MRtrix3 Streamline Tractography Generation¶
Library: MRtrix3 | Docker Image: mrtrix3/mrtrix3
Function¶
Generates streamline tractograms using various algorithms (iFOD2, FACT, etc.) from FOD or tensor images.
Modality: FOD image (from dwi2fod) or tensor image, plus optional seed/mask/ROI images.
Typical Use: Generating whole-brain or ROI-seeded tractograms.
Key Parameters¶
Key Points¶
iFOD2 (default) is probabilistic and handles crossing fibers. Use -select for target count. -cutoff controls termination.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
source |
File |
Yes | Input FOD or tensor image | |
output |
string |
Yes | Output tractogram filename | |
algorithm |
string |
No | Tracking algorithm (iFOD2/Tensor_Det/Tensor_Prob) | -algorithm |
seed_image |
File |
No | Seed image for tractography | -seed_image |
select |
int |
No | Number of streamlines to select | -select |
cutoff |
double |
No | FOD amplitude cutoff for termination | -cutoff |
act |
File |
No | ACT tissue-segmented image | -act |
step |
double |
No | Step size (mm) | -step |
angle |
double |
No | Maximum angle between steps (degrees) | -angle |
maxlength |
double |
No | Maximum streamline length (mm) | -maxlength |
Accepted Input Extensions¶
- source:
.mif,.nii,.nii.gz,.mgh,.mgz - seed_image:
.mif,.nii,.nii.gz,.mgh,.mgz - act:
.mif,.nii,.nii.gz,.mgh,.mgz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
tractogram |
File |
$(inputs.output) |
log |
File |
tckgen.log |
Output Extensions¶
- tractogram:
.tck
Docker Tags¶
Available versions: latest, 3.0.8, 3.0.7, 3.0.5, 3.0.4, 3.0.3
Categories¶
- Diffusion MRI > MRtrix3 > Tractography