00280 {
00281    int nopt=1 ;
00282    int nzz, ii,jj,kk , ntt,nxx,nyy,nxy , nup ;
00283    float tomax,tomin , tshift , fmin,fmax , gmin,gmax , f0,f1 , g0,g1 ;
00284    float ffmin,ffmax , ggmin,ggmax ;
00285    MRI_IMAGE * flim , * glim ;
00286    float * far , * gar ;
00287    int ignore=0 , BAD=0 ;
00288 
00289    /*- scan command line -*/
00290 
00291    if( argc < 2 || strcmp(argv[1],"-help") == 0 ) TS_syntax(NULL) ;
00292 
00293    mainENTRY("3dTshift main"); machdep(); AFNI_logger("3dTshift",argc,argv);
00294    PRINT_VERSION("3dTshift");
00295 
00296    SHIFT_set_method( MRI_FOURIER ) ;
00297 
00298    while( nopt < argc && argv[nopt][0] == '-' ){
00299 
00300       if( strcmp(argv[nopt],"-BAD") == 0 ){
00301         BAD = 1 ; nopt++ ; continue ;
00302       }
00303 
00304       if( strncmp(argv[nopt],"-verbose",5) == 0 ){
00305          TS_verbose++ ;
00306          nopt++ ; continue ;
00307       }
00308 
00309       if( strcmp(argv[nopt],"-ignore") == 0 ){  /* 15 Feb 2001 */
00310          TS_ignore = (int) strtod(argv[++nopt],NULL) ;
00311          if( TS_ignore < 0 ) TS_syntax("-ignore value is negative!") ;
00312          nopt++ ; continue ;
00313       }
00314 
00315       if( strncmp(argv[nopt],"-Fourier",4) == 0 || strncmp(argv[nopt],"-fourier",4) == 0 ){
00316          SHIFT_set_method( MRI_FOURIER ) ;
00317          nopt++ ; continue ;
00318       }
00319 
00320       if( strncmp(argv[nopt],"-cubic",4) == 0 || strncmp(argv[nopt],"-Cubic",4) == 0 ){
00321          SHIFT_set_method( MRI_CUBIC ) ;
00322          nopt++ ; continue ;
00323       }
00324 
00325       if( strncmp(argv[nopt],"-quintic",4) == 0 || strncmp(argv[nopt],"-Quintic",4) == 0 ){
00326          SHIFT_set_method( MRI_QUINTIC ) ;
00327          nopt++ ; continue ;
00328       }
00329 
00330       if( strncmp(argv[nopt],"-heptic",4) == 0 || strncmp(argv[nopt],"-Heptic",4) == 0 ){
00331          SHIFT_set_method( MRI_HEPTIC ) ;
00332          nopt++ ; continue ;
00333       }
00334 
00335       if( strncmp(argv[nopt],"-linear",4) == 0 || strncmp(argv[nopt],"-Linear",4) == 0 ){
00336          SHIFT_set_method( MRI_LINEAR ) ;
00337          nopt++ ; continue ;
00338       }
00339 
00340       if( strcmp(argv[nopt],"-TR") == 0 ){
00341          char * eptr ;
00342          if( ++nopt >= argc ) TS_syntax("-TR needs an argument!") ;
00343          TS_TR = strtod( argv[nopt] , &eptr ) ;
00344          if( TS_TR <= 0.0 ) TS_syntax("illegal value after -TR!") ;
00345 
00346          if( strcmp(eptr,"ms")==0 || strcmp(eptr,"msec")==0 ){
00347             TS_tunits = UNITS_MSEC_TYPE ;
00348          } else if( strcmp(eptr,"s")==0 || strcmp(eptr,"sec")==0 ){
00349             TS_tunits = UNITS_SEC_TYPE ;
00350          } else if( strcmp(eptr,"Hz")==0 || strcmp(eptr,"Hertz")==0 ){
00351             TS_tunits = UNITS_HZ_TYPE ;
00352          }
00353 
00354          nopt++ ; continue ;
00355       }
00356 
00357       if( strcmp(argv[nopt],"-tzero") == 0 ){
00358          if( ++nopt >= argc ) TS_syntax("-tzero needs an argument!") ;
00359          TS_tzero = strtod( argv[nopt] , NULL ) ;
00360          if( TS_tzero < 0.0 ) TS_syntax("illegal value after -tzero!") ;
00361          nopt++ ; continue ;
00362       }
00363 
00364       if( strcmp(argv[nopt],"-slice") == 0 ){
00365          if( ++nopt >= argc ) TS_syntax("-slice needs an argument!") ;
00366          TS_slice = strtod( argv[nopt] , NULL ) ;
00367          if( TS_slice < 0 ) TS_syntax("illegal value after -slice!") ;
00368          nopt++ ; continue ;
00369       }
00370 
00371       if( strcmp(argv[nopt],"-prefix") == 0 ){
