Opened region containing a foreign frame/box surrounding the brain

[Yuliya Patsyuk]

Dear Frank,

I am experiencing an issue with the new version of the software where, by opening a (custom) region, there seems to be a box surrounding the brain considered as part of the imported region (see screenshot below). This happens on both MacOS and Windows, and it seems to be affecting tract generation as the number of tracts for the same region used, e.g., as seed, differs when generated with the new version (containing the box) and the previous one (not having the box). The external frame does not appear when opening the same region in the previous versions of the software.

Could you please assist me with this problem?

Thank you in advance.  

Kind regards,
Yuliya Patsyuk

[Yuliya Patsyuk]

Dear Frank,

Related to this, I have tried a workaround by creating an ROI computed as an intersection between the ROI containing both the correct region and the box and a manually drawn region just around the anatomical region of interest. This way, the resulting ROI excludes the frame around the region. However, to do this for every region and every participant is a bit cumbersome. Do you perhaps have a suggestion on why this might be happening after updating the software to the latest version?

Thank you.

Kind regards,

Yuliya Patsyuk

[Frank Yeh]

Hi Yuliya,

    Knowing where goes wrong is much harder than fixing it in this case. If I can reproduce the issue on my side, then I will have a chance to find the cause and fix it.

    Thus this is why I would request a sample of the data to reproduce the problem. Otherwise, I have very little clue to search for the location of the bug.

Best regards,

Frank

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[Yuliya Patsyuk]

Hi Frank,

Thank you for your response. I have uploaded the requested data.

Kind regards,

Yuliya

[Frank Yeh]

Sorry for my delayed reply.

I checked the data. The mask has "nan" values filled outside the DWI box, and DSI Studio wrongly took them in.

I am updating DSI Studio so that it will ignore the nan values: https://github.com/frankyeh/DSI-Studio/actions/runs/6252913672

Frank

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[Yuliya Patsyuk]

Hi Frank,

Everything works perfectly now, indeed!

Thank you a lot for your help.

Best,

Yuliya