Issues with matching CLI/MATLAB results with DSI Studio GUI results

[Aesha Jain]

Hi Frank,

I am trying to reproduce my GUI-based fiber tracking results when running via CLI (and/or MATLAB). When I track a single subject in the GUI, I use:

• Angular threshold: 4
• Max seeds: 0
• Max tracts: 1,000,000 

With those settings, the tract output looks as expected. However, when I run multiple subjects using the CLI/MATLAB, the resulting tracts don’t match the GUI output (they look substantially different / incomplete). I also tried batch tractography using a higher track-to-voxel ratio, but the output still isn’t what I get from the GUI.

Could you share the recommended way to make the CLI/MATLAB run match the GUI tracking as closely as possible? Specifically, are there any additional GUI defaults (stopping criteria, step size, smoothing, QA thresholds, seeding behavior, etc.) that I might be missing in the CLI/MATLAB setup?

The screenshot below is the one that I generate in GUI and this is exactly what I am trying to recreate using CLI or Matlab. 

Below attached are the Screenshots of the output generated using CLI/Matlab.

Thanks so much for your time and guidance,

Best,

Aesha 

[Frank Yeh]

Could you post the console output from the GUI? and also the command line log output?
Comparing them side by side may give a hint.

Frank

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[Aesha Jain]

Hi Frank,
I've uploaded output files in the dropbox. Thank you!

Aesha 

[Frank Yeh]

There are many differences in the parameters as listed in the log files. The biggest difference is the difference of the pipeline (trk vs atk)
To get identical results, either using --action=trk for the CLI. or use [Tractography (Batch)][Step B4: Automated Tracking...] for the GUI

On Fri, Feb 20, 2026 at 11:21 AM Aesha Jain <jain.ae...@gmail.com> wrote:

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