Save tracts in native space- QSDR .fib with DTI-TK 4d tensor nifit conversion

[Christa Wille]

Hello, 

I am using your software to process tractography data of skeletal muscle. I am interested in working with my tract data in Matlab for additional analyses but I am having trouble exporting my data in the native space (screenshot of ROI+tracts in DSI and in Matlab attached). I understand that I need to use a QSDR .fib file to do this but I am using the code you have provided at the link below to convert a DTI-TK 4D tensor nifti file to DSI studio .fib format. Do you have any suggestions as to how to create a QSDR .fib file while converting from a nifit file to DSI studio format? 

http://dsi-studio.labsolver.org/Manual/data-exchange-between-dsi-studio-and-mrtrix

 

Thank you in advance for you time,

Christa Wille

[Frank Yeh]

Hi Christa,

    QSDR only works for brain data. The only option is native space analysis.

Best regards,

Frank

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[Christa Wille]

Hi Frank, 

Thanks for your quick response. Good to know about QSDR. Can you explain what you mean by native space analysis? That is what I am hoping to do but I'm struggling trying to save the tract data in native space. I'm open to other suggestions if you have any. 

Thanks again for your time,
Christa

[Frank Yeh]

The native space here means either using DTI or GQI. They won't apply spatial wrapping to the data.

Hope this helps.

Frank

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[Christa Wille]

Hi Frank, 

Thanks for your continued help, few more follow up questions. I apologize for not knowing this but what reconstruction method is used in code provided in the link below? I use the section of code provided to convert a DTI-TK 4D nifit file to DSI .fib format. 

http://dsi-studio.labsolver.org/Manual/data-exchange-between-dsi-studio-and-mrtrix

Convert a DTI-TK 4D Tensor Nifti file to DSI Studio format

Without this conversion/code, I am not able to maintain the correct directions/bvecs when I use the GUI to reconstruct fib files. I am loading my .nii/DTI data from FSL. When using the GUI the check btables does not work but I could also try manually flipping the b-table using [Step T2 reconstruction][B-table][flip by]... Regardless, when I do use the GUI to reconstruct the .fib file I am still not able to save my tract data relative to the native space using either the DTI or the GQI reconstruction methods. I have tried saving the current tracts relative to the template space, T1/T2 space, and just using save current tracts as (screen shot attached, tracts in blue/yellow, roi in T1 space in purple. The tracts were generated using/within that ROI). 

Any additional clarification/resources would be appreciated. 

Thanks,
Christa

[Frank Yeh]

DSI Studio saves data in voxel coordinates, not the NIFTI's "srow" space. Even if you use space to T1w space, the results are still voxel coordinates.

Multiplying the tracts coordinates with spatial resolution and then add a translocation (usually the recorded in NIFTI's srow) will turn results into the "space" you are looking for.

Hope this works out.

Frank

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[Christa Wille]

Got it, very helpful. I will give this a shot. Thank you!