Automatic Fiber Tracking

Use --action=atk to initiate automatic fiber tracking.

Automatic fiber tracking maps individual bundles using deterministic fiber tracking and tract recognition. The implementation is detailed in Yeh, Fang-Cheng. “Shape analysis of the human association pathways.” Neuroimage 223 (2020): 117329.

Examples

1. Run fiber tracking on all fib.gz files to map all association pathways:

dsi_studio --action=atk --source=*.fz

2. Track specific bundles (e.g., corticospinal tracts and optic radiation):

dsi_studio --action=atk --source=*.fz --track_id=Corticos,Optic

3. Output tracts in the template space:

dsi_studio --action=atk --source=*.fz --template_track

Core Functions

Parameter Default Description
source   Specify fib.gz files for automatic bundle tracking.
track_id Arcuate,Cingulum,Aslant,InferiorFronto,InferiorLongitudinal,SuperiorLongitudinal,Uncinate,Fornix,Corticos,ThalamicR,Optic,Lemniscus,Reticular,Corpus Specify the bundle names, separated by commas. Partial names are accepted. Example: --track_id=arcuate tracks left and right arcuate fasciculus.
template 0 Specify the template for tracking. Supported templates:
0: ICBM152
1: CIVM_mouse
2: Neonate
3: INDI_rhesus
4: Pitt_Marmoset
5: WHS_SD_rat
tolerance 22,26,30 Set tolerance for bundle recognition (in mm). Larger values may include more variation but increase false positives.
track_voxel_ratio 2.0 Set the track-to-voxel ratio for streamline count. Higher values improve mapping but increase computation time.
check_ending 1 (default: 0 for cingulum) Removes tracts terminating in high anisotropy locations.
thread_count Hardware max Specify the number of CPU cores used for computation.
yield_rate 0.00001 Terminates tracking early if no new fibers are generated.
default_mask 0 Specify whether to use the default mask.
overwrite 0 Specify whether to overwrite existing files.
trk_format tt.gz Set the output format for tractography files. Supported formats: .tt.gz, .trk, .trk.gz, .tck, .txt, .mat, .nii, .nii.gz.

Optional Functions

The majority of parameters used in –action=trk are also supported.