Ejemplo n.º 1
0
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 */
}
Ejemplo n.º 2
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[])
{
  MRIS *mris_in,*mris_out;
  Progname=argv[0];
  if (argc < 3)
  {
    usage_exit(-1);
  }
  mris_in=MRISread(argv[1]);
  mris_out=MRISextractMainComponent(mris_in,0,1,0);
  MRISwrite(mris_out,argv[2]);
  MRISfree(&mris_out);
  MRISfree(&mris_in);
  fprintf(stderr,"\ndone\n\n");
  return 0;
}
Ejemplo n.º 4
0
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 */
}
Ejemplo n.º 5
0
static int
MRISfindOptimalRigidPosition(MRI_SURFACE *mris, MRI *mri, INTEGRATION_PARMS *parms) {
  double    dx, dy, dz, old_sse, sse, pct_change, dt, dx_total, dy_total, dz_total ;
  int       i ;

  i = 0 ;
  sse = compute_surface_dist_sse(mris, mri) ;
  dt = .1 ;

  dx_total = dy_total = dz_total = 0;
  do {
    old_sse = sse ;
    compute_rigid_gradient(mris, mri, &dx, &dy, &dz) ;
    apply_rigid_gradient(mris, dx*dt, dy*dt, dz*dt) ;
    sse = compute_surface_dist_sse(mris, mri) ;
    dx_total += dt*dx ;
    dy_total += dt*dy ;
    dz_total += dt*dz ;
    pct_change = 100.0 * ((old_sse - sse) / old_sse) ;
    if (pct_change < 0) {
      dt *=-1 ;
      apply_rigid_gradient(mris, dx*dt, dy*dt, dz*dt) ;
      dx_total += dt*dx ;
      dy_total += dt*dy ;
      dz_total += dt*dz ;
    }

    if (Gdiag & DIAG_WRITE) {
      char fname[STRLEN] ;
      sprintf(fname, "lh.%4.4d", ++parms->start_t) ;
      MRISwrite(mris, fname) ;
    }
    if (FZERO(sse))
      break ;
  } while (pct_change > .01);

  printf("after rigid positioning, delta = (%2.0f, %2.0f, %2.0f)\n", dx_total, dy_total, dz_total) ;
  return(NO_ERROR) ;
}
Ejemplo n.º 6
0
int
main(int argc, char *argv[])
{
  char         **av, *in_surf_fname, *out_fname, fname[STRLEN], *cp ;
  int          ac, nargs, msec, err ;
  MRI_SURFACE  *mris ;
  struct timeb then ;
  float        max_dim ;

  char cmdline[CMD_LINE_LEN] ;

  make_cmd_version_string
  (argc, argv,
   "$Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $",
   "$Name: stable5 $", cmdline);

  /* rkt: check for and handle version tag */
  nargs = handle_version_option
          (argc, argv,
           "$Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $",
           "$Name: stable5 $");
  if (nargs && argc - nargs == 1)
  {
    exit (0);
  }
  argc -= nargs;

#ifdef FS_CUDA
  /* print GPU device info */
  MRISCdeviceInfo();
#endif // FS_CUDA

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

  memset(&parms, 0, sizeof(parms)) ;
  parms.dt = .05 ;
  parms.projection = PROJECT_ELLIPSOID ;
  parms.tol = .5 /*1e-1*/ ;
  parms.n_averages = 1024 ;
  parms.min_averages = 0 ;
  parms.l_angle = 0.0 /* L_ANGLE */ ;
  parms.l_area = 0.0 /* L_AREA */ ;
  parms.l_neg = 0.0 ;
  parms.l_dist = 1.0 ;
  parms.l_spring = 0.0 ;
  parms.l_area = 1.0 ;
  parms.l_boundary = 0.0 ;
  parms.l_curv = 0.0 ;
  parms.niterations = 25 ;
  parms.write_iterations = 1000 ;
  parms.a = parms.b = parms.c = 0.0f ;  /* ellipsoid parameters */
  parms.dt_increase = 1.01 /* DT_INCREASE */;
  parms.dt_decrease = 0.99 /* DT_DECREASE*/ ;
  parms.error_ratio = 1.03 /*ERROR_RATIO */;
  parms.integration_type = INTEGRATE_LINE_MINIMIZE ;
  parms.momentum = 0.9 ;
  parms.desired_rms_height = -1.0 ;
  parms.base_name[0] = 0 ;
  parms.Hdesired = 0.0 ;   /* a flat surface */
  parms.nbhd_size = 7 ;
  parms.max_nbrs = 8 ;

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

  parms.scale = scale ;

  if (argc != 3) // catches args beyond the expected two
  {
    usage_exit() ;
  }

  parms.base_dt = base_dt_scale * parms.dt ;
  in_surf_fname = argv[1] ;
  out_fname = argv[2] ;

  printf("%s\n",vcid);
  printf("  %s\n",MRISurfSrcVersion());
  fflush(stdout);

  if (parms.base_name[0] == 0)
  {
    FileNameOnly(out_fname, fname) ;
    cp = strchr(fname, '.') ;
    if (cp)
    {
      strcpy(parms.base_name, cp+1) ;
    }
    else
    {
      strcpy(parms.base_name, "sphere") ;
    }
  }

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

  MRISaddCommandLine(mris, cmdline) ;

  fprintf(stderr, "reading original vertex positions...\n") ;
  if (!FZERO(disturb))
  {
    mrisDisturbVertices(mris, disturb) ;
  }
  if (quick == 0)
  {
    // don't need original properties unless preserving metric
    err = MRISreadOriginalProperties(mris, orig_name) ;
    if(err)
    {
      exit(1);
    }
  }
  if (smooth_avgs > 0)
  {
    MRISsaveVertexPositions(mris, TMP_VERTICES) ;
    MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
    MRISaverageVertexPositions(mris, smooth_avgs) ;
    MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
    MRISrestoreVertexPositions(mris, TMP_VERTICES) ;
  }

  if (!FZERO(ralpha) || !FZERO(rbeta) || !FZERO(rgamma))
  {
    MRISrotate(mris,mris,RADIANS(ralpha),RADIANS(rbeta),RADIANS(rgamma)) ;
    //                if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
    MRISwrite(mris, "rot") ;
  }
  fprintf(stderr, "unfolding cortex into spherical form...\n");
  if (talairach)
  {
    MRIStalairachTransform(mris, mris) ;
    MRISwrite(mris, "tal") ;
  }

  if (xform_fname)
  {
    LTA *lta ;
    MRI *mri ;
    TRANSFORM transform ;

    lta = LTAread(xform_fname) ;
    if (lta == NULL)
    {
      ErrorExit(ERROR_NOFILE, "%s: could not load %s", xform_fname) ;
    }
    mri = MRIread(vol_fname) ;
    if (mri == NULL)
    {
      ErrorExit(ERROR_NOFILE, "%s: could not load %s", vol_fname) ;
    }
    transform.type = lta->type ;
    transform.xform = (void *)lta ;
    MRIStransform(mris, mri, &transform, mri) ;
    MRIfree(&mri) ;
    LTAfree(&lta) ;
    MRISwrite(mris, "xfm") ;
  }
#if 0
  max_dim = MAX(abs(mris->xlo), abs(mris->xhi)) ;
  max_dim = MAX(abs(max_dim), abs(mris->ylo)) ;
  max_dim = MAX(abs(max_dim), abs(mris->yhi)) ;
  max_dim = MAX(abs(max_dim), abs(mris->zlo)) ;
  max_dim = MAX(abs(max_dim), abs(mris->zhi)) ;
#else
  max_dim = MAX(abs(mris->xhi-mris->xlo), abs(mris->yhi-mris->ylo)) ;
  max_dim = MAX(max_dim,abs(mris->zhi-mris->zlo)) ;
#endif
  if (max_dim > .75*DEFAULT_RADIUS)
  {
    float ratio = .75*DEFAULT_RADIUS / (max_dim) ;
    printf("scaling brain by %2.3f...\n", ratio) ;
    MRISscaleBrain(mris, mris, ratio) ;
  }

  if (target_radius < 0)
  {
    target_radius = sqrt(mris->total_area / (4*M_PI)) ;
    printf("setting target radius to be %2.3f to match surface areas\n",
           target_radius) ;
  }
  //  MRISsampleAtEachDistance(mris, parms.nbhd_size, parms.max_nbrs) ;
  if (!load && inflate)
  {
    INTEGRATION_PARMS inflation_parms ;

    MRIScenter(mris, mris) ;
    memset(&inflation_parms, 0, sizeof(INTEGRATION_PARMS)) ;
    strcpy(inflation_parms.base_name, parms.base_name) ;
    inflation_parms.write_iterations = parms.write_iterations ;
    inflation_parms.niterations = inflate_iterations ;
    inflation_parms.l_spring_norm = l_spring_norm ;
    inflation_parms.l_spring = inflate_spring ;
    inflation_parms.l_nlarea = inflate_nlarea ;
    inflation_parms.l_area = inflate_area ;
    inflation_parms.n_averages = inflate_avgs ;
    inflation_parms.l_expand = l_expand ;
    inflation_parms.l_tspring = inflate_tspring ;
    inflation_parms.l_sphere = l_sphere ;
    inflation_parms.l_convex = l_convex ;
#define SCALE_UP 2
    inflation_parms.a = SCALE_UP*DEFAULT_RADIUS ;
    inflation_parms.tol = inflate_tol ;
    inflation_parms.integration_type = INTEGRATE_MOMENTUM ;
    inflation_parms.momentum = 0.9 ;
    inflation_parms.dt = inflate_dt ;

    /* store the inflated positions in the v->c? field so that they can
      be used in the repulsive term.
    */
    /*    inflation_parms.l_repulse_ratio = .1 ;*/
    MRISsaveVertexPositions(mris, CANONICAL_VERTICES) ;
    if (l_expand > 0)
    {
      MRISexpandSurface(mris, target_radius/2, &inflation_parms, 0, 1) ;
      l_expand = parms.l_expand = 0 ;
    }
    MRIScenter(mris, mris) ;
    mris->x0 = mris->xctr ;
    mris->y0 = mris->yctr ;
    mris->z0 = mris->zctr ;
    MRISinflateToSphere(mris, &inflation_parms) ;
    if (inflation_parms.l_expand > 0)
    {
      inflation_parms.l_expand = 0 ;
      inflation_parms.niterations += (inflate_iterations*.1) ;
      MRISinflateToSphere(mris, &inflation_parms) ;
    }
    MRISscaleBrain(mris, mris, target_radius/(DEFAULT_RADIUS*SCALE_UP)) ;
    parms.start_t = inflation_parms.start_t ;
    MRISresetNeighborhoodSize(mris, nbrs) ;
  }

  if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
  {
    MRISwrite(mris, "before") ;
  }
  MRISprojectOntoSphere(mris, mris, target_radius) ;
  if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
  {
    MRISwrite(mris, "after") ;
  }
  fprintf(stderr,"surface projected - minimizing metric distortion...\n");
  MRISsetNeighborhoodSize(mris, nbrs) ;
  if (quick)
  {
    if (!load)
    {
#if 0
      parms.n_averages = 32 ;
      parms.tol = .1 ;
      parms.l_parea = parms.l_dist = 0.0 ;
      parms.l_nlarea = 1 ;
#endif
      MRISprintTessellationStats(mris, stderr) ;
      MRISquickSphere(mris, &parms, max_passes) ;
    }
  }
  else
  {
    MRISunfold(mris, &parms, max_passes) ;
  }
  if (remove_negative)
  {
    parms.niterations = 1000 ;
    MRISremoveOverlapWithSmoothing(mris,&parms) ;
  }
  if (!load)
  {
    fprintf(stderr, "writing spherical brain to %s\n", out_fname) ;
    MRISwrite(mris, out_fname) ;
  }

  msec = TimerStop(&then) ;
  fprintf(stderr, "spherical transformation took %2.2f hours\n",
          (float)msec/(1000.0f*60.0f*60.0f));
  exit(0) ;
  return(0) ;  /* for ansi */
}
int
main(int argc, char *argv[]) {
  char         **av, *avg_surf_name, *canon_surf_name, fname[STRLEN],
  *mdir, ico_fname[STRLEN], *hemi, *out_sname ;
  int          ac, nargs, i, vno, n ;
  VERTEX       *v ;
  MRI_SURFACE  *mris_ico ;
  MRI_SP       *mrisp_total ;
  LTA          *lta ;
  VOL_GEOM     vg;
  float        average_surface_area = 0.0 ;
  MATRIX *XFM=NULL;
  GCA_MORPH *gcam=NULL;

  memset((void *) &vg, 0, sizeof (VOL_GEOM));

  /* rkt: check for and handle version tag */
  nargs = handle_version_option 
    (argc, argv, 
     "$Id: mris_make_average_surface.c,v 1.29 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) ;

  mdir = getenv("FREESURFER_HOME") ;
  if (!mdir)
    ErrorExit(ERROR_BADPARM, 
              "%s: no FREESURFER_HOME in environment.\n",Progname);
  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }
  if (sdir == NULL) {
    sdir =  getenv("SUBJECTS_DIR");
    if (!sdir)
      ErrorExit(ERROR_BADPARM, 
                "%s: no SUBJECTS_DIR in environment.\n",Progname);
  }
  if (sdirout == NULL) sdirout = sdir;
  if (argc < 6) usage_exit() ;

  hemi = argv[1] ;
  avg_surf_name = argv[2] ;
  canon_surf_name = argv[3] ;
  out_sname = argv[4] ;

  printf("---------------------------------------------------\n");
  printf("hemi            = %s\n",hemi);
  printf("avg_surf_name   = %s\n",avg_surf_name);
  printf("canon_surf_name = %s\n",canon_surf_name);
  printf("out_sname       = %s\n",out_sname);
  printf("xform           = %s\n",xform_name);
  printf("---------------------------------------------------\n");
  printf("\n\n");
  fflush(stdout);

#define SCALE 1
  mrisp_total = MRISPalloc(SCALE, 3) ;
  for (n = 0, i = 5 ; i < argc ; i++) {
    MRI *mri;
    MRI_SURFACE *mris;
    MRI_SP *mrisp;

    printf("\n---------------------------------------------------\n");
    printf("#@# processing subject %d/%d %s...\n", i-4,argc-5,argv[i]) ;
    fflush(stdout);

    // read sphere.reg
    sprintf(fname, "%s/%s/surf/%s.%s", sdir, argv[i], hemi, canon_surf_name) ;
    printf("  Reading %s\n",fname);
    fflush(stdout);
    mris = MRISread(fname) ;
    if (!mris) {
      ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
                Progname, fname) ;
      exit(1);
    }
    // get "pial" surface vertex into ->origx, origy, origz
    if (MRISreadOriginalProperties(mris, orig_name) != NO_ERROR)
      ErrorExit(ERROR_BADFILE,"%s: could not read orig file for %s.\n",
                Progname, argv[1]);
    // read transform
    if (0) {
      sprintf(fname, "%s/%s/mri/transforms/%s", sdir, argv[i], xform_name) ;
      lta = LTAreadEx(fname) ;
      if (!lta)
        ErrorExit(ERROR_BADPARM, 
                  "%s: could not read transform from %s", Progname, fname) ;
    }

