OK, so I found a couple of little bugs in how tckedit was applying the masking. This was affecting how many tracks were being written to the output file, over and above the discrepancy introduced by chopping individual streamlines into multiple segments. Re-checking the track file subsequently using tckedit was also being deceiving, as the original minimum length criterion from tracking was being re-applied even though nothing was specified at the command-line, and many of the cropped track segments were not long enough. I’ve also made tckedit provide the number of track ‘segments’ written to the output file as part of its progress message.
Alternatives for checking the contents of track files include tckinfo -count (which will manually check the number of tracks in the file, over and above what’s reported in the header), and tckstats (which calculates statistics on streamlines length, and will also warn about the presence of null streamlines, which is often indicative of an error).
Thanks for the report; the fixes will be included as part of a reasonably-sized update that will hopefully get pushed out within the next 24 hours.
Rob