Dear MRtrix experts,
I have an acquisition with one B=0 and 29-off directions with B=1000, I need to find the Structural Connectivity matrix, so I preprocessed the data as shown in the guide and then created the Basis Functions:
dwi2response dhollander sub-01_den_preproc_unbiased.mif wm.txt gm.txt csf.txt -voxels voxels.mif
dwi2fod msmt_csd sub-01_den_preproc_unbiased.mif -mask mask.mif wm.txt wmfod.mif gm.txt gmfod.mif csf.txt csffod.mif
mrconvert -coord 3 0 wmfod.mif - | mrcat csffod.mif gmfod.mif - vf.mif
However when opening with:
mrview vf.mif -odf.load_sh wmfod.mif
I can see no GM, see screenshot
I think this is due to the fact that I have only 2 shells (B=0 and B=1000) to find 3 tissues, is it correct?
Assuming it is true, I installed MRtrix3Tissue and used the ss3t_csd_beta1 command:
ss3t_csd_beta1 sub-01_den_preproc_unbiased.mif wm.txt wmfod.mif gm.txt gmfod.mif csf.txt csffod.mif -mask mask.mif
however I get the following error "
ss3t_csd_beta1: [ERROR] shconv fod_csf_0.mif wresp_csf_bz.txt sh_csf_bz_1.mif -mask mask.mif (ss3t_csd_beta1:163)
ss3t_csd_beta1: [ERROR] Information from failed command:
ss3t_csd_beta1:
shconv: [ERROR] unknown option “-mask”
Even removing the option -mask mask.mif did not fix:
ss3t_csd_beta1: [ERROR] sh2amp sh_csf_bz_1.mif grad_bz.txt sig_csf_bz_1.mif -gradient (ss3t_csd_beta1:166)
ss3t_csd_beta1: [ERROR] Information from failed command:
ss3t_csd_beta1:
sh2amp: [ERROR] unknown option “-gradient”
Can you help me please?
I appreciated!