Thank you very much Rob for your explanation and suggestions, they are very useful. I’ll take your advice and go for dynamic seeding:
tckgen -act 5tissue_pm_nocoreg.mif -backtrack -seed_dynamic wmfod_norm.mif csffod_norm.mif -select 10000000 tracks_10mio_dynamic.tck
tcksift2 -act 5tissue_pm_coreg.mif tracks_10mio_dynamic.tck wmfod_norm.mif sift2_weigths.csv
I have just one last question: is it ok if I use wmfod_norm.mif and csffod_norm.mif as input for seed_dynamic option? Basing on my data (5 b0, 100 volumes acquired with b=3000) and on this previous discussion (Full processing pipeline with single phase-encoding direction in MS - #2 by rsmith), I used the multi-tissue CSD algorithm to derive FODs but provided only the WM and CSF response functions:
dwi2fod msmt_csd dwi_den_preproc.mif -mask brain_mask.mif -fslgrad bvecs.bvec bvals.bval wm_response.txt wmfod.mif csf_response.txt csffod.mif
I thank you in advance for your attention and help.
Best,
Laura