示例#1
0
/*---------------------------------------------------------------*/
int main(int argc, char *argv[]) {
  int nargs,n,err;
  MRIS *SurfReg[100];
  MRI *SrcVal, *TrgVal;
  char *base;
  COLOR_TABLE *ctab=NULL;

  nargs = handle_version_option (argc, argv, vcid, "$Name:  $");
  if (nargs && argc - nargs == 1) exit (0);
  argc -= nargs;
  cmdline = argv2cmdline(argc,argv);
  uname(&uts);
  getcwd(cwd,2000);

  Progname = argv[0] ;
  argc --;
  argv++;
  ErrorInit(NULL, NULL, NULL) ;
  DiagInit(NULL, NULL, NULL) ;
  if (argc == 0) usage_exit();
  parse_commandline(argc, argv);
  check_options();
  if (checkoptsonly) return(0);
  dump_options(stdout);

  // Load in surface registrations
  for(n=0; n<nsurfs;n++){
    printf("%d Loading %s\n",n+1,SurfRegFile[n]);
    base = fio_basename(SurfRegFile[n],".tri");
    if(strcmp(base,"ic7")==0){
      // Have to do it this way to rescale. Need to find a better more robust way.
      printf("   reading as ico 7, rescaling radius to 100\n");
      SurfReg[n] = ReadIcoByOrder(7, 100);
    }
    else
      SurfReg[n] = MRISread(SurfRegFile[n]);
    free(base);
    if(SurfReg[n]==NULL) exit(1);
  }

  // Load in source data
  SrcVal = NULL;
  if(DoSynthRand) {
    if (SynthSeed < 0) SynthSeed = PDFtodSeed();
    printf("INFO: synthesizing, seed = %d\n",SynthSeed);
    srand48(SynthSeed);
    MRIrandn(SrcVal->width, SrcVal->height, SrcVal->depth,
             SrcVal->nframes,0, 1, SrcVal);
  }
  else if(DoSynthOnes != 0) {
    printf("INFO: filling input with all 1s\n");
    MRIconst(SrcVal->width, SrcVal->height, SrcVal->depth,
             SrcVal->nframes, 1, SrcVal);
  }
  else if(AnnotFile) {
    printf("Loading annotation %s\n",AnnotFile);
    err = MRISreadAnnotation(SurfReg[0], AnnotFile);
    if(err) exit(1);
    SrcVal = MRISannotIndex2Seg(SurfReg[0]);
    ctab = CTABdeepCopy(SurfReg[0]->ct);
  }
  else if(LabelFile) {
    LABEL *srclabel;
    printf("Loading label %s\n",LabelFile);
    srclabel = LabelRead(NULL, LabelFile);
    if(srclabel == NULL) exit(1);
    SrcVal = MRISlabel2Mask(SurfReg[0],srclabel,NULL);
    printf("   %d points in input label\n",srclabel->n_points);
    LabelFree(&srclabel);
  }
  else {
    printf("Loading %s\n",SrcValFile);
    SrcVal = MRIread(SrcValFile);
    if(SrcVal==NULL) exit(1);
  }

  // Apply registration to source
  TrgVal = MRISapplyReg(SrcVal, SurfReg, nsurfs, ReverseMapFlag, DoJac, UseHash);
  if(TrgVal == NULL) exit(1);

  // Save output
  if(AnnotFile){
    printf("Converting to target annot\n");
    err = MRISseg2annot(SurfReg[nsurfs-1],TrgVal,ctab);
    if(err) exit(1);
    printf("Writing %s\n",TrgValFile);
    MRISwriteAnnotation(SurfReg[nsurfs-1], TrgValFile);
  } 
  else if(LabelFile){
    LABEL *label;
    label = MRISmask2Label(SurfReg[nsurfs-1], TrgVal, 0, 10e-5);
    printf("   %d points in output label\n",label->n_points);
    err = LabelWrite(label,TrgValFile);
    if(err){
      printf("ERROR: writing label file %s\n",TrgValFile);
      exit(1);
    }
    LabelFree(&label);
  }
  else{
    printf("Writing %s\n",TrgValFile);
    MRIwrite(TrgVal,TrgValFile);
  }
  
  printf("mris_apply_reg done\n");
  return 0;
}
示例#2
0
/*---------------------------------------------------------------*/
int main(int argc, char *argv[]) {
    int nargs,r,c,s,n,segid,err;
    double val;

    nargs = handle_version_option (argc, argv, vcid, "$Name: stable5 $");
    if (nargs && argc - nargs == 1) exit (0);
    argc -= nargs;
    cmdline = argv2cmdline(argc,argv);
    uname(&uts);
    getcwd(cwd,2000);

    Progname = argv[0] ;
    argc --;
    argv++;
    ErrorInit(NULL, NULL, NULL) ;
    DiagInit(NULL, NULL, NULL) ;
    if (argc == 0) usage_exit();
    parse_commandline(argc, argv);
    check_options();
    if (checkoptsonly) return(0);
    dump_options(stdout);

    SUBJECTS_DIR = getenv("SUBJECTS_DIR");
    if (SUBJECTS_DIR == NULL) {
        printf("ERROR: SUBJECTS_DIR not defined in environment\n");
        exit(1);
    }

    if (DoDavid) {
        printf("Loading David's stat file\n");
        nitems = LