Matlab code for validation of dipy LiFE implementation

life_for_dipy_test.m

feOpenLocalCluster;
dwiFile       = './small_25_eye.nii';
fibers = load('./dipy_fibers.mat', 'fibers');
fibers_trans = {};
for ff=1:length(fibers.fibers)
    fibers_trans{ff} = fibers.fibers{ff}';
end

fg = fgCreate('name', 'dipy', 'fibers', fibers_trans);
fgWrite(fg, 'dipy_fg.mat');
fe = feConnectomeInit(dwiFile, 'dipy_fg.mat');

img = niftiRead('small_25_eye.nii');
sig = [];
for c=1:length(fe.roi.coords)
   this_sig = img.data(fe.roi.coords(c, 1), fe.roi.coords(c, 2), fe.roi.coords(c, 3), 2:end);
sig = [sig;this_sig - mean(this_sig)];
end
sig = squeeze(sig);
sig_r = reshape(sig', 1, 62*25);

fe.dSig = double(sig_r); 

fe = feSet(fe,'fit',feFitModel(feGet(fe,'mfiber'),feGet(fe,'dsigdemeaned'),'bbnnls'));
rmse   = feGet(fe,'vox rmse');

[Y,I] = sort(fe.diffusion_S0_img);
sig_low_b0 = fe.diffusion_signal_img(I(1),:);

w = fe.fit.weights;
save('matlab_rmse', 'rmse');
save('matlab_weights.mat', 'w');