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In Computers in biology and medicine

INTRODUCTION : MRI T2* relaxometry protocols are often used for Liver Iron Quantification in patients with hemochromatosis. Several methods exist to semi-automatically segment parenchyma and exclude vessels for this calculation.

PURPOSE : To determine if inclusion of multiple echoes inputs to Convolutional Neural Networks (CNN) improves automated liver and vessel segmentation in MRI T2* relaxometry protocols and to determine if the resultant segmentations agree with manual segmentations for liver iron quantification analysis.

METHODS : Multi echo Gradient Recalled Echo (GRE) MRI sequence for T2* relaxometry was performed for 79 exams on 31 patients with hemochromatosis for iron quantification analysis. 275 axial liver slices were manually segmented as ground truth masks. A batch normalized U-Net with variable input width to incorporate multiple echoes is used for segmentation, using DICE as the accuracy metric. ANOVA is used to evaluate significance of channel width changes in segmentation accuracy. Linear regression is used to model the relationship of channel width on segmentation accuracy. Liver segmentations are applied to relaxometry data to calculate liver T2* yielding liver iron concentration(LIC) derived from literature based calibration curves. Manual and CNN based LIC values are compared with Pearson correlation. Bland altman plots are used to visualize differences between manual and CNN based LIC values.

RESULTS : Performance metrics are tested on 55 hold out slices. Linear regression indicates that there is a monotonic increase of DICE with increasing channel depth (p = 0.001) with a slope of 3.61e-3. ANOVA indicates a significant increase segmentation accuracy over single channel starting at 3 channels. Incorporation of all channels results in an average DICE of 0.86, an average increase of 0.07 over single channel. The calculated LIC from CNN segmented livers agrees well with manual segmentation (R = 0.998, slope = 0.914, p«0.001), with an average absolute difference 0.27 ± 0.99 mg Fe/g or 1.34 ± 4.3%.

CONCLUSION : More input echoes yields higher model accuracy until the noise floor. Echos beyond the first three echo times in GRE based T2* relaxometry do not contribute significant information for segmentation of liver for LIC calculation. Deep learning models with three channel width allow for generalization of model to protocols of more than three echoes, effectively a universal requirement for relaxometry. Deep learning segmentations achieve a good accuracy compared with manual segmentations with minimal preprocessing. Liver iron values calculated from hand segmented liver and Neural network segmented liver were not statistically different from each other.

Liu Michael, Vanguri Rami, Mutasa Simukayi, Ha Richard, Liu Yu-Cheng, Button Terry, Jambawalikar Sachin


Deep learning, Liver iron concentration, MRI, Machine learning, Segmentation