test_dmri_FA_image_processing

 --- Extract DTI 4D-NIfTI.gz, bvec, bval files

0001 %
0002 % --- Extract DTI 4D-NIfTI.gz, bvec, bval files
0003 %
0004 dti_dicom_dir   = '/home/cbi-data4/rhayashi/DWI/4';
0005 output_dir      = '/home/cbi-data4/rhayashi/DWI/test_FA_image';
0006 basename        = 'data'; 
0007 
0008 dmri_4D_image_extract(dti_dicom_dir, output_dir, basename);
0009     % creates
0010     %  output_dir/basename.nii.gz
0011     %  output_dir/basename_bvec
0012     %  output_dir/basename_bval
0013 
0014 %
0015 % --- Motion Correction
0016 %
0017 data_4d_file = [output_dir, '/', basename, '.nii.gz'];
0018 dmri_4D_image_correct(data_4d_file);
0019     % will put files into the same directory.
0020     %   (_ecc is added as a postfix.)
0021     %   data_ecc.nii.gz
0022     %   data_ecc_bvec
0023     %   data_ecc_bval
0024 
0025 %
0026 % --- Extract brain image and brain mask from 4D-NIfTI.gz
0027 %
0028 data_4d_ecc_file = [output_dir, '/', basename, '_ecc.nii.gz'];
0029 threshold = 0.18;
0030 brain_image_extract(data_4d_ecc_file, threshold);
0031     % will put files into the same directory.
0032     %   (_brain, _brain_mask is added as a postfix.)
0033     %   data_ecc_brain.nii.gz
0034     %   data_ecc_brain_mask.nii.gz
0035 
0036 %
0037 % --- Create FA image
0038 %
0039 brain_mask_file = [output_dir, '/data_ecc_brain_mask.nii.gz'];
0040 bvec_file       = [output_dir, '/data_ecc_bvec'];
0041 bval_file       = [output_dir, '/data_ecc_bval'];
0042 basename        = 'data_ecc_FA';
0043 
0044 dmri_FA_image_create(data_4d_ecc_file, ...
0045                     bval_file, bvec_file, ...
0046                     brain_mask_file, ...
0047                     output_dir, ...
0048                     basename);
0049     % will put files into the same directory.
0050     %    output_dir/basename.nii.gz