C++ ISOPTION函数代码示例

int
main(int argc, char *argv[]) {
  char         **av, *in_fname, *out_fname ;
  int          ac, nargs ;
  MRI_SURFACE  *mris ;
  float        alpha, beta, gamma ;

  /* rkt: check for and handle version tag */
  nargs = handle_version_option (argc, argv, "$Id: mris_rotate.c,v 1.6 2011/03/02 00:04:33 nicks Exp $", "$Name: stable5 $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

  Progname = argv[0] ;
  ErrorInit(NULL, NULL, NULL) ;
  DiagInit(NULL, NULL, NULL) ;

  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }

  if (argc < 6)
    usage_exit() ;

  in_fname = argv[1] ;
  if (sscanf(argv[2], "%f", &alpha) != 1)
    ErrorExit(ERROR_BADPARM, "%s: could not scan alpha from %s",
              Progname, argv[2]) ;
  if (sscanf(argv[3], "%f", &beta) != 1)
    ErrorExit(ERROR_BADPARM, "%s: could not scan beta from %s",
              Progname, argv[3]) ;
  if (sscanf(argv[4], "%f", &gamma) != 1)
    ErrorExit(ERROR_BADPARM, "%s: could not scan gamma from %s",
              Progname, argv[4]) ;
  out_fname = argv[5] ;

  mris = MRISfastRead(in_fname) ;
  if (!mris)
    ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
              Progname, in_fname) ;

  alpha = RADIANS(alpha) ;
  beta = RADIANS(beta) ;
  gamma = RADIANS(gamma) ;
  MRIScenter(mris, mris) ;
  MRISrotate(mris, mris, alpha, beta, gamma) ;
  if (!mris)
    ErrorExit(ERROR_NOFILE, "%s: could not rotate surface", Progname) ;

  if (Gdiag & DIAG_SHOW)
    fprintf(stderr, "writing rotated surface to %s\n", out_fname) ;
  MRISwrite(mris, out_fname) ;

  exit(0) ;
  return(0) ;  /* for ansi */
}

int
main(int argc, char *argv[]) {
  char        **av, *out_vol ;
  int         ac, nargs ;
  MRI         *mri_time1, *mri_time2, *mri_tmp, *mri_atrophy ;
  TRANSFORM   *transform1, *transform2 ;

  /* rkt: check for and handle version tag */
  nargs = handle_version_option (argc, argv, "$Id: mri_map_atrophy.c,v 1.4 2011/03/02 00:04:22 nicks Exp $", "$Name: stable5 $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

  Progname = argv[0] ;
  ErrorInit(NULL, NULL, NULL) ;
  DiagInit(NULL, NULL, NULL) ;

  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }

  if (argc < 6)
    usage_exit() ;

  out_vol = argv[argc-1] ;

  printf("reading volume from %s...\n", argv[1]) ;
  mri_time1 = MRIread(argv[1]) ;
  if (!mri_time1)
    ErrorExit(ERROR_NOFILE, "%s: could not read MRI volume %s", Progname, argv[2]) ;
  mri_time2 = MRIread(argv[2]) ;
  if (!mri_time2)
    ErrorExit(ERROR_NOFILE, "%s: could not read MRI volume %s", Progname, argv[2]) ;

  transform1 = TransformRead(argv[3]) ;
  if (!transform1)
    ErrorExit(ERROR_NOFILE, "%s: could not read transform from %s", Progname, argv[3]) ;

  transform2 = TransformRead(argv[4]) ;
  if (!transform2)
    ErrorExit(ERROR_NOFILE, "%s: could not read transform from %s", Progname, argv[4]) ;

  mri_tmp = TransformApplyType(transform1, mri_time1, NULL, SAMPLE_NEAREST);
  MRIfree(&mri_time1) ;
  mri_time1 = mri_tmp ;
  mri_tmp = TransformApplyType(transform2, mri_time2, NULL, SAMPLE_NEAREST);
  MRIfree(&mri_time2) ;
  mri_time2 = mri_tmp ;
  mri_atrophy = make_atrophy_map(mri_time1, mri_time2, NULL, transform1, transform2, gray_labels, ngray, csf_labels, ncsf) ;

