MRtrix3 DWI Denoising (MP-PCA)¶
Library: MRtrix3 | Docker Image: mrtrix3/mrtrix3
Function¶
Removes thermal noise from diffusion MRI data using Marchenko-Pastur PCA exploiting data redundancy across diffusion directions.
Modality: 4D diffusion-weighted NIfTI with multiple diffusion directions (minimum ~30 recommended).
Typical Use: First step in DWI preprocessing to improve SNR.
Key Parameters¶
Key Points¶
Should be run FIRST, before any other processing. Requires sufficient number of diffusion directions. Noise map useful for QC.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input DWI image | |
output |
string |
Yes | Output denoised image | |
noise |
string |
No | Output noise map filename | -noise |
extent |
string |
No | Sliding window extent (e.g., 5,5,5) | -extent |
mask |
File |
No | Processing mask | -mask |
Accepted Input Extensions¶
- input:
.mif,.nii,.nii.gz,.mgh,.mgz - mask:
.mif,.nii,.nii.gz,.mgh,.mgz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
denoised |
File |
$(inputs.output) |
noise_map |
File |
`${ |
| if (inputs.noise) | ||
| else | ||
| } | ||
| ` | ||
log |
File |
dwidenoise.log |
Output Extensions¶
- denoised:
.mif,.nii,.nii.gz - noise_map:
.mif,.nii,.nii.gz
Docker Tags¶
Available versions: latest, 3.0.8, 3.0.7, 3.0.5, 3.0.4, 3.0.3
Categories¶
- Diffusion MRI > MRtrix3 > Preprocessing