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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