Fiber-Tracking Parameter Setting (Command Line)

[Darren Lee]

Dear Dr. Yeh 

I am writing to seek clarification regarding Fiber Tracking using the CLI. I noticed that the tractography results generated via the CLI differ substantially from those obtained through the GUI.  Below is the CLI command I used:

dsi_studio \
--action=trk \
--source=${sub}/dwi/dsi_studio/${sub}_src.gqi.fz \
--output=${sub}/dwi/dsi_studio/${sub}_whole_brain_CLI \
--trk_format=trk \
--tip_iteration=2 \
--step_size=0.5 \
--turning_angle=55 \
--min_length=20 \
--max_length=200 \
--random_seed=42

From the screenshot, the tractogram labeled whole_brain in Step T3d: Tracts was generated via the GUI, while sub-0001_whole_brain_CLI was generated via the CLI. There appears to be a significant discrepancy between the tract distributions produced by the two methods. All tracking parameters configured in the GUI are shown under Step T3c: Options.  Could you please advise how I should modify my CLI command to ensure that the results closely match those obtained via the GUI?

Best regards,

Darren  

[Darren Lee]

Dear Dr. Yeh,

I have resolved the issue. It was caused by an incorrect overwrite setting on my end.

My apologies for the confusion.

Best regards,
Darren

On Mon, 2 Mar 2026 at 23:50, Darren Lee <darre...@gmail.com> wrote:

Hi Yeh, 

   

    In the CLI, I used --parameter_id to copy all the tracking parameters from the GUI, and the resulting whole-brain tractogram is similar to the one obtained from the GUI.  

    I have another quick question: when using --parameter_id, do I still need to manually set the output parameters (e.g., --output and --trk_format)? My updated CLI command is as follows:

sub=sub-0001

dsi_studio \
--action=trk \
--source=${sub}/dwi/dsi_studio/${sub}_src.gqi.fz \
--output=${sub}/dwi/dsi_studio/${sub}_whole_brain_CLI \
--trk_format=trk \

--parameter_id=c9A99193FE8D5123Fba3FcbA041b4843c40420Fba803FcCDCC4C3Ec

. However, I noticed that the output file is named whole_brain_template_GUI.tt.tt, which differs from the filename and format I specified using --output and --trk_format. 




  Additionally, when I loaded the CLI-generated file into DSI Studio, the whole-brain tractogram did not appear to be in the original space. I have attached a screenshot for reference.Additionally, when I loaded the CLI-generated file into DSI-Studio, the whole-brain tractogram did not appear to be in the original space. I have attached a screenshot for reference.




Best regards,

Darren  




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[Darren Lee]

Hi Yeh, 

   

    In the CLI, I used --parameter_id to copy all the tracking parameters from the GUI, and the resulting whole-brain tractogram is similar to the one obtained from the GUI.  

    I have another quick question: when using --parameter_id, do I still need to manually set the output parameters (e.g., --output and --trk_format)? My updated CLI command is as follows:

sub=sub-0001

dsi_studio \
--action=trk \
--source=${sub}/dwi/dsi_studio/${sub}_src.gqi.fz \
--output=${sub}/dwi/dsi_studio/${sub}_whole_brain_CLI \
--trk_format=trk \

--parameter_id=c9A99193FE8D5123Fba3FcbA041b4843c40420Fba803FcCDCC4C3Ec

. However, I noticed that the output file is named whole_brain_template_GUI.tt.tt, which differs from the filename and format I specified using --output and --trk_format. 




  Additionally, when I loaded the CLI-generated file into DSI Studio, the whole-brain tractogram did not appear to be in the original space. I have attached a screenshot for reference.Additionally, when I loaded the CLI-generated file into DSI-Studio, the whole-brain tractogram did not appear to be in the original space. I have attached a screenshot for reference.




Best regards,

Darren  




On Mon, 2 Mar 2026 at 16:25, Darren Lee <darre...@gmail.com> wrote:

[Frank Yeh]

Glad this is resolved.
Best regards,

Frank

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[Darren Lee]

Hi Yeh,

I'm currently using Autotrack for OpticaRadiationLeft. In the GUI interface, parameters such as min_length and max_length can be set manually, while in the CLI these parameters cannot be specified when using --action=atk. I used the following CLI command and found that no streamlines were generated:

    dsi_studio --action=atk --source=sub-0001_src.gqi.fz --trk_format=trk.gz --track_id=ProjectionBasalGanglia_OpticRadiationL

However, in the GUI the streamlines for the OpticRadiationL tract can be generated successfully (see the attached screenshot).

Alternatively, in the CLI I tried using --action=trk with the following command:

    dsi_studio --action=trk --source=sub-0001_src.gqi.fz --output=sub-0001_OR_L --trk_format=trk --track_id=OpticRadiationL --parameter_id=c9A99193Fb803FdbF041b9643db803Fba04CDCC4C3Ec

The resulting tract was similar to what I obtained in the GUI using Autotrack.

Since the GUI is not available on our High-Performance Computing environment, I have to rely on the CLI. Given this limitation, would it be appropriate to use --action=trk with the corresponding track_id (and parameter_id) as a replacement for --action=atk in this case? 

For reference, the .fz file and the resulting .trk file (generated using --action=trk with --track_id=OpticRadiationL) have been uploaded via a private link for data sharing on the DSI Studio Google Group website.

Best regards,
Darren