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.


*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/ . <p> This text file is included in DSI Studio package (For Mac, right-click on 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