Tracks out of the white region


From a HCP subject we would like to get a mask which contains those tracks calculated according to HCP MRtrix tutorial.

Considering the paper: Jeurissen, B. et al (2014). Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data. NeuroImage, 103, 411-426. The white matter is defined as:

WM value > 0.95 and FA>0.7.

In other to get this mask, we used the wm.mif file (obtained from 5TTgen command) and we applied on it a threshold > 0.95 (using fsl -thr 0.95).

Checking the visualization of the fibers (actually a subset of 100 fibers through tckedit command) on our white matter mask, we see fiber voxels placed out of the mask.
Are we using a wrong criterion to definition of the mask where the tracks should be?

We attach one picture indicating with blue circles some examples of what we are seeing.
In white: our mask, In red: tracks

Thank you very much in advance.

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I think there is confusion between the mask that would be used to estimate the responses for multi-tissue CSD, and the use of that same 5TT partial volume map during the completely unrelated tractography stage, which in the HCP tutorial is performed with Anatomically Constrained Tractography enabled. You’ll note that the thresholds used in ACT are quite different, kicking if when PGM > 0.5 or PCSF > 0.5 for instance - i.e. not PWM > 0.95. So it’s not unexpected to find streamlines outside the PWM > 0.95 region…

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Ooh, I understand! Sorry for the confusion.
Thanks for your quick response.