How tck2connectome processes the label 0 in the nodes.mif

Hi there,

I used the tck2connectome with the cortical parcellation result i_brain.mif. The label of i_brain.mif is from 0, which denotes the background, to 84. As anticipated, a connectome with the size 8484 will be obtained, however, I got the connectome with the size 8585.

I checked the URL (Structural connectome construction — MRtrix 3.0 documentation), it seems to say it does matter for the i_brain.mif with a label 0. But I want to know what happens behind and how can I fix this problem to have a connectome with the size 84*84, by either post-processing the connectome.csv or modifying the code below.

“tck2connectome -symmetric -zero_diagonal -tck_weights_in sift_tck.txt tracks.tck i_brain.mif connectome.csv -out_assignment connectome_assignments.csv -keep_unassigned -force -nthreads 40”


Did nobody meet this problem?


I think your problem is that you have the -keep_unassigned flag in your tck2connectome call. This adds and extra row/column with the unassigned tracts. I hope this helps.

Best regards,


Hi Manuel,

Thanks for your kind response. Sorry for replying late, I have to handle some other issues.
You are right, the option of ‘-keep_unassigned’ lets the connectome have an additional row and column that are caused by the node with label 0.

I can remove this option, the additional row could be removed successfully. however, this incurs another question.
I have a patient whose left hippocampus or left entorhinal disappeared. However, if I do not add the -keep_unassigned option, the connectome may have less than 84 rows. I could hardly locate the disappeared node(s) from the connectome itself.
Is there any other solution to resolving this?