Example for using HySCO and 'write HySCO corrected images'

This example shows how to use apply a HySCO-estimated field-inhomogeneity to other images using the write HySCO corrected images option.

Assume, we have acquired a DTI dataset with blip-up phase-encoding direction consisting of a b=0 image and six diffusion weighted images. Additionally, for the correction, we have acquired a b=0-weighted image with blip-down phase-encoding. The goal now is, to estimate the field-inhomogeneity using the pair of b=0 images using HySCO and then apply the inhomogeneity to the diffusion weighted images.

Before we start, the following files exist in our data directory:

1. Run HySCO using b=0 weighted images.

The field-inhomogeneity is estimated based on the b=0-weighted image pair using HySCO:

This generates three new files in our data directory:

The files 'ublip-up-b0.nii' and 'ublip-down-b0.nii' are the corrected b=0 images and the file 'HySCO-blip-up-down-b0.nii' stores the inhomogeneity. The specific filenames will vary in your case, however, corrected images always get the prefix 'u' and the inhomogeneity always starts with HySCO_*.

2. Apply inhomogeneity to other diffusion weighted images

We now correct the diffusion-weighted images using the 'write HySCO corrected images' option:

We locate and insert the six diffusion-weighted images as 'Other blip-up images' (since they were acquired with the same phase-encoding direction as the blip-up image in HySCO) and the HySCO generated field-inhomgeneity. The batch looks like this:

Upon completion, this generates six undistorted diffusion-weighted image data stored ind the files with prefix 'u':

3. Notes and remarks

• The same result is obtained when using the diffusion-weighted images in the field 'Other blip-up images' in HySCO (see step 1). However, the 'write HySCO corrected images' option is useful, when additional images need to be corrected.

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