bvecs flipping and tractography results

[Catherine Tang]

Hello,

I've noticed that each time I loaded my bvecs manually after loading my nii.gz, the bvecs y-direction is automatically flipped in dsistudio (i compared it with the bvec.txt i have). I'd like to understand/check if this is correct.

Some background about the dataset - we used in-house scripts to correct the data for motion and artifacts, the data's bvecs has only been x-flipped by us for FSL processing, and the image is in a typical DTI space, but not native DTI space. They are rigid-body registered relative to the T1, but with 2 mm voxels.

I did not turn on check b-table during QSDR and had done QC check. After I obtained the tractography results, I checked the direction for some regions and it seemed correct to me. However, I still get some weird tracks on the surface for the two participants i've tested (attached, sub2 is more problematic). Thus, I'm not sure if it's a bvecs flipping issue or some other issues that I overlooked.

Thanks!

Catherine

[Frank Yeh]

Hi Catherine,

    Have you checked the quality of your DWI? 

    Hope this video helps: http://dsi-studio.labsolver.org/Manual/Parse-DICOM#TOC-Quality-Inspection

    If you still cannot find the problem, please send me a sample of the data (src file) using the link provided in the DSI Studio website.

Best,

Frank

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[Catherine Tang]

Hi Frank,

After carefully looking through the data, I think the problem has to do with the white matter mask coverage in reconstruction, where eye ball regions were included in the mask. I tried erosion etc but it could not make localized changes. It looks like the nodif_brain_mask we generated from FSL covers more non-white matter areas than the one from DSIstudio. Do you have any recommendations regarding situations like this(e.g., manual editing?)? I also attached the src.gz for your reference.

Thanks so much!

Catherine

 data.nii.gz.src.gz

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[Frank Yeh]

The mask does not need to be very accurate. Most analyses in DSI Studio do not need a precise mask.

You can even assign threshold=0 to cover the entire space, and the results should be mostly consistent (or even identical).

Hope this addresses your concerns.

Best,

Frank