Commands are not recognised in LQT Matlab-based

[Triana Karnadipa]

Dear Prof. Frank,

I hope you’re well. I’m reaching out for guidance on using DSI Studio commands in MATLAB’s Lesion Quantification Toolkit to create a disconnection matrix. The command I used is:

eval(['! ' cfg.dsi_path ' --action=ana --source=' fullfile(cfg.source_path, source_fib) ' --tract=' fullfile(cfg.source_path, all_tracts) ' --roi=' cfg.lesion_path...
    ' --output=' out_file ' --connectivity=' cfg.parcel_path ' --connectivity_type=end'...
    ' --connectivity_threshold=0 --export=tdi']);

Here are the specifics:

• cfg.source_path points to an HCP1065 fiber file.
• The parcellation file used is Schaefer2018_100Parcels_7Networks_order_plus_subcort.

However, the following error messages appeared when executing the command:

• WARNING: --connectivity is not used/recognized. Did you mean --dt_metric1?
• WARNING: --connectivity_type is not used/recognized.
• WARNING: --connectivity_threshold is not used/recognized.
• WARNING: --export is not used/recognized. Did you mean --regions?

I have checked the DSI Studio documentation, and the commands appear to match the syntax provided. Would you be able to provide any guidance or feedback on these errors?

Thank you very much for your time and help.

Best regards,
Triana Karnadipa

[Frank Yeh]

Could you post the complete log output?

--
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/a4e79d8b-0d1f-48a0-a0da-cf793745c26fn%40googlegroups.com.

[Triana Karnadipa]

Dear Prof. Frank,

I have sent the logfile in the drop box link provided at the front page. Thank you for your quick response and help. 

Kind regards,

Triana 

[Frank Yeh]

Sorry I did not see any file uploaded.

It would be easier if you just post the content here.

Frank

--
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/faa16e4c-a795-4ea9-84a5-18c0302fbe66n%40googlegroups.com.

[Frank Yeh]

I checked the log file you sent me by email. It seems that you are using an older version of DSI Studio, and you may need to update it.

Also, please watch the tutorial videos at https://practicum.labsolver.org about the usage of CLI.

There are also working examples at https://dsi-studio.labsolver.org/

This may help troubleshooting the problem.

Best,

Frank

[Triana Karnadipa]

Dear Prof. Frank,

I hope this message finds you well. I have updated DSI Studio, but the issue with unrecognised commands persists. I have also double-checked the commands against the documentation:

• CLI Analysis Documentation
• CLI Template-Based Tractography Documentation

The commands appear to be correct, but I’m still encountering the problem. I would greatly appreciate your insight on how I might resolve this issue.

Thank you for your time and assistance.

[Frank Yeh]

I am willing to help, but there is no detailed description about the command used and description about problem.

I won't be able to assist you with limited information.

Also, you may need to complete the tutorial videos in order to use the command correctly. 

Best regards

Frank

To view this discussion visit https://groups.google.com/d/msgid/dsi-studio/408f7636-37b4-499e-a49a-f3109df50028n%40googlegroups.com.

[Triana Karnadipa]

Dear Prof. Frack,

I attached the log file here. Thank you so much for your quick response and help. 

Kind regards,

Triana 

[Triana Karnadipa]

Dear Prof. Frank,

I attached the logfile here. Thank you for your quick response and help. 

Kind regards,

Triana 

On Saturday, 16 November 2024 at 01:21:10 UTC+13 Frank Yeh wrote:

[Frank Yeh]

The error is related to the matlab code in LQT, which is not maintained by DSI Studio.

You may contact LQT team and see if they have a solution.

Best regards

Frank

To view this discussion visit https://groups.google.com/d/msgid/dsi-studio/07214ee9-c5f3-4dd2-9b79-167aaf9c460bn%40googlegroups.com.

[Triana Karnadipa]

Dear Prof. Yeh,

Thank you for your previous feedback—it was very helpful. I identified the issue and successfully installed my custom atlas in DSI Studio, fixed the syntax, and ran the tract analysis in Windows PowerShell. The process completed successfully, but the output values are all zeros. I tried this with 20 different lesion masks, and the results remained the same.

I’m wondering if you might have any insight into why this is happening. I’ve attached the script, output files, and CSV results for your reference.

Thank you for your time and guidance.

Best regards,

Triana Karnadipa

[Frank Yeh]

I took a quick look at the code, but the command passed to DSI Studio
does not make sense to me.

It could be that I am not familiar with the lesion-symptom mapping.
Perhaps you may explain more about your goal and the idea behind your
study, and I will see what I can do to assist you.

Best regards,
Frank

> To view this discussion visit https://groups.google.com/d/msgid/dsi-studio/98ddb169-ae9f-4f08-91f3-b95353e301can%40googlegroups.com.