00372          if( ++nopt >= argc ) TS_syntax("-prefix needs an argument!") ;
00373          MCW_strncpy( TS_prefix , argv[nopt] , THD_MAX_PREFIX ) ;
00374          if( !THD_filename_ok(TS_prefix) ) TS_syntax("illegal value after -prefix") ;
00375          nopt++ ; continue ;
00376       }
00377 
00378       if( strcmp(argv[nopt],"-rlt") == 0 ){
00379          TS_rlt = 1 ;
00380          nopt++ ; continue ;
00381       }
00382 
00383       if( strcmp(argv[nopt],"-rlt+") == 0 ){
00384          TS_rlt = 2 ;
00385          nopt++ ; continue ;
00386       }
00387 
00388       if( strcmp(argv[nopt],"-tpattern") == 0 ){
00389          if( ++nopt >= argc ) TS_syntax("-tpattern needs an argument!") ;
00390          TS_tpattern = argv[nopt] ;
00391          nopt++ ; continue ;
00392       }
00393 
00394       fprintf(stderr,"*** Unknown option: %s\n",argv[nopt]) ; exit(1) ;
00395 
00396    }  /* end of scan command line */
00397 
00398    /*- open dataset; extract values, check for errors -*/
00399 
00400    if( nopt >= argc ) TS_syntax("Need a dataset input?!") ;
00401    if( TS_verbose ) printf("++ opening input dataset header\n") ;
00402    TS_dset = THD_open_dataset( argv[nopt] ) ;
00403    if( TS_dset == NULL ) TS_syntax("Can't open input dataset!") ;
00404 
00405    nxx = DSET_NX(TS_dset) ;                      /* get dimensions */
00406    nyy = DSET_NY(TS_dset) ; nxy = nxx * nyy ;
00407    nzz = DSET_NZ(TS_dset) ;
00408    ntt = DSET_NVALS(TS_dset) ;
00409 
00410    if( DSET_NVALS(TS_dset) < 2 ) TS_syntax("Dataset has only 1 value per voxel!") ;
00411    if( TS_slice >= nzz ) TS_syntax("-slice value is too large") ;
00412 
00413    if( TS_ignore > ntt-5 ) TS_syntax("-ignore value is too large") ;
00414 
00415    if( TS_dset->taxis == NULL ){
00416       if( TS_TR == 0.0 || TS_tpattern == NULL )
00417          TS_syntax("dataset has no time axis => you must supply -TR and -tpattern!") ;
00418 
00419    } else if( TS_tpattern == NULL && TS_dset->taxis->toff_sl == NULL ){
00420       TS_syntax("dataset is already aligned in time!") ;
00421    }
00422 
00423    if( TS_TR == 0.0 ){                                    /* set TR from dataset */
00424       TS_TR     = DSET_TIMESTEP(TS_dset) ;
00425       TS_tunits = TS_dset->taxis->units_type ;
00426       if( TS_verbose )
00427          printf("++ using dataset TR = %g %s\n",TS_TR,UNITS_TYPE_LABEL(TS_tunits)) ;
00428    }
00429 
00430    if( TS_tpattern != NULL ){                                    /* set pattern */
00431       TS_tpat = TS_parse_tpattern( nzz , TS_TR , TS_tpattern ) ;
00432    } else {
00433       if( TS_dset->taxis->nsl != nzz )
00434          TS_syntax("dataset temporal pattern is malformed!") ; /* should not happen */
00435 
00436       TS_tpat = (float *) malloc( sizeof(float) * nzz ) ;
00437       memcpy( TS_tpat , TS_dset->taxis->toff_sl , sizeof(float)*nzz ) ;
00438    }
00439    if( TS_verbose ){
00440       printf("++ using tpattern = ") ;
00441       for( ii=0 ; ii < nzz ; ii++ ) printf("%g ",TS_tpat[ii]) ;
00442       printf("%s\n",UNITS_TYPE_LABEL(TS_tunits)) ;
00443    }
00444 
00445    tomin = WAY_BIG ; tomax = -WAY_BIG ;                      /* check pattern */
00446    for( ii=0 ; ii < nzz ; ii++ ){
00447       if( TS_tpat[ii] > tomax ) tomax = TS_tpat[ii] ;
00448       if( TS_tpat[ii] < tomin ) tomin = TS_tpat[ii] ;
00449    }
00450    if( tomin < 0.0 || tomax > TS_TR )
00451       TS_syntax("some value in tpattern is outside 0..TR") ;
00452    else if( tomin >= tomax )
00453       TS_syntax("temporal pattern is already aligned in time!") ;
00454 
00455    if( TS_slice >= 0 && TS_slice < nzz ){                   /* set common time point */