  MRIwrite(mri_atrophy, out_vol) ;

  exit(0) ;
  return(0) ;  /* for ansi */
}

int
main(int argc, char *argv[]) {
  char   **av ;
  int    ac, nargs ;
  MRI    *mri_src, *mri_dst = NULL ;
  char   *in_fname, *out_fname ;

  /* rkt: check for and handle version tag */
  nargs = handle_version_option (argc, argv, "$Id: mri_polv.c,v 1.6 2011/03/02 00:04:24 nicks Exp $", "$Name: stable5 $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

  Progname = argv[0] ;
  ErrorInit(NULL, NULL, NULL) ;
  DiagInit(NULL, NULL, NULL) ;

  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }

  if (argc < 1)
    argc = 1 ;

  if (argc < 1)
    ErrorExit(ERROR_BADPARM, "%s: no input name specified", Progname) ;
  in_fname = argv[1] ;

  if (argc < 2)
    ErrorExit(ERROR_BADPARM, "%s: no output name specified", Progname) ;
  out_fname = argv[2] ;

  if (verbose)
    fprintf(stderr, "reading from %s...", in_fname) ;
  mri_src = MRIread(in_fname) ;
  if (!mri_src)
    ErrorExit(ERROR_NO_FILE, "%s: could not open source file %s",
              Progname, in_fname) ;

  if (verbose)
    fprintf(stderr, "done.\ncalculating plane of least variance...") ;
  mri_dst = MRIcentralPlaneOfLeastVarianceNormal(mri_src, NULL, window_size) ;
  if (!mri_dst)
    ErrorExit(ERROR_BADPARM, "%s: plane of least variance calculation failed",
              Progname) ;

  if (verbose)
    fprintf(stderr, "\ndone. writing output to %s", out_fname) ;
  MRIwrite(mri_dst, out_fname) ;
  if (verbose)
    fprintf(stderr, "\n") ;
  exit(0) ;
  return(0) ;
}

int
main(int argc, char *argv[]) {
  char   **av ;
  int    ac, nargs ;
  MRI    *mri_src, *mri_dst ;
  char   *in_fname, *out_fname ;
  int    label, nvox ;

  /* rkt: check for and handle version tag */
  nargs = handle_version_option (argc, argv, "$Id: mri_copy_values.c,v 1.5 2011/03/02 00:04:14 nicks Exp $", "$Name:  $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

  Progname = argv[0] ;
  ErrorInit(NULL, NULL, NULL) ;
  DiagInit(NULL, NULL, NULL) ;

  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }

  if (argc < 2)
    ErrorExit(ERROR_BADPARM, "%s: no input name specified", Progname) ;
  in_fname = argv[1] ;

  if (argc < 3)
    ErrorExit(ERROR_BADPARM, "%s: no value specified", Progname) ;
  label = atoi(argv[2]) ;

  if (argc < 4)
    ErrorExit(ERROR_BADPARM, "%s: no output name specified", Progname) ;
  out_fname = argv[3] ;

  fprintf(stderr, "reading from %s...\n", in_fname) ;
  mri_src = MRIread(in_fname) ;
  if (!mri_src)
    ErrorExit(ERROR_NOFILE, "%s: could not read input volume %s",
              Progname, in_fname) ;
  mri_dst = MRIread(out_fname) ;
  if (!mri_dst)
    ErrorExit(ERROR_NOFILE, "%s: could not read destination volume %s",
              Progname, out_fname) ;
  nvox = MRIcopyLabel(mri_src, mri_dst, label) ;
  fprintf(stderr, "%d voxels copied from input to output volume...\n", nvox);

  fprintf(stderr, "writing to %s...\n", out_fname) ;
  MRIwrite(mri_dst, out_fname) ;
  MRIfree(&mri_dst) ;
  MRIfree(&mri_src) ;
  exit(0) ;
  return(0) ;
}

int
main(int argc, char *argv[]) {
  char   **av ;
  int    ac, nargs, i ;
  MRI    *mri_src, *mri_dst = NULL ;
  char   *in_fname, *out_fname ;

  /* rkt: check for and handle version tag */
  nargs = handle_version_option (argc, argv, "$Id: mri_reduce.c,v 1.7 2011/03/02 00:04:24 nicks Exp $", "$Name: stable5 $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

  Progname = argv[0] ;
  ErrorInit(NULL, NULL, NULL) ;
  DiagInit(NULL, NULL, NULL) ;

