Segmentation of Fornix_Cingulum

Hi Mrtrix community,

I am new to mrtrix. I use this structure (Beginner: Connectome pipeline (Updated)) for tractography and structural connectivity.
I wan to extract Fronix, Cingulum bundle , and corpus callosum.

How can i do this?

Thanks in advanced.

Hi Neda,

What I would suggest is to:

  1. do the whole brain tractography first.
  2. with tckedit you can select fornix, cingulum or cc, just under the options type -include “mask”

You can make mask yourself in mrview roi editor on your existing data or you can download atlas segmentations from various internet source.
Note that you would usually need to corregister to MNI space first for the latter option.


Thanks David.