% mexReadDWIList: read dwi images, gradient files, and b values
%
% Usage:
% [dwi4D, bVector, gradMatrix, b0Image3D] = mexReadDWIList(txtFile, params)
% [dwi4D, bVector, gradMatrix] = mexReadDWIList(txtFile)
%
% INPUT
% txtFile : file name which includes DWI files, b values, gradient files.
% * ******in data.txt*******************
% * 650 grad1.txt dwi1.nii index1.txt
% * 1500 grad2.txt dwi2.nii index2.txt
% * 3000 grad3.txt dwi3.nii index3.txt
% * ************************************
% * Each line is for a single shell data.
% * If the dimension N in grad.txt is smaller than the dimension M in dwi.nii, the first M-N dimension in dwi.hpp is for b0 image
% * index.txt (optional) shows the index requested for reading.
% * dwi.hdr can be stored as VectorImage or Image
% *
% * ******in data.txt*********************
% * b1.txt grad1.txt dwi1.nii index1.txt
% * b2.txt grad2.txt dwi2.nii index2.txt
% * b3.txt grad3.txt dwi3.nii index3.txt
% * **************************************
% * b.txt and grad.txt should have the same dimension. In this format, it is not necessary to have the same b values in b1.txt, b2.txt, etc
%
%
% params.b0Image : A 3D image for b0. If it is set, then the b0 image should not be in the data.txt,
% which means the dimension of grad1.txt and dwi.nii.gz should have the same size.
% If it is not set and grad1.txt and dwi.nii.gz have the same size, then the values of b0Image are all one.
%
% params.normalize : If it is true, then normalize the DWI data using b0 image.
% The default value is true
%
% params.bThreshold : If it is positive, then correct b values by grouping the b values whose difference is smaller than the bThreshold.
% The default value is -1
%
% params.correctDWI : correct DWI values if it is more than the value in b0 image or if it is no more than 0.
% params.warn : if it is true, print some warnings if the dwi values are abnormal (i.e. zero, negative, larger than b0 value)
%
%
%
% OUTPUT
% dwi4D : 4D dwi image
% bVector : vector of b values
% grad : Nx3 matrix, each row is a point in sphere.
% b0Image : 3D b0 image
%
% Copyright (c) 2013, Jian Cheng <jian.cheng.1983@gmail.com>
%
