Single-Shell (+B0) 3-Tissue CSD

1

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

Screenshot
Screenshot1739×1043 110 KB

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!

1 Like
2

Hello @michefabb ,
I think you can first overlay voxels.mif onto DWI image. You should see three colors of voxels.

Many Thanks,
Suren

3

@suren thanks for your reply. It looks the voxels.mif shows only the voxels used to create the Basis Functions of each tissue, but apparently does not fix the issue with GM.

Any possible help?

@ThijsDhollander @jdtournier do you have any suggestion?