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

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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

Connectivity analysis (HCP-MMP & AAL3 atlases)

dsi_studio --action=trk \
           --source=subject.fib.gz \
           --output=no_file \
           --connectivity=HCP-MMP,AAL3 \
           --connectivity_value=count,qa

Bundle-specific tracking by parameter ID

dsi_studio --action=trk \
           --source=subject.fib.gz \
           --parameter_id=c9A99193Fba3F2EFF013Fcb2041b96438813dcb \
           --output=subject_bundle.tt.gz

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Core Options

Option	Default	Description
--action	(required)	Must be trk.
--source	(required)	Path to your .fib.gz (or .fz) file.
--output	Depends on format	Output file or directory. Extensions depend on the specified format.
--thread_count	Hardware threads	Number of threads to use.
--report	—	Write the raw tracking report (.txt).
--parameter_id	—	Load all tracking parameters from a saved parameter code.
--refine	—	Number of “trim + reseed” iterations after initial tracking.
--tip_iteration	0 or 16	Specify pruning iterations. Default is 16 for track_id or dt_threshold_index.
--random_seed	0	Seed for random number generation in fiber tracking. Set to an integer to vary seed sequences.

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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.

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ROI / Region Options

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

--seed=<file>
--roi=<file_or_atlas:region>[,dilation,erosion,smoothing,…]
--roi2=…
--roa=…
--end=…
--ter=…
--nend=…
--lim=…

Actions

• Actions: dilation, erosion, defragment, negate, flipx, flipy, flipz, etc.
• Merge Volumes: You can merge multiple volumes using +:

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

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Post-Tracking & Export Options

Option	Description
--delete_repeat	Remove duplicate streamlines within a specified voxel distance.
--recognize	Apply atlas-based bundle recognition.
--mni_track	Save tracts in MNI space.
--end_point	Save a .txt or .mat file of all endpoint coordinates.
--export	Export options for statistics and visualizations: stat, tdi, tdi_color, report:index, etc.

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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).

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Connectivity Options

Option	Default	Description
--connectivity	—	Comma-separated list of atlases or ROI files (e.g., AAL2,HCP-MMP).
--connectivity_value	count	Metrics to compute for each matrix entry: count, length, qa, etc.
--connectivity_threshold	0.001	Threshold to binarize connection weights before graph measures.