  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }

  if (argc < 1)
    argc = 1 ;

  if (argc < 1)
    ErrorExit(ERROR_BADPARM, "%s: no input name specified", Progname) ;
  in_fname = argv[1] ;

  if (argc < 2)
    ErrorExit(ERROR_BADPARM, "%s: no output name specified", Progname) ;
  out_fname = argv[2] ;

  fprintf(stderr, "reading from %s...", in_fname) ;
  mri_src = MRIread(in_fname) ;

  i = 0 ;
  do {
    if (i)
      mri_src = MRIcopy(mri_dst, NULL) ;
    fprintf(stderr, "\nreducing by 2");

    mri_dst = MRIallocSequence(mri_src->width/2, mri_src->height/2, mri_src->depth/2, MRI_FLOAT, mri_src->nframes);
    MRIreduce(mri_src, mri_dst) ;
    MRIfree(&mri_src) ;
  } while (++i < reductions) ;

  fprintf(stderr, "\nwriting to %s", out_fname) ;
  MRIwrite(mri_dst, out_fname) ;
  fprintf(stderr, "\n") ;
  exit(0) ;
  return(0) ;
}

int
main(int argc, char *argv[]) {
  char   **av ;
  int    ac, nargs ;
  MRI    *mri_src, *mri_ref, *mri_tmp ;
  double accuracy ;
  MRI_REGION box ;

  /* rkt: check for and handle version tag */
  nargs = handle_version_option (argc, argv, "$Id: mri_label_accuracy.c,v 1.2 2011/03/02 00:04:22 nicks Exp $", "$Name: stable5 $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

  Progname = argv[0] ;
  ErrorInit(NULL, NULL, NULL) ;
  DiagInit(NULL, NULL, NULL) ;

  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }

  if (argc < 3)
    usage_exit(1) ;

  mri_src = MRIread(argv[1]) ;
  if (mri_src == NULL)
    ErrorExit(ERROR_BADPARM, "%s: could not read input volume %s\n", Progname,argv[1]);
  MRIboundingBox(mri_src, 0, &box) ;
  mri_tmp = MRIextractRegionAndPad(mri_src, NULL, &box, PAD) ;
  MRIfree(&mri_src) ; mri_src = mri_tmp ;
  if (mri_src->type == MRI_SHORT)
  {
    mri_tmp = MRIchangeType(mri_src, MRI_FLOAT, 0, 0, 0) ;
    MRIfree(&mri_src) ; mri_src = mri_tmp ;
  }

  mri_ref = MRIread(argv[2]) ;
  if (mri_ref == NULL)
    ErrorExit(ERROR_BADPARM, "%s: could not read reference volume %s\n", Progname,argv[1]);
  MRIboundingBox(mri_ref, 0, &box) ;
  mri_tmp = MRIextractRegionAndPad(mri_ref, NULL, &box, PAD) ;
  MRIfree(&mri_ref) ; mri_ref = mri_tmp ;

  accuracy = MRIcomputeLabelAccuracy(mri_src, mri_ref, MRI_MEAN_MIN_DISTANCE, stdout) ;

  if (Gdiag_fp)
    fclose(Gdiag_fp) ;
  exit(0) ;
  return(0) ;
}

int
main(int argc, char *argv[]) {
  char         **av ;
  int          ac, nargs, nsize ;
  MRI_SURFACE  *mris ;
  MRI          *mri ;

  nargs = handle_version_option (argc, argv, "$Id: mris_nudge.c,v 1.2 2011/03/02 00:04:31 nicks Exp $", "$Name: stable5 $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

  Gx = Gy = Gz = -1 ;
  Progname = argv[0] ;
  ErrorInit(NULL, NULL, NULL) ;
  DiagInit(NULL, NULL, NULL) ;

  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }

  if (argc < 7)
    usage_exit(1) ;

  mris = MRISread(argv[1]) ;
  if (mris == NULL)
    ErrorExit(ERROR_NOFILE, "%s: could not read surface from %s", Progname, argv[1]) ;
  MRIScomputeMetricProperties(mris) ;
  MRISstoreMetricProperties(mris) ;

  mri = MRIread(argv[2]) ;
  if (mri == NULL)
    ErrorExit(ERROR_NOFILE, "%s: could not read volume from %s", Progname, argv[2]) ;

  target_vnos[nvertices] = atoi(argv[3]) ;
  target_vals[nvertices] = atof(argv[4]) ;
  nsize = atoi(argv[5]) ;

  printf("nudging %d vertex region around vertex %d to target val %2.1f\n", 
         nsize, target_vnos[nvertices], target_vals[nvertices]) ;
  nvertices++ ;

