Segment GMWMI corresponding to cortical/subcortical segmentation

Hello Mrtrix Experts,

  1. I have used “labelconvert” and “labelsgmfix” commands to obtain nodes_fixSGM.mif in the diffusion space.
  2. I have also used “5tt2gmwmi” command to obtain gmwmi_b0.mif in the diffusion space.

However, i dont see a perfect/complete overlay of the gmwmi_b0.mif over the cortical/subcortical segmentations from nodes_fixSGM.mif. Is it possible to segment the gmwmi_b0.mif based on the cortical/subcortical segmentations from nodes_fixSGM.mif? I am interested in looking at the interaction between the grey matter cortical/subcortical measures and white matter measures from their corresponding interface.

BW
Jay

Hi Jay,
What algorithm was used to generate the 5TT image?

Cheers,
Arkiev

Hi Arkiev,

I used the 5ttgen fsl command to generate the 5TT image.

BW
Jay