the along tracts FA of the white matter tracts obtained with FSL probtrackX. Does someone know if there is any already existent tool for this purpose?

I've the tracts generated by the probabilistic tractography of the FDT diffusion (.nii files) and also the fractional anisotropy images and I would like to visualize the FA trend along the tracts.

Any help would be greatly appreciated.

Alberto Stani