MRtrix Tutorial #4: Preprocessing смотреть онлайн

Chapter 4 of the MRtrix tutorial of Andy's Brain Book: https://tinyurl.com/ycww9u94

Table of Contents:

0:00 Overview of Preprocessing
0:24 Denoising the Data
0:58 Examining the Residuals
2:03 Preparing for Distortion Correction
3:46 Preprocessing with dwifslpreproc
5:38 Checking the Output of dwifslpreproc
6:32 Bias Correction with dwibiascorrect
7:28 Creating a mask with dwi2mask

ANTs Installation: http://stnava.github.io/ANTs/

Commands Used:

Denoising:

dwidenoise sub-02_dwi.mif sub-02_den.mif -noise noise.mif
mrcalc sub-02_dwi.mif sub-02_den.mif -subtract residual.mif
mrview residual.mif

Converting the PA Images:

mrconvert sub-CON02_ses-preop_acq-PA_dwi.nii.gz PA.mif
mrconvert PA.mif -fslgrad sub-02_PA.bvec sub-02_PA.bval - | mrmath - mean mean_b0_PA.mif -axis 3

Extracting b0 images from the AP dataset, and concatenating the b0 images across both AP and PA images:

dwiextract sub-02_den.mif - -bzero | mrmath - mean mean_b0_AP.mif -axis 3
mrcat mean_b0_AP.mif mean_b0_PA.mif -axis 3 b0_pair.mif


Preprocessing with dwifslpreproc:

dwifslpreproc sub-02_den.mif sub-02_den_preproc.mif -nocleanup -pe_dir AP -rpe_pair -se_epi b0_pair.mif -eddy_options " --slm=linear --data_is_shelled"


Checking the preprocessing output:

mrview sub-02_den_preproc.mif -overlay.load sub-02_dwi.mif


Bias-correcting the data and creating a mask:

dwibiascorrect ants sub-02_den_preproc.mif sub-02_den_preproc_unbiased.mif -bias bias.mif
dwi2mask sub-02_den_preproc_unbiased.mif mask.mif
mrview mask.mif