  MRISerodeRipped(mris, nsize) ;
  MRISrepositionSurface(mris, mri, target_vnos, target_vals, nvertices, nsize, sigma) ;

  MRISunrip(mris) ;
  printf("writing repositioned surface to %s\n", argv[6]) ;
  MRISwrite(mris, argv[6]) ;
  return(0) ;
}

/***-------------------------------------------------------****/
int main(int argc, char *argv[])
{
  int  nargs, index, ac, nvolumes;
  char **av ;
  MRI  *mri_and = NULL, *mri ;

  /* rkt: check for and handle version tag */
  nargs = handle_version_option (argc, argv, vcid, "$Name:  $");
  if (nargs && argc - nargs == 1)
    exit (0);
  Progname = argv[0] ;
  argc -= nargs;
  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
  {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }

  nvolumes = argc-2 ;
  if (nvolumes <= 0)
    usage_exit() ;
  printf("processing %d input files\n", nvolumes) ;

  ErrorInit(NULL, NULL, NULL) ;
  DiagInit(NULL, NULL, NULL) ;

  for (index = 0 ; index < nvolumes ; index++)
  {
    char *fname = argv[index+1] ;
    printf("processing input volume %d of %d: %s\n",
           index+1, nvolumes, fname) ;
    mri = MRIread(fname) ;
    if (index == 0)
      mri_and = MRIcopy(mri, NULL) ;
    else
      MRIand(mri, mri_and, mri_and, 0) ;

    MRIfree(&mri) ;
  }

  printf("writing output to %s\n", argv[argc-1]) ;
  MRIwrite(mri_and, argv[argc-1]) ;
  exit(0);

} /* end main() */

int
main(int argc, char *argv[]) 
{
  MRI_SURFACE  *mris ;
  char         **av, *in_fname, *out_fname ;
  int          ac, nargs ;
  MRI          *mri_distance ;

  /* rkt: check for and handle version tag */
  nargs = handle_version_option
          (argc, argv,
           "$Id: mris_distance_map.c,v 1.2 2011/03/02 00:04:31 nicks Exp $",
           "$Name: stable5 $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

  Progname = argv[0] ;
  ErrorInit(NULL, NULL, NULL) ;
  DiagInit(NULL, NULL, NULL) ;

  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }

  if (argc < 3) usage_exit() ;

  in_fname = argv[1] ;
  out_fname = argv[2] ;
  mris = MRISread(in_fname) ;
  if (mris == NULL)
    ErrorExit(ERROR_NOFILE, "%s: could not load surface %s", Progname, out_fname) ;

  mri_distance = MRIScomputeDistanceMap(mris, NULL, ref_vertex_no) ;

  MRIwrite(mri_distance, out_fname) ;
  MRISfree(&mris) ;

  exit(0) ;

  return(0) ;  /* for ansi */
}

int
main(int argc, char *argv[]) {
  char         **av, *in_fname, *out_fname ;
  int          ac, nargs ;
  MRI_SURFACE  *mris ;
  float        radius, scale ;

  /* rkt: check for and handle version tag */
  nargs = handle_version_option (argc, argv, "$Id: mris_rescale.c,v 1.5 2011/03/02 00:04:33 nicks Exp $", "$Name:  $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

  Progname = argv[0] ;
  ErrorInit(NULL, NULL, NULL) ;
  DiagInit(NULL, NULL, NULL) ;

