Dear MRtrix experts,
I would like to obtain an estimate of the CSF signal fraction from single-shell data. I tried two different approaches and I would be glad to hear your feedback:
- Response function estimation followed by Single-Shell 3-Tissue CSD (Single-Shell 3-Tissue CSD (SS3T-CSD) | MRtrix3Tissue):
- dwi2response dhollander preprocessed_dwi.mif wm.txt gm.txt csf.txt
-
ss3t_csd_beta1 preprocessed_dwi.mif wm.txt wm.mif gm.txt gm.mif csf.txt csf.mif -mask brain_mask.mif
After that, to get a signal fraction, I normalize the 3 compartments to sum to unity: for CSF csf/(wm+gm+csf)
- Response function estimation followed by Multi-Shell Multi-Tissue CSD:
- dwi2response dhollander preprocessed_dwi.mif wm.txt gm.txt csf.txt
-
dwi2fod msmt_csd preprocessed_dwi.mif wm.txt wm.mif csf.txt csf.mif -mask brain_mask.mif
Again, I normalize the 2 compartments (WM and CSF) to sum to unity: for CSF csf/(wm+csf)
When comparing the two approaches, the values that I obtain with the second approach are larger than those obtained with the first approach. I understand that, for single-shell data, MSMT CSD is limited to resolve 2 compartments and this may result in an overestimated CSF signal fraction. Thus, I would tend to use, for this specific application, the SS3T CSD approach. On the other hand, I was wondering whether there are any drawbacks that I should consider when using MRtrix3Tissue, which is still a fork of the main MRtrix3.
Thanks a lot for your help!
Cheers,
Vincenzo