00005 {
00006    THD_3dim_dataset *dset ;
00007    char *prefix=NULL , *fname ;
00008    int narg=1 , flags=0 , ii , verb=0 , newid=1 , denote=0 , floatize=0 ;
00009    niftiwr_opts_t options ;
00010 
00011    PRINT_VERSION("3dAFNItoNIFTI");
00012 
00013    if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
00014       printf("Usage: 3dAFNItoNIFTI [options] dataset\n"
00015              "Reads an AFNI dataset, writes it out as a NIfTI-1.1 (.nii) file.\n"
00016              "\n"
00017              "NOTES:\n"
00018              "* The nifti_tool program can be used to manipulate\n"
00019              "   the contents of a NIfTI-1.1 file.\n"
00020              "* The input dataset can actually be in any input format\n"
00021              "   that AFNI can read directly (e.g., MINC-1).\n"
00022              "* There is no 3dNIFTItoAFNI program, since AFNI programs\n"
00023              "   can directly read .nii files.  If you wish to make such\n"
00024              "   a conversion anyway, one way to do so is like so:\n"
00025              "     3dcalc -a ppp.nii -prefix ppp -expr 'a'\n"
00026              "\n"
00027              "OPTIONS:\n"
00028              "  -prefix ppp = Write the NIfTI-1.1 file as 'ppp.nii'.\n"
00029              "                  Default: the dataset's prefix is used.\n"
00030 #ifdef HAVE_ZLIB
00031              "                  If you want a compressed file, try\n"
00032              "                  using a prefix like 'ppp.nii.gz'.\n"
00033 #endif
00034              "  -verb       = Be verbose = print progress messages.\n"
00035              "                  Repeating this increases the verbosity\n"
00036              "                  (maximum setting is 3 '-verb' options).\n"
00037              "  -float      = Force the output dataset to be 32-bit\n"
00038              "                  floats.  This option should be used when\n"
00039              "                  the input AFNI dataset has different\n"
00040              "                  float scale factors for different sub-bricks,\n"
00041              "                  an option that NIfTI-1.1 does not support.\n"
00042              "\n"
00043              "The following options affect the contents of the AFNI extension\n"
00044              "field that is written by default into the NIfTI-1.1 header:\n"
00045              "\n"
00046              "  -pure       = Do NOT write an AFNI extension field into\n"
00047              "                  the output file.  Only use this option if\n"
00048              "                  needed.  You can also use the 'nifti_tool'\n"
00049              "                  program to strip extensions from a file.\n"
00050              "  -denote     = When writing the AFNI extension field, remove\n"
00051              "                  text notes that might contain subject\n"
00052              "                  identifying information.\n"
00053              "  -oldid      = Give the new dataset the input dataset's\n"
00054              "                  AFNI ID code.\n"
00055              "  -newid      = Give the new dataset a new AFNI ID code, to\n"
00056              "                  distinguish it from the input dataset.\n"
00057              "     **** N.B.:  -newid is now the default action.\n"
00058             ) ;
00059       exit(0) ;
00060    }
00061 
00062    mainENTRY("3dAFNItoNIFTI main"); machdep();
00063 
00064    /*--- check options ---*/
00065 
00066    while( narg < argc && argv[narg][0] == '-' ){
00067 
00068      if( strcmp(argv[narg],"-newid") == 0 ){  /* 11 May 2005 - RWCox */
