Command-Line Interface for DSI Studio

Contents
1 Fiber tracking
1.1 Parameters
1.2 Example
2 Image Reconstruction
2.1 Parameters:
2.2 Example

Fiber tracking

The fiber tracking function on DSI Studio can be executed by using command line. After fiber tracking, a log file named tracking_log.txt will be generated. The result can be saved as a .txt file or .trk file. The detail for tracking commands is as follows. For parameters not assigned explicitly, default values will be used instead.

Parameters

action: use "trk" to perform fiber tracking

source: specify the .fib file for tracking.

method: tracking methods 0:streamline (default), 1:rk4

initial_dir: initial direction 0:random (default), 1:main

interpolation:interpolation methods (0:trilinear, 1:gaussian radial)

thread_count: specify the thread count. 1 for single thread. 2 for two threads...

seed: specify the seeding file. Supported file format includes text files, Analyze files, and nifti files.

roi: specify the roi file. Supported file format includes text files, Analyze files, and nifti files. Multiple input is supported.

roi2: specify the second roi

roa: specify the roa

end: specify the endpoint

fiber_count: specify the number of fibers to be generated. If seed number is preferred, use seed_count instead.

    output: specify the output file that stores the tracking result. Supported file format include text file and .trk file.

    step_size, turning_angle, interpo_angle, fa_threshold, smoothing, min_length, max_length: refer to tracking manual for detail. The step_size, min_length, and max_length are at a scale of minimeter.

Example

c:\dsi_studio.exe --action=trk --source=test.fib.gz --method=0 --fiber_count=10000 --output=track.trk

c:\dsi_studio --action=trk --source=subject1.fib --method=0 --seed=wholeBrain.nii --roi=my_roi1.nii --roi2=myroi2.nii --seed_count=5000

--fa_threshold=0.0241 --turning_angle=80 --step_size=.5 --smoothing=0.85 --min_length=20 --max_length=140 --output=track.txt

*The default value will be used if the parameters have no value assigned.

Image Reconstruction

The reconstruction on DSI Studio can be executed by command line. For parameters not assigned explicitly, default values will be used instead.

Parameters:

    action: use "rec" for image reconstruction

    source: assign the .src file for reconstruction

    mask: assign the mask file. You may skip this parameter to use the default mask.

    method: assign the reconstruction methods. 0:DSI, 1:DTI, 2:Funk-Randon QBI, 3:Spherical Harmonic QBI, 4:GQI. For detail, please refer to the reconstruction page.

param0, param1, param2...: the parameters for reconstruction. For DSI, param0 stands for the width of the hanning filter, and other parameters are not used. For GQI, param0 is the ratio of the mean diffusion distance.

record_odf: use "--record_odf=1" to record the odf.

odf_order: assign the dimension of the odf. Supported values are 4,5,6,and 8, resulting in dimension of 162, 252, 362, 642, respectively, default value=8.

num_fiber: the maximum count of the resolving fibers for each voxel, default=3.

Example

1.DSI reconstruction with hanning filter of 16 and record the ODF

dsi_studio --action=rec --source=20081006_M025Y_1Grid.src.gz --method=0 --param0=16 --record_odf=1

2.GQI reconstruction with 1.25 mean diffusion distance

dsi_studio --action=rec --source=20081006_M025Y_1Shell.src.gz --mask=mask100.txt --method=4 --param0=1.25

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