00456       TS_tzero = TS_tpat[TS_slice] ;
00457    } else if( TS_tzero < 0.0 ){
00458       TS_tzero = 0.0 ;
00459       for( ii=0 ; ii < nzz ; ii++ ) TS_tzero += TS_tpat[ii] ;
00460       TS_tzero /= nzz ;
00461    }
00462    if( TS_verbose ) printf("++ common time point set to %g\n",TS_tzero) ;
00463 
00464    /*- copy input dataset, modify it to be the output -*/
00465 
00466    if( TS_verbose ) printf("++ copying input dataset bricks\n") ;
00467 
00468    TS_oset = EDIT_full_copy( TS_dset , TS_prefix ) ;
00469    if( TS_oset == NULL ) TS_syntax("Can't copy input dataset!") ;
00470    DSET_unload( TS_dset ) ;
00471 
00472    if( THD_is_file(DSET_HEADNAME(TS_oset)) )
00473       TS_syntax("output dataset already exists!") ;
00474 
00475    tross_Copy_History( TS_dset , TS_oset ) ;
00476    tross_Make_History( "3dTshift" , argc,argv , TS_oset ) ;
00477 
00478    /*- reconfigure the time axis -*/
00479 
00480    EDIT_dset_items( TS_oset ,
00481                        ADN_ntt    , ntt       ,  /* in case not already set */
00482                        ADN_ttdel  , TS_TR     ,  /* may have changed */
00483                        ADN_tunits , TS_tunits ,  /* may have changed */
00484                        ADN_nsl    , 0         ,  /* will have no offsets when done */
00485 #if 0
00486                        ADN_ttorg  , 0.0       ,  /* in case not already set */
00487                        ADN_ttdur  , 0.0       ,  /* in case not already set */
00488 #endif
00489                     ADN_none ) ;
00490 
00491    /*---- do the temporal shifting! ----*/
00492 
00493    nup = csfft_nextup_one35( ntt+4 ) ;
00494    ignore = TS_ignore ;
00495 
00496    if( TS_verbose && SHIFT_get_method() == MRI_FOURIER )
00497       printf("++ Time series length = %d; FFT length set to %d\n",ntt,nup) ;
00498 
00499    for( kk=0 ; kk < nzz ; kk++ ){       /* loop over slices */
00500 
00501       tshift = (TS_tzero - TS_tpat[kk]) / TS_TR ;    /* rightward fractional shift */
00502 #if 1
00503       if( !BAD ) tshift = -tshift ;   /* 24 Apr 2003 -- OOG */
00504 #endif
00505 
00506       if( TS_verbose )
00507          printf("++ slice %d: fractional shift = %g\n",kk,tshift) ;
00508 
00509       if( fabs(tshift) < 0.001 ) continue ;          /* skip this slice */
00510 
00511       for( ii=0 ; ii < nxy ; ii+=2 ){   /* loop over voxel pairs in slice */
00512 
00513          flim = THD_extract_series( ii+kk*nxy , TS_oset , 0 ) ;  /* get this voxel */
00514          far  = MRI_FLOAT_PTR(flim) ;
00515 
00516          if( TS_rlt == 0 ){
00517             for( ffmin=ffmax=far[ignore],jj=ignore+1 ; jj < ntt ; jj++ ){
00518                     if( far[jj] < ffmin ) ffmin = far[jj] ;
00519                else if( far[jj] > ffmax ) ffmax = far[jj] ;
00520             }
00521          }
00522 
00523          THD_linear_detrend( ntt-ignore , far+ignore , &f0,&f1 ) ;   /* remove trend */
00524 
00525          for( fmin=fmax=far[ignore],jj=ignore+1 ; jj < ntt ; jj++ ){
00526                  if( far[jj] < fmin ) fmin = far[jj] ;   /* range of data: after */
00527             else if( far[jj] > fmax ) fmax = far[jj] ;
00528          }
00529 
00530          if( ii < nxy-1 ){                                       /* get next voxel */
00531             glim = THD_extract_series( ii+kk*nxy+1 , TS_oset , 0 ) ;
00532             gar  = MRI_FLOAT_PTR(glim) ;
00533 
00534             if( TS_rlt == 0 ){
00535                for( ggmin=ggmax=gar[ignore],jj=ignore+1 ; jj < ntt ; jj++ ){
00536                        if( gar[jj] < ggmin ) ggmin = gar[jj] ;
00537                   else if( gar[jj] > ggmax ) ggmax = gar[jj] ;
