Tckgen running forever and selecting 1 streamline

5

if I choose 2 ROIs, should I use connectome2tck from ROI 1:2 and from ROI 2:1, then average the output of tckstats ? Or is one direction enough?

All commands in MRtrix3 intended to deal with structural connectome data are carefully and deliberately designed with the implicit symmetry of those data in mind. So connectome2tck does not consider the requests “-nodes 1,2” and “-nodes 2,1” to be any different to one another. Indeed tck2connectome outputs an upper diagonal matrix by default to reflect this; though I think that choice may have upset more people than not :-/

If I am also interested in FA/MD values between these ROIs, is there a command to derive those values from streamlines?

There’s multiple ways in which this can be done:

  • Construct the full connectome based on the desired contrast, and then just extract from that matrix the values for the particular edges that are of interest; see Wiki page

  • Take that set of streamlines, use tcksample to sample the values of the parametric map along each streamline (likely taking e.g. the mean along each streamline so that there’s a single scalar value per streamline), then take e.g. the mean of these values across all streamlines.

  • Use tckmap followed by mrthreshold to produce a binary mask for that set of streamlines, and then use mrstats -mask to compute the e.g. mean values of those quantities within that mask.

Rob

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