00006 {
00007    int iarg ;
00008    THD_3dim_dataset *inset , *outset ;
00009    int keep_bot=-1 , keep_top , nz ;
00010    int add_I=0 , add_S=0 , add_A=0 , add_P=0 , add_L=0 , add_R=0 ;
00011    char * prefix="zcutup" ;
00012 
00013    /*-- help? --*/
00014 
00015    if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
00016       printf("Usage: 3dZcutup [options] dataset\n"
00017              "Cuts slices off a dataset in its z-direction, and writes a new\n"
00018              "dataset.  The z-direction and number of slices in a dataset\n"
00019              "can be determined using the 3dinfo program.\n"
00020              "Options:\n"
00021              " -keep b t   = Keep slices numbered 'b' through 't', inclusive.\n"
00022              "                 This is a mandatory option.  If you want to\n"
00023              "                 create a single-slice dataset, this is allowed,\n"
00024              "                 but AFNI may not display such datasets properly.\n"
00025              "                 A single slice dataset would have b=t.  Slice\n"
00026              "                 numbers start at 0.\n"
00027              " -prefix ppp = Write result into dataset with prefix 'ppp'\n"
00028              "                 [default = 'zcutup']\n"
00029              "Notes:\n"
00030              " * You can use a sub-brick selector on the input dataset.\n"
00031              " * 3dZcutup won't overwrite an existing dataset (I hope).\n"
00032              " * This program is adapted from 3dZeropad, which does the\n"
00033              "     same thing, but along all 3 axes.\n"
00034              " * You can glue datasets back together in the z-direction\n"
00035              "     using program 3dZcat.  A sample C shell script that\n"
00036              "     uses these progams to carry out an analysis of a large\n"
00037              "     dataset is:\n"
00038              "\n"
00039              "  #!/bin/csh\n"
00040              "  # Cut 3D+time dataset epi07+orig into individual slices\n"
00041              "\n"
00042              "  foreach sl ( `count -dig 2 0 20` )\n"
00043              "    3dZcutup -prefix zcut${sl} -keep $sl $sl epi07+orig\n"
00044              "\n"
00045              "    # Analyze this slice with 3dDeconvolve separately\n"
00046              "\n"
00047              "    3dDeconvolve -input zcut${sl}+orig.HEAD            \\\n"
00048              "                 -num_stimts 3                         \\\n"
00049              "                 -stim_file 1 ann_response_07.1D       \\\n"
00050              "                 -stim_file 2 antiann_response_07.1D   \\\n"
00051              "                 -stim_file 3 righthand_response_07.1D \\\n"
00052              "                 -stim_label 1 annulus                 \\\n"
00053              "                 -stim_label 2 antiann                 \\\n"
00054              "                 -stim_label 3 motor                   \\\n"
00055              "                 -stim_minlag 1 0  -stim_maxlag 1 0    \\\n"
00056              "                 -stim_minlag 2 0  -stim_maxlag 2 0    \\\n"
00057              "                 -stim_minlag 3 0  -stim_maxlag 3 0    \\\n"
00058              "                 -fitts zcut${sl}_fitts                \\\n"
00059              "                 -fout -bucket zcut${sl}_stats\n"
00060              "  end\n"
00061              "\n"
00062              "  # Assemble slicewise outputs into final datasets\n"
00063              "\n"
00064              "  time 3dZcat -verb -prefix zc07a_fitts zcut??_fitts+orig.HEAD\n"
00065              "  time 3dZcat -verb -prefix zc07a_stats zcut??_stats+orig.HEAD\n"
00066              "\n"
00067              "  # Remove individual slice datasets\n"
00068              "\n"
00069              "  /bin/rm -f zcut*\n"
00070            ) ;
00071       exit(0) ;