00538                }
00539             }
00540 
00541             THD_linear_detrend( ntt-ignore , gar+ignore , &g0,&g1 ) ;
00542 
00543             for( gmin=gmax=gar[ignore],jj=ignore+1 ; jj < ntt ; jj++ ){
00544                     if( gar[jj] < gmin ) gmin = gar[jj] ;
00545                else if( gar[jj] > gmax ) gmax = gar[jj] ;
00546             }
00547          } else {
00548             gar  = NULL ;
00549          }
00550 
00551          if( gar != NULL )
00552             SHIFT_two_rows( ntt-ignore,nup, tshift,far+ignore , tshift, gar+ignore ) ;
00553          else
00554             SHIFT_two_rows( ntt-ignore,nup, tshift,far+ignore , tshift, NULL ) ;
00555 
00556          for( jj=ignore ; jj < ntt ; jj++ ){
00557                  if( far[jj] < fmin ) far[jj] = fmin ;           /* clip to input range */
00558             else if( far[jj] > fmax ) far[jj] = fmax ;
00559             switch( TS_rlt ){                                    /* restore trend? */
00560                case 0:
00561                   far[jj] += (f0 + (jj-ignore)*f1) ;
00562                        if( far[jj] < ffmin ) far[jj] = ffmin ;
00563                   else if( far[jj] > ffmax ) far[jj] = ffmax ;
00564                break ;
00565 
00566                case 2:
00567                   far[jj] += f0 ;
00568                break ;
00569             }
00570          }
00571 
00572          if( gar != NULL ){
00573             for( jj=ignore ; jj < ntt ; jj++ ){
00574                     if( gar[jj] < gmin ) gar[jj] = gmin ;
00575                else if( gar[jj] > gmax ) gar[jj] = gmax ;
00576                switch( TS_rlt ){
00577                   case 0:
00578                      gar[jj] += (g0 + (jj-ignore)*g1) ;
00579                           if( gar[jj] < ggmin ) gar[jj] = ggmin ;
00580                      else if( gar[jj] > ggmax ) gar[jj] = ggmax ;
00581                   break ;
00582 
00583                   case 2:
00584                      gar[jj] += g0 ;
00585                   break ;
00586                }
00587             }
00588          }
00589 
00590          /* put back into dataset */
00591 
00592          THD_insert_series( ii+kk*nxy , TS_oset , ntt , MRI_float , far , 0 ) ;
00593          if( gar != NULL )
00594             THD_insert_series( ii+kk*nxy+1 , TS_oset , ntt , MRI_float , gar , 0 ) ;
00595 
00596          /* throw out the trash */
00597 
00598          mri_free(flim) ; if( gar != NULL ) mri_free(glim) ;
00599       }
00600    }
00601 
00602    DSET_write( TS_oset ) ;
00603    if( TS_verbose ) fprintf(stderr,"++ Wrote output: %s\n",DSET_BRIKNAME(TS_oset)) ;
00604    exit(0) ;
00605 }

00144 {
00145    int ii ;
00146    float tframe , tsl ;
00147    float * tpat ;
00148 
00149    tpat = (float *) malloc( sizeof(float) * nzz ) ;
00150    for( ii=0 ; ii < nzz ; ii++ ) tpat[ii] = 0.0 ;
00151 
00152    tframe = TR / nzz ;  /* time per slice */
00153 
00154    if( nzz > 1 && tpattern[0] == '@' ){
00155       FILE * fp ;
00156 
00157       /*--- read pattern file (ignore EOFs!) ---*/
00158 
00159       fp = fopen( tpattern+1 , "r" ) ;
00160       if( fp == NULL ){
00161          fprintf(stderr,"*** Cannot open tpattern file %s\n",tpattern+1) ;
00162          exit(1) ;
00163       } else {
00164          for( ii=0 ; ii < nzz ; ii++ ){
00165             fscanf( fp , "%f" , tpat + ii ) ;
00166             if( tpat[ii] < 0.0 || tpat[ii] > TR ){
00167                fprintf(stderr,"*** Illegal value %g in tpattern file %s\n",
00168                        tpat[ii] , tpattern+1 ) ;
00169                exit(1) ;
00170             }
00171          }
00172          fclose( fp ) ;
