Checking tractography codes

1

Hi Mrtrix3 community,

I’m new to MRtrix3 and tractography analysis, and I’d like to share my code with this community for feedback. Currently my data is a single shell diffusion (b value =1500).

Here are the following codes I have used so far:

  1. Converting
    mrconvert DICOM_dwi-64db1500-acc6_dir-PA_20240212123741_3.nii dwi_raw.mif -fslgrad dicom_dwi-64db1500-acc6_dir-PA_20230511121012_3.bvec dicom_dwi-64db1500-acc6_dir-PA_20230511121012_3.bval

  2. Denoising
    dwidenoise dwi_raw.mif dwi_den.mif -noise noise.mif

  3. Calculating the difference between the raw and denoised images
    mrcalc dwi_raw.mif dwi_den.mif -subtract residual.mif

  4. Unringing
    mrdegibbs dwi_den.mif dwi_den_unr.mif –axes 0,1

  5. Motion and distortion correction
    a. mrconvert dicom_dwi-b0_acq-acc6_dir-AP_20230511121012_9.nii AP.mif
    b. mrconvert AP.mif - | mrmath - mean mean_b0_AP.mif -axis 3
    c. dwiextract dwi_den_unr_with_gradients.mif - -bzero | mrmath - mean mean_b0_PA.mif -axis 3
    d. mrcat mean_b0_PA.mif mean_b0_AP.mif –axis 3 b0_pair.mif
    e. dwifslpreproc dwi_den_unr_with_gradients.mif dwi_den_unr_preproc.mif -nocleanup -pe_dir PA -rpe_pair -se_epi b0_pair.mif -eddy_options " --slm=linear "

  6. Bias field Correction
    dwibiascorrect ants dwi_den_unr_preproc.mif dwi_den_unr_preproc_unbiased.mif -bias bias.mif

  7. Brain mask estimation
    dwi2mask dwi_den_unr_preproc_unbiased.mif mask_den_unr_preproc_unb.mif
    In this step, the dwi2mask command did not work as well and had a few holes. I used the following steps to change the default setting.
    mrconvert dwi_den_unr_preproc_unbiased.mif sub-02_unbiased.nii
    bet2 sub-02_unbiased.nii sub-02_masked_0.3 -m -f 0.3
    mrconvert sub-02_masked_0.3_mask.nii.gz mask_0.3.mif

  8. Response function estimation
    dwi2response tournier dwi_den_unr_preproc_unbiased.mif wm.txt -mask mask_0.3.mif -voxels voxels.mif

  9. Estimation of Fiber Orientation Distributions
    dwi2fod csd dwi_den_unr_preproc_unbiased.mif wm.txt wmfod.mif -mask mask_0.3.mif

  10. Intensity Normalization
    mtnormalise wmfod.mif wmfod_norm.mif -mask mask_0.3.mif

For now this is what I have. Please let me know what you think.

Thank you for all your help.