NORDIC denoising in MicaPipe

[PaulBautin]

What is the current behaviour?

• The dMRI data was previously denoised using the MPPCA (Marchenko-Pastur Principal
  Component Analysis) method, implemented in MRtrix3's dwidenoise command.
  Reference: https://mrtrix.readthedocs.io/en/dev/reference/commands/dwidenoise.html

What is the motivation / use case for changing the behaviour?

• 7T dMRI image SNR is low.

NORDIC references:

• Original Paper: https://doi.org/10.1016/j.neuroimage.2020.117539
• GitHub Repository: https://github.com/SteenMoeller/NORDIC_Raw

Before running:

• Ensure MATLAB version 2017b or newer is installed with the Image Processing Toolbox and Signal Processing Toolbox.
• Clone the NORDIC GitHub repository.

Input data:

• This script is tested with a 2mm dMRI image from the Edden dataset available at: https://openneuro.org/datasets/ds004666/versions/1.0.5
• Note: Requires dMRI magnitude and phase images.
• Note: Not yet able to test 1.5mm dMRI images, > 16 GB RAM is required.

Alternative denoising method:

• DIPY's patch2self Roundup of denoising and unringing algorithms from ISMRM nipreps/dmriprep#132
  Reference: https://docs.dipy.org/stable/examples_built/preprocessing/denoise_patch2self.html
• MRtrix MPPCA method (dwidenoise) now supports complex input data, which could help correcting for non-Gaussian noise biases present in magnitude-reconstructed MRI images.

Implementation considerations:

• The NORDIC method could be adapted for other MRI modalities such as fMRI or ASL.
• Implementing NORDIC similarly to the FIX tool used in micapipe fMRI (similar Matlab requirements?).

Test:

Code

# Input and output file paths
img_magn_in='/home/pabaua/dev_mni/data/test_nordic/sub-01_ses-2mm_dir-AP_run-01_part-mag_dwi.nii.gz'
img_phase_in='/home/pabaua/dev_mni/data/test_nordic/sub-01_ses-2mm_dir-AP_run-01_part-phase_dwi.nii.gz'
img_out='sub-01_ses-2mm_dir-AP_run-01_dwi_nordic' # Do not put extension .nii
nordic_matlab_dir='/home/pabaua/dev_mni/NORDIC_Raw/'  # Directory containing NIFTI_NORDIC.m

# Arguments for the MATLAB function
ARG_temporal_phase=3
ARG_phase_filter_width=3
ARG_DIROUT='/home/pabaua/dev_mni/results/nordic/'

# Run MATLAB command with the specified arguments
matlab -nodisplay -nojvm -nosplash -nodesktop -r " \
try; \
addpath('${nordic_matlab_dir}'); \
ARG.temporal_phase = ${ARG_temporal_phase}; \
ARG.phase_filter_width = ${ARG_phase_filter_width}; \
ARG.DIROUT = '${ARG_DIROUT}'; \
NIFTI_NORDIC('${img_magn_in}', '${img_phase_in}', '${img_out}', ARG); \
end; \
quit;" \
>> ${ARG_DIROUT}/log_NORDIC_$(date '+%Y-%m-%d').txt

# Run dwidenoise on dMRI magnitude image
dwidenoise ${img_magn_in} ${ARG_DIROUT}/sub-01_ses-2mm_dir-AP_run-01_dwi_mppca.nii.gz