  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }

  if (argc < 3)
    usage_exit() ;

  in_fname = argv[1] ;
  out_fname = argv[2] ;

  mris = MRISread(in_fname) ;
  if (!mris)
    ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
              Progname, in_fname) ;
  radius = MRISaverageRadius(mris) ;
  scale = DEFAULT_RADIUS / radius ;
  MRISscaleBrain(mris, mris, scale) ;
  MRISwrite(mris, out_fname) ;

  exit(0) ;
  return(0) ;  /* for ansi */
}

int
main(int argc, char *argv[]) {
  char          **av, *out_fname, *in_fname ;
  int           ac, nargs ;
  MRI_SURFACE   *mris ;
  MRI           *mri_interior, *mri_template = NULL, *mri_buffer = NULL;

  char cmdline[CMD_LINE_LEN] ;

  make_cmd_version_string
  (argc, argv,
   "$Id: mris_fill.c,v 1.6 2011/03/02 00:04:32 nicks Exp $", "$Name:  $",
   cmdline);

  /* rkt: check for and handle version tag */
  nargs = handle_version_option (argc, argv, "$Id: mris_fill.c,v 1.6 2011/03/02 00:04:32 nicks Exp $", "$Name:  $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

  Progname = argv[0] ;
  ErrorInit(NULL, NULL, NULL) ;
  DiagInit(NULL, NULL, NULL) ;

  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }

  if (argc != 3)
    usage_exit() ;

  in_fname = argv[1] ;
  out_fname = argv[2] ;

  fprintf(stderr, "reading surface from %s...\n", in_fname) ;
  mris = MRISread(in_fname) ;

  if (template)

int
main(int argc, char *argv[]) {
  char   **av, fname[STRLEN] ;
  int    ac, nargs, i ;
  char   *in_fname, *out_fname ;
  int          msec, minutes, seconds ;
  struct timeb start ;

  /* rkt: check for and handle version tag */
  nargs = handle_version_option (argc, argv, "$Id: main_template.c,v 1.5 2011/03/02 00:04:40 nicks Exp $", "$Name:  $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

  Progname = argv[0] ;
  ErrorInit(NULL, NULL, NULL) ;
  DiagInit(NULL, NULL, NULL) ;

  TimerStart(&start) ;

  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }

  if (argc < 3)
    usage_exit(1) ;


  msec = TimerStop(&start) ;
  seconds = nint((float)msec/1000.0f) ;
  minutes = seconds / 60 ;
  seconds = seconds % 60 ;
  fprintf(stderr, "inverse operator application took %d minutes"
          " and %d seconds.\n", minutes, seconds) ;
  exit(0) ;
  return(0) ;
}

int
main(int argc, char *argv[])
{
  char         *in_fname, *out_fname, **av, *xform_fname, fname[STRLEN] ;
  MRI          *mri_in, *mri_tmp ;
  int          ac, nargs, msec, minutes, seconds;
  int          input, ninputs ;
  struct timeb start ;
  TRANSFORM    *transform = NULL ;
  char         cmdline[CMD_LINE_LEN], line[STRLEN], *cp, subject[STRLEN], sdir[STRLEN], base_name[STRLEN] ;
  FILE         *fp ;

  make_cmd_version_string
    (argc, argv,
     "$Id: mri_fuse_intensity_images.c,v 1.2 2011/06/02 14:05:10 fischl Exp $",
     "$Name:  $", cmdline);

  /* rkt: check for and handle version tag */
  nargs = handle_version_option
    (argc, argv,
     "$Id: mri_fuse_intensity_images.c,v 1.2 2011/06/02 14:05:10 fischl Exp $",
     "$Name:  $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

  setRandomSeed(-1L) ;
  Progname = argv[0] ;

  DiagInit(NULL, NULL, NULL) ;
  ErrorInit(NULL, NULL, NULL) ;

  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
  {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }

  if (argc < 5)
    ErrorExit
      (ERROR_BADPARM,
       "usage: %s [<options>] <longitudinal time point file> <in vol> <transform file> <out vol> \n",
       Progname) ;
  in_fname = argv[2] ;
  xform_fname = argv[3] ;
  out_fname = argv[4] ;

  transform = TransformRead(xform_fname) ;
  if (transform == NULL)
    ErrorExit(ERROR_NOFILE, "%s: could not read transform from %s", Progname, xform_fname) ;
  TimerStart(&start) ;