    // read T1 volume
    sprintf(fname, "%s/%s/mri/T1.mgz", sdir, argv[i]) ;
    if (fio_FileExistsReadable(fname)) mri = MRIreadHeader(fname,MRI_MGH_FILE);
    else {
      sprintf(fname, "%s/%s/mri/T1", sdir, argv[i]) ;
      mri = MRIreadHeader(fname, MRI_UCHAR); // MRI_CORONAL_SLICE_DIRECTORY) ;
    }
    printf("  Read %s\n",fname);
    fflush(stdout);

    if (!mri)
      ErrorExit(ERROR_BADPARM, 
                "%s: could not read reference MRI volume from %s",
                Progname, fname) ;

    // save current vertex position into ->cx
    MRISsaveVertexPositions(mris, CANONICAL_VERTICES) ;
    // get the vertex position from ->origx, ... 
    // (get the "pial" vertex position)
    MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
    MRIScomputeMetricProperties(mris) ;
    printf("  Surface area: %2.1f cm^2\n", mris->total_area/100) ;
    fflush(stdout);
    average_surface_area += mris->total_area ;

    // this means that we transform "pial" surface

    if (xform_name)
    {
      if (!strcmp(xform_name,"talairach.xfm")) {
        printf("  Applying linear transform\n");
        fflush(stdout);
        XFM = DevolveXFMWithSubjectsDir(argv[i], NULL, "talairach.xfm", sdir);
        if (XFM == NULL) exit(1);
        MRISmatrixMultiply(mris, XFM);
        MatrixFree(&XFM);
      } else if (!strcmp(xform_name,"talairach.m3z")) {
        printf("  Applying GCA Morph\n");
        fflush(stdout);
        sprintf(fname, "%s/%s/mri/transforms/talairach.m3z", sdir, argv[i]) ;
        gcam = GCAMreadAndInvert(fname);
        if (gcam == NULL) exit(1);
        GCAMmorphSurf(mris, gcam);
        GCAMfree(&gcam);
      } else {
        printf("ERROR: don't know what to do with %s\n",xform_name);
        exit(1);
      }
    }

    // save transformed position in ->orig 
    // (store "pial" vertices position in orig)
    MRIScomputeMetricProperties(mris) ;
    MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
    // get the vertex position from ->cx 
    // (note that this is not transformed)  sphere.reg vertices
    MRISrestoreVertexPositions(mris, CANONICAL_VERTICES) ;
    // mris contains sphere.reg in vertex and pial vertices in orig
    // map to a theta-phi space and accumulate values
    mrisp = MRIScoordsToParameterization(mris, NULL, SCALE, ORIGINAL_VERTICES) ;
    MRISPaccumulate(mrisp, mrisp_total, 0) ;
    MRISPaccumulate(mrisp, mrisp_total, 1) ;
    MRISPaccumulate(mrisp, mrisp_total, 2) ;
    MRISPfree(&mrisp) ;
    MRISfree(&mris) ;
    MRIfree(&mri) ;
    //LTAfree(&lta) ;
    fflush(stdout);
    n++ ;
  }
  printf("Finished loading all data\n");
  average_surface_area /= (float)n ;
  printf("Avg surf area = %g cm\n",average_surface_area/100.0);
  fflush(stdout);

  // mrisp_total lost info on the modified surface
  sprintf(ico_fname, "%s/lib/bem/ic%d.tri", mdir, ico_no) ;
  printf("Reading icosahedron from %s...\n", ico_fname) ;
  mris_ico = ICOread(ico_fname) ;
  if (!mris_ico)
    ErrorExit(ERROR_NOFILE, "%s: could not read icosahedron file %s\n",
              Progname,ico_fname) ;
  MRISscaleBrain(mris_ico, mris_ico,
                 DEFAULT_RADIUS/MRISaverageRadius(mris_ico)) ;
  // save current ico position to ->cx, cy, cz
  MRISsaveVertexPositions(mris_ico, CANONICAL_VERTICES) ;
  // using mrisp_total to calculate position into ->origx, origy, origz 
  // (orig is the "pial" vertices)
  MRIScoordsFromParameterization(mrisp_total, mris_ico, ORIGINAL_VERTICES) ;
  // copy geometry info
  memcpy((void *) &mris_ico->vg, (void *) &vg, sizeof (VOL_GEOM));

  if (Gdiag_no >= 0 && Gdiag_no < mris_ico->nvertices) {
    int n ;
    VERTEX *vn ;

    v = &mris_ico->vertices[Gdiag_no] ;
    printf( "v %d: x = (%2.2f, %2.2f, %2.2f)\n",
            Gdiag_no, v->origx, v->origy, v->origz) ;
    for (n = 0 ; n < v->vnum ; n++) {
      vn = &mris_ico->vertices[v->v[n]] ;
      printf( "v %d: x = (%2.2f, %2.2f, %2.2f)\n",
              v->v[n], vn->origx, vn->origy, vn->origz) ;
    }
  }
  // write *h.sphere.reg
  sprintf(fname, "%s/%s/surf/%s.%s", 
          sdirout, out_sname, hemi, canon_surf_name) ;
  if (Gdiag & DIAG_SHOW)
    printf("writing average canonical surface to %s\n", fname);
  MRISwrite(mris_ico, fname) ;

  // get "pial vertices" from orig
  MRISrestoreVertexPositions(mris_ico, ORIG_VERTICES);
  for (vno = 0 ; vno < mris_ico->nvertices ; vno++) {
    v = &mris_ico->vertices[vno] ;
    // n = number of subjects
    v->x /= (float)n ;
    v->y /= (float)n ;
    v->z /= (float)n ;
  }
  if (normalize_area) {
    MRIScomputeMetricProperties(mris_ico) ;
    printf("setting group surface area to be %2.1f cm^2 (scale=%2.2f)\n",
           average_surface_area/100.0,
           sqrt(average_surface_area/mris_ico->total_area)) ;

#if 0
    MRISscaleBrain(mris_ico, mris_ico,
                   sqrt(average_surface_area/mris_ico->total_area)) ;
#else
    mris_ico->group_avg_surface_area = average_surface_area ;
#endif
    MRIScomputeMetricProperties(mris_ico) ;
  }

  sprintf(fname, "%s/%s/surf/%s.%s", sdirout,out_sname, hemi, avg_surf_name) ;
  printf("writing average %s surface to %s\n", avg_surf_name, fname);
  MRISwrite(mris_ico,  fname) ;

  if (0) {
    char path[STRLEN] ;
    LTA  *lta ;

    FileNamePath(fname, path) ;
    lta = LTAalloc(1, NULL) ;
    // write to a different location
    sprintf(fname, "%s/../mri/transforms/%s", path,xform_name) ;
    LTAwriteEx(lta, fname) ;
    LTAfree(&lta) ;
  }

  MRISfree(&mris_ico) ;
  MRISPfree(&mrisp_total) ;

  printf("mris_make_average_surface done\n");

  exit(0) ;
  return(0) ;  /* for ansi */
}
Ejemplo n.º 8
0
int
main(int argc, char *argv[]) {
  int           nargs, msec, order, i, number, vno, nnum, m, k, b1, b2, cno, flag=0, fno;
  struct timeb  then ;
  MRIS          *mris_in, *mris_out, *mris_high;
  MRI_SP        *mrisp ;
  VERTEX        *vm_out, *vm_high, *v;
  float         s_jkm, area;

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

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

  if (argc < 4)
    ErrorExit(ERROR_BADPARM,
              "usage: %s <input surface> <orig surface> <finest order> <output surface>", Progname);

  TimerStart(&then) ;

  order = atoi (argv[3]);
  fprintf(stdout, "Set %s as the finest scale level\n", argv[3]);
  if (order > 7)
    ErrorExit(ERROR_BADPARM, "the highest order is 7\n");

  /*Spherical Wavelet Analysis*/

  if (ANALYSIS&&!CURV) {
    mris_in = MRISread(argv[1]) ;
    if (!mris_in)
      ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
                Progname, argv[1]) ;
    fprintf(stdout, "Reading input spherical surface from %s\n", argv[1]);
    MRISreadOriginalProperties(mris_in, argv[2]) ;
    fprintf(stdout, "Reading original surface from %s orig area is %f\n", argv[2],mris_in->orig_area);

    mris_out = ReadIcoByOrder(order, 100);
    for (m = 0; m<mris_out->nvertices; m++)
      mris_out->vertices[m].nsize=1;
    mrisp = MRISPalloc(1, 3);
#if 1
    MRIScoordsToParameterization(mris_in, mrisp, 1, ORIGINAL_VERTICES) ;
    MRISPblur(mrisp, mrisp, 1, 0);
    MRISPblur(mrisp, mrisp, 1, 1);
    MRISPblur(mrisp, mrisp, 1, 2);
    MRIScoordsFromParameterization(mrisp, mris_out) ;
#else
    MRISreadOriginalProperties(mris_out, argv[2]) ;
#endif
#if 1 /*just to test if the parameterization is correct */
    MRISsaveVertexPositions(mris_out, TMP_VERTICES) ;
    MRISrestoreVertexPositions(mris_out, ORIGINAL_VERTICES) ;
    MRISupdateSurface(mris_out);
    fprintf(stderr, "original area becomes %f\n", mris_out->total_area);
    center_brain(mris_out, mris_out);
    MRISscaleBrain(mris_out, mris_out, sqrt(100000.0f/mris_out->total_area)) ;
    MRISupdateSurface(mris_out);
    for (fno=0; fno<mris_out->nfaces; fno++)
      area += mris_out->faces[fno].area;
    fprintf(stderr, "original area becomes %f\n", area);
    //MRISwrite(mris_out, "/space/xrt/1/users/btquinn/buckner_paper/010223_61223/surf/lh.sampled") ;
    MRISsaveVertexPositions(mris_out, ORIGINAL_VERTICES) ;
    MRISrestoreVertexPositions(mris_out, TMP_VERTICES) ;
#endif

    /* Initialize Ij,k*/
    for (vno = 0 ; vno<mris_out->nvertices; vno++) {
      vm_out = &mris_out->vertices[vno];
      vm_out->val = 1;
    }

    /*Iteratively compute Ij,k*/
    for (i=order;i>0;i--) {
      mris_high = ReadIcoByOrder(i, 100); //higher order surface
      for (m = 0; m<mris_high->nvertices; m++)
        mris_high->vertices[m].nsize=1;
      MRISsetNeighborhoodSize(mris_high, 3) ;
      number = IcoNVtxsFromOrder(i-1); //the start of m vertices
      for (m = number; m<mris_high->nvertices; m++) {
        vm_out = &mris_out->vertices[m];
        vm_high = &mris_high->vertices[m];
        flag=0;
        for (nnum=0; nnum<vm_high->vnum; nnum++)
          if ( vm_high->v[nnum]<number ) //A(j,m)
          {
            k = vm_high->v[nnum];
            v = &mris_out->vertices[k];
            v->val += 0.5*vm_out->val ;
          }
        for (; nnum<vm_high->v2num; nnum++)
          if ( vm_high->v[nnum]<number ) //B(j,m)
          {
            k = vm_high->v[nnum];
            if (flag==0) b1=k;
            else b2=k;
            flag++;
            v = &mris_out->vertices[k];
            v->val += 0.125*vm_out->val ;
          }
        for (; nnum<vm_high->v3num; nnum++)
          if ( vm_high->v[nnum]<number ) //C(j,m)
          {
            k = vm_high->v[nnum];
            flag=0; //C has to be a second-order neighbor of B
            for (cno=mris_high->vertices[b1].vnum; cno<mris_high->vertices[b1].v2num;cno++)
              if (mris_high->vertices[b1].v[cno]==k) flag=1;
            for (cno=mris_high->vertices[b2].vnum; cno<mris_high->vertices[b2].v2num;cno++)
              if (mris_high->vertices[b2].v[cno]==k) flag=1;
            if (flag) {
              v = &mris_out->vertices[k];
              v->val -= 0.0625*vm_out->val ;
            }
          }
      }
    }


    /*Analysis Stage I:*/
    for (i=order;i>0;i--) {
      mris_high = ReadIcoByOrder(i, 100); //higher order surface
      for (m = 0; m<mris_high->nvertices; m++)
        mris_high->vertices[m].nsize=1;
      MRISsetNeighborhoodSize(mris_high, 3) ;

      number = IcoNVtxsFromOrder(i-1); //the start of m vertices
      /* compute Yj,m for each m vertices */
      for (m = number; m<mris_high->nvertices; m++) {
        vm_out = &mris_out->vertices[m];
        vm_high = &mris_high->vertices[m];
        flag=0;
        for (nnum=0; nnum<vm_high->vnum; nnum++)  //first order neighborhood
          if ( vm_high->v[nnum]<number ) //neighbor A(j,m)
          {
            k = vm_high->v[nnum] ;
            v = &mris_out->vertices[k];
            vm_out->origx -= 0.5*v->origx;
            vm_out->origy -= 0.5*v->origy;
            vm_out->origz -= 0.5*v->origz;
          }
        for (; nnum<vm_high->v2num; nnum++) //second order neighborhood
          if ( vm_high->v[nnum]<number ) //neighbor B(j,m)
          {
            k = vm_high->v[nnum] ;
            if (flag==0) b1=k;
            else b2=k;
            flag++;
            v = &mris_out->vertices[k];
            vm_out->origx -= 0.125*v->origx;
            vm_out->origy -= 0.125*v->origy;
            vm_out->origz -= 0.125*v->origz;
          }
        for (; nnum<vm_high->v3num; nnum++)
          if ( vm_high->v[nnum]<number ) //neighbor C(j,m)
          {
            k = vm_high->v[nnum] ;
            flag=0; //C has to be a second-order neighbor of B
            for (cno=mris_high->vertices[b1].vnum; cno<mris_high->vertices[b1].v2num;cno++)
              if (mris_high->vertices[b1].v[cno]==k) flag=1;
            for (cno=mris_high->vertices[b2].vnum; cno<mris_high->vertices[b2].v2num;cno++)
              if (mris_high->vertices[b2].v[cno]==k) flag=1;
            if (flag) {
              v = &mris_out->vertices[k];
              vm_out->origx += 0.0625*v->origx;
              vm_out->origy += 0.0625*v->origy;
              vm_out->origz += 0.0625*v->origz;
            }
          }
      }


      /*Analysis Stage II: */
      /*Compute Lamda(j,k) using the Yita(j,m)*/
      for (m = number; m<mris_high->nvertices; m++) {
        vm_out = &mris_out->vertices[m];
        vm_high = &mris_high->vertices[m];
        for (nnum=0; nnum<vm_high->vnum; nnum++)
          if ( vm_high->v[nnum]<number ) //A(j,m)
          {
            k = vm_high->v[nnum];
            v = &mris_out->vertices[k];
            s_jkm = vm_out->val/2/v->val;
            v->origx += s_jkm*vm_out->origx;
            v->origy += s_jkm*vm_out->origy;
            v->origz += s_jkm*vm_out->origz;
          }

      }

    }

    MRISsaveVertexPositions(mris_out, TMP_VERTICES) ;
    MRISrestoreVertexPositions(mris_out, ORIGINAL_VERTICES) ;
#if 0
    for (m=0;m<mris_out->nvertices;m++)
      if (mris_out->vertices[m].z>6)
        fprintf(stdout, "%d %f %f %f\n", m,mris_out->vertices[m].x, mris_out->vertices[m].y, mris_out->vertices[m].z);
    //mris_high = ReadIcoByOrder(0, 100);
    //for (m=0;m<mris_high->nvertices;m++)
    //{mris_high->vertices[m].x=mris_out->vertices[m].x;
    //mris_high->vertices[m].y=mris_out->vertices[m].y;
    //mris_high->vertices[m].z=mris_out->vertices[m].z;
    //}
    //MRISwrite(mris_high, "/space/xrt/1/users/btquinn/buckner_paper/010223_61223/surf/lh.sampled") ;
#endif
    fprintf(stdout, "Writing wavelets coefficient of original surface to %s\n", argv[4]);
    MRISwrite(mris_out,argv[4] ) ;
    MRISrestoreVertexPositions(mris_out, TMP_VERTICES) ;
    MRISPfree(&mrisp) ;
    MRISfree(&mris_in) ;
    /*End of Analysis*/
  } else if (ANALYSIS&&CURV) {
    mris_in = MRISread(argv[1]) ;
    if (!mris_in)
      ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
                Progname, argv[1]) ;
    fprintf(stdout, "Reading input spherical surface from %s\n", argv[1]);

