Reorienting dwi data and bvecs

1

Hello!
After acquiring diffusion weighted MRI data, and converting the DICOM to .nii.gz files, we found that the axes in our volumes are wrong: when displaying the .nii.gz volumes, the y- and z-axis are exchanged and the z-axis has a flipped sign. :flushed: We are now trying to reorient the images while maintaining the correct b-vectors. Our code is the following:

mrconvert -json_import dwidata.json -fslgrad dwidata.bvec dwidata.bval dwidata.nii.gz dwidata.mif
mrconvert -axes 0,2,1,3 dwidata.mif dwidata_axisswap.mif
mrtransform -flip 2 dwidata_axisswap.mif dwidata_axisswap_flip.mif
mrconvert -strides 1,2,3,4 dwidata_axisswap_flip.mif dwidata_axisswap_flip_strides.mif

If we now extract the bval and bvec and re-convert the data to nifti

mrconvert -export_grad_fsl reorient.bvec reorient.bval dwidata_axisswap_flip_strides.mif dwidata_axisswap_flip_strides.nii.gz

and run dtifit on the data

dtifit -k dwidata_axisswap_flip_strides.nii.gz -r reorient.bvec -b reorient bval -m mask mask.nii.gz -o reorient

the principal diffusion direction do not seem to be correct!

grafik

(this is the V1-file from the dtifit overlaid on the FA-volume)

So it seems that the bvecs were not transformed correspondingly with the image axes…

We are happy about any suggestions, ideas, comments!

2

Dear @LauraNeuro,

There is a simple method to output the correct gradient directions:

  1. run dwigradcheck on your original data and export the corrected diffusion table -
for_each */ : dwigradcheck IN/dwi/dwi.mif -export_grad_mrtrix IN/dwi/fixed_bvecs.txt
  1. run mrconvert using the fixed gradient table -
for_each */ : mrconvert IN/dwi/dwi.mif IN/dwi/dwi_fixed.mif -grad IN/dwi/fixed_bvecs.txt

Hope this helps,

Nick

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3

I’d double-check the Dicom export by directly converting the Dicom to .mif: DICOM handling — MRtrix 3.0 documentation. You might find that you do not need any adjustments.

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4

I didn’t explain: both images have now correct labels thanks to axes switchs and flips through mrtrix commands but in one case (top picture) there was a flip in the bvec which was not present (bottom picture) when using the dwigradcheck command suggested by Nick

5

Hi Nick, great tip, thank you! Thanks to you, we could go from this situation:

V1_reo_flip_stridesm
V1_reo_flip_stridesm1338×366 121 KB

to this:

classic_V1_reo_flip_stridesm_fixed
classic_V1_reo_flip_stridesm_fixed1341×362 121 KB

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6

Great, thanks to @bjeurissen who made this nifty tool!

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7

@rsmith did the implementation in MRtrix!

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