  FileNamePath(argv[1], sdir) ;
  cp = strrchr(sdir, '/') ; 
  if (cp)
  {
    strcpy(base_name, cp+1) ;
    *cp = 0 ;  // remove last component of path, which is base subject name
  }
  ninputs = 0 ;
  fp = fopen(argv[1], "r") ;
  if (fp == NULL)
    ErrorExit(ERROR_NOFILE, "%s: could not read time point file %s", Progname, argv[1]) ;

  do
  {
    cp = fgetl(line, STRLEN-1, fp) ;
    if (cp != NULL && strlen(cp) > 0)
    {
      subjects[ninputs] = (char *)calloc(strlen(cp)+1, sizeof(char)) ;
      strcpy(subjects[ninputs], cp) ;
      ninputs++ ;
    }
  } while (cp != NULL && strlen(cp) > 0) ;
  fclose(fp) ;
  printf("processing %d timepoints in SUBJECTS_DIR %s...\n", ninputs, sdir) ;
  for (input = 0 ; input < ninputs ; input++)
  {
    sprintf(subject, "%s.long.%s", subjects[input], base_name) ;
    printf("reading subject %s - %d of %d\n", subject, input+1, ninputs) ;
    sprintf(fname, "%s/%s/mri/%s", sdir, subject, in_fname) ;
    mri_tmp = MRIread(fname) ;
    if (!mri_tmp)
      ErrorExit(ERROR_NOFILE, "%s: could not read input MR volume from %s",
                Progname, fname) ;
    MRImakePositive(mri_tmp, mri_tmp) ;
    if (input == 0)
    {
      mri_in =
        MRIallocSequence(mri_tmp->width, mri_tmp->height, mri_tmp->depth,
                         mri_tmp->type, ninputs) ;
      if (!mri_in)
        ErrorExit(ERROR_NOMEMORY,
                  "%s: could not allocate input volume %dx%dx%dx%d",
                  mri_tmp->width,mri_tmp->height,mri_tmp->depth,ninputs) ;
      MRIcopyHeader(mri_tmp, mri_in) ;
    }
//.........这里部分代码省略.........

int
main(int argc, char *argv[])
{
  char        **av, *in_fname, *out_fname ;
  int         ac, nargs, i, label ;
  MRI         *mri_in, *mri_out, *mri_kernel, *mri_smoothed ;

  /* rkt: check for and handle version tag */
  nargs = handle_version_option
          (argc, argv,
           "$Id: mri_extract_label.c,v 1.13 2011/03/02 00:04:15 nicks Exp $",
           "$Name:  $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

  Progname = argv[0] ;
  ErrorInit(NULL, NULL, NULL) ;
  DiagInit(NULL, NULL, NULL) ;

  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
  {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }

  if (argc < 4)
    usage_exit() ;

  in_fname = argv[1] ;
  out_fname = argv[argc-1] ;

  printf("reading volume from %s...\n", in_fname) ;
  mri_in = MRIread(in_fname) ;
  if (!mri_in)
    ErrorExit(ERROR_NOFILE, "%s: could not read MRI volume %s", Progname,
              in_fname) ;
  if (out_like_fname)
  {
    MRI *mri_tmp = MRIread(out_like_fname) ;
    if (!mri_tmp)
      ErrorExit
      (ERROR_NOFILE,
       "%s: could not read template volume from %s",
       out_like_fname) ;
    mri_out = MRIalloc(mri_tmp->width,
                       mri_tmp->height,
                       mri_tmp->depth,
                       mri_tmp->type) ;
    /*    MRIcopyHeader(mri_tmp, mri_out) ;*/
    MRIfree(&mri_tmp) ;
  }
  else
    mri_out = MRIclone(mri_in, NULL) ;

  for (i = 2 ; i < argc-1 ; i++)
  {
    label = atoi(argv[i]) ;
    printf("extracting label %d (%s)\n", label, cma_label_to_name(label)) ;
    extract_labeled_image(mri_in, transform, label, mri_out) ;
  }
  if (!FZERO(sigma))
  {
    printf("smoothing extracted volume...\n") ;
    mri_kernel = MRIgaussian1d(sigma, 10*sigma) ;
    mri_smoothed = MRIconvolveGaussian(mri_out, NULL, mri_kernel) ;
    MRIfree(&mri_out) ;
    mri_out = mri_smoothed ;
  }
  /* removed for gcc3.3
   * vsprintf(out_fname, out_fname, (va_list) &label) ;
   */
  if (dilate > 0)
  {
    int i ;
    printf("dilating output volume %d times...\n", dilate) ;
    for (i = 0 ; i < dilate ; i++)
      MRIdilate(mri_out, mri_out) ;
  }
  if (erode > 0)
  {
    int i ;
    printf("eroding output volume %d times...\n", erode) ;
    for (i = 0 ; i < erode ; i++)
      MRIerode(mri_out, mri_out) ;
  }
  printf("writing output to %s.\n", out_fname) ;
  MRIwrite(mri_out, out_fname) ;

  if (exit_none_found && (nvoxels == 0))
  {
    printf("No voxels with specified label were found!\n");
    exit(1);
  }

  exit(0) ;
  return(0) ;  /* for ansi */
//.........这里部分代码省略.........