    MRISreadCurvatureFile(mris_in, argv[2]) ;
    fprintf(stdout, "Reading input from %s\n", argv[2]);

    mris_out = ReadIcoByOrder(order, 100);
    for (m = 0; m<mris_out->nvertices; m++)
      mris_out->vertices[m].nsize=1;
    //mrisp = MRISPalloc(1, 3);
    mrisp = MRIStoParameterization(mris_in, NULL, 1, 0) ;
    //MRISPblur(mrisp, mrisp, 1, 0);
    MRISfromParameterization(mrisp, mris_out, 0) ;
    //MRISwriteCurvature(mris_out,"/space/xrt/1/users/btquinn/buckner_paper/010223_61223/surf/lh.thickness.sampled");
    /* Initialize Ij,k*/
    for (vno = 0 ; vno<mris_out->nvertices; vno++) {
      vm_out = &mris_out->vertices[vno];
      vm_out->val = 1;
    }

    /*Iteratively compute Ij,k*/
    for (i=order;i>0;i--) {
      mris_high = ReadIcoByOrder(i, 100); //higher order surface
      for (m = 0; m<mris_high->nvertices; m++)
        mris_high->vertices[m].nsize=1;
      MRISsetNeighborhoodSize(mris_high, 3) ;
      number = IcoNVtxsFromOrder(i-1); //the start of m vertices
      for (m = number; m<mris_high->nvertices; m++) {
        vm_out = &mris_out->vertices[m];
        vm_high = &mris_high->vertices[m];
        flag=0;
        for (nnum=0; nnum<vm_high->vnum; nnum++)
          if ( vm_high->v[nnum]<number ) //A(j,m)
          {
            k = vm_high->v[nnum];
            v = &mris_out->vertices[k];
            v->val += 0.5*vm_out->val ;
          }
        for (; nnum<vm_high->v2num; nnum++)
          if ( vm_high->v[nnum]<number ) //B(j,m)
          {
            k = vm_high->v[nnum];
            if (flag==0) b1=k;
            else b2=k;
            flag++;
            v = &mris_out->vertices[k];
            v->val += 0.125*vm_out->val ;
          }
        for (; nnum<vm_high->v3num; nnum++)
          if ( vm_high->v[nnum]<number ) //C(j,m)
          {
            k = vm_high->v[nnum];
            flag=0; //C has to be a second-order neighbor of B
            for (cno=mris_high->vertices[b1].vnum; cno<mris_high->vertices[b1].v2num;cno++)
              if (mris_high->vertices[b1].v[cno]==k) flag=1;
            for (cno=mris_high->vertices[b2].vnum; cno<mris_high->vertices[b2].v2num;cno++)
              if (mris_high->vertices[b2].v[cno]==k) flag=1;
            if (flag) {
              v = &mris_out->vertices[k];
              v->val -= 0.0625*vm_out->val ;
            }
          }
      }
    }


    /*Analysis Stage I:*/
    for (i=order;i>0;i--) {
      mris_high = ReadIcoByOrder(i, 100); //higher order surface
      for (m = 0; m<mris_high->nvertices; m++)
        mris_high->vertices[m].nsize=1;
      MRISsetNeighborhoodSize(mris_high, 3) ;

      number = IcoNVtxsFromOrder(i-1); //the start of m vertices
      /* compute Yj,m for each m vertices */
      for (m = number; m<mris_high->nvertices; m++) {
        vm_out = &mris_out->vertices[m];
        vm_high = &mris_high->vertices[m];
        flag=0;
        for (nnum=0; nnum<vm_high->vnum; nnum++)  //first order neighborhood
          if ( vm_high->v[nnum]<number ) //neighbor A(j,m)
          {
            k = vm_high->v[nnum] ;
            v = &mris_out->vertices[k];
            vm_out->curv -= 0.5*v->curv;
          }
        for (; nnum<vm_high->v2num; nnum++) //second order neighborhood
          if ( vm_high->v[nnum]<number ) //neighbor B(j,m)
          {
            k = vm_high->v[nnum] ;
            if (flag==0) b1=k;
            else b2=k;
            flag++;
            v = &mris_out->vertices[k];
            vm_out->curv -= 0.125*v->curv;
          }
        for (; nnum<vm_high->v3num; nnum++)
          if ( vm_high->v[nnum]<number ) //neighbor C(j,m)
          {
            k = vm_high->v[nnum] ;
            flag=0; //C has to be a second-order neighbor of B
            for (cno=mris_high->vertices[b1].vnum; cno<mris_high->vertices[b1].v2num;cno++)
              if (mris_high->vertices[b1].v[cno]==k) flag=1;
            for (cno=mris_high->vertices[b2].vnum; cno<mris_high->vertices[b2].v2num;cno++)
              if (mris_high->vertices[b2].v[cno]==k) flag=1;
            if (flag) {
              v = &mris_out->vertices[k];
              vm_out->curv += 0.0625*v->curv;
            }
          }
      }


      /*Analysis Stage II: */
      /*Compute Lamda(j,k) using the Yita(j,m)*/
      for (m = number; m<mris_high->nvertices; m++) {
        vm_out = &mris_out->vertices[m];
        vm_high = &mris_high->vertices[m];
        for (nnum=0; nnum<vm_high->vnum; nnum++)
          if ( vm_high->v[nnum]<number ) //A(j,m)
          {
            k = vm_high->v[nnum];
            v = &mris_out->vertices[k];
            s_jkm = vm_out->val/2/v->val;
            v->curv += s_jkm*vm_out->curv;
          }

      }
    }

    fprintf(stdout, "Writing wavelets coefficient of original surface to %s\n", argv[4]);
    MRISwriteCurvature(mris_out,argv[4] ) ;
    MRISPfree(&mrisp) ;
    MRISfree(&mris_in) ;
    /*End of Analysis*/
  } else if (SYNTHESIS) /*Spherical Wavelet Synthesis*/
  {
    mris_out = ReadIcoByOrder(order, 100); //higher order surface
    fprintf(stdout, "Creating a %d order spherical surface\n", order);
    MRISreadOriginalProperties(mris_out, argv[1]) ;
    fprintf(stdout, "Reading wavelet coefficients from %s\n", argv[1]);
    for (m = 0; m<mris_out->nvertices; m++)
      mris_out->vertices[m].nsize=1;
    MRISsetNeighborhoodSize(mris_out, 3) ;

    if (COMPARE) {
      mris_in = MRISread(fname);
      for (i=1; i<IcoNVtxsFromOrder(order-1); i++) {
        if (mris_out->vertices[i].origx==0)
          area =  fabs(mris_out->vertices[i].origx-mris_in->vertices[i].x);
        else area = fabs((mris_out->vertices[i].origx-mris_in->vertices[i].x)/mris_out->vertices[i].origx);
        if ( area>5 ) {
          mris_out->vertices[i].origx = mris_in->vertices[i].x ;
          fprintf(stdout, "%d %f\n", i, area);
        }
        if (mris_out->vertices[i].origy==0)
          area =  fabs(mris_out->vertices[i].origy-mris_in->vertices[i].y);
        else area = fabs((mris_out->vertices[i].origy-mris_in->vertices[i].y)/mris_out->vertices[i].origy);
        if ( area>5 ) {
          mris_out->vertices[i].origy = mris_in->vertices[i].y ;
          fprintf(stdout, "%d %f\n", i, area);
        }
        if (mris_out->vertices[i].origz==0)
          area =  fabs(mris_out->vertices[i].origz-mris_in->vertices[i].z);
        else area = fabs((mris_out->vertices[i].origz-mris_in->vertices[i].z)/mris_out->vertices[i].origz);
        if ( area>5 ) {
          mris_out->vertices[i].origz = mris_in->vertices[i].z ;
          fprintf(stdout, "%d %f\n", i, area);
        }
      }
      MRISfree(&mris_in);
    }

    fprintf(stdout, "Recover the surface using %s order coefficients\n",argv[2]);
    number = IcoNVtxsFromOrder(atoi(argv[2]));
    for (m = number; m<mris_out->nvertices; m++) {
      mris_out->vertices[m].origx = 0;
      mris_out->vertices[m].origy = 0;
      mris_out->vertices[m].origz = 0;
    }

    /*Initialize Ij,k*/
    for (vno = 0; vno<mris_out->nvertices; vno++) {
      vm_out = &mris_out->vertices[vno];
      vm_out->val = 1;
    }

    /*Iteratively compute Ij,k*/
    for (i=order;i>0;i--) {
      mris_high = ReadIcoByOrder(i, 100); //higher order surface
      for (m = 0; m<mris_high->nvertices; m++)
        mris_high->vertices[m].nsize=1;
      MRISsetNeighborhoodSize(mris_high, 3) ;
      number = IcoNVtxsFromOrder(i-1); //the start of m vertices
      for (m = number; m<mris_high->nvertices; m++) {
        vm_out = &mris_out->vertices[m];
        vm_high = &mris_high->vertices[m];
        flag=0;
        for (nnum=0; nnum<vm_high->vnum; nnum++)
          if ( vm_high->v[nnum]<number ) //A(j,m)
          {
            k = vm_high->v[nnum];
            v = &mris_out->vertices[k];
            v->val += 0.5*vm_out->val ;
          }
        for (; nnum<vm_high->v2num; nnum++)
          if ( vm_high->v[nnum]<number ) //B(j,m)
          {
            k = vm_high->v[nnum];
            if (flag==0) b1=k;
            else b2=k;
            flag++;
            v = &mris_out->vertices[k];
            v->val += 0.125*vm_out->val ;
          }
        for (; nnum<vm_high->v3num; nnum++)
          if ( vm_high->v[nnum]<number ) //C(j,m)
          {
            k = vm_high->v[nnum];
            flag=0; //C has to be a second-order neighbor of B
            for (cno=mris_high->vertices[b1].vnum; cno<mris_high->vertices[b1].v2num;cno++)
              if (mris_high->vertices[b1].v[cno]==k) flag=1;
            for (cno=mris_high->vertices[b2].vnum; cno<mris_high->vertices[b2].v2num;cno++)
              if (mris_high->vertices[b2].v[cno]==k) flag=1;
            if (flag) {
              v = &mris_out->vertices[k];
              v->val -= 0.0625*vm_out->val ;
            }
          }
      }
    }


    for (i=1;i<=order;i++) {
      mris_high = ReadIcoByOrder(i, 100); //higher order surface
      for (m = 0; m<mris_high->nvertices; m++)
        mris_high->vertices[m].nsize=1;
      MRISsetNeighborhoodSize(mris_high, 3) ;
      number = IcoNVtxsFromOrder(i-1); //the start of m vertices

      /* Synthesis Stage I */
      /* Compute Lamda(j+1,k) using the Yita(j,m) */
      for (m = number; m<mris_high->nvertices; m++) {
        vm_out = &mris_out->vertices[m];
        vm_high = &mris_high->vertices[m];
        for (nnum=0; nnum<vm_high->vnum; nnum++)
          if ( vm_high->v[nnum]<number ) //A(j,m)
          {
            k = vm_high->v[nnum];
            v = &mris_out->vertices[k];
            s_jkm = vm_out->val/2/v->val;
            v->origx -= s_jkm*vm_out->origx;
            v->origy -= s_jkm*vm_out->origy;
            v->origz -= s_jkm*vm_out->origz;
          }
      }

      /* compute Lamda(j+1,m) for each m vertices */
      for (m = number; m<mris_high->nvertices; m++) {
        vm_out = &mris_out->vertices[m];
        vm_high = &mris_high->vertices[m];
        flag=0;
        for (nnum=0; nnum<vm_high->vnum; nnum++)  //first order neighborhood
          if ( vm_high->v[nnum]<number ) //neighbor A(j,m)
          {
            k = vm_high->v[nnum] ;
            v = &mris_out->vertices[k];
            vm_out->origx += 0.5*v->origx;
            vm_out->origy += 0.5*v->origy;
            vm_out->origz += 0.5*v->origz;
          }
        for (; nnum<vm_high->v2num; nnum++) //second order neighborhood
          if ( vm_high->v[nnum]<number ) //neighbor B(j,m)
          {
            k = vm_high->v[nnum] ;
            if (flag==0) b1=k;
            else b2=k;
            flag++;
            v = &mris_out->vertices[k];
            vm_out->origx += 0.125*v->origx;
            vm_out->origy += 0.125*v->origy;
            vm_out->origz += 0.125*v->origz;
          }
        for (; nnum<vm_high->v3num; nnum++) //third order neighborhood
          if ( vm_high->v[nnum]<number ) //neighbor C(j,m)
          {
            k = vm_high->v[nnum] ;
            flag=0; //C has to be a second-order neighbor of B
            for (cno=mris_high->vertices[b1].vnum; cno<mris_high->vertices[b1].v2num;cno++)
              if (mris_high->vertices[b1].v[cno]==k) flag=1;
            for (cno=mris_high->vertices[b2].vnum; cno<mris_high->vertices[b2].v2num;cno++)
              if (mris_high->vertices[b2].v[cno]==k) flag=1;
            if (flag) {
              v = &mris_out->vertices[k];
              vm_out->origx -= 0.0625*v->origx;
              vm_out->origy -= 0.0625*v->origy;
              vm_out->origz -= 0.0625*v->origz;
            }
          }
      }
    }

    MRISsaveVertexPositions(mris_out, TMP_VERTICES) ;
    MRISrestoreVertexPositions(mris_out, ORIGINAL_VERTICES) ;
    fprintf(stdout, "Writing recovered surface to %s\n", argv[4]);
    MRISwrite(mris_out, argv[4]) ;
#if 0
    mris_high = ReadIcoByOrder(4, 100);
    for (m=0;m<mris_high->nvertices;m++) {
      mris_high->vertices[m].x=mris_out->vertices[m].x;
      mris_high->vertices[m].y=mris_out->vertices[m].y;
      mris_high->vertices[m].z=mris_out->vertices[m].z;
    }
    MRISwrite(mris_high, "/space/xrt/1/users/btquinn/buckner_paper/010223_61223/surf/lh.wavelet.recon") ;
#endif
    MRISrestoreVertexPositions(mris_out, TMP_VERTICES) ;
    /*End of Synthesis*/
  }

  MRISfree(&mris_out);
  MRISfree(&mris_high) ;
  msec = TimerStop(&then) ;
  fprintf(stdout, "spherical wavelet took %2.1f minutes\n", (float)msec/(1000.0f*60.0f));
  exit(0) ;
  return(0) ;
}
Ejemplo n.º 9
0
int
main(int argc, char *argv[])
{
  char         **av, surf_fname[STRLEN], *template_fname, *hemi, *sphere_name,
  *cp, *subject, fname[STRLEN] ;
  int          ac, nargs, ino, sno, nbad = 0, failed, n,nfields;
  VERTEX *v;
  VALS_VP *vp;
  MRI_SURFACE  *mris ;
  MRI_SP       *mrisp, /* *mrisp_aligned,*/ *mrisp_template ;
  INTEGRATION_PARMS parms ;