00069        newid = 1 ; narg++ ; continue ;
00070      }
00071 
00072      if( strcmp(argv[narg],"-oldid") == 0 ){  /* 15 Jul 2005 - RWCox */
00073        newid = 0 ; narg++ ; continue ;
00074      }
00075 
00076      if( strcmp(argv[narg],"-denote") == 0 ){ /* 11 Jul 2005 - RWCox */
00077        denote = 1 ; narg++ ; continue ;
00078      }
00079 
00080      if( strcmp(argv[narg],"-float") == 0 ){  /* 14 Jul 2005 - RWCox */
00081        floatize = 1 ; narg++ ; continue ;
00082      }
00083 
00084      if( strcmp(argv[narg],"-pure") == 0 ){   /* 11 May 2005 - RWCox */
00085        putenv("AFNI_NIFTI_NOEXT=YES") ;
00086        narg++ ; continue ;
00087      }
00088 
00089      if( strcmp(argv[narg],"-prefix") == 0 ){
00090        prefix = argv[++narg] ;
00091        if( !THD_filename_ok(prefix) || prefix[0] == '-' )
00092          ERROR_exit("-prefix is illegal: %s\n",prefix) ;
00093        narg++ ; continue ;
00094      }
00095 
00096      if( strcmp(argv[narg],"-verb") == 0 ){
00097        verb++ ; narg++ ; continue ;
00098      }
00099 
00100      ERROR_exit("Unknown option: %s\n",argv[narg]);
00101    }
00102 
00103    /*--- get the dataset ---*/
00104 
00105    if( narg >= argc )
00106      ERROR_exit("No dataset on command line?\n");
00107 
00108    dset = THD_open_dataset( argv[narg] ) ;
00109    if( !ISVALID_DSET(dset) )
00110      ERROR_exit("Can't open dataset %s\n",argv[narg]);
00111 
00112    /*--- deal with the filename ---*/
00113 
00114    if( prefix == NULL ) prefix = DSET_PREFIX(dset) ;
00115 
00116    if( newid ) dset->idcode = MCW_new_idcode() ;  /* 11 May 2005 */
00117 
00118    fname = malloc( strlen(prefix)+16 ) ;
00119    strcpy(fname,prefix) ;
00120    if( strstr(fname,".nii") == NULL ) strcat(fname,".nii") ;
00121 
00122    options.infile_name = nifti_strdup(fname) ;
00123    options.debug_level = verb ;
00124 
00125    /*--- 14 Jul 2005: floatization ---*/
00126 
00127    if( floatize ){
00128      int nvals=DSET_NVALS(dset) , nxyz=DSET_NVOX(dset) , tt ;
00129      float fac , *far ;
00130 
00131      DSET_mallocize(dset); DSET_load(dset);
00132      if( !DSET_LOADED(dset) ) ERROR_exit("Can't load input dataset from disk") ;
00133      if( verb ) INFO_message("Converting dataset to floats (in memory)") ;
00134 
00135      /* loop over sub-bricks */
00136 
00137      for( ii=0 ; ii < nvals ; ii++ ){
00138        fac = DSET_BRICK_FACTOR(dset,ii) ; if( fac == 0.0f ) fac = 1.0f ;
00139        tt  = DSET_BRICK_TYPE(dset,ii) ;
00140 
00141        /* if already floats and scale fac is 1.0, don't need to do anything */
00142 
00143        if( fac == 1.0f && (tt == MRI_float || tt == MRI_complex) ) continue ;
00144 
00145        /* create output space */
00146 
00147        far = (float *)calloc( nxyz , sizeof(float) ) ;
00148 
00149        /* scale input to output */
00150 
00151        EDIT_coerce_scale_type( nxyz , fac ,
00152                                DSET_BRICK_TYPE(dset,ii),DSET_BRICK_ARRAY(dset,ii) ,
00153                                MRI_float , far ) ;
00154 
00155        /* replace input with output, and fix scale factor */
00156 
00157        EDIT_substitute_brick( dset , ii , MRI_float , far ) ;
00158        EDIT_BRICK_FACTOR( dset , ii , 0.0 ) ;
00159      } /* end of loop over sub-bricks */
00160    } /* end of floatizationing */
00161 
00162    /*--- Go Baby, Go! ---*/
00163 
00164    if( denote ) THD_anonymize_write(1) ; /* sets a flag for attribute output */
00165    ii = THD_write_nifti( dset , options ) ; /* actually write the damn thing */
00166    exit(0) ;
00167 }