MRtrix3 Tractogram to Connectome¶
Library: MRtrix3 | Docker Image: mrtrix3/mrtrix3
Function¶
Constructs a structural connectivity matrix by counting streamlines connecting pairs of regions from a parcellation.
Modality: Tractogram (.tck) plus parcellation volume (integer-labeled 3D NIfTI).
Typical Use: Building structural connectivity matrices from tractography and parcellation.
Key Parameters¶
Key Points¶
Output is NxN matrix. Use SIFT/SIFT2 filtered tractogram for quantitative connectomics. -symmetric recommended.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input_tracks |
File |
Yes | Input tractogram | |
parcellation |
File |
Yes | Parcellation image (atlas) | |
output |
string |
Yes | Output connectivity matrix filename | |
assignment_radial_search |
double |
No | Radial search distance for node assignment (mm) | -assignment_radial_search |
scale_length |
boolean |
No | Scale by streamline length | -scale_length |
scale_invlength |
boolean |
No | Scale by inverse streamline length | -scale_invlength |
scale_invnodevol |
boolean |
No | Scale by inverse node volume | -scale_invnodevol |
stat_edge |
string |
No | Edge statistic (sum/mean/min/max) | -stat_edge |
symmetric |
boolean |
No | Make matrix symmetric | -symmetric |
zero_diagonal |
boolean |
No | Zero the diagonal of the matrix | -zero_diagonal |
Accepted Input Extensions¶
- input_tracks:
.tck - parcellation:
.mif,.nii,.nii.gz,.mgh,.mgz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
connectome |
File |
$(inputs.output) |
log |
File |
tck2connectome.log |
Output Extensions¶
- connectome:
.csv
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