  /* rkt: check for and handle version tag */
  nargs = handle_version_option
          (argc, argv,
           "$Id: mris_make_template.c,v 1.27 2011/03/02 00:04:33 nicks Exp $",
           "$Name: stable5 $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

  memset(&parms, 0, sizeof(parms)) ;
  Progname = argv[0] ;
  ErrorInit(NULL, NULL, NULL) ;
  DiagInit(NULL, NULL, NULL) ;
  /* setting default values for vectorial registration */
  setParms(&parms);

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

  if (argc < 5) usage_exit() ;

  /* multiframe registration */
  if (multiframes) parms.flags |= IP_USE_MULTIFRAMES;

  if (!strlen(subjects_dir))  /* not specified on command line*/
  {
    cp = getenv("SUBJECTS_DIR") ;
    if (!cp)
      ErrorExit(ERROR_BADPARM,
                "%s: SUBJECTS_DIR not defined in environment.\n",
                Progname) ;
    strcpy(subjects_dir, cp) ;
  }
  hemi = argv[1] ;
  sphere_name = argv[2] ;
  template_fname = argv[argc-1] ;
  if (1 || !FileExists(template_fname))  /* first time - create it */
  {
    fprintf(stderr, "creating new parameterization...\n") ;
    if (multiframes)
    {
      mrisp_template = MRISPalloc(scale, atlas_size * IMAGES_PER_SURFACE );
      /*    if (no_rot)  /\* don't do rigid alignment *\/ */
      /*     mrisp_aligned = NULL ; */
      /*    else */
      /*     mrisp_aligned = MRISPalloc(scale, PARAM_FRAMES);  */
    }
    else
    {
      mrisp_template = MRISPalloc(scale, PARAM_IMAGES);
      /*    if (no_rot)  /\* don't do rigid alignment *\/ */
      /*     mrisp_aligned = NULL ; */
      /*    else */
      /*     mrisp_aligned = MRISPalloc(scale, PARAM_IMAGES);  */
    }

  }
  else
  {
    fprintf(stderr, "reading template parameterization from %s...\n",
            template_fname) ;
    /* mrisp_aligned = NULL ; */
    mrisp_template = MRISPread(template_fname) ;
    if (!mrisp_template)
      ErrorExit(ERROR_NOFILE, "%s: could not open template file %s",
                Progname, template_fname) ;
  }

  argv += 3 ;
  argc -= 3 ;
  for (ino = 0 ; ino < argc-1 ; ino++)
  {
    failed = 0 ;
    subject = argv[ino] ;
    fprintf(stderr, "\nprocessing subject %s (%d of %d)\n", subject,
            ino+1, argc-1) ;
    sprintf(surf_fname, "%s/%s/surf/%s.%s",
            subjects_dir, subject, hemi, sphere_name) ;
    fprintf(stderr, "reading spherical surface %s...\n", surf_fname) ;
    mris = MRISread(surf_fname) ;
    if (!mris)
    {
      nbad++ ;
      ErrorPrintf(ERROR_NOFILE, "%s: could not read surface file %s",
                  Progname, surf_fname) ;
      exit(1) ;
    }
    if (annot_name)
    {
      if (MRISreadAnnotation(mris, annot_name) != NO_ERROR)
        ErrorExit(ERROR_BADPARM,
                  "%s: could not read annot file %s",
                  Progname, annot_name) ;
      MRISripMedialWall(mris) ;
    }

    MRISsaveVertexPositions(mris, CANONICAL_VERTICES) ;
    MRIScomputeMetricProperties(mris) ;
    MRISstoreMetricProperties(mris) ;

    if (Gdiag & DIAG_WRITE)
    {
      char *cp1 ;

      FileNameOnly(template_fname, fname) ;
      cp = strchr(fname, '.') ;
      if (cp)
      {
        cp1 = strrchr(fname, '.') ;
        if (cp1 && cp1 != cp)
          strncpy(parms.base_name, cp+1, cp1-cp-1) ;
        else
          strcpy(parms.base_name, cp+1) ;
      }
      else
        strcpy(parms.base_name, "template") ;
      sprintf(fname, "%s.%s.out", hemi, parms.base_name);
      parms.fp = fopen(fname, "w") ;
      printf("writing output to '%s'\n", fname) ;
    }

    /* multiframe registration */
    if (multiframes)
    {
      nfields=parms.nfields;

      for ( n = 0; n < mris->nvertices ; n++) /* allocate the VALS_VP
                                                                 structure */
      {
        v=&mris->vertices[n];
        vp=calloc(1,sizeof(VALS_VP));
        vp->nvals=nfields;
        vp->orig_vals=(float*)malloc(nfields*sizeof(float)); /* before
                                                                blurring */
        vp->vals=(float*)malloc(nfields*sizeof(float));     /* values used by
                                                               MRISintegrate */
        v->vp=(void*)vp;
      }

      /* load the different fields */
      for (n = 0 ; n < parms.nfields ; n++)
      {
        if (parms.fields[n].name != NULL)
        {
          sprintf(surf_fname, "%s/%s/%s/%s.%s", subjects_dir,
                  subject, overlay_dir, hemi, parms.fields[n].name) ;
          printf("reading overlay file %s...\n", surf_fname) ;
          if (MRISreadValues(mris, surf_fname) != NO_ERROR)
            ErrorExit(ERROR_BADPARM, "%s: could not read overlay file %s",
                      Progname, surf_fname) ;
          MRIScopyValuesToCurvature(mris) ;
        }
        else if (ReturnFieldName(parms.fields[n].field))
        {
          /* read in precomputed curvature file */
          sprintf(surf_fname, "%s/%s/surf/%s.%s", subjects_dir,
                  subject, hemi, ReturnFieldName(parms.fields[n].field)) ;
          // fprintf(stderr,"\nreading field %d from %s(type=%d,frame=%d)\n",parms.fields[n].field,surf_fname,parms.fields[n].type,parms.fields[n].frame);
          if (MRISreadCurvatureFile(mris, surf_fname) != NO_ERROR)
          {
            fprintf(stderr,"\n\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n");
            fprintf(stderr, "%s: could not read curvature file '%s'\n",
                    Progname, surf_fname) ;
            failed = 1;
            break;
          }
        }
        else
        {                       /* compute curvature of surface */
          sprintf(surf_fname, "%s/%s/surf/%s.%s", subjects_dir,
                  subject, hemi, surface_names[parms.fields[n].field]) ;
          /*if(parms.fields[n].field==0)
           sprintf(fname, "inflated") ;
           else
           sprintf(fname, "smoothwm") ;*/
          //fprintf(stderr,"\ngenerating field %d(type=%d,frame=%d) (from %s)\n",parms.fields[n].field,parms.fields[n].type,parms.fields[n].frame,surf_fname);
          //     MRISsaveVertexPositions(mris, TMP_VERTICES) ;
          if (MRISreadVertexPositions(mris, surf_fname) != NO_ERROR)
          {
            fprintf(stderr,"\n\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n");
            ErrorPrintf(ERROR_NOFILE, "%s: could not read surface file %s",
                        Progname, surf_fname) ;
            fprintf(stderr,"setting up correlation coefficient to zero\n");
            parms.fields[n].l_corr=parms.fields[n].l_pcorr=0.0;
            failed=1;
            break;
          }

          if (nbrs > 1) MRISsetNeighborhoodSize(mris, nbrs) ;
          MRIScomputeMetricProperties(mris) ;
          MRIScomputeSecondFundamentalForm(mris) ;
          MRISuseMeanCurvature(mris) ;
          MRISaverageCurvatures(mris, navgs) ;
          MRISrestoreVertexPositions(mris, CANONICAL_VERTICES) ;
        }
        /*    if(parms.fields[n].field!=SULC_CORR_FRAME)*/
        MRISnormalizeField(mris,parms.fields[n].type,
                           parms.fields[n].which_norm); /* normalize values */
        MRISsetCurvaturesToOrigValues(mris,n);
        MRISsetCurvaturesToValues(mris,n);
      }

      if (failed)
      {
        fprintf(stderr,"\n\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n");
        fprintf(stderr,"Subject %s Failed",subject);
        fprintf(stderr,"XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n\n");
        /* free cal structure*/
        for ( n = 0; n < mris->nvertices ; n++)
        {
          v=&mris->vertices[n];
          vp=(VALS_VP*)v->vp;
          free(vp->orig_vals);
          free(vp->vals);
          free(vp);
          v->vp=NULL;
        }
        /* free surface */
        MRISfree(&mris);
        /* go onto the next subject */
        continue;
      }
    }

    if (multiframes && (!no_rot))
    { /* rigid body alignment */
      parms.frame_no = 3 ;  /* don't use single field correlation functions */
      parms.l_corr = parms.l_pcorr = 0.0f ;

      parms.mrisp = MRIStoParameterization(mris, NULL, scale, 0) ;
      parms.mrisp_template = mrisp_template ;

      MRISrigidBodyAlignVectorGlobal(mris, &parms, 1.0, 64.0, 8) ;
      if (Gdiag & DIAG_WRITE) MRISwrite(mris, "sphere.rot.global") ;
      MRISrigidBodyAlignVectorLocal(mris, &parms) ;
      if (Gdiag & DIAG_WRITE) MRISwrite(mris, "sphere.rot.local") ;
      MRISPfree(&parms.mrisp) ;
      MRISsaveVertexPositions(mris, CANONICAL_VERTICES) ;
    };
    if ((!multiframes) && (!no_rot) && ino > 0)
    { /* rigid body alignment */
      sprintf(surf_fname, "%s/%s/surf/%s.%s",
              subjects_dir, subject, hemi, "sulc") ;
      if (MRISreadCurvatureFile(mris, surf_fname) != NO_ERROR)
      {
        ErrorPrintf(Gerror, "%s: could not read curvature file '%s'\n",
                    Progname, surf_fname) ;
        nbad++ ;
        MRISfree(&mris) ;
        continue ;
      }
      parms.frame_no = 3 ; /* use sulc for rigid registration */
      parms.mrisp = MRIStoParameterization(mris, NULL, scale, 0) ;
      parms.mrisp_template = mrisp_template ;
      parms.l_corr = 1.0f ;

      MRISrigidBodyAlignGlobal(mris, &parms, 1.0, 64.0, 8) ;
      if (Gdiag & DIAG_WRITE)
        MRISwrite(mris, "sphere.rot.global") ;
      MRISrigidBodyAlignLocal(mris, &parms) ;
      if (Gdiag & DIAG_WRITE)
        MRISwrite(mris, "sphere.rot.local") ;
      MRISPfree(&parms.mrisp) ;
      MRISsaveVertexPositions(mris, CANONICAL_VERTICES) ;
    }

    if (multiframes)
    {
      for (n = 0; n < parms.nfields ; n++)
      {
        MRISsetOrigValuesToCurvatures(mris,n);
        MRISaverageCurvatures(mris, parms.fields[n].navgs) ;
        mrisp = MRIStoParameterization(mris, NULL, scale, 0) ;
        MRISPcombine(mrisp,
                     mrisp_template,
                     parms.fields[n].frame * IMAGES_PER_SURFACE) ;
        MRISPfree(&mrisp) ;
      }
      /* free the VALS_VP structure */
      for ( n = 0; n < mris->nvertices ; n++)
      {
        v=&mris->vertices[n];
        vp=(VALS_VP*)v->vp;
        free(vp->orig_vals);
        free(vp->vals);
        free(vp);
        v->vp=NULL;
      }
      MRISfree(&mris) ;
    }
    else
    {
      for (sno = 0; sno < SURFACES ; sno++)
      {
        if (curvature_names[sno])  /* read in precomputed curvature file */
        {
          sprintf(surf_fname, "%s/%s/surf/%s.%s",
                  subjects_dir, subject, hemi, curvature_names[sno]) ;
          if (MRISreadCurvatureFile(mris, surf_fname) != NO_ERROR)
          {
            nbad++ ;
            ErrorPrintf(Gerror, "%s: could not read curvature file '%s'\n",
                        Progname, surf_fname) ;
            failed = 1 ;
            break ;
          }
          /* the two next lines were not in the original code */
          MRISaverageCurvatures(mris, navgs) ;
          MRISnormalizeCurvature(mris, which_norm) ;
        } else                       /* compute curvature of surface */
        {
          sprintf(surf_fname, "%s/%s/surf/%s.%s",
                  subjects_dir, subject, hemi, surface_names[sno]) ;
          if (MRISreadVertexPositions(mris, surf_fname) != NO_ERROR)
          {
            ErrorPrintf(ERROR_NOFILE, "%s: could not read surface file %s",
                        Progname, surf_fname) ;
            nbad++ ;
            failed = 1 ;
            break ;
          }

          if (nbrs > 1)
            MRISsetNeighborhoodSize(mris, nbrs) ;
          MRIScomputeMetricProperties(mris) ;
          MRIScomputeSecondFundamentalForm(mris) ;
          MRISuseMeanCurvature(mris) ;
          MRISaverageCurvatures(mris, navgs) ;
          MRISrestoreVertexPositions(mris, CANONICAL_VERTICES) ;
          MRISnormalizeCurvature(mris, which_norm) ;
        }
        fprintf(stderr, "computing parameterization for surface %s...\n",
                surf_fname);
        if (failed)
        {
          continue ;
          MRISfree(&mris) ;
        }
        mrisp = MRIStoParameterization(mris, NULL, scale, 0) ;
        MRISPcombine(mrisp, mrisp_template, sno*3) ;
        MRISPfree(&mrisp) ;
      }
      MRISfree(&mris) ;
    }
  }

#if 0
  if (mrisp_aligned)  /* new parameterization - use rigid alignment */
  {
    MRI_SP *mrisp_tmp ;

    if (Gdiag & DIAG_WRITE)
    {
      char *cp1 ;

      FileNameOnly(template_fname, fname) ;
      cp = strchr(fname, '.') ;
      if (cp)
      {
        cp1 = strrchr(fname, '.') ;
        if (cp1 && cp1 != cp)
          strncpy(parms.base_name, cp+1, cp1-cp-1) ;
        else
          strcpy(parms.base_name, cp+1) ;
      }
      else
        strcpy(parms.base_name, "template") ;
      sprintf(fname, "%s.%s.out", hemi, parms.base_name);
      parms.fp = fopen(fname, "w") ;
      printf("writing output to '%s'\n", fname) ;
    }
    for (ino = 0 ; ino < argc-1 ; ino++)
    {
      subject = argv[ino] ;
      if (Gdiag & DIAG_WRITE)
        fprintf(parms.fp, "processing subject %s\n", subject) ;
      fprintf(stderr, "processing subject %s\n", subject) ;
      sprintf(surf_fname, "%s/%s/surf/%s.%s",
              subjects_dir, subject, hemi, sphere_name) ;
      fprintf(stderr, "reading spherical surface %s...\n", surf_fname) ;
      mris = MRISread(surf_fname) ;
      if (!mris)
        ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
                  Progname, surf_fname) ;
      MRIScomputeMetricProperties(mris) ;
      MRISstoreMetricProperties(mris) ;
      MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
      sprintf(surf_fname, "%s/%s/surf/%s.%s",
              subjects_dir, subject, hemi, "sulc") ;
      if (MRISreadCurvatureFile(mris, surf_fname) != NO_ERROR)
        ErrorExit(Gerror, "%s: could not read curvature file '%s'\n",
                  Progname, surf_fname) ;
      parms.frame_no = 3 ;
      parms.mrisp = MRIStoParameterization(mris, NULL, scale, 0) ;
      parms.mrisp_template = mrisp_template ;
      parms.l_corr = 1.0f ;

