I have single shell DWI data with b=0 & b=1000, with no distortion correction unfortunately, so I have not been using ACT. I’ve run through the entire pipeline and I get the result below for my tractography. I shouldn’t expect so many streamlines in the grey matter.
From reading the docs and many forum posts, I ran the dhollander algorithm to get the tissue response functions and then only calculate the ODF for WM and CSF because of single shell data:
dwi2response dhollander dwi2.mif response_wm.txt response_gm.txt response_csf.txt -mask dwi_mask.mif -voxels voxels.mif -force dwi2fod msmt_csd dwi2.mif response_wm.txt FOD_WM.mif response_csf.txt FOD_CSF.mif -mask dwi_mask_dilated.mif -force
However, this gives me a FOD_WM that looks weird for the b0 volume. I’m not entirely sure what to expect here, but my suspicion is this may be throwing off the tractography.
The previous iteration of my pipeline only calculated WM and GM ODFs, but I’ve changed it due to recommendations on the forum. Yet, the tractography from that iteration and the WM FOD looks much better. Here is the WM FOD:
and the corresponding tractography:
What is going on? Should I stick with my original pipeline? The only differences were the WM/CSF vs WM/GM and adding global intensity normalisation, but I don’t believe that would make such a change… Do I need a white matter mask in my tcksift2 command? Right now I’m simply feeding the DWI mask to -proc_mask.