Seeking Advice on Fiber Tracking Parameters

[Yijie Li (一生破晓)]

Dear Dr. Yeh,

I am writing to seek your advice on the parameter settings for fiber tracking in DSI Studio. I am currently using the --action=trk function on the HCP-YA GQI data from FiberDataHub. Currently, I am running the following command:
/data/yijie/software/dsi-studio/dsi_studio --action=trk --source=gqi_file --tract_count=100000 --step_size=1 --method=1

After converting the resulting .tt.gz file to VTK format and visualizing it in 3D Slicer, I noticed a high number of apparent false-positive streamlines (shown in purple), which form looping structures in the example image.

Could you please advise on recommended parameter settings to help reduce these artifacts? Any suggestions or best practices for improving tractography quality in this context would be greatly appreciated.  Alternatively, I would prefer to avoid using QSDR-reconstructed files because QSDR applies nonlinear warping to MNI space, whereas I hope to generate tractography in native space for subsequent registration experiments.

Thank you for your time and assistance.

Best regards,
Yijie Li

[Frank Yeh]

Increasing anisotropy threshold or angular threshold can help reduce
those false results.
Frank

On Thu, Mar 5, 2026 at 10:31 AM Yijie Li (一生破晓) <li624...@gmail.com> wrote:
>
> Dear Dr. Yeh,
>
> I am writing to seek your advice on the parameter settings for fiber tracking in DSI Studio. I am currently using the --action=trk function on the HCP-YA GQI data from FiberDataHub. Currently, I am running the following command:
> /data/yijie/software/dsi-studio/dsi_studio --action=trk --source=gqi_file --tract_count=100000 --step_size=1 --method=1
>
> After converting the resulting .tt.gz file to VTK format and visualizing it in 3D Slicer, I noticed a high number of apparent false-positive streamlines (shown in purple), which form looping structures in the example image.
>

> Could you please advise on recommended parameter settings to help reduce these artifacts? Any suggestions or best practices for improving tractography quality in this context would be greatly appreciated. Alternatively, I would prefer to avoid using QSDR-reconstructed files because QSDR applies nonlinear warping to MNI space, whereas I hope to generate tractography in native space for subsequent registration experiments.
>
> Thank you for your time and assistance.
>
> Best regards,
> Yijie Li
>

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