      MRISrigidBodyAlignGlobal(mris, &parms, 1.0, 32.0, 8) ;
      if (Gdiag & DIAG_WRITE)
        MRISwrite(mris, "sphere.rot.global") ;
      MRISrigidBodyAlignLocal(mris, &parms) ;
      if (Gdiag & DIAG_WRITE)
        MRISwrite(mris, "sphere.rot.local") ;
      MRISPfree(&parms.mrisp) ;

#if 0
      /* write out rotated surface */
      sprintf(surf_fname, "%s.rot", mris->fname) ;
      fprintf(stderr, "writing out rigidly aligned surface to '%s'\n",
              surf_fname) ;
      MRISwrite(mris, surf_fname) ;
#endif

      /* now generate new parameterization using the optimal alignment */
      for (sno = 0; sno < SURFACES ; sno++)
      {
        if (curvature_names[sno])  /* read in precomputed curvature file */
        {
          sprintf(surf_fname, "%s/%s/surf/%s.%s",
                  subjects_dir, subject, hemi, curvature_names[sno]) ;
          if (MRISreadCurvatureFile(mris, surf_fname) != NO_ERROR)
            ErrorExit(Gerror, "%s: could not read curvature file '%s'\n",
                      Progname, surf_fname) ;
        } else                       /* compute curvature of surface */
        {
          sprintf(surf_fname, "%s/%s/surf/%s.%s",
                  subjects_dir, subject, hemi, surface_names[sno]) ;
          if (MRISreadVertexPositions(mris, surf_fname) != NO_ERROR)
            ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
                      Progname, surf_fname) ;

          if (nbrs > 1)
            MRISsetNeighborhoodSize(mris, nbrs) ;
          MRIScomputeMetricProperties(mris) ;
          MRIScomputeSecondFundamentalForm(mris) ;
          MRISuseMeanCurvature(mris) ;
          MRISaverageCurvatures(mris, navgs) ;
          MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
          MRISnormalizeCurvature(mris) ;
        }
        fprintf(stderr, "computing parameterization for surface %s...\n",
                surf_fname);
        mrisp = MRIStoParameterization(mris, NULL, scale, 0) ;
        MRISPcombine(mrisp, mrisp_aligned, sno*3) ;
        MRISPfree(&mrisp) ;
      }
      MRISfree(&mris) ;
    }

    if (Gdiag & DIAG_WRITE)
      fclose(parms.fp) ;

    mrisp_tmp = mrisp_aligned ;
    mrisp_aligned = mrisp_template ;
    mrisp_template = mrisp_tmp ;
    MRISPfree(&mrisp_aligned) ;
  }
#endif
  fprintf(stderr,
          "writing updated template with %d subjects to %s...\n",
          argc-1-nbad, template_fname) ;
  MRISPwrite(mrisp_template, template_fname) ;
  MRISPfree(&mrisp_template) ;
  exit(0) ;
  return(0) ;  /* for ansi */
}
Ejemplo n.º 10
0
int
main(int argc, char *argv[]) {
  int          ac, nargs ;
  char         **av, *cp, surf_name[100], *hemi, *subject_name, *label_name,
               *out_fname ;
  MRI_SURFACE  *mris ;
  LABEL        *label ;

  /* rkt: check for and handle version tag */
  nargs = handle_version_option (argc, argv, "$Id: label2patch.c,v 1.7 2016/12/10 22:57:39 fischl Exp $", "$Name:  $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

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

  /* read in command-line options */
  ac = argc ;
  av = argv ;
  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }
  
  if (argc < 4)
    print_usage() ;

  subject_name = argv[1] ;
  hemi = argv[2] ;
  label_name = argv[3] ;
  out_fname = argv[4] ;

  if (strlen(subjects_dir) == 0)
  {
    cp = getenv("SUBJECTS_DIR") ;
    if (!cp)
      ErrorExit(ERROR_BADPARM, "no subjects directory in environment.\n") ;
    strcpy(subjects_dir, cp) ;
  }

  sprintf(surf_name,"%s/%s/surf/%s.%s",subjects_dir,subject_name,hemi,surface);
  fprintf(stderr, "reading %s...\n", surf_name) ;
  mris = MRISread(surf_name) ;
  if (!mris)
    ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s\n",
              surf_name) ;
  MRIScomputeMetricProperties(mris) ;
  label = LabelRead(subject_name, label_name) ;
  if (ndilate)
    LabelDilate(label, mris, ndilate, CURRENT_VERTICES) ;
  if (nerode)
    LabelErode(label, mris, nerode) ;
  if (nclose)
  {
    LabelDilate(label, mris, nclose, CURRENT_VERTICES) ;
    LabelErode(label, mris, nclose) ;
  }

  LabelRipRestOfSurface(label, mris) ;
  MRISripFaces(mris) ;
  if (writesurf)
  {
     MRISwrite(mris, out_fname) ;
  }
  else
     MRISwritePatch(mris, out_fname) ;

  if (verbose)
    fprintf(stderr, "done.\n") ;
  exit(0) ;
  return(0) ;  /* ansi */
}
Ejemplo n.º 11
0
int
main(int argc, char *argv[])
{
  char **av, *surf_fname, *template_fname, *out_fname, fname[STRLEN],*cp;
  int ac, nargs,err, msec ;
  MRI_SURFACE  *mris ;
  MRI_SP       *mrisp_template ;

  char cmdline[CMD_LINE_LEN] ;
  struct  timeb start ;

  make_cmd_version_string
  (argc, argv,
   "$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $",
   "$Name: stable5 $",
   cmdline);

  /* rkt: check for and handle version tag */
  nargs = handle_version_option
          (argc, argv,
           "$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $",
           "$Name: stable5 $");
  if (nargs && argc - nargs == 1)
  {
    exit (0);
  }
  argc -= nargs;

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

  memset(&parms, 0, sizeof(parms)) ;
  parms.projection = PROJECT_SPHERE ;
  parms.flags |= IP_USE_CURVATURE ;
  parms.tol = 0.5 ;    // was 1e-0*2.5
  parms.min_averages = 0 ;
  parms.l_area = 0.0 ;
  parms.l_parea = 0.1f ;  // used to be 0.2
  parms.l_dist = 5.0 ; // used to be 0.5, and before that 0.1
  parms.l_corr = 1.0f ;
  parms.l_nlarea = 1 ;
  parms.l_pcorr = 0.0f ;
  parms.niterations = 25 ;
  parms.n_averages = 1024 ;   // used to be 256
  parms.write_iterations = 100 ;
  parms.dt_increase = 1.01 /* DT_INCREASE */;
  parms.dt_decrease = 0.99 /* DT_DECREASE*/ ;
  parms.error_ratio = 1.03 /*ERROR_RATIO */;
  parms.dt_increase = 1.0 ;
  parms.dt_decrease = 1.0 ;
  parms.l_external = 10000 ;   /* in case manual label is specified */
  parms.error_ratio = 1.1 /*ERROR_RATIO */;
  parms.integration_type = INTEGRATE_ADAPTIVE ;
  parms.integration_type = INTEGRATE_MOMENTUM /*INTEGRATE_LINE_MINIMIZE*/ ;
  parms.integration_type = INTEGRATE_LINE_MINIMIZE ;
  parms.dt = 0.9 ;
  parms.momentum = 0.95 ;
  parms.desired_rms_height = -1.0 ;
  parms.nbhd_size = -10 ;
  parms.max_nbrs = 10 ;

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

  if (nsigmas > 0)
  {
    MRISsetRegistrationSigmas(sigmas, nsigmas) ;
  }
  parms.which_norm = which_norm ;
  if (argc < 4)
  {
    usage_exit() ;
  }

  printf("%s\n", vcid) ;
  printf("  %s\n",MRISurfSrcVersion());
  fflush(stdout);

  surf_fname = argv[1] ;
  template_fname = argv[2] ;
  out_fname = argv[3] ;

  if (parms.base_name[0] == 0)
  {
    FileNameOnly(out_fname, fname) ;
    cp = strchr(fname, '.') ;
    if (cp)
    {
      strcpy(parms.base_name, cp+1) ;
    }
    else
    {
      strcpy(parms.base_name, "sphere") ;
    }
  }

  fprintf(stderr, "reading surface from %s...\n", surf_fname) ;
  mris = MRISread(surf_fname) ;
  if (!mris)
    ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
              Progname, surf_fname) ;

  if (parms.var_smoothness)
  {
    parms.vsmoothness = (float *)calloc(mris->nvertices, sizeof(float)) ;
    if (parms.vsmoothness == NULL)
    {
      ErrorExit(ERROR_NOMEMORY, "%s: could not allocate vsmoothness array",
                Progname) ;
    }
    parms.dist_error = (float *)calloc(mris->nvertices, sizeof(float)) ;
    if (parms.dist_error == NULL)
    {
      ErrorExit(ERROR_NOMEMORY, "%s: could not allocate dist_error array",
                Progname) ;
    }
    parms.area_error = (float *)calloc(mris->nvertices, sizeof(float)) ;
    if (parms.area_error == NULL)
    {
      ErrorExit(ERROR_NOMEMORY, "%s: could not allocate area_error array",
                Progname) ;
    }
    parms.geometry_error = (float *)calloc(mris->nvertices, sizeof(float)) ;
    if (parms.geometry_error == NULL)
    {
      ErrorExit(ERROR_NOMEMORY, "%s: could not allocate geometry_error array",
                Progname) ;
    }
  }

  MRISresetNeighborhoodSize(mris, 1) ;
  if (annot_name)
  {
    if (MRISreadAnnotation(mris, annot_name) != NO_ERROR)
      ErrorExit(ERROR_BADPARM,
                "%s: could not read annot file %s",
                Progname, annot_name) ;
    MRISripMedialWall(mris) ;
  }

  MRISsaveVertexPositions(mris, TMP2_VERTICES) ;
  MRISaddCommandLine(mris, cmdline) ;
  if (!FZERO(dalpha) || !FZERO(dbeta) || !FZERO(dgamma))
    MRISrotate(mris, mris, RADIANS(dalpha), RADIANS(dbeta),
               RADIANS(dgamma)) ;

  if (curvature_fname[0])
  {
    fprintf(stderr, "reading source curvature from %s\n",curvature_fname) ;
    MRISreadCurvatureFile(mris, curvature_fname) ;
  }
  if (single_surf)
  {
    char        fname[STRLEN], *cp, surf_dir[STRLEN], hemi[10]  ;
    MRI_SURFACE *mris_template ;
    int         sno, tnbrs=3 ;

    FileNamePath(template_fname, surf_dir) ;
    cp = strrchr(template_fname, '/') ;
    if (cp == NULL) // no path - start from beginning of file name
    {
      cp = template_fname ;
    }
    cp = strchr(cp, '.') ;
    if (cp == NULL)
      ErrorExit(ERROR_NOFILE,
                "%s: could no scan hemi from %s",
                Progname, template_fname) ;
    strncpy(hemi, cp-2, 2) ;
    hemi[2] = 0 ;
    fprintf(stderr, "reading spherical surface %s...\n", template_fname) ;
    mris_template = MRISread(template_fname) ;
    if (mris_template == NULL)
    {
      ErrorExit(ERROR_NOFILE, "") ;
    }
#if 0
    if (reverse_flag)
    {
      MRISreverse(mris_template, REVERSE_X, 1) ;
    }
#endif
    MRISsaveVertexPositions(mris_template, CANONICAL_VERTICES) ;
    MRIScomputeMetricProperties(mris_template) ;
    MRISstoreMetricProperties(mris_template) ;

    if (noverlays > 0)
    {
      mrisp_template = MRISPalloc(scale, IMAGES_PER_SURFACE*noverlays);
      for (sno = 0; sno < noverlays ; sno++)
      {
        sprintf(fname, "%s/../label/%s.%s", surf_dir, hemi, overlays[sno]) ;
        if (MRISreadValues(mris_template, fname)  != NO_ERROR)
          ErrorExit(ERROR_NOFILE,
                    "%s: could not read overlay from %s",
                    Progname, fname) ;
        MRIScopyValuesToCurvature(mris_template) ;
        MRISaverageCurvatures(mris_template, navgs) ;
        MRISnormalizeCurvature(mris_template, which_norm) ;
        fprintf(stderr,
                "computing parameterization for overlay %s...\n",
                fname);
        MRIStoParameterization(mris_template, mrisp_template, scale, sno*3) ;
        MRISPsetFrameVal(mrisp_template, sno*3+1, 1.0) ;
      }
    }
    else
    {
      mrisp_template = MRISPalloc(scale, PARAM_IMAGES);
      for (sno = 0; sno < SURFACES ; sno++)
      {
        if (curvature_names[sno])  /* read in precomputed curvature file */
        {
          sprintf(fname, "%s/%s.%s", surf_dir, hemi, curvature_names[sno]) ;
          if (MRISreadCurvatureFile(mris_template, fname) != NO_ERROR)
            ErrorExit(Gerror,
                      "%s: could not read curvature file '%s'\n",
                      Progname, fname) ;

