dmri_4D_image_correct

 This functions applies FSL Eddy Current Correction to the
 Diffusion weighted data(4D image)
 [Usage]
    dmri_4D_image_correct(niftigz_file);

 [Input]
    niftigz_file    : Diffusion weighted data(4D image). 
                      (.nii.gz)
 [Output]
    none

 [Output files]
    Diffusion weighted data(4D image) after applying Eddy Current Correction.
    The output filename is original + _ecc

 [See also]
    https://users.fmrib.ox.ac.uk/~behrens/fdt_docs/fdt_eddy.html
    Eddy currents in the gradient coils induce (approximate) stretches
    and shears in the diffusion weighted images. These distortions are
    different for different gradient directions. Eddy Current Correction
    corrects for these distortions, and for simple head motion, using
    affine registration to a reference volume.

 [Example]
    dmri_4D_image_correct('/home/cbi/org/DTI_data.nii.gz');
       creates /home/cbi/org/DTI_data_m.nii.gz
               /home/cbi/org/DTI_data_m.bvec
               /home/cbi/org/DTI_data_m.bval

 Copyright (C) 2011, ATR All Rights Reserved.
 License : New BSD License(see VBMEG_LICENSE.txt)

0001 function dmri_4D_image_correct(niftigz_file)
0002 % This functions applies FSL Eddy Current Correction to the
0003 % Diffusion weighted data(4D image)
0004 % [Usage]
0005 %    dmri_4D_image_correct(niftigz_file);
0006 %
0007 % [Input]
0008 %    niftigz_file    : Diffusion weighted data(4D image).
0009 %                      (.nii.gz)
0010 % [Output]
0011 %    none
0012 %
0013 % [Output files]
0014 %    Diffusion weighted data(4D image) after applying Eddy Current Correction.
0015 %    The output filename is original + _ecc
0016 %
0017 % [See also]
0018 %    https://users.fmrib.ox.ac.uk/~behrens/fdt_docs/fdt_eddy.html
0019 %    Eddy currents in the gradient coils induce (approximate) stretches
0020 %    and shears in the diffusion weighted images. These distortions are
0021 %    different for different gradient directions. Eddy Current Correction
0022 %    corrects for these distortions, and for simple head motion, using
0023 %    affine registration to a reference volume.
0024 %
0025 % [Example]
0026 %    dmri_4D_image_correct('/home/cbi/org/DTI_data.nii.gz');
0027 %       creates /home/cbi/org/DTI_data_m.nii.gz
0028 %               /home/cbi/org/DTI_data_m.bvec
0029 %               /home/cbi/org/DTI_data_m.bval
0030 %
0031 % Copyright (C) 2011, ATR All Rights Reserved.
0032 % License : New BSD License(see VBMEG_LICENSE.txt)
0033 
0034 %
0035 % --- Previous check
0036 %
0037 if ~exist('niftigz_file', 'var')
0038     error('Please check arguments.');
0039 end
0040 if exist(niftigz_file, 'file') ~= 2
0041     error('Input file not found.');
0042 end
0043 
0044 %
0045 % --- Main Procedure
0046 %
0047 disp('Applying Eddy current correction...');
0048 start = tic;
0049 [p, f, e] = fileparts(niftigz_file(1:end-7)); % -7 => .nii.gz
0050 bvec_file = [p, '/', f, '.bvec'];
0051 bval_file = [p, '/', f, '.bval'];
0052 
0053 c_niftigz_file = [p, '/', f, '_m.nii.gz'];
0054 c_bvec_file    = [p, '/', f, '_m.bvec'];
0055 c_bval_file    = [p, '/', f, '_m.bval'];
0056 
0057 command = ['eddy_correct ' niftigz_file, ' ' c_niftigz_file, ' 0'];
0058 [status, cmdout] = dmri_system(command, '-echo');
0059 if status ~= 0
0060     error('Please check input arguments');
0061 end
0062 
0063 % bvec correction and new bvec file is saved as FSL readable format.
0064 disp('Applying bvec correction..');
0065 ecclog = [p, '/', f, '_m.ecclog'];
0066 corrected_bvec_file = ecc_bvecs(ecclog, bvec_file);
0067 mv_cmd = ['mv ' corrected_bvec_file, ' ', c_bvec_file];
0068 system(mv_cmd);
0069 
0070 % just copy and rename bval file
0071 cp_cmd = ['cp ' bval_file, ' ', c_bval_file];
0072 system(cp_cmd);
0073 disp('Finished.');
0074 toc(start);