Finding % of tracts that cross significant voxels in tractogram

1

Hi MRtrix3 Team,

I’m doing a tractography analysis where I’m interested in finding out if a percentage of tracks in my tractogram have crossed certain significant voxels (I have MNI coordinates for these ROIs). As I’m unfamiliar with this, does anyone know how I could go about this?

Many thanks

2

Probably the simplest approach here is to generate a mask ROI of your selected voxels, then run something like:

tckedit your_tracks.tck -include your_ROI.nii output.tck

and then compare the count field in the output of tckinfo your_tracks.tck and tckinfo output.tck – i.e. the number of streamlines in the orignal tractogram, compared to the number that were selected by using your_ROI.nii as an inclusion ROI.

For anything more complex than that (e.g. if you have multiple ROIs), you could also try tck2connectome.

3

Thank you so much for your help! It has worked wonders.