          /* the two next lines were not in the original code */
          MRISaverageCurvatures(mris_template, navgs) ;
          MRISnormalizeCurvature(mris_template, which_norm) ;
        }
        else                         /* compute curvature of surface */
        {
          sprintf(fname, "%s/%s.%s", surf_dir, hemi, surface_names[sno]) ;
          if (MRISreadVertexPositions(mris_template, fname) != NO_ERROR)
            ErrorExit(ERROR_NOFILE,
                      "%s: could not read surface file %s",
                      Progname, fname) ;

          if (tnbrs > 1)
          {
            MRISresetNeighborhoodSize(mris_template, tnbrs) ;
          }
          MRIScomputeMetricProperties(mris_template) ;
          MRIScomputeSecondFundamentalForm(mris_template) ;
          MRISuseMeanCurvature(mris_template) ;
          MRISaverageCurvatures(mris_template, navgs) ;
          MRISrestoreVertexPositions(mris_template, CANONICAL_VERTICES) ;
          MRISnormalizeCurvature(mris_template, which_norm) ;
        }
        fprintf(stderr,
                "computing parameterization for surface %s...\n",
                fname);
        MRIStoParameterization(mris_template, mrisp_template, scale, sno*3) ;
        MRISPsetFrameVal(mrisp_template, sno*3+1, 1.0) ;
      }
    }
  }
  else
  {
    fprintf(stderr, "reading template parameterization from %s...\n",
            template_fname) ;
    mrisp_template = MRISPread(template_fname) ;
    if (!mrisp_template)
      ErrorExit(ERROR_NOFILE, "%s: could not open template file %s",
                Progname, template_fname) ;
    if (noverlays > 0)
    {
      if (mrisp_template->Ip->num_frame != IMAGES_PER_SURFACE*noverlays)
        ErrorExit(ERROR_BADPARM,
                  "template frames (%d) doesn't match input (%d x %d) = %d\n",
                  mrisp_template->Ip->num_frame, IMAGES_PER_SURFACE,noverlays,
                  IMAGES_PER_SURFACE*noverlays) ;
    }
  }
  if (use_defaults)
  {
    if (*IMAGEFseq_pix(mrisp_template->Ip, 0, 0, 2) <= 1.0)  /* 1st time */
    {
      parms.l_dist = 5.0 ;
      parms.l_corr = 1.0 ;
      parms.l_parea = 0.2 ;
    }
    else   /* subsequent alignments */
    {
      parms.l_dist = 5.0 ;
      parms.l_corr = 1.0 ;
      parms.l_parea = 0.2 ;
    }
  }

  if (nbrs > 1)
  {
    MRISresetNeighborhoodSize(mris, nbrs) ;
  }
  MRISprojectOntoSphere(mris, mris, DEFAULT_RADIUS) ;
  mris->status = MRIS_PARAMETERIZED_SPHERE ;
  MRIScomputeMetricProperties(mris) ;
  if (!FZERO(parms.l_dist))
  {
    MRISscaleDistances(mris, scale) ;
  }
#if 0
  MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
  MRISzeroNegativeAreas(mris) ;
  MRISstoreMetricProperties(mris) ;
#endif
  MRISstoreMeanCurvature(mris) ;  /* use curvature from file */
  MRISsetOriginalFileName(orig_name) ;
  if (inflated_name)
  {
    MRISsetInflatedFileName(inflated_name) ;
  }
  err = MRISreadOriginalProperties(mris, orig_name) ;
  if (err != 0)
  {
    printf("ERROR %d from MRISreadOriginalProperties().\n",err);
    exit(1);
  }

  if (MRISreadCanonicalCoordinates(mris, canon_name) != NO_ERROR)
    ErrorExit(ERROR_BADFILE, "%s: could not read canon surface %s",
              Progname, canon_name) ;

  if (reverse_flag)
  {
    MRISreverse(mris, REVERSE_X, 1) ;
    MRISsaveVertexPositions(mris, TMP_VERTICES) ;
    MRISrestoreVertexPositions(mris, CANONICAL_VERTICES) ;
    MRISreverse(mris, REVERSE_X, 0) ;
    MRISsaveVertexPositions(mris, CANONICAL_VERTICES) ;
    MRISrestoreVertexPositions(mris, TMP_VERTICES) ;
    MRIScomputeMetricProperties(mris) ;
  }
#if 0
  MRISsaveVertexPositions
  (mris, CANONICAL_VERTICES) ;  // uniform spherical positions
#endif
  if (starting_reg_fname)
    if (MRISreadVertexPositions(mris, starting_reg_fname) != NO_ERROR)
    {
      exit(Gerror) ;
    }

  if (multiframes)
  {
    if (use_initial_registration)
      MRISvectorRegister(mris, mrisp_template, &parms, max_passes,
                         min_degrees, max_degrees, nangles) ;
    parms.l_corr=parms.l_pcorr=0.0f;
#if 0
    parms.l_dist = 0.0 ;
    parms.l_corr = 0.0 ;
    parms.l_parea = 0.0 ;
    parms.l_area = 0.0 ;
    parms.l_parea = 0.0f ;
    parms.l_dist = 0.0 ;
    parms.l_corr = 0.0f ;
    parms.l_nlarea = 0.0f ;
    parms.l_pcorr = 0.0f ;
#endif
    MRISvectorRegister(mris,
                       mrisp_template,
                       &parms,
                       max_passes,
                       min_degrees,
                       max_degrees,
                       nangles) ;
  }
  else
  {
    double l_dist = parms.l_dist ;
    if (multi_scale > 0)
    {
      int i ;

      parms.l_dist = l_dist * pow(5.0, (multi_scale-1.0)) ;
      parms.flags |= IPFLAG_NOSCALE_TOL ;
      parms.flags &= ~IP_USE_CURVATURE ;
      for (i = 0 ; i < multi_scale ; i++)
      {
        printf("*************** round %d, l_dist = %2.3f **************\n", i,
               parms.l_dist) ;
        MRISregister(mris, mrisp_template,
                     &parms, max_passes,
                     min_degrees, max_degrees, nangles) ;
        parms.flags |= IP_NO_RIGID_ALIGN ;
        parms.flags &= ~IP_USE_INFLATED ;
        parms.l_dist /= 5 ;
      }

      if (parms.nbhd_size < 0)
      {
        parms.nbhd_size *= -1 ;
        printf("**** starting 2nd epoch, with long-range distances *****\n");
        parms.l_dist = l_dist * pow(5.0, (multi_scale-2.0)) ;
        for (i = 1 ; i < multi_scale ; i++)
        {
          printf("*********** round %d, l_dist = %2.3f *************\n", i,
                 parms.l_dist) ;
          MRISregister(mris, mrisp_template,
                       &parms, max_passes,
                       min_degrees, max_degrees, nangles) ;
          parms.l_dist /= 5 ;
        }
      }
      printf("****** final curvature registration ***************\n") ;
      if (parms.nbhd_size > 0)
      {
        parms.nbhd_size *= -1 ;  // disable long-range stuff
      }
      parms.l_dist *= 5 ;
      parms.flags |= (IP_USE_CURVATURE | IP_NO_SULC);
      MRISregister(mris, mrisp_template,
                   &parms, max_passes,
                   min_degrees, max_degrees, nangles) ;
    }
    else
      MRISregister(mris, mrisp_template,
                   &parms, max_passes,
                   min_degrees, max_degrees, nangles) ;

  }
  if (remove_negative)
  {
    parms.niterations = 1000 ;
    MRISremoveOverlapWithSmoothing(mris,&parms) ;
  }
  fprintf(stderr, "writing registered surface to %s...\n", out_fname) ;
  MRISwrite(mris, out_fname) ;
  if (jacobian_fname)
  {
    MRIScomputeMetricProperties(mris) ;
    compute_area_ratios(mris) ;  /* will put results in v->curv */
#if 0
    MRISwriteArea(mris, jacobian_fname) ;
#else
    MRISwriteCurvature(mris, jacobian_fname) ;
#endif
  }

  msec = TimerStop(&start) ;
  if (Gdiag & DIAG_SHOW)
    printf("registration took %2.2f hours\n",
           (float)msec/(1000.0f*60.0f*60.0f));
  MRISPfree(&mrisp_template) ;
  MRISfree(&mris) ;
  exit(0) ;
  return(0) ;  /* for ansi */
}
Ejemplo n.º 12
0
int main(int argc, char *argv[]) {
  MRIS *mris;
  char  *in_orig_fname=NULL, *in_seg_fname=NULL,*out_fname=NULL;
  MRI *mri_orig=NULL,*mri_seg=NULL,*mri_out=NULL;
  int nargs,n;
  char fname[512];

  Progname=argv[0];
  fprintf(stderr,"\n");
  MRI_TOPOLOGY_PARMSdefault(&parms);

  for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
    nargs = get_option(argc, argv) ;
    argc -= nargs ;
    argv += nargs ;
  }
  if (parms.tesselation_mode==-1)
    parms.tesselation_mode=parms.connectivity;
  if (argc<4) {
    fprintf(stderr, "\nUsage: %s options input_orig_file input_segmented_file output_folder\n", Progname);
    exit(1);
  };

  in_orig_fname=argv[argc-3];
  in_seg_fname = argv[argc-2];
  out_fname = argv[argc-1];

  fprintf(stderr,"************************************************************"
          "\nThe input orig volume is %s"
          "\nThe input segmented volume is %s"
          "\nThe output volume is %s"
          "\nIf this is incorrect, please exit quickly the program (Ctl-C)\n",in_orig_fname,in_seg_fname,out_fname);
  for (n=0;n<parms.nlabels;n++)
    fprintf(stderr,"label = %d: %s \n",parms.labels[n],cma_label_to_name(parms.labels[n]));
  if (parms.using_gca_maps)
    fprintf(stderr,"mixing parameters: alpha=%1.3f , beta=%1.3f \n",parms.alpha,parms.beta);
  else {
    parms.beta=1.0f;
    parms.alpha=1.0f;
  }
  fprintf(stderr,"connectivity = %d\n",parms.connectivity);

  mri_orig=MRIread(in_orig_fname);
  if (!mri_orig && parms.using_gca_maps)
    Error("orig volume: orig volume could not be read\n");
  mri_seg=MRIread(in_seg_fname);
  if (!mri_seg)
    Error("segmented volume: segmented volume could not be read\n");


  //check euler characteristic of initial surface
  if (parms.initial_surface_file) {
    int i,j,k,val,euler,pnvertices,  pnfaces, pnedges;
    MRI *mri_tmp;
    mri_tmp=MRIclone(mri_seg,NULL);
    for (k=0;k<mri_seg->depth;k++)
      for (j=0;j<mri_seg->height;j++)
        for (i=0;i<mri_seg->width;i++)
          for (n=0;n<parms.nlabels;n++) {
            val=MRIgetVoxVal(mri_seg,i,j,k, 0);
            if (val==parms.labels[n]) {
              MRIsetVoxVal(mri_tmp,i,j,k,0,1);
              break;
            }
          }
    mris=MRIScreateSurfaceFromVolume(mri_tmp,1,parms.connectivity);
    euler=MRIScomputeEulerNumber(mris,&pnvertices,&pnfaces,&pnedges);
    fprintf(stderr,"\ninitial euler characteristic = %d, %d vertices, %d faces, %d edges"
            ,euler,pnvertices,pnfaces,pnedges);
    MRISwrite(mris,parms.initial_surface_file);
    MRISfree(&mris);
    MRIfree(&mri_tmp);
  }

  mri_out=MRIcorrectTopology(mri_orig,mri_seg,NULL,&parms);

  if (parms.nlabels == 1) {
    MRI *mri_tmp ;

    // turn off all voxels that are going to be on in the output
    MRImask(mri_seg, mri_out, mri_seg, 1, 0) ;
    /* whatever ones are left are now incorrect and should be labeled
      something else
    */
    resegment_erased_voxels(mri_orig, mri_seg, mri_seg, parms.labels[0]) ;
    MRIreplaceValues(mri_out, mri_out, 1, parms.labels[0]) ;
    mri_tmp = MRIcopy(mri_seg, NULL) ;
    MRIcopyLabel(mri_out, mri_tmp, parms.labels[0]) ;
    MRIfree(&mri_out) ;
    mri_out = mri_tmp ;
    //  check_volume(mri_save, mri_out, parms.labels[0]) ;
  }
  MRIwrite(mri_out,out_fname);

  ////TEMPORARY VALIDATION STUFF //////////////////////////////////////////////////////////////////
  //////////////////////////////////////////////////////////////////////////////////////////////////
  /////////////////////////////////////////////////////////////////////////////////////////////////
#if 0
  //validation of the algo
  {
    FILE *f;
    MRIS *mristb[20],*mrisr;
    int n,i,j,k,depth,height,width,count,count2;
    int tab[20]={4,43,51,12,52,13,54,18,53,17,49,10,50,11};//,6,7,10,11,12,13,17,18,43,44,45,46,49,50,51,52,53,54};
    MRI *mri_val=MRIclone(parms.mri_seg,NULL);
    parms.nlabels=1;

    depth=parms.mri_seg->depth;
    height=parms.mri_seg->height;
    width=parms.mri_seg->width;
    for (n=0;n<14;n++) {
      MRIfree(&parms.mri_output);
      MRIfree(&parms.mri_bin);
      MRIfree(&parms.mri_dist);
      MRIfree(&parms.mri_fcost);
      MRIfree(&parms.mri_bcost);
      MRIfree(&parms.mri_fprior);
      MRIfree(&parms.mri_bprior);
      MRIfree(&parms.mri_labeled);
      segmentationFree(&parms.F_Bseg);
      segmentationFree(&parms.F_Rseg);
      segmentationFree(&parms.B_Bseg);
      segmentationFree(&parms.B_Rseg);
      CCSfree(&parms.F_Bccs);
      CCSfree(&parms.F_Rccs);
      CCSfree(&parms.B_Bccs);
      CCSfree(&parms.B_Rccs);

      parms.labels[0]=tab[n];
      MRIcorrectTopology(parms.mri_orig,parms.mri_seg,&parms.mri_output,mris
                         ,parms.labels,parms.nblabels,parms.f_c,parms);



      MRISwrite(*mris,"./tmp");
      mristb[n]=MRISread("./tmp");
#if 0
      count=0;
      count2=0;
      for (k=0;k<depth;k++)
        for (j=0;j<height;j++)
          for (i=0;i<width;i++) {
            if (MRIvox(parms.mri_seg,i,j,k)==parms.labels[0])
              count2++;
            if (MRIvox(parms.mri_output,i,j,k)==1) {
              MRIvox(mri_val,i,j,k)++;
              if (MRIvox(parms.mri_seg,i,j,k)!=parms.labels[0])
                count++;
            } else if (MRIvox(parms.mri_seg,i,j,k)==parms.labels[0])
              count++;
          }
      fprintf(stderr,"\n yeh %d %d %f \n",count,count2,100.*count/count2);
      sprintf(fname,"./label%d",tab[n]);
      f=fopen(fname,"a+");
      fprintf(f,"\n %d %d %f ",count,count2,(float)100.*count/count2);
      fclose(f);
#endif

#if 0
      sprintf(fname,"./surf%d",n);
      MRISwrite(mristb[n],fname);
      MRISsmoothSurface2(mristb[n],5,0.5,0);
      MRISsmoothSurface2(mristb[n],5,0.25,2);
      MRISsmoothSurface2(mristb[n],10,0.05,5);
      sprintf(fname,"./surfsmooth%d",n);
      mristb[n]->type=MRIS_TRIANGULAR_SURFACE;//MRIS_BINARY_QUADRANGLE_FILE;
      MRISwrite(mristb[n],fname);

      MRISsetNeighborhoodSize(mristb[n],3) ;
      MRIScomputeMetricProperties(mristb[n]) ;
      MRIScomputeSecondFundamentalForm(mristb[n]) ;
      MRISuseMeanCurvature(mristb[n]);
      MRISaverageCurvatures(mristb[n],2) ;
      MRISnormalizeCurvature(mristb[n], NORM_MEAN) ;
      sprintf(fname,"./curv%d",n);
      MRISwriteCurvature(mristb[n],fname);
#endif
    }

#if 0
    mrisr=MRISconcatenateQuadSurfaces(n,mristb);
    mrisr->type=MRIS_TRIANGULAR_SURFACE;
    MRISwrite(mrisr,"./lh.ZURFACE");


    //    for(k=0;k<mrisr->nvertices;k++)
    // mrisr->vertices[k].curv=0.3;

    //MRISnormalizeCurvature(mrisr, NORM_MEAN) ;
    MRISwriteCurvature(mrisr,"./ZURFACE_CURVATURE");
    for (k=0;k<mrisr->nvertices;k++)
      mrisr->vertices[k].curv=mrisr->vertices[k].val;
    MRISwriteCurvature(mrisr,"./ZURFACE_VAL");
#endif

    n=0;
    count=0;
    for (k=0;k<depth;k++)
      for (j=0;j<height;j++)
        for (i=0;i<width;i++) {
          if (MRIgetVoxVal(mri_val,i,j,k,0)>=1) {
            n++;
            if (MRIsetVoxVal(mri_val,i,j,k,0)>1)
              count++;
          }
        }
    //    sprintf(fname,"./labeltotal");
    /// f=fopen(fname,"a+");
    //fprintf(f,"\n %s %d %d %f ",in_seg_fname,count,n,(float)100.*count/n);
    //fclose(f);




#if 0
    MRIwrite(mri_val,"/tmp/tmp");
#endif

    fprintf(stderr,"\n WE HAVE %d %d %f   \n",count,n,100.*count/n);

