we are currently setting up a MRtrix pipeline for multishell data (3 shells, b 1000/1750/2500, 1.75 mm isotropic resolution) for probabilistic tractography and are a bit unsure which steps work best for our data.
This is roughly how we would like to proceed:
After preprocessing, converting to mif format, generating a mask and registering T1 images to DWI images we would like to take the following steps:
# Generation of 5tt.mif files
# Response function estimation using –dhollander option dwi2response dhollander dwi.mif wm_response.txt gm_response.txt csf_response.txt
# FOD dwi2fod msmt_csd -mask mask.mif dwi.mif wm_response.txt wm.mif gm_response.txt gm.mif csf_response.txt csf.mif
# Multi-tissue informed log-domain intensity normalisation mtnormalise wmfod.mif wmfod_norm.mif gm.mif gm_norm.mif csf.mif csf_norm.mif -mask mask.mif
So far the steps were quite clear to us. (Depending on the following steps we might not even need the 5tt.mif files).
For the following steps we are not quite sure which steps to use as there is no gold-standard/ state-of-the-art pipeline available especially for multi-shell data.
tckglobal doesn’t take the anatomically-constrained tractography (ACT) into account. But isn’t ACT very important in the end?
tckgen OR tckglobal?
As sift2 doesn’t remove streamlines – can we therefore reduce the number of fibres in the step before (generating tracts)?
tcksift OR tcksift2
We are aiming for the best quality in data analyses and computation time should not be an issue.
We appreciate your help! Thank you in advance,