Issues with -seed_cutoff value option in tckgen

Hi everyone,

I am optimizing my procedure by adding an additional option of FOD cut off value in order to set a minimum value for seeding tracks. I am using FOD values getting from wmfod image, pretty straight forward with options of -seed_gmwmi. I’d like to add one more option of -seed_cutoff value (which is 1.9 in this case). However when I loaded all variables in a command line, number of seeds exceeded my determined number of 10mio without any updating of streamlines and selected streamlines. The process seemed like never ends. Could you please check if my command line is correct? I am very appreciated.

tckgen -act 5tt.mif -backtrack -seed_gmwmi gmwm.mif -select 10000000 wmfod.mif -seed_cutoff 1.9 tracks_10mio.tck

Notice that there was not any error pops up in Mrtrix.

I’d like to add one more option of -seed_cutoff value (which is 1.9 in this case).


Have you tried running the command without this option? I don’t know how you’ve “optimised” your procedure in order to select this value, but given the default is 0.05, this value is rather extreme. While FOD amplitudes this large may be observed in the core of deep single-fibre WM bundles, given you’re using GM-WM interface seeding, where the FODs are typically more complex and hence peak FOD amplitudes are reduced, the command is likely not able to find a single location that both lies on the GM-WM interface and has an FOD amplitude greater than this value. This won’t produce an error, since you’ve not technically done anything “wrong”; but the command will alert you to the fact that it’s not able to satisfy your request.


Thanks so much Rob. Actually the cutoff value was 0.19. My typo of 1.9 leading the process came endless.