Automatic Fiber Tracking
use –action=
atkto 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
*Run fiber tracking on all fib.gz files to map the left and arcuate fasciculus
dsi_studio --action=atk --source=*.fib.gz --track_id=Arcuate
*Run fiber tracking on all fib.gz files and output tracts to the template space
dsi_studio --action=atk --source=*.fib.gz --export_template_trk=1
Core Functions
| Parameters | Default | Description |
|---|---|---|
| source | specify the src.gz or fib.gz file for automatic bundle tracking. | |
| track_id | Fasciculus,Cingulum,Aslant,Corticos,Thalamic_R,Reticular,Optic,Fornix,Corpus |
specify the id number or the name of the bundle. The id can be found in /atlas/ICBM152/HCP1065.tt.gz.txt . <p> This text file is included in DSI Studio package (For Mac, right-click on dsi_studio_64.app to find content). You can specify partial name of the bundle: <p> example:<p> for tracking left and right arcuate fasciculus, assign –track_id=0,1 or –track_id=arcuate (DSI Studio will find bundles with names containing ‘arcuate’, case insensitive) <p> example:<p> for tracking left and right arcuate and cingulum, assign –track_id=0,1,2,3 or –track_id=arcuate,cingulum |
| tolerance | 16,18,20 |
the tolerance for the bundle recognition. The unit is in mm. Multiple values can be assigned using comma separator. A larger value may include larger track variation but also subject to more false results. |
| tip | 32 |
iterations of topology-informed pruning. A higher value will apply more pruning that removes noisy tracks |
| track_voxel_ratio | 2 |
the track-voxel ratio for the total number of streamline count. A larger value gives better mapping with the expense of computation time. |
| check_ending | 1 |
remove tracts if they terminate in high anisotropy locations. |
Other Options
| Parameters | Default | Description |
|---|---|---|
| thread_count | hardware max | Specify number of CPU cores used in computation |
| length_ratio | 1.25 |
the diffusion sampling length ratio for GQI reconstruction. This is only used if the source file is an SRC file. |
| For small bundles (e.g. right arcuate), a larger value may cause a large computation burden. | ||
| default_mask | 0 |
Specify whether default mask is used. |
| overwrite | 0 |
Specify whether to overwrite existing files. |
| output | the directory of the source file | Specify the output directory. |
| export_stat | 1 |
Specify whether to output track statistics. |
| export_trk | 1 |
Specify whether to output tractography file. |
| export_template_trk | 0 |
Specify whether to output tractography in the template space. |
| trk_format | tt.gz |
Specifythe output format of the tractography. Supported formats include tt.gz trk trk.gz tck txt mat nii nii.gz |