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I am using Phase Correlation to register 3D data. There's a clear distinction in the y direction so the resulting shifts seem to be correct. But since there is a lot of similarity in the x direction therefore resulting in spikes. Does anyone have suggestions on any processing techniques that could help get better results.

This is my phase correlation code at the moment.

function peak = PhaseCorrelation(fftr, tar)
dim = GetPad(fftr); 
fftt = fftn(tar, dim);
% calculate the power spectrum to remove the magnitude
cp_vol = CrossPowerSpectrum(fftr, fftt);
% go back to the time domain and find the peak
shift_vol = ifftn(cp_vol);
shift_vol = fftshift(shift_vol);
shift_vol = imgaussfilt(abs(shift_vol), 5);
[~, ind] = max(abs(shift_vol(:)));
[xsh, ysh, zsh] = ind2sub(size(shift_vol), ind);
peak = [xsh, ysh, zsh];
peak = GetOffsetShift(peak, dim);
end

function [shift] = GetOffsetShift(peak, dim)
shift(1:2) = (peak(1:2) - dim(1:2)/2) - 1;
if length(dim) == 3 % 3D shifts
    if peak(3) > dim(3)/2
        shift(3) = (peak(3) - dim(3)/2);
    else
        shift(3) = (peak(3) + dim(3)/2);
    end
else % 2D shifts
    % dont have to change the shift of the third dimension
    shift(3) = peak(3);
end

function [res] = CrossPowerSpectrum(A, B)
y = A.*conj(B);
scale = abs(y);
res = y./scale;
end

function [new_dim] = GetPad(ref)
dim = nextpow2(size(ref));
new_dim = 2.^dim;
end

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