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 --export_template_trk=1
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 : ICBM1521 : CIVM_mouse2 : Neonate3 : INDI_rhesus4 : Pitt_Marmoset5 : 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. |
export_stat |
1 |
Specify whether to output tracking statistics. |
export_trk |
1 |
Specify whether to output the tractography file. |
export_template_trk |
0 |
Specify whether to output tractography in the template space. |
trk_format |
tt.gz |
Set the output format for tractography files. Supported formats: .tt.gz , .trk , .trk.gz , .tck , .txt , .mat , .nii , .nii.gz . |
stat_format |
stat.txt |
Specify the output format for statistics files (must be in text format). |
output |
Output directory of the first file in --source |
Specify the output directory. |
Notes:
- Fiber Tracking Parameters: The following parameters are also supported:
--otsu_threshold
--fa_threshold
--turning_angle
--step_size
--smoothing
--tip_iteration
- Length Constraints: Parameters like
--min_length
and--max_length
are not supported, as length constraints are automatically determined from the atlas. - Report Generation: Use the
--report
parameter to save the auto-tracking report to a file.