  }
#endif
  //////////////////////////////////////////////////////////////////////////////////
  //////////////////////////////////////////////////////////////////////////////////

  if (parms.final_surface_file) {
    int euler,pnvertices,  pnfaces, pnedges;
    mris=MRIScreateSurfaceFromVolume(mri_out,1,parms.connectivity);
    euler=MRIScomputeEulerNumber(mris,&pnvertices,&pnfaces,&pnedges);
    fprintf(stderr,"\nfinal euler characteristic = %d, %d vertices, %d faces, %d edges"
            ,euler,pnvertices,pnfaces,pnedges);
    sprintf(fname,"%s",parms.final_surface_file);
    MRISwrite(mris,fname);

#if 0
    MRISsmoothSurface(mris,7,0.2);
    strcat(fname,"_smooth");
    MRISwrite(mris,fname);
    if (parms.fit) {
      sprintf(fname,parms.surfname);
      strcat(fname,"_fit");
      MRISmatchSurfaceToLabel(parms.mris,parms.mri_output,1,NULL,NULL,parms.f_c);
      MRISwrite(parms.mris,fname);
    }
#endif
    MRISfree(&mris);
  }

  if (mri_out)
    MRIfree(&mri_out);
  if (mri_orig)
    MRIfree(&mri_orig);
  if (mri_seg)
    MRIfree(&mri_seg);
  fprintf(stderr,"\n");
  return NO_ERROR;
}
Ejemplo n.º 13
0
static int
MRISrepositionToInnerSkull(MRI_SURFACE *mris, MRI *mri_smooth, INTEGRATION_PARMS *parms) {
  MRI   *mri_dist, *mri_bin, *mri_kernel, *mri_bin_smooth, *mri_dist_smooth ;
  float l_spring, sigma ;
  int   i, ic_order, avgs ;

  parms->niterations = 1000 ;
  if (parms->momentum < 0.0)
    parms->momentum = 0.0 /*0.75*/ ;

  mri_bin = MRIbinarize(mri_smooth, NULL, 15, 0, TARGET_VAL) ;
  mri_dist = MRIdistanceTransform(mri_bin, NULL, TARGET_VAL, 10*mri_bin->width, DTRANS_MODE_SIGNED, NULL) ;
  MRIwrite(mri_bin, "bin.mgz") ;
  MRIwrite(mri_dist, "dist.mgz") ;
  MRISscaleBrain(mris, mris, 0.5) ;  // start inside

  mri_kernel = MRIgaussian1d(2, 0) ;
  mri_bin_smooth = MRIconvolveGaussian(mri_bin, NULL, mri_kernel) ;
  MRIwrite(mri_bin_smooth, "bin_smooth.mgz") ;
  MRISfindOptimalRigidPosition(mris, mri_bin_smooth, parms) ;
  MRIfree(&mri_kernel) ;
  MRIfree(&mri_bin_smooth) ;
  avgs = parms->n_averages = 32 ;
  l_spring = parms->l_spring_norm ;
  for (ic_order = 3 ; ic_order <= 3 ; ic_order++) {
    if (ic_order != ic_init) {
      MRI_SURFACE *mris_new ;
      char fname[STRLEN], *mdir ;

      mdir = getenv("FREESURFER_HOME") ;
      if (!mdir)
        ErrorExit(ERROR_BADPARM, "FREESURFER_HOME not defined in environment") ;

      sprintf(fname, "%s/lib/bem/ic%d.tri", mdir, ic_order) ;
      mris_new = MRISread(fname) ;
      MRISupsampleIco(mris, mris_new) ;
      MRISfree(&mris) ;
      mris = mris_new ;
    }

    printf("********************** using ICO order %d *********************\n", ic_order) ;
    parms->n_averages = avgs ;
    parms->l_spring_norm = l_spring ;
    for (sigma = 16.0, i = 0 ; i < 7 ; i++, sigma /= 2) {
      printf("******************** pass %d, sigma = %2.2f, avgs = %d ******************\n",
             i+1, sigma, parms->n_averages) ;
      parms->sigma = sigma ;
      MRISsetVals(mris,parms->sigma) ;
      MRIScopyValToVal2(mris) ;
      MRISsetVals(mris, 0) ;  // 0 mm from fat
      parms->mri_brain = mri_dist ;


      mri_kernel = MRIgaussian1d(sigma, 0) ;
      mri_dist_smooth = MRIconvolveGaussian(mri_dist, NULL, mri_kernel) ;
      MRIfree(&mri_kernel) ;
      if (i == 0) {
        MRIwrite(mri_dist_smooth, "dist_smooth.mgz") ;

        MRISwrite(mris, "lh.0000") ;
      }
      MRISsetVals(mris, 0) ;
      MRISpositionSurface(mris, mri_dist, mri_dist_smooth, parms) ;
      parms->l_spring_norm /= 2;
      parms->n_averages /= 2 ;
    }
  }

  MRIfree(&mri_bin) ;
  MRIfree(&mri_dist) ;
  return(NO_ERROR) ;
}
Ejemplo n.º 14
0
int
MRISpositionOptimalSphere(MRI_SURFACE *mris, MRI *mri_inner, float sample_dist) {
  double  r, rmin, rmax, min_sse, min_r, min_x0, min_y0, min_z0, x0, y0, z0, sse,
  xmin, xmax, ymin, ymax, zmin, zmax, delta_r, delta_x, delta_y, delta_z ;
  int     scale ;

  MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
  MRIScomputeMetricProperties(mris) ;
  rmin = mris->radius*.5 ;
  rmax = mris->radius*1.5 ;
  min_x0 = mris->xctr ;
  min_y0 = mris->yctr ;
  min_z0 = mris->zctr ;
  min_r = mris->radius ;

  MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
  MRISprojectOntoTranslatedSphere(mris, mris, min_r, min_x0, min_y0, min_z0) ;
  min_sse = compute_surface_sse(mris, mri_inner, sample_dist) ;
  delta_r = DELTA_R ;
  for (r = rmin ; r <= rmax ; r += delta_r) {
    MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
    MRISprojectOntoTranslatedSphere(mris, mris, r, min_x0, min_y0, min_z0) ;
    sse = compute_surface_sse(mris, mri_inner, sample_dist) ;
    if (sse < min_sse) {
      min_sse = sse ;
      min_r = r ;
      printf("new min sse %2.0f, found at r=%2.1f mm, c = (%2.1f, %2.1f, %2.1f)\n",
             min_sse, min_r, min_x0, min_y0, min_z0) ;
    }
  }
  MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
  MRISprojectOntoTranslatedSphere(mris, mris, min_r, min_x0, min_y0, min_z0) ;
  MRISwrite(mris, "lh.minr") ;
  for (scale = 8 ; scale >= 1 ; scale /=2) {
    printf("scale = %d\n", scale) ;
    xmin = min_x0-scale ;
    xmax = min_x0+scale ;
    ymin = min_y0-scale ;
    ymax = min_y0+scale ;
    zmin = min_z0-scale ;
    zmax = min_z0+scale ;
    rmin = min_r*(1.0-scale/128.0) ;
    rmax = min_r*(1.0+scale/128.0) ;
    delta_x = mri_inner->xsize*scale/16 ;
    delta_y = mri_inner->ysize*scale/16 ;
    delta_z = mri_inner->zsize*scale/16 ;
    delta_r = DELTA_R*scale ;
    if (delta_x > (xmax-xmin)/3)
      delta_x = (xmax-xmin)/3 ;
    if (delta_y > (ymax-ymin)/3)
      delta_y = (ymax-ymin)/3 ;
    if (delta_z > (zmax-zmin)/3)
      delta_z = (zmax-zmin)/3 ;
    if (delta_r > (rmax-rmin)/3)
      delta_r = (rmax-rmin)/3 ;

    for (x0 = xmin ; x0 <= xmax ; x0 += delta_x) {
      for (y0 = ymin ; y0 <= ymax ; y0 += delta_y) {
        for (z0 = zmin ; z0 <= zmax ; z0 += delta_z) {
          for (r = rmin ; r <= rmax ; r += delta_r) {
            MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
            MRISprojectOntoTranslatedSphere(mris, mris, r, x0, y0, z0) ;
            sse = compute_surface_sse(mris, mri_inner, sample_dist) ;
            if (sse < min_sse) {
              min_sse = sse ;
              min_r = r ;
              min_x0 = x0 ;
              min_y0 = y0 ;
              min_z0 = z0 ;
              printf("new min sse %2.0f, found at r=%2.1f mm, c = (%2.1f, %2.1f, %2.1f)\n",
                     min_sse, min_r, min_x0, min_y0, min_z0) ;
            }
          }
        }
      }
    }
    {
      char fname[STRLEN] ;
      MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
      MRISprojectOntoTranslatedSphere(mris, mris, min_r, min_x0, min_y0, min_z0) ;
      sprintf(fname, "lh.min_scale%d", scale) ;
      MRISwrite(mris, fname) ;
    }
  }

  MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
  MRISprojectOntoTranslatedSphere(mris, mris, min_r, min_x0, min_y0, min_z0) ;
  return(NO_ERROR) ;
}
Ejemplo n.º 15
0
int
main(int argc, char *argv[]) {
  char          **av, fname[STRLEN], *T1_fname, *PD_fname, *output_dir, *mdir ;
  int           ac, nargs, msec, s ;
  MRI_SURFACE   *mris ;
  MRI           *mri_flash1, *mri_flash2, *mri_masked, *mri_masked_smooth, *mri_kernel,
  *mri_mean, *mri_dif, *mri_binary, *mri_distance ;
  MRI *mri_smooth, *mri_grad, *mri_inner ;
  struct timeb  then ;
  double        l_spring ;
  MRI_SEGMENTATION *mriseg ;


  /* rkt: check for and handle version tag */
  nargs = handle_version_option (argc, argv, "$Id: mris_AA_shrinkwrap.c,v 1.5 2011/03/02 00:04:34 nicks Exp $", "$Name: stable5 $");
  if (nargs && argc - nargs == 1)
    exit (0);
  argc -= nargs;

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

  memset(&parms, 0, sizeof(parms)) ;

  parms.projection = NO_PROJECTION ;
  parms.tol = 0.05 ;
  parms.check_tol = 1 ;
  parms.ignore_energy = 1 ;
  parms.dt = 0.5f ;
  parms.base_dt = BASE_DT_SCALE*parms.dt ;

  parms.l_spring_norm = 1 ;
  parms.l_shrinkwrap = 0 ;
  parms.l_intensity = 1 ;

  parms.niterations = 0 ;
  parms.write_iterations = 0 /*WRITE_ITERATIONS */;
  parms.integration_type = INTEGRATE_MOMENTUM ;
  parms.momentum = 0.0 /*0.8*/ ;
  parms.l_intensity = 1 ;
  parms.dt_increase = 1.0 /* DT_INCREASE */;
  parms.dt_decrease = 0.50 /* DT_DECREASE*/ ;
  parms.error_ratio = 50.0 /*ERROR_RATIO */;
  /*  parms.integration_type = INTEGRATE_LINE_MINIMIZE ;*/
  parms.l_surf_repulse = 0.0 ;
  parms.l_repulse = 0 /*1*/ ;

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

  mdir = getenv("FREESURFER_HOME") ;
  if (!mdir)
    ErrorExit(ERROR_BADPARM, "FREESURFER_HOME not defined in environment") ;

  if (argc < 4)
    usage_exit() ;

  /* set default parameters for white and gray matter surfaces */
  parms.niterations = 1000 ;
  if (parms.momentum < 0.0)
    parms.momentum = 0.0 /*0.75*/ ;

  TimerStart(&then) ;
  T1_fname = argv[1] ;
  PD_fname = argv[2] ;
  output_dir = argv[3] ;
  fprintf(stderr, "reading volume %s...\n", T1_fname) ;
  mri_flash1 = MRIread(T1_fname) ;
  if (!mri_flash1)
    ErrorExit(ERROR_NOFILE, "%s: could not read input volume %s", Progname, T1_fname) ;

  mri_flash2 = MRIread(PD_fname) ;
  if (!mri_flash2)
    ErrorExit(ERROR_NOFILE, "%s: could not read input volume %s", Progname, T1_fname) ;

  //  setMRIforSurface(mri_flash1);
  sprintf(fname, "%s/lib/bem/ic%d.tri", mdir, ic_init) ;
  mris = MRISread(fname) ;
  if (!mris)
    ErrorExit(ERROR_NOFILE, "%s: could not read icosahedron %s", Progname, fname) ;

  mri_mean = MRImean(mri_flash1, NULL, 5) ;
  MRIwrite(mri_mean, "mean.mgz") ;

  mri_dif = MRIabsdiff(mri_flash1, mri_flash2, NULL) ;
  MRIwrite(mri_dif, "dif.mgz") ;

  mriseg = MRIsegment(mri_mean, 30, 100000) ;
  s = MRIsegmentMax(mriseg) ;
  mri_masked = MRIsegmentToImage(mri_flash1, NULL, mriseg, s) ;
  MRIwrite(mri_masked, "mask.mgz") ;
  MRIsegmentFree(&mriseg) ;

  // MRIthresholdMask(mri_dif, mri_masked, mri_dif, 1, 0) ;
  // MRIwrite(mri_dif, "dif_masked.mgz") ;


  mri_kernel = MRIgaussian1d(2, 0) ;
  mri_smooth = MRIconvolveGaussian(mri_dif, NULL, mri_kernel) ;
  MRIwrite(mri_smooth, "smooth.mgz") ;
  MRIScopyVolGeomFromMRI(mris, mri_smooth) ;
  mris->useRealRAS = 1 ;

  initialize_surface_position(mris, mri_dif, 1, &parms) ;
  MRISwrite(mris, "init") ;
  MRISrepositionToInnerSkull(mris, mri_smooth, &parms) ;

  exit(0) ;
  mri_grad = MRIsobel(mri_smooth, NULL, NULL) ;
  MRIwrite(mri_grad, "grad.mgz") ;
  mri_inner = MRIfindInnerBoundary(mri_dif, mri_grad, NULL, 5.0) ;
  MRIwrite(mri_inner, "inner.mgz") ;
  MRIbinarize(mri_inner, mri_inner, 10, 0, 128) ;

  MRISpositionOptimalSphere(mris, mri_inner, 6) ;
  MRISwrite(mris, "optimal") ;
  exit(0) ;
  parms.sigma = 4 / mri_flash1->xsize ;
  // mri_dist = create_distance_map(mri_masked, NULL, BORDER_VAL, OUTSIDE_BORDER_STEP) ;
  MRISsetVals(mris,parms.sigma) ;
  MRIScopyValToVal2(mris) ;
  MRISsetVals(mris, 0) ;
  sprintf(parms.base_name, "%s_inner_skull%s%s", "test", output_suffix, suffix) ;
  parms.mri_brain = mri_masked ;
  l_spring = parms.l_spring_norm ;
  mri_kernel = MRIgaussian1d(parms.sigma, 0) ;


  mri_binary = MRIbinarize(mri_dif, mri_binary, 40, 0, 128) ;
  MRIwrite(mri_binary, "bin.mgz") ;
  mri_distance = MRIdistanceTransform(mri_binary, NULL, 128, 100, DTRANS_MODE_SIGNED, NULL) ;
  MRIwrite(mri_distance, "dist.mgz") ;
  mri_masked_smooth = MRIconvolveGaussian(mri_distance, NULL, mri_kernel) ;
  MRIfree(&mri_kernel) ;
  MRIwrite(mri_masked_smooth, "dif_smooth.mgz") ;

