I have a question regarding the usage of the Brainnetome Atlas in MRtrix. So far I have worked with the Desikan-Killiany and the Destrieux Atlas to create connectomes, which was fairly straightforward. However, with the BN Atlas I encountered a weird issue while preparing the atlas files for the connectome generation. I tried to follow the instructions from the BATMAN Tutorial (Appendix) but I keep running into an error.
I have the annotation files ready (lh.BN_atlas.annot and rh.BN_atlas.annot) and when I open them in freeview it all looks perfectly fine (node names are all present and based on BN atlas). So, I am trying to use the freesurfer command mri_aparc2aseg --old-ribbon -s my_subject --annot BN_atlas --o BN_atlas.mgz. Using the outcome file for tck2connectome gives me an error stating that basically all my nodes are missing. When I check the BN_atlas.mgz with freeview it seems like the node names are now based on the FreesurferColorLUT instead of the BN_atlas LUT. It appears as if the mri_aparc2_aseg command is messing it up, but I have no clue why. Using labelconvert make things even worse, removing all the nodes from the file.
Is there anyone who has used different atlases than Desikan or Destrieux who knows why this error occurs and what I could do about it? Thank you very much in advance!