You have some fibers, and you want to know how many pass through a particular mask and then go on to intersect each target ROI? There's more than one way to do it.

If you only need to know how many fibers from bayesianTracts.Bfloat go through the ROI in tractMask.nii.gz and then hit a target, you can do

  cat bayesianTracts.Bfloat | procstreamlines -waypointfile tractMask.nii.gz | cbsmat -seedfile -targetfile ROI.nii.gz -outputroot result_

This would give you the target counts. It won't tell you which voxel in tractMask.nii.gz connects to which target, though.

If you want to know the connectivity of each voxel in tractMask.nii.gz, then I would do as you suggest and use that image as the seed file, then run cbsmat on the output.