  MRISwrite(mris, "inner_skull.tri") ;

  msec = TimerStop(&then) ;
  fprintf(stderr,"positioning took %2.1f minutes\n", (float)msec/(60*1000.0f));
  exit(0) ;
  return(0) ;  /* for ansi */
}
Ejemplo n.º 16
0
int
main(int argc, char *argv[])
{
  char               **av, *in_fname, *out_fname, fname[STRLEN], path[STRLEN] ;
  int                ac, nargs, start_t, pass ;
  MRI_SURFACE        *mris ;

  char cmdline[CMD_LINE_LEN] ;

  make_cmd_version_string
  (argc, argv,
   "$Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $",
   "$Name: stable5 $", cmdline);

  /* rkt: check for and handle version tag */
  nargs = handle_version_option
          (argc, argv,
           "$Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 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)
  {
    print_help() ;
  }

  in_fname = argv[1] ;
  out_fname = argv[2] ;
  FileNamePath(out_fname, path) ;

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

  MRISaddCommandLine(mris, cmdline) ;
  MRISremoveTriangleLinks(mris) ;
  fprintf(stderr, "smoothing surface tessellation for %d iterations...\n",
          niterations);

  MRIScomputeMetricProperties(mris) ;
  MRISstoreMetricProperties(mris) ;
  MRISsetNeighborhoodSize(mris, nbrs) ;
#define DT 0.5
  if (gaussian_norm > 0)
  {
    int i, done, start_avgs = gaussian_avgs, j ;

    done = 0;
    start_t = 0 ;
    pass = 0 ;
    do
    {
      for (i = start_t ; i < niterations+start_t ; i++)
      {
        MRIScomputeMetricProperties(mris) ;
        MRISsaveVertexPositions(mris, TMP_VERTICES) ;
        for (j = 0 ; j < 5 ; j++)
        {
          MRISaverageVertexPositions(mris, 2) ; // turn flat spikes into tubular ones
          MRIScomputeMetricProperties(mris) ;
          MRIScomputeSecondFundamentalForm(mris) ;
          MRIShistoThresholdGaussianCurvatureToMarked(mris, (float)(mris->nvertices-20)/mris->nvertices) ;
        }
        MRISrestoreVertexPositions(mris, TMP_VERTICES) ;
        MRIScomputeMetricProperties(mris) ;
        MRISsmoothSurfaceNormals(mris, gaussian_avgs) ;
        MRISclearMarks(mris) ;
        MRISthresholdGaussianCurvatureToMarked(mris, 10, 50);
        MRIScomputeSecondFundamentalForm(mris) ;
        MRIShistoThresholdGaussianCurvatureToMarked(mris, (float)(mris->nvertices-20)/mris->nvertices) ;
        MRISthresholdGaussianCurvatureToMarked(mris, 10, 50);
        if ((write_iterations > 0) && ((i % write_iterations) == 0))
        {
          char fname[STRLEN] ;

          sprintf(fname, "%s%04d", out_fname, i) ;
          printf("writing snapshot to %s...\n", fname) ;
          MRISwrite(mris, fname) ;
          if (Gdiag & DIAG_WRITE)
          {
            MRISuseGaussianCurvature(mris) ;
            sprintf(fname, "%s_K%04d", out_fname, i) ;
            printf("writing curvature to %s...\n", fname) ;
            MRISwriteCurvature(mris, fname) ;
            sprintf(fname, "%s_marked%04d", out_fname, i) ;
            printf("writing marks to %s...\n", fname) ;
            MRISwriteMarked(mris, fname) ;
          }
        }
        for (j = 0 ; j <= 5*nint(1/DT) ; j++)
        {
          MRISmarkedSpringTerm(mris, l_spring) ;
          MRISaverageGradients(mris, gaussian_avgs) ;
          MRISmomentumTimeStep(mris, momentum, DT, 1, gaussian_avgs) ;
          MRISclearGradient(mris) ;
          MRIScomputeMetricProperties(mris) ;
          MRISsmoothSurfaceNormals(mris, gaussian_avgs) ;
          {
            int vno ;
            VERTEX *v ;

            for (vno = 0 ; vno < mris->nvertices ; vno++)
            {
              v = &mris->vertices[vno] ;
              if (v->marked > 0)
              {
                v->K = 1.0/(v->marked) ;
              }
              else
              {
                v->K = 0 ;
              }
            }
          }
        }
      }
      MRISclearGradient(mris) ;
      if (gaussian_avgs == 2)
      {
        if (pass++ > 4)
        {
          done = 1 ;
        }
        else
        {
          int num = count_big_curvatures(mris, 2) ;
          printf("------------------------------------------------------\n") ;
          printf("------------------------------------------------------\n") ;
          printf("------------------ pass %d (num=%d) ------------------\n",
                 pass, num) ;
          printf("------------------------------------------------------\n") ;
          printf("------------------------------------------------------\n") ;
          gaussian_avgs = start_avgs ;
        }
      }
      else
      {
        gaussian_avgs /= 2 ;
        if (done ==0)
        {
          printf("----------------- setting avgs to %d -----------------\n", gaussian_avgs) ;
        }
      }
      start_t = i ;
    }
    while (!done) ;

#if 0
    // more smoothing with principal curvatures
    gaussian_avgs = start_avgs ;
    printf("--------------------------------------------------------------------------\n") ;
    printf("--------------------------------------------------------------------------\n") ;
    printf("---------------------- starting threshold smoothing ----------------------\n") ;
    printf("--------------------------------------------------------------------------\n") ;
    printf("--------------------------------------------------------------------------\n") ;
    do
    {
      for (i = start_t ; i < niterations+start_t ; i++)
      {
        MRIScomputeMetricProperties(mris) ;
        MRIScomputeSecondFundamentalForm(mris) ;
        MRISsmoothSurfaceNormals(mris, 16) ;
#define KTHRESH 1.5  // everything with kmin less than this will not move
        MRISthresholdPrincipalCurvatures(mris, KTHRESH) ;
        MRISspringTermWithGaussianCurvature(mris, gaussian_norm, l_spring) ;
        MRISaverageGradients(mris, gaussian_avgs) ;
        MRISmomentumTimeStep(mris, 0, 0.1, 1, gaussian_avgs) ;
        MRISclearGradient(mris) ;
        if ((write_iterations > 0) && (((i+1) % write_iterations) == 0))
        {
          char fname[STRLEN] ;

          sprintf(fname, "%s%04d", out_fname, i+1) ;
          printf("writing snapshot to %s...\n", fname) ;
          MRISwrite(mris, fname) ;
          if (Gdiag & DIAG_WRITE/* && DIAG_VERBOSE_ON*/)
          {
            MRISuseGaussianCurvature(mris) ;
            sprintf(fname, "%s_K%04d", out_fname, i+1) ;
            printf("writing curvature to %s...\n", fname) ;
            MRISwriteCurvature(mris, fname) ;
          }
        }
      }
      MRISclearGradient(mris) ;
      done = (gaussian_avgs == 2) ;
      gaussian_avgs /= 2 ;
      if (done ==0)
      {
        printf("---------------------- setting avgs to %d ----------------------\n", gaussian_avgs) ;
      }
      start_t = i ;
    }
    while (!done) ;
#endif
  }
  else
  {
    MRISaverageVertexPositions(mris, niterations) ;
  }

  fprintf(stderr, "smoothing complete - recomputing first and second "
          "fundamental forms...\n") ;
  MRIScomputeMetricProperties(mris) ;

  if (rescale)
  {
    MRISscaleBrainArea(mris) ;
  }
  MRIScomputeSecondFundamentalForm(mris) ;
  MRISuseMeanCurvature(mris) ;
  MRISaverageCurvatures(mris, navgs) ;
  if (normalize_flag)
  {
    MRISnormalizeCurvature(mris, which_norm) ;
  }
  sprintf(fname, "%s.%s", mris->hemisphere == LEFT_HEMISPHERE?"lh":"rh",
          curvature_fname);
  if (no_write == 0)
  {
    fprintf(stderr, "writing smoothed curvature to %s/%s\n", path,fname) ;
    MRISwriteCurvature(mris, fname) ;
    sprintf(fname, "%s.%s", mris->hemisphere == LEFT_HEMISPHERE?"lh":"rh",
            area_fname);
    fprintf(stderr, "writing smoothed area to %s/%s\n", path, fname) ;
    MRISwriteArea(mris, fname) ;
  }

  if (Gdiag & DIAG_SHOW)
  {
    fprintf(stderr, "writing smoothed surface to %s\n", out_fname) ;
  }
  MRISwrite(mris, out_fname) ;
  exit(0) ;
  return(0) ;  /* for ansi */
}
Ejemplo n.º 17
0
int main(int argc, char *argv[]) {
  tesselation_parms *parms;
  MRIS **mris_table, *mris,*mris_corrected;
  MRI *mri;

  char cmdline[CMD_LINE_LEN] ;

  make_cmd_version_string 
    (argc, argv, 
     "$Id: mri_mc.c,v 1.22 2011/03/02 00:04:23 nicks Exp $", "$Name: stable5 $", 
     cmdline);
  Progname=argv[0];

  if (argc > 1 && (stricmp(argv[1], "-d") == 0)) {
    downsample = atoi(argv[2]) ;
    argc -= 2;
    argv += 2 ;
    printf("downsampling input volume %d times\n", downsample) ;
  }

  if (argc < 4) {
    fprintf(stderr,"\n\nUSAGE: mri_mc input_volume "
            "label_value output_surface [connectivity]");
    fprintf(stderr,
            "\noption connectivity: 1=6+,2=18,3=6,4=26 (default=1)\n\n");
    exit(-1);
  }

  parms=(tesselation_parms*)calloc(1,sizeof(tesselation_parms));
  if (!parms)
    ErrorExit(ERROR_NOMEMORY, "tesselation parms\n") ;
  mri=MRIread(argv[1]);
  if (downsample > 0) {
    MRI *mri_tmp ;
    mri_tmp = MRIdownsample2(mri, NULL) ;
    MRIfree(&mri) ;
    mri = mri_tmp ;
  }
  {
    MRI *mri_tmp ;
    mri_tmp = MRIalloc(mri->width+2, mri->height+2, mri->depth+2, mri->type) ;
    MRIextractInto(mri, mri_tmp, 
                   0, 0, 0, 
                   mri->width, mri->height, mri->depth, 
                   1, 1, 1) ;
    MRIfree(&mri) ;
    mri = mri_tmp ;
  }
  MRIreInitCache(mri);
  if (mri->type != MRI_UCHAR) {
    MRI *mri_tmp ;
    float min_val, max_val ;

    MRIvalRange(mri, &min_val, &max_val) ;
    if (min_val < 0 || max_val > 255)
      ErrorExit
        (ERROR_UNSUPPORTED, 
         "%s: input volume (val range [%2.1f %2.1f]) must be "
         "convertible to UCHAR",
         Progname, min_val, max_val) ;
    printf("changing type of input volume to 8 bits/voxel...\n") ;
    mri_tmp = MRIchangeType(mri, MRI_UCHAR, 0.0, 0.999, TRUE) ;
    MRIfree(&mri) ;
    mri = mri_tmp ;
  }

  parms->mri=mri;

  parms->number_of_labels=1; //only one single label
  parms->label_values=(int*)malloc(sizeof(int));
  parms->label_values[0]=atoi(argv[2]);//label;
  parms->ind=0;
  mris_table=(MRIS**)malloc(sizeof(MRIS*)); //final surface information
  parms->mris_table=mris_table;
  if ((!parms->label_values) || (!mris_table))
    ErrorExit(ERROR_NOMEMORY, "labels/surfaces tables\n") ;

  if (argc==5) parms->connectivity=atoi(argv[4]);//connectivity;
  else parms->connectivity=1;

  initTesselationParms(parms);

  generateMCtesselation(parms);

  free(parms->label_values);
  mris=parms->mris_table[0];
  free(parms->mris_table);
  freeTesselationParms(&parms);

  {
    float dist,max_e=0.0;
    int n,p,vn0,vn2;
    VERTEX *v,*vp;
    fprintf(stderr,"computing the maximum edge length...");
    for (n = 0 ; n < mris->nvertices ; n++) {
      v=&mris->vertices[n];
      for (p = 0 ; p < v->vnum ; p++) {
        vp = &mris->vertices[v->v[p]];
        dist=SQR(vp->x-v->x)+SQR(vp->y-v->y)+SQR(vp->z-v->z);
        if (dist>max_e) max_e=dist;
      }
    }
    fprintf(stderr,"%f mm",sqrt(max_e));
    fprintf(stderr,"\nreversing orientation of faces...");
    for (n = 0 ; n < mris->nfaces ; n++) {
      vn0=mris->faces[n].v[0];
      vn2=mris->faces[n].v[2];
      /* vertex 0 becomes vertex 2 */
      v=&mris->vertices[vn0];
      for (p = 0 ; p < v->num ; p++)
        if (v->f[p]==n)
          v->n[p]=2;
      mris->faces[n].v[2]=vn0;
      /* vertex 2 becomes vertex 0 */
      v=&mris->vertices[vn2];
      for (p = 0 ; p < v->num ; p++)
        if (v->f[p]==n)
          v->n[p]=0;
      mris->faces[n].v[0]=vn2;
    }
  }

  fprintf(stderr,"\nchecking orientation of surface...");
  MRISmarkOrientationChanges(mris);
  mris_corrected=MRISextractMainComponent(mris,0,1,0);

  MRISfree(&mris);

  fprintf(stderr,"\nwriting out surface...");
  MRISaddCommandLine(mris_corrected, cmdline) ;
  if (mriConformed(mri) == 0) {
    printf("input volume is not conformed - using useRealRAS=1\n") ;
    mris_corrected->useRealRAS = 1 ;
  }
  //  getVolGeom(mri, &mris_corrected->vg);
  MRISwrite(mris_corrected,argv[3]);
  fprintf(stderr,"done\n");

  MRIfree(&mri);
  MRISfree(&mris_corrected);

  return 0;
}
Ejemplo n.º 18
0
int
main(int argc, char *argv[]) {
  char               **av, *in_fname, *out_fname, path[STRLEN], fname[STRLEN],
  hemi[STRLEN], *cp ;
  int                ac, nargs ;
  MRI_SURFACE        *mris ;

  /* rkt: check for and handle version tag */
  nargs = handle_version_option (argc, argv, "$Id: mris_reverse.c,v 1.10 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] ;

  if (patch_flag) {
    FileNamePath(in_fname, path) ;
    FileNameOnly(in_fname, hemi) ;
    cp = strchr(hemi, '.') ;
    if (cp)
      *cp = 0 ;
    else
      ErrorExit(ERROR_BADPARM, "%s: could not scan hemisphere from %s\n",
                in_fname) ;
    sprintf(fname, "%s/%s.%s", path, hemi, ORIG_NAME) ;
    mris = MRISread(fname) ;
    if (!mris)
      ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
                Progname, fname) ;
    if (MRISreadPatch(mris, in_fname) != NO_ERROR)
      ErrorExit(Gerror, "%s: could not read patch\n", Progname) ;
  } else {
    mris = MRISread(in_fname) ;
    if (!mris)
      ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
                Progname, in_fname) ;
  }

  FileNamePath(out_fname, path) ;
  MRISreverse(mris, which, 1) ;
  if (Gdiag & DIAG_SHOW)
    fprintf(stderr, "writing reversed surface to %s\n", out_fname) ;
  mris->type = MRIS_TRIANGULAR_SURFACE ;
  if (patch_flag)
    MRISwritePatch(mris, out_fname) ;
  else
    MRISwrite(mris, out_fname) ;
  exit(0) ;
  return(0) ;  /* for ansi */
}