Batch generation of multiple connectivity matrices or tractography outputs from a single .fib.gz file with varying tracking parameters?

[Jaime Castillo]

Hello Frank,

I’m working on a research project involving deterministic tractography using DSI Studio, and I would like to ask whether it is possible to automate the generation of multiple connectivity matrices (or tractography outputs, e.g. .trk files) from a single .fib.gz source, each using different tracking parameters (e.g., tracking_threshold, angular_threshold, etc.).

I’m aware of the batch processing feature to process multiple subjects, but in my case, the goal is to run several fiber tracking sessions on the same dataset, varying parameters systematically (e.g., Monte Carlo-style analysis of uncertainty propagation). Is there any way to achieve this directly through the command line or a scriptable interface within DSI Studio?

Thanks in advance for your help, and thank you for developing and maintaining such a powerful tool!

Best regards,
Jaime

[Frank Yeh]

Yes, this is doable. You may use Python and bash script to call the command line at different parameters.

Best

Frank

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[Jaime Castillo]

Hi Frank,

Thank you for your reply.

Just to confirm — I’m trying to use DSI Studio through the command line to generate multiple connectivity matrices and tractographies by varying tracking parameters in an automated way (using Python or Bash scripts as you suggested).

However, I’ve encountered issues depending on the environment. Could you please clarify:

• Which operating system(s) and/or version(s) of DSI Studio support full command-line functionality without launching the GUI?

• Is it possible to run --action=trk or similar actions in a headless (non-GUI) Linux environment or Docker container?

Thank you very much for your help!

Best regards,
Jaime

[Frank Yeh]

>
> Which operating system(s) and/or version(s) of DSI Studio support full command-line functionality without launching the GUI?

All of them. Once CLI is used, GUI won't start.

>
> Is it possible to run --action=trk or similar actions in a headless (non-GUI) Linux environment or Docker container?

Yes, we do this all the time.

Best regards,
Frank

>
> Thank you very much for your help!
>
> Best regards,
> Jaime
>
>
> El domingo, 13 de julio de 2025 a las 17:28:40 UTC+2, Frank Yeh escribió:
>>
>> Yes, this is doable. You may use Python and bash script to call the command line at different parameters.
>>
>> Best
>> Frank
>>
>> Jaime Castillo <jaime.cast...@gmail.com> 於 2025年7月13日 週日 上午11:26 寫道：
>>>
>>> Hello Frank,
>>>
>>> I’m working on a research project involving deterministic tractography using DSI Studio, and I would like to ask whether it is possible to automate the generation of multiple connectivity matrices (or tractography outputs, e.g. .trk files) from a single .fib.gz source, each using different tracking parameters (e.g., tracking_threshold, angular_threshold, etc.).
>>>
>>> I’m aware of the batch processing feature to process multiple subjects, but in my case, the goal is to run several fiber tracking sessions on the same dataset, varying parameters systematically (e.g., Monte Carlo-style analysis of uncertainty propagation). Is there any way to achieve this directly through the command line or a scriptable interface within DSI Studio?
>>>
>>> Thanks in advance for your help, and thank you for developing and maintaining such a powerful tool!
>>>
>>> Best regards,
>>> Jaime
>>>
>>> --
>>> You received this message because you are subscribed to the Google Groups "DSI Studio" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+...@googlegroups.com.
>>> To view this discussion visit https://groups.google.com/d/msgid/dsi-studio/4dffc1ad-f344-40f6-90ca-89baf6cf4fadn%40googlegroups.com.
>
> --
> You received this message because you are subscribed to the Google Groups "DSI Studio" group.
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> To view this discussion visit https://groups.google.com/d/msgid/dsi-studio/3ac8b38c-8e94-4506-9ce1-e3d45357c989n%40googlegroups.com.