Combining diffusion data across slabs

[Christa Wille]

Hello, 

I'm working on tractography of skeletal muscle in the thigh and curious if you have any suggestions/resources for stitching DWI data across multiple slabs. We collect our DWI data in 2 slabs to capture the entire thigh but in the image attached you can see that there is significant discontinuity in our tracts at the slab boundaries. I have tried several different options for combining the data from each slab in the overlap region (mean vs max vs image with best SNR) and I've tried some different image registration techniques to ensure the slabs are aligned but I always seem to have some level of discontinuity at the slab boundary/overlap. See screenshot attached with discontinuity ~1/4 of the way down from the most cranial/top of the ROI. Happy to share more data/details/examples of what I've done but open to any other ideas if you've dealt with this before. 

Thanks,
Christa

[Frank Yeh]

Hi Christa,

     This is a challenging task, and it is likely that the b-table was not correctly rotated with the image registration.

     Did you rotate the NIFTI or SRC files before stitching them together?

Best,

Frank

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[Christa Wille]

Hi Frank, 

Thanks for the quick follow up. In short, no I don't rotate them before I stitch them together. All of the image manipulations/rotations occur after they are stitched together. 

I'm working through each step of the pre-processing and image manipulations that I do and trying to document each step a little more clearly. I will follow up in the next couple days with more details on exactly what we are doing to our data prior to tractography. 

Thanks,
Christa