Thanks for the software!
Here I am exploring some new-born brain with multiple shells.
As far as I can understand there are three options available:
- csd: standard single-shell single-tissue CSD (SSST-CSD);
- msmt_csd: multi-shell multi-tissue CSD (MSMT-CSD)
- ss3t_csd: single-shell 3-tissue CSD
As the tissue is not myelinated, this case seems to fall in the missing one: multi-shell single tissue.
Do you have any suggestion for this?
What I tried so far was:
dwi2response fa <dwi.nii.gz> <output_average_response.txt> -grad <bvals_bvects.txt> -shell 844,1048,1570
Where dwi is a 199 timepoints with 7 b=0 and 64 for each shell.
The <output_average_response.txt> is a single row with 6 floats.
Therefore when running
dwi2fod msmt_csd <dwi.nii.gz> <output_average_response.txt> -grad <bvals_bvects.txt> -mask <mask.nii.gz> -shell 844,1048,1570
What I got is:
[ERROR] number of rows in response function must match number of b-value shells
Have not tried
dwi2response msmt_5tt as there is no clear distinction between WM and GM, moreover they are ex vivo data, so no CSF…