I am almost completely new to dwi analysis and MRtrix, so I apologise if these are fairly obvious questions.
I want to do fascicle tracking using a region-to-region method. e.g. hMT+ to hMT+. I have followed this pipeline and have ended with a whole brain tractography with 100K tracks. I was hoping for some advice on how to register my T1 anatomical scan to the dwi data (Flirt/fnirt would be my first guess, but if the MRtrix community advise another package, please let me know), so that I can then transform the ROI’s created in the T1 space into the dwi space, and then use these for the ROI to ROI analysis. Which brings me onto my next question. Does anyone have any advice on the best way to do this? I assume it would be something along the lines of running: tckgen wmfod.mif MTtracks.tck -seed_image lh_MTroi_dwiSpace.mif -mask mask.mif -select 100k. Where lh_MTroi_dwiSpace.mif is an anatomical ROI transformed into the dwi space. I also assume this would be the tracks running through this ROI and not necessarily the ROI to ROI tracks? Once again, any advice on this would be appreciated. I also see track numbers in the order of 10 million, not 10K as per the tutorials. Is this simply altered by changing the -select 100k to -select 10m?
For completeness here is each step I currently take: Please feel free to tell me if anything is obviously incorrect here.
Convert from nii.gz to .mif
mrconvert AP.nii.gz AP.mif -fslgrad AP.bvec AP.bval
mrconvert PA.nii.gz PA.mif -fslgrad PA.bvec PA.bval
mrconvert PA.mif -coord 3 0 PA_b0.mif
mrconvert AP.mif -coord 3 0 AP_b0.mif
mrcat AP_b0.mif PA_b0.mif b0s.mif -axis 3
Preprocess dwi data
dwipreproc AP.mif dwi_preprocessed.mif -pe_dir AP -rpe_pair -se_epi b0s.mif
Mask dwi data
dwi2mask dwi_preprocessed.mif mask.mif
Estimate response function for spherical deconvolution
dwi2response dhollander dwi_preprocessed.mif wm_response.txt, gm_response.txt csf_response.txt
Perform constrained spherical deconvolution on the response function
dwi2fod msmt_csd dwi_preprocessed.mif response_wm.txt wmfod.mif response_gm.txt gm.mif response_csf.txt csf.mif
Perform whole-brain tractography with 100,000 tracks
tckgen wmfod.mif whole_brain_100k.tck -seed_image mask_dwi.mif -select 100k