00072    }
00073 
00074    mainENTRY("3dZcutup main") ; machdep() ; AFNI_logger("3dZcutup",argc,argv) ;
00075    PRINT_VERSION("3dZcutup") ;
00076 
00077    /*-- read command line options --*/
00078 
00079    iarg = 1 ;
00080    while( iarg < argc && argv[iarg][0] == '-' ){
00081 
00082       /*- -prefix -*/
00083 
00084       if( strcmp(argv[iarg],"-prefix") == 0 ){
00085          prefix = argv[++iarg] ;
00086          if( !THD_filename_ok(prefix) ){
00087             fprintf(stderr,"*** Illegal string after -prefix!\n"); exit(1) ;
00088          }
00089          iarg++ ; continue ;
00090       }
00091 
00092       /*- -keep -*/
00093 
00094       if( strcmp(argv[iarg],"-keep") == 0 ){
00095          if( iarg+2 >= argc ){
00096            fprintf(stderr,"*** Need 2 arguments after -keep!\n"); exit(1);
00097          }
00098          keep_bot = strtol( argv[++iarg] , NULL , 10 ) ;
00099          keep_top = strtol( argv[++iarg] , NULL , 10 ) ;
00100          if( keep_bot < 0 || keep_top > keep_top ){
00101             fprintf(stderr,"*** Nonsense values after -keep!\n"); exit(1);
00102          }
00103          iarg++ ; continue ;
00104       }
00105 
00106       /*- what the hell? -*/
00107 
00108       fprintf(stderr,"*** Illegal option: %s\n",argv[iarg]) ; exit(1) ;
00109    }
00110 
00111    /*- check to see if the user asked for something, anything -*/
00112 
00113    if( keep_bot < 0 ){
00114       fprintf(stderr,"*** Don't you want to -keep SOMETHING!?\n"); exit(1);
00115    }
00116 
00117    /*-- read the input dataset --*/
00118 
00119    if( iarg >= argc ){
00120       fprintf(stderr,"*** No input dataset on command line!\n"); exit(1);
00121    }
00122 
00123    inset = THD_open_dataset( argv[iarg] ) ;
00124    if( inset == NULL ){
00125       fprintf(stderr,"*** Can't open dataset %s\n",argv[iarg]); exit(1);
00126    }
00127 
00128    nz = DSET_NZ(inset) ;
00129    if( keep_top >= nz ){
00130       fprintf(stderr,"*** -keep %d %d goes past last slice %d\n",
00131               keep_bot,keep_top,nz-1 ) ;
00132       exit(1) ;
00133    }
00134 
00135    /*-- set orientation codes correctly --*/
00136 
00137    switch( inset->daxes->zzorient ){
00138       case ORI_R2L_TYPE:
00139          add_R = -keep_bot ; add_L = keep_top - (nz-1) ; break ;
00140       case ORI_L2R_TYPE:
00141          add_L = -keep_bot ; add_R = keep_top - (nz-1) ; break ;
00142       case ORI_P2A_TYPE:
00143          add_P = -keep_bot ; add_A = keep_top - (nz-1) ; break ;
00144       case ORI_A2P_TYPE:
00145          add_A = -keep_bot ; add_P = keep_top - (nz-1) ; break ;
00146       case ORI_I2S_TYPE:
00147          add_I = -keep_bot ; add_S = keep_top - (nz-1) ; break ;
00148       case ORI_S2I_TYPE:
00149          add_S = -keep_bot ; add_I = keep_top - (nz-1) ; break ;
00150       default:
00151          fprintf(stderr,"*** Unknown orientation code in dataset!\n");
00152          exit(1) ;
00153    }
00154 
00155    outset = THD_zeropad( inset ,
00156                          add_I, add_S, add_A, add_P, add_L, add_R,
00157                          prefix , ZPAD_PURGE ) ;
00158 
00159    if( outset == NULL ){
00160       fprintf(stderr,"*** 3dZcutup: Some error occurred in processing!\n") ;
00161       exit(1) ;
00162    }
00163 
00164 STATUS("checking output filename") ;
00165 
00166    if( THD_is_file(DSET_HEADNAME(outset)) ){
00167       fprintf(stderr,
00168               "*** 3dZcutup: output file %s already exists - FATAL ERROR!\n",
00169               DSET_HEADNAME(outset) ) ;
00170       exit(1) ;
00171    }
00172 
00173 STATUS("making history") ;
00174 
00175    tross_Copy_History( inset , outset ) ;
00176    tross_Make_History( "3dZcutup" , argc,argv , outset ) ;
00177 
00178 STATUS("writing output") ;
00179 
00180    DSET_write(outset) ;
00181    fprintf(stderr,"++ output dataset: %s\n",DSET_BRIKNAME(outset)) ;
00182    exit(0) ;
00183 }