MRtrix3 Tensor Metric Extraction¶
Library: MRtrix3 | Docker Image: mrtrix3/mrtrix3
Function¶
Extracts scalar metrics (FA, MD, AD, RD, eigenvalues, eigenvectors) from a fitted diffusion tensor image.
Modality: Diffusion tensor image (4D NIfTI from dwi2tensor).
Typical Use: Generating FA, MD, and other scalar diffusion maps from tensor.
Key Parameters¶
, -fa (output FA map), -adc (output MD map), -ad (output AD), -rd (output RD), -vector (output eigenvectors)
Key Points¶
Multiple outputs can be generated in a single run. FA range 0-1. Specify each desired output explicitly.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input tensor image | |
fa |
string |
No | Output FA map filename | -fa |
adc |
string |
No | Output mean diffusivity (ADC) map filename | -adc |
ad |
string |
No | Output axial diffusivity map filename | -ad |
rd |
string |
No | Output radial diffusivity map filename | -rd |
vector |
string |
No | Output eigenvector map filename | -vector |
value |
string |
No | Output eigenvalue map filename | -value |
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 |
|---|---|---|
fa_map |
File |
`${ |
| if (inputs.fa) | ||
| else | ||
| } | ||
| ` | ||
md_map |
File |
`${ |
| if (inputs.adc) | ||
| else | ||
| } | ||
| ` | ||
ad_map |
File |
`${ |
| if (inputs.ad) | ||
| else | ||
| } | ||
| ` | ||
rd_map |
File |
`${ |
| if (inputs.rd) | ||
| else | ||
| } | ||
| ` | ||
log |
File |
tensor2metric.log |
Output Extensions¶
- fa_map:
.mif,.nii,.nii.gz - md_map:
.mif,.nii,.nii.gz - ad_map:
.mif,.nii,.nii.gz - rd_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 > Tensor/FOD