Example batches of recommended ACID pipelines
2. Susceptibility artifact correction using HYperelastic Susceptibility Artifact Correction (HySCO)
For diffusion data, which were acquired with Echo-Planar-Imaging (EPI) and thus suffered from susceptibility distortion, we recommend the example batch "ECMOCOandHySCOandDTIfit.mat", which is located in the ACID toolbox in the folder "ExampleBatches" or here.
This batch (in addition to the steps in 1.1 also) corrects for susceptibility distortions using HySCO. For using this batch, you need to acquire, in addition to the normal DTI dataset, one b=0 image with reversed phase-encoding direction, i.e. you need blip-up and blip-down b=0 images. If you have further question about the phase encoding direction, please read our papers (see HySCO), contact your local physicist, or send us an email via the SPM mail base. Figure 2b shows an example for an FA map that is distorted by susceptibility artifacts.
Fig. 2: The effect of susceptibility distortion for DTI data acquired in diffusion Echo-Planar-Imaging (EPI) demonstrated for the corpus callosum. The genu in the FA map (arrow) that is estimated calculated from the original data is misaligned (b) as compared to the pseudo ground truth structural high-resolution image (a). After applying HySCO (c) the position of the genu in the FA map corresponds to the structural ground truth map.
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