00173       }
00174 
00175    } else if( nzz > 1 &&
00176              (strcmp(tpattern,"alt+z")==0 || strcmp(tpattern,"altplus")==0) ){
00177 
00178       /*--- set up alternating in the +z direction ---*/
00179 
00180       tsl = 0.0 ;
00181       for( ii=0 ; ii < nzz ; ii+=2 ){
00182          tpat[ii] = tsl ; tsl += tframe ;
00183       }
00184       for( ii=1 ; ii < nzz ; ii+=2 ){
00185          tpat[ii] = tsl ; tsl += tframe ;
00186       }
00187 
00188    } else if( nzz > 1 && strcmp(tpattern,"alt+z2")==0 ){  /* 22 Feb 2005 */
00189 
00190       /*--- set up alternating in the +z direction ---*/
00191 
00192       tsl = 0.0 ;
00193       for( ii=1 ; ii < nzz ; ii+=2 ){
00194          tpat[ii] = tsl ; tsl += tframe ;
00195       }
00196       for( ii=0 ; ii < nzz ; ii+=2 ){
00197          tpat[ii] = tsl ; tsl += tframe ;
00198       }
00199 
00200    } else if( nzz > 1 &&
00201              (strcmp(tpattern,"alt-z")==0 || strcmp(tpattern,"altminus")==0) ){
00202 
00203       /*--- set up alternating in the -z direction ---*/
00204 
00205       tsl = 0.0 ;
00206       for( ii=nzz-1 ; ii >=0 ; ii-=2 ){
00207          tpat[ii] = tsl ; tsl += tframe ;
00208       }
00209       for( ii=nzz-2 ; ii >=0 ; ii-=2 ){
00210          tpat[ii] = tsl ; tsl += tframe ;
00211       }
00212 
00213    } else if( nzz > 1 && strcmp(tpattern,"alt-z2") == 0 ){  /* 22 Feb 2005 */
00214 
00215       /*--- set up alternating in the -z direction ---*/
00216 
00217       tsl = 0.0 ;
00218       for( ii=nzz-2 ; ii >=0 ; ii-=2 ){
00219          tpat[ii] = tsl ; tsl += tframe ;
00220       }
00221       for( ii=nzz-1 ; ii >=0 ; ii-=2 ){
00222          tpat[ii] = tsl ; tsl += tframe ;
00223       }
00224 
00225    } else if( nzz > 1 &&
00226              (strcmp(tpattern,"seq+z")==0 || strcmp(tpattern,"seqplus")==0) ){
00227 
00228       /*--- set up sequential in the +z direction ---*/
00229 
00230       tsl = 0.0 ;
00231       for( ii=0 ; ii < nzz ; ii++ ){
00232          tpat[ii] = tsl ; tsl += tframe ;
00233       }
00234 
00235    } else if( nzz > 1 &&
00236              (strcmp(tpattern,"seq-z")==0 || strcmp(tpattern,"seqminus")==0) ){
00237 
00238       /*--- set up sequential in the -z direction ---*/
00239 
00240       tsl = 0.0 ;
00241       for( ii=nzz-1 ; ii >=0 ; ii-- ){
00242          tpat[ii] = tsl ; tsl += tframe ;
00243       }
00244 
00245    } else if( nzz == 1 ||
00246              (strcmp(tpattern,"zero")==0 || strcmp(tpattern,"simult")==0) ){
00247 
00248       /*--- do nothing [leave it all zeros] ---*/
00249 
00250    } else {
00251       fprintf(stderr,"*** Unknown tpattern = %s\n",tpattern) ;
00252       exit(1) ;
00253    }
00254 
00255    return tpat ;
00256 }

00012 {
00013    if( str != NULL ){
00014       fprintf(stderr,"*** Fatal Error: %s\n",str) ; exit(1) ;
00015    }
00016 
00017    printf("Usage: 3dTshift [options] dataset\n"
00018           "Shifts voxel time series from the input dataset so that the separate\n"
00019           "slices are aligned to the same temporal origin.  By default, uses the\n"
00020           "slicewise shifting information in the dataset header (from the 'tpattern'\n"
00021           "input to program to3d).\n"
00022           "\n"
00023           "Method:  detrend -> interpolate -> retrend (optionally)\n"
00024           "\n"
00025           "The input dataset can have a sub-brick selector attached, as documented\n"
00026           "in '3dcalc -help'.\n"
00027           "\n"
00028           "The output dataset time series will be interpolated from the input to\n"
00029           "the new temporal grid.  This may not be the best way to analyze your\n"
