Visualization Error

[Steven Jay Granger]

Hi Frank, 

I hope you are well.

I have been having trouble visualizing streamlines via the command line. Here is the call: /Users/stevegranger/Desktop/dsi_studio.app/Contents/MacOS/dsi_studio --action=vis --source=src_base.src.gz.icbm152.qsdr.1.25.R66.fib.gz --track="count_connect.trk.gz" --cmd="slice_off+set_view,0+save_image,tractography1.jpg,1024 800"

It seems that the image renders in the lower left-hand corner of a wider window. Almost as though there is some mosaic view turned on. Is there a way to modify where in the jpg the images render in the frame? 

Best,

Steve 

[Frank Yeh]

Hi Steve,

    Mac command line visualization has been a long issue in DSI Studio (I am sorry about that), but I will re-visit it again and see if Qt has a better solution.

    Are you using the most recent version of DSI Studio? Just want to make sure we are on the same command-line syntax to make sure it works for you.

Best,

Frank

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[Steven Jay Granger]

Hi Frank, 

I believe I am working with the August 30th 2021 build at the moment. Thanks so much for taking a look at this! 

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Steven J. Granger | Graduate Student Researcher

Center for the Neurobiology of Learning and Memory

Department of Neurobiology and Behavior

University of California, Irvine

gran...@uci.edu 

[Frank Yeh]

Thanks I will check and see if there is a solution.

Frank

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[Steven Jay Granger]

Thank you Frank! 

I may have missed this as well, but is there a way to specify an ROI file somewhere in the --vis action? 

Best,

Steve 

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[Frank Yeh]

Not implemented yet but I am listing this on my to-do list.

Frank

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[Frank Yeh]

This problem is likely due to the retina display in Mac. You may try turning it off and see if it works.

I am still looking for a solution but currently, I don't have a Mac with a retina display to fix the bug.

I will have this issue open and hopefully, either a future Qt version will fix it internally, or I can find a workaround.

Frank

[Steven Jay Granger]

Hi Frank,

Thank you for your time on this. 

A related question for you...have you tried running the vis commands through a docker container? 

I know this is rather specific, but I am having another internal error related to DSI studio's use of the Qt plugin. 

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[Frank Yeh]

Not really, but one version of the docker container has Qt linking problem. This has been recently fixed.

You may test again and let me know if there is still an error message.

Best regards,

Frank

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[Steven Jay Granger]

Hi Frank, 

Thanks so much for the quick response! 

Under which version of docker DSI is the issue fixed under? 

Alternatively, are there any other ways to visualize trk files that don't rely on DSI studio? That is to say if I can't fix the issue with the new docker version of DSI studio. 

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[Frank Yeh]

DIPY has a tractography viewer that can visualize trk files.

Frank

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[Steven Jay Granger]

Hi Frank, 

Thanks for the direction. 

I was able to run DIPY on a sample dataset released with DIPY but had some trouble with the header of the trk file created with DSI studio. 

Have you been able to use DIPY in the past to visualize trk files from DSI-studio? 

Hoping to gather any resources I can get ahold of to solve this issue. 

Thank you so much again for your time. I realize this isn't exactly an issue with DSI-studio itself. 

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[Frank Yeh]

There was a discussion in the past (either at DIPY or DSI Studio discussion group) about the trk orientation differences.

You may try flipping the coordinates and see if there is a good match.

Best regards,

Frank

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[Steven Jay Granger]

Thank you Frank! 

For what it's worth...turns out the optimized TRK loader for nibabel was the trick for my very specific purposes (https://github.com/nipy/nibabel/issues/943).

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[Frank Yeh]

Yes, I remembered this discussion thread (thanks for bringing it up), and there is a solution to speed up the loading.

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