Fiber Tracking

Use --action=trk to perform deterministic whole-brain or ROI-based fiber tracking in DSI Studio (Yeh et al. PLoS ONE 8(11):e80713, 2013). Additionally, you can compute tract-to-region connectomes, tract statistics, track-density images, cluster or recognize known bundles, and even perform differential analysis—all from this single command.

For automatic atlas-based bundle mapping, see --action=atk instead:
Atlas-Based Tracking Documentation

Examples

Whole-brain deterministic tracking

dsi_studio --action=trk \
           --source=subject.fib.gz \
           --output=subject_all.tt.gz

Seed-and-target ROI tracking

dsi_studio --action=trk \
           --source=subject.fib.gz \
           --seed=wholeBrain.nii.gz \
           --roi=regionA.nii.gz \
           --roi2=regionB.nii.gz \
           --output=streamlines.tt.gz

Mapping the left arcuate fasciculus and derive is tract-to-region connectome at HCP-MMP parcellation

dsi_studio --action=trk \
           --source=subject.fib.gz \
           --track_id=ArcuateFasciculusL \
           --connectivity=HCP-MMP

Core Options

Option	Default	Description
`--action`	(required)	Must be `trk`.
`--source`	(required)	Path to your `.fib.gz` (or `.fz`) file.
`--output`		Output tractography file (e.g. –output=tract.tt.gz) or directory (e.g. –output=/path).
`--track_id`	(optional)	Specify the name of the bundle to be mapped (e.g. –track_id=ArcuateFasciculusL ). The complete list can be found here
`--tip_iteration`	`0` or `16`	Specify pruning iterations. Default is `16` for `track_id` or `dt_threshold_index`.
`--thread_count`	Hardware threads	Number of threads to use.

Tracking Parameters

Option	Default	Description
`--method`	Algorithm in file	Tracking algorithm. `0=streamline`, `1=RK4`, etc.
`--tract_count`	`0`	Number of tracts to generate (alternative to seed count).
`--seed_count`	Auto	Number of seeds to launch. Overrides `tract_count`.
`--track_voxel_ratio`	`0.5`	Seeds-per-voxel ratio.
`--turning_angle`	`0` (random)	Maximum allowable turning angle (deg). Default is random between 15° and 90°.
`--step_size`	`0` (random)	Step size in mm. Default is random between 1–3 voxels.
`--smoothing`	`0`	Fraction of previous direction to mix in (0-1).
`--min_length`	Dataset-specific	Minimum fiber length (mm).
`--max_length`	Dataset-specific	Maximum fiber length (mm).
`--otsu_threshold`	FA threshold × 0.6	Default threshold for FA-based seeding.
`--threshold_index`	—	Use a different diffusion index (e.g., QA) for termination instead of FA.
`--check_ending`	Off for whole-brain tracking	Drop tracks that do not terminate within any ROI.
`--parameter_id`	—	Load all tracking parameters from a parameter code.
`--random_seed`	`0`	Seed for random number generation in fiber tracking. Set to an integer to vary seed sequences.

ROI / Region Options

The following region types can be specified (comma-separated actions are applied in order):

--seed=<file>
--roi=<file_or_atlas:region>,<other region file>,<region actions>,... 
--roi2=…
--roa=…
--end=…
--ter=…
--nend=…
--lim=…

Region Actions

Region Actions: dilation, erosion, defragment, negate, flipx, flipy, flipz, etc.

Merge Volumes: You can also add more volumes using ,:

--roi=left.nii.gz,right.nii.gz,dilation,smoothing

Post-Tracking Routine

Option	Description
`--output=<file>`	Save tractography result (e.g., `--output=result.tt.gz`).
`--trk_format=<format>`	Set default tract format if `--output` is not specified (e.g., `--trk_format=tt.gz`).
`--delete_repeat=<length>`	Remove duplicate streamlines within the specified voxel distance (e.g., `--delete_repeat=8`).
`--delete_by_length=<length>`	Remove streamlines shorter than the specified voxel length.
`--cluster=<method>,<count>,<detail>,<output>`	Perform clustering (e.g., `--cluster=0,50,8,cluster.txt`). • `method`: 0 = single linkage, 1 = k-means, 2 = EM • `detail`: only used in method 0
`--recognize=<file>`	Apply atlas-based bundle recognition and save recognized tracts.
`--template_track=<file>`	Save tracts in template voxel space.
`--mni_track=<file>`	Save tracts in MNI space.
`--end_point=<file>`	Save endpoint coordinates (both ends) to `.txt` or `.mat`.
`--end_point1=<file>`	Save starting point coordinates to `.txt` or `.mat`.
`--end_point2=<file>`	Save endpoint coordinates to `.txt` or `.mat`.
`--export=<type>,<type>,...`	Export tract data (e.g., `--export=stat,tdi,`) • `<type>`: stat = tract statistics, tdi = track density image, tdi2= track density image with x2 resolution
`--profile=<metrics>,<type>,<bandwidth>`	Get tract profile, for example: `--profile=dti_fa:3:1` exports `FA` profile along `fiber direction (left first)` using `bandwidth = 1`.
	`<type>`: 0=x direction, 1=y direction, 2=z direction, 3=fiber orientation (left first), 4=fiber orientation (posterior first), 5=fiber orientation (superior first), 6=fiber orientation (right first), 7=fiber orientation (anterior first), 8=fiber orientation (inferior first)

Connectivity Matrix (Connectome)

Option	Description
`--connectivity=<atlases>`	A comma-separated list of brain parcellation atlases (NIfTI files or atlas names recognized by DSI Studio, e.g., `AAL2,HCP-MMP`). The specified parcellations are used to compute region-to-region (R2R) and tract-to-region (T2R) connectomes.
`--connectivity_type=<types>`	Defines how streamlines contribute to the structural connectivity. Use `pass` to include streamlines that pass through ROIs (pass-through), or `end` to include streamline by checking the endpoints. Multiple types can be specified using commas to export multiple connectomes in a single run, e.g., `--connectivity_type=pass,end`.
`--connectivity_value=<metrics>`	Selects which connectivity metric(s) to export. The default value `all` exports all supported metrics. To export a subset, provide a comma-separated list of metric keywords (matched by name), e.g., `--connectivity_value=volume,fa`.
`--connectivity_output=<outputs>`	Specifies which outputs to save. The default value `matrix` saves region-to-region and tract-to-region matrices as `.connectivity.mat` (MATLAB v4 square matrix). Specify `connectogram` saves `.connectogram.txt` for visualization with CIRCUS. Specify `network` saves graph-theoretic network measures as `*.network_measures.txt`; Example: `--connectivity_output=matrix,network`.

Differential Tracking

Option	Description
`--dt_metric1`	Metric for baseline tracking (e.g., `qa`).
`--dt_metric2`	Metric for comparison tracking (e.g., `nqa`).
`--dt_threshold`	Percent change threshold for differential analysis.
`--dt_threshold_type`	Type of threshold: `0=(m1−m2)/m1`, `1=(m1−m2)/m2`, `2=abs(m1−m2)`.