00030           "data, but it can be convenient.\n"
00031           "\n"
00032           "Warnings:\n"
00033           "* Please recall the phenomenon of 'aliasing': frequencies above 1/(2*TR) can't\n"
00034           "  be properly interpolated.  For most 3D FMRI data, this means that cardiac\n"
00035           "  and respiratory effects will not be treated properly by this program.\n"
00036           "\n"
00037           "* The images at the beginning of a high-speed FMRI imaging run are usually\n"
00038           "  of a different quality than the later images, due to transient effects\n"
00039           "  before the longitudinal magnetization settles into a steady-state value.\n"
00040           "  These images should not be included in the interpolation!  For example,\n"
00041           "  if you wish to exclude the first 4 images, then the input dataset should\n"
00042           "  be specified in the form 'prefix+orig[4..$]'.  Alternatively, you can\n"
00043           "  use the '-ignore ii' option.\n"
00044           "\n"
00045           "* It seems to be best to use 3dTshift before using 3dvolreg.\n"
00046           "\n"
00047           "Options:\n"
00048           "  -verbose      = print lots of messages while program runs\n"
00049           "\n"
00050           "  -TR ddd       = use 'ddd' as the TR, rather than the value\n"
00051           "                  stored in the dataset header using to3d.\n"
00052           "                  You may attach the suffix 's' for seconds,\n"
00053           "                  or 'ms' for milliseconds.\n"
00054           "\n"
00055           "  -tzero zzz    = align each slice to time offset 'zzz';\n"
00056           "                  the value of 'zzz' must be between the\n"
00057           "                  minimum and maximum slice temporal offsets.\n"
00058           "            N.B.: The default alignment time is the average\n"
00059           "                  of the 'tpattern' values (either from the\n"
00060           "                  dataset header or from the -tpattern option)\n"
00061           "\n"
00062           "  -slice nnn    = align each slice to the time offset of slice\n"
00063           "                  number 'nnn' - only one of the -tzero and\n"
00064           "                  -slice options can be used.\n"
00065           "\n"
00066           "  -prefix ppp   = use 'ppp' for the prefix of the output file;\n"
00067           "                  the default is 'tshift'.\n"
00068           "\n"
00069           "  -ignore ii    = Ignore the first 'ii' points. (Default is ii=0.)\n"
00070           "                  The first ii values will be unchanged in the output\n"
00071           "                  (regardless of the -rlt option).  They also will\n"
00072           "                  not be used in the detrending or time shifting.\n"
00073           "\n"
00074           "  -rlt          = Before shifting, the mean and linear trend\n"
00075           "  -rlt+         = of each time series is removed.  The default\n"
00076           "                  action is to add these back in after shifting.\n"
00077           "                  -rlt  means to leave both of these out of the output\n"
00078           "                  -rlt+ means to add only the mean back into the output\n"
00079           "                  (cf. '3dTcat -help')\n"
00080           "\n"
00081           "  -Fourier = Use a Fourier method (the default: most accurate; slowest).\n"
00082           "  -linear  = Use linear (1st order polynomial) interpolation (least accurate).\n"
00083           "  -cubic   = Use the cubic (3rd order) Lagrange polynomial interpolation.\n"
00084           "  -quintic = Use the quintic (5th order) Lagrange polynomial interpolation.\n"
00085           "  -heptic  = Use the heptic (7th order) Lagrange polynomial interpolation.\n"
00086           "\n"
00087           "  -tpattern ttt = use 'ttt' as the slice time pattern, rather\n"
00088           "                  than the pattern in the input dataset header;\n"
00089           "                  'ttt' can have any of the values that would\n"
00090           "                  go in the 'tpattern' input to to3d, described below:\n"
00091           "\n"
00092           "   alt+z = altplus   = alternating in the plus direction\n"
00093           "   alt+z2            = alternating, starting at slice #1 instead of #0\n"
00094           "   alt-z = altminus  = alternating in the minus direction\n"
00095           "   alt-z2            = alternating, starting at slice #nz-2 instead of #nz-1\n"
00096           "   seq+z = seqplus   = sequential in the plus direction\n"
00097           "   seq-z = seqminus  = sequential in the minus direction\n"
00098           "   @filename         = read temporal offsets from 'filename'\n"
00099           "\n"
00100           "  For example if nz = 5 and TR = 1000, then the inter-slice\n"
00101           "  time is taken to be dt = TR/nz = 200.  In this case, the\n"
00102           "  slices are offset in time by the following amounts:\n"
00103           "\n"
00104           "             S L I C E   N U M B E R\n"
00105           "   tpattern    0   1   2   3   4   Comment\n"
00106           "   --------- --- --- --- --- ---   -------------------------------\n"
00107           "   altplus     0 600 200 800 400   Alternating in the +z direction\n"
00108           "   alt+z2    400   0 600 200 800   Alternating, but starting at #1\n"
00109           "   altminus  400 800 200 600   0   Alternating in the -z direction\n"
00110           "   alt-z2    800 200 600   0 400   Alternating, starting at #nz-2 \n"
00111           "   seqplus     0 200 400 600 800   Sequential  in the -z direction\n"
00112           "   seqplus   800 600 400 200   0   Sequential  in the -z direction\n"
00113           "\n"
00114           "  If @filename is used for tpattern, then nz ASCII-formatted numbers\n"
00115           "  are read from the file.  These indicate the time offsets for each\n"
00116           "  slice. For example, if 'filename' contains\n"
00117           "     0 600 200 800 400\n"
00118           "  then this is equivalent to 'altplus' in the above example.\n"
00119           "  (nz = number of slices in the input dataset)\n"
00120           "\n"
00121           "N.B.: if you are using -tpattern, make sure that the units supplied\n"
00122           "      match the units of TR in the dataset header, or provide a\n"
00123           "      new TR using the -TR option.\n"
00124           "\n"
00125           "As a test of how well 3dTshift interpolates, you can take a dataset\n"
00126           "that was created with '-tpattern alt+z', run 3dTshift on it, and\n"
00127           "then run 3dTshift on the new dataset with '-tpattern alt-z' -- the\n"
00128           "effect will be to reshift the dataset back to the original time\n"
00129           "grid.  Comparing the original dataset to the shifted-then-reshifted\n"
00130           "output will show where 3dTshift does a good job and where it does\n"
00131           "a bad job.\n"
00132           "\n"
00133           "-- RWCox - 31 October 1999\n"
00134         ) ;
00135 
00136    printf("\n" MASTER_SHORTHELP_STRING ) ;
00137 
00138    exit(0) ;
00139 }