int
main(int argc, char *argv[]) {
  char          **av, *hemi, *subject_name, *cp, fname[STRLEN];
  char          *parc_name, *annot_name ;
  int           ac, nargs, vno, i ;
  MRI_SURFACE   *mris ;
  MRI           *mri_parc ;
  VERTEX        *v ;
  double        d ;
  Real          x, y, z, xw, yw, zw ;

  /* rkt: check for and handle version tag */
  nargs = handle_version_option (argc, argv,
                                 "$Id: mris_sample_parc.c,v 1.31 2016/12/11 14:33:38 fischl Exp $", "$Name:  $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

  Progname = argv[0] ;
  ErrorInit(NULL, NULL, NULL) ;
  DiagInit(NULL, NULL, NULL) ;

  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }

  if (argc < 4)
    usage_exit() ;

  subject_name = argv[1] ;
  hemi = argv[2] ;
  parc_name = argv[3] ;
  annot_name = argv[4] ;

  if (strlen(sdir) == 0)  /* if not specified explicitly as option */
  {
    cp = getenv("SUBJECTS_DIR") ;
    if (!cp)
      ErrorExit(ERROR_BADPARM,
                "%s: SUBJECTS_DIR not defined in environment.\n", Progname) ;
    strcpy(sdir, cp) ;
  }

  if (parc_name[0] == '/')  // full path specified
    strcpy(fname, parc_name) ;
  else
    sprintf(fname, "%s/%s/mri/%s", sdir, subject_name, parc_name) ;
  printf("reading parcellation volume from %s...\n", fname) ;
  mri_parc = MRIread(fname) ;
  if (!mri_parc)
    ErrorExit(ERROR_NOFILE, "%s: could not read input volume %s",
              Progname, fname) ;

  if (mask_fname) {
    MRI *mri_mask, *mri_tmp ;

    mri_tmp = MRIread(mask_fname) ;
    if (mri_tmp == NULL)
      ErrorExit(ERROR_BADPARM, "%s: could not load mask volume %s", Progname, mask_fname) ;
    mri_mask = MRIclone(mri_tmp, NULL) ;
    MRIcopyLabel(mri_tmp, mri_mask, mask_val) ;
    MRIdilate(mri_mask, mri_mask) ;
    MRIdilate(mri_mask, mri_mask) ;
    MRIdilate(mri_mask, mri_mask) ;
    MRIdilate(mri_mask, mri_mask) ;
    MRIfree(&mri_tmp) ;
    mri_tmp = MRIclone(mri_parc, NULL) ;
    MRIcopyLabeledVoxels(mri_parc, mri_mask, mri_tmp, mask_val) ;
    MRIfree(&mri_parc) ;
    mri_parc = mri_tmp ;
    if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
      MRIwrite(mri_parc, "p.mgz") ;
    MRIfree(&mri_mask) ;
  }

  for (i = 0 ; i < ntrans ; i++) {
    MRIreplaceValues(mri_parc, mri_parc, trans_in[i], trans_out[i]) ;
  }
  sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject_name, hemi, surf_name) ;
  printf("reading input surface %s...\n", fname) ;
  mris = MRISread(fname) ;
  if (!mris)
    ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
              Progname, fname) ;
  MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
  MRIScomputeMetricProperties(mris) ;
  if (avgs > 0)
    MRISaverageVertexPositions(mris, avgs) ;

  if (FZERO(proj_mm)) {
    if (MRISreadCurvatureFile(mris, thickness_name) != NO_ERROR)
      ErrorExit(ERROR_NOFILE, "%s: could not read thickness file %s",
                Progname, thickness_name) ;
  }

  if (color_table_fname) {
//.........这里部分代码省略.........