Hi Jackson
Your seed mask is not in diffusion space. If you draw the LGN e.g. on the FA map and give that as input to probtrackx you will get results. If you want to use a different than diffusion seed space you need to provide transformations to/from that space (—xfm and —invxfm options).
Cheers
Stam
On 19 Feb 2014, at 18:04, Jackson Smith <[log in to unmask]> wrote:
> Hello,
>
> I have had the same problem. Only, I used no exclusion mask. I tried an unconstrained tractography session that was seeded from a mask. The fdt_paths file only has values in seed mask voxels and the value is always the number of streamlines generated per seed.
>
> An example of this is located on jalapeno, here: /home/fs0/jsmith/scratch/M124x.Olympia
> Results from probtrackX are in subdirectory ./tractography/test
> The seed mask is class.msk/LGN_Right.nii.gz
>
> I cannot imagine what the problem might be. I ran dtifit with the same diffusion weighted images, b-values, and b-vectors as a quality check, and the results looked fine.
>
> Kind regards,
> Jackson
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