dmri_FA_image_create

 Create fractional anisotropy image using dtifit command(fsl)
 [Usage]
    dmri_FA_image_create(niftigz_file,
                         bval_file, bvec_file,
                         brain_mask_file,
                         output_dir,
                         output_name);
 [Input]
    niftigz_file    : gzipped Nifti file(.nii.gz)
                      4D series of data volumes.
    bval_file       : A text file containing a list of b values applied 
                      during each volume acquisition. The order of entries 
                      in this file must match the order of volumes in 
                      the input data and entries in the gradient 
                       directions text file. 
    bvec_file       : A text file containing a list of gradient directions 
                      applied during diffusion weighted volumes. The order 
                      of entries in this file must match the order of volumes 
                      in the input data series. 
    brain_mask_file : gzipped Nifti file(.nii.gz)
                      BET binary brain mask.
                      A single binarised volume in diffusion space 
                      containing ones inside the brain and zeroes 
                      outside the brain.
         output_dir : output directory.
        output_name : output filename.
                      output_dir/output_name.nii.gz will be created.
         
 [See also]
    http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_dtifit.html

 [Output]
    none


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

0001 function dmri_FA_image_create(niftigz_file, ...
0002                               bval_file, bvec_file, ...
0003                               brain_mask_file, ...
0004                               output_dir, ...
0005                               output_name)
0006 % Create fractional anisotropy image using dtifit command(fsl)
0007 % [Usage]
0008 %    dmri_FA_image_create(niftigz_file,
0009 %                         bval_file, bvec_file,
0010 %                         brain_mask_file,
0011 %                         output_dir,
0012 %                         output_name);
0013 % [Input]
0014 %    niftigz_file    : gzipped Nifti file(.nii.gz)
0015 %                      4D series of data volumes.
0016 %    bval_file       : A text file containing a list of b values applied
0017 %                      during each volume acquisition. The order of entries
0018 %                      in this file must match the order of volumes in
0019 %                      the input data and entries in the gradient
0020 %                       directions text file.
0021 %    bvec_file       : A text file containing a list of gradient directions
0022 %                      applied during diffusion weighted volumes. The order
0023 %                      of entries in this file must match the order of volumes
0024 %                      in the input data series.
0025 %    brain_mask_file : gzipped Nifti file(.nii.gz)
0026 %                      BET binary brain mask.
0027 %                      A single binarised volume in diffusion space
0028 %                      containing ones inside the brain and zeroes
0029 %                      outside the brain.
0030 %         output_dir : output directory.
0031 %        output_name : output filename.
0032 %                      output_dir/output_name.nii.gz will be created.
0033 %
0034 % [See also]
0035 %    http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_dtifit.html
0036 %
0037 % [Output]
0038 %    none
0039 %
0040 %
0041 % Copyright (C) 2011, ATR All Rights Reserved.
0042 % License : New BSD License(see VBMEG_LICENSE.txt)
0043 
0044 %
0045 % --- Previous check
0046 %
0047 if nargin ~= 6
0048     error('Please check input argument.');
0049 end
0050 if exist(niftigz_file, 'file') ~= 2
0051     error('Specified diffusion weighted data file not found.');
0052 end
0053 if exist(bval_file, 'file') ~= 2
0054     error('Specified bval_file not found.');
0055 end
0056 if exist(bvec_file, 'file') ~= 2
0057     error('Specified bvec_file not found.');
0058 end
0059 if exist(brain_mask_file, 'file') ~= 2
0060     error('Specified brain_mask file(.nii.gz) not found.');
0061 end
0062 if ~ischar(output_dir)
0063     error('output_dir should be specified by character string.');
0064 end
0065 if ~ischar(output_name)
0066     error('output_name should be specified by character string.');
0067 end
0068 if exist(output_dir, 'dir') ~= 7
0069     mkdir(output_dir);
0070 end
0071 
0072 %
0073 % --- Main Procedure
0074 %
0075 disp('Creating fractional anisotropy image.');
0076 start = tic;
0077 base_name = [output_dir, '/', output_name];
0078 command = ['dtifit -k ', niftigz_file, ...
0079            ' -m '       , brain_mask_file, ...
0080            ' -r '       , bvec_file, ...
0081            ' -b '       , bval_file, ...
0082            ' -o '       , base_name];
0083 
0084 [status, cmdout] = dmri_system(command, '-echo');
0085 if status ~= 0
0086     error('Please check input arguments.');
0087 end
0088 
0089 % Remove unnecesary files.
0090 delete([base_name, '_L*.nii.gz']);
0091 delete([base_name, '_M*.nii.gz']);
0092 delete([base_name, '_S*.nii.gz']);
0093 delete([base_name, '_V*.nii.gz']);
0094 
0095 % Rename
0096 command = ['mv ' base_name, '_FA.nii.gz', ' ', base_name, '.nii.gz'];
0097 [status, comret] = system(command, '-echo');
0098 
0099 toc(start);