AFNI Tractography (3dTrackID)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Performs deterministic, mini-probabilistic, or full probabilistic white matter tractography using diffusion tensor data.
Modality: DTI parameter volumes (from 3dDWItoDT with -eigs) and integer-labeled ROI mask.
Typical Use: White matter tractography and structural connectivity analysis in AFNI diffusion pipelines.
Key Parameters¶
-mode (DET/MINIP/PROB), -dti_in (DTI prefix), -netrois (ROI file), -prefix (output prefix), -mask (brain/WM mask)
Key Points¶
Three tracking modes with different speed/accuracy tradeoffs. Outputs tract files, connectivity matrices, and statistics. Requires 3dDWItoDT output with -eigs flag.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
mode |
enum |
Yes | Tracking mode (DET=deterministic, MINIP=mini-probabilistic, PROB=probabilistic) | -mode |
dti_in |
string |
Yes | DTI input prefix (basename, files staged via dti_files) | -dti_in |
dti_files |
File[] |
Yes | DTI parameter files from 3dDWItoDT (HEAD/BRIK pairs, staged into working dir) | |
netrois |
File |
Yes | Network ROI file (integer-labeled mask) | -netrois |
prefix |
string |
Yes | Output prefix | -prefix |
mask |
File |
No | Brain mask (WM mask recommended) | -mask |
logic |
enum |
No | Logic for multi-ROI tracking (default OR) | -logic |
algopt |
File |
No | Algorithm options file | -algopt |
unc_min_FA |
double |
No | Minimum FA for uncertainty calc | -unc_min_FA |
unc_min_V |
double |
No | Minimum confidence for uncertainty | -unc_min_V |
alg_Thresh_FA |
double |
No | FA threshold for tracking | -alg_Thresh_FA |
alg_Thresh_ANG |
double |
No | Angle threshold (degrees) for tracking | -alg_Thresh_ANG |
alg_Thresh_Len |
double |
No | Minimum tract length (mm) | -alg_Thresh_Len |
alg_Nseed_X |
int |
No | Number of seeds per voxel (X direction) | -alg_Nseed_X |
alg_Nseed_Y |
int |
No | Number of seeds per voxel (Y direction) | -alg_Nseed_Y |
alg_Nseed_Z |
int |
No | Number of seeds per voxel (Z direction) | -alg_Nseed_Z |
nifti |
boolean |
No | Output in NIfTI format | -nifti |
no_indipair_out |
boolean |
No | Do not output individual pairwise maps | -no_indipair_out |
write_rois |
boolean |
No | Write out ROI volumes | -write_rois |
write_opts |
boolean |
No | Write out tracking options | -write_opts |
pair_out_power |
boolean |
No | Output power-averaged map | -pair_out_power |
Accepted Input Extensions¶
- netrois:
.nii,.nii.gz,.HEAD - mask:
.nii,.nii.gz,.HEAD
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
tracts |
File |
$(inputs.prefix)*.trk, $(inputs.prefix)*.niml.tract |
connectivity_matrix |
File |
$(inputs.prefix)*.grid |
stats |
File |
$(inputs.prefix)*.stats |
log |
File |
$(inputs.prefix).log |
Output Extensions¶
- tracts:
.trk,.niml.tract - connectivity_matrix:
.grid - stats:
.stats
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Diffusion MRI > AFNI > Tractography