convert_dicom_nifti

 Convert DICOM to RAS-NIFTI and LAS-Analyze file by using dcm2nii
  Note: DICOM directory should include only DICOM files
 --- Usage 1
  convert_dicom_nifti;
    : Select DICOM file by GUI
 --- Usage 2
  [RASname,LASname,ORGname] = convert_dicom_nifti(dicom_file,output_dir)
   RASname : RASname with path
   LASname : LASname with path
   ORGname : Original name with path
             (Not reorienting case, This value will be returned)
 Masa-aki Sato 2010-01-10
      rhayashi 2010-05-13 supported not reorienting case

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

0001 function    [RASname,LASname,ORGname] = ...
0002     convert_dicom_nifti(dicom_file,output_dir)
0003 % Convert DICOM to RAS-NIFTI and LAS-Analyze file by using dcm2nii
0004 %  Note: DICOM directory should include only DICOM files
0005 % --- Usage 1
0006 %  convert_dicom_nifti;
0007 %    : Select DICOM file by GUI
0008 % --- Usage 2
0009 %  [RASname,LASname,ORGname] = convert_dicom_nifti(dicom_file,output_dir)
0010 %   RASname : RASname with path
0011 %   LASname : LASname with path
0012 %   ORGname : Original name with path
0013 %             (Not reorienting case, This value will be returned)
0014 % Masa-aki Sato 2010-01-10
0015 %      rhayashi 2010-05-13 supported not reorienting case
0016 %
0017 % Copyright (C) 2011, ATR All Rights Reserved.
0018 % License : New BSD License(see VBMEG_LICENSE.txt)
0019 
0020 RASname = []; % RASname with path
0021 LASname = []; % LASname with path
0022 ORGname = []; % Original name
0023               % (Not reorienting case, This value will be return)
0024 
0025 % path for 'dcm2nii' program
0026 prog_path = [];
0027 
0028 % select DICOM directory
0029 if ~exist('dicom_file','var'), 
0030     [this] = file_dialog;
0031     this.dialog_title = 'Select one of DICOM files';
0032     [dicom_dir, dicom_file] = visible(this);
0033     if length(dicom_file) == 0, return; end
0034     dicom_file = [dicom_dir filesep dicom_file{1}];
0035 else
0036     [dicom_dir, fname, fext] = fileparts(dicom_file);
0037 end
0038 
0039 if ~exist('output_dir','var') || isempty(output_dir)
0040     output_dir = dicom_dir; 
0041 end;
0042 disp('============================================');
0043 disp('DICOM to LAS Analyze and RAS NIfTI');
0044 disp('Start converting...');
0045 
0046 % --- Convert DICOM to NIFTI file by 'dcm2nii'
0047 convert_dicom_nifti_cmd(dicom_file, output_dir, prog_path);
0048 
0049 % --- Output files by 'dcm2nii': Three set of NIFTI files are saved
0050 %  fname.hdr/img    : original image
0051 %  o+fname.hdr/img  : reoriented image with RAS orientation
0052 %  co+fname.hdr/img : reoriented & cropped image with RAS orientation
0053 
0054 % dcm2nii logfile name
0055 logname = [output_dir, '/dcm2nii.log'];
0056 
0057 % Select RAS NIFTI file and delete other orientation files
0058 [RASname,fname] = select_nii_ras_fname(logname, output_dir);
0059 if isempty(RASname)
0060     ORGname = [output_dir, filesep, fname];
0061     fprintf('Saved ORG NIFTI file: %s\n', ORGname);
0062     fprintf('RAS/LAS file did not create.\n');
0063 else
0064     LASname = [output_dir filesep, 'LAS_' fname];
0065 
0066     % Convert RAS-NIFTI to LAS-Analyze file
0067     convert_nifti_to_las(RASname,LASname);
0068 
0069     fprintf('Saved RAS NIFTI   file: %s\n',RASname)
0070     fprintf('Saved LAS Analyze file: %s\n',LASname)
0071 end
0072 
0073 disp('Finished converting.');
0074 disp('============================================');
0075 
0076 return
0077 
0078 % check .hdr file exist
0079 %fname = vb_get_ext_fname(dicom_dir,'.hdr');
0080 %
0081 %if ~isempty(fname),
0082 %    error('There are Analyze file in the directory');
0083 %end
0084 
0085 %if ~exist('dicom_file','var') || isempty(dicom_file)
0086 %    dicom_file = vb_get_ext_fname(dicom_dir);
0087 %else
0088 %    dcm_file = [dicom_dir filesep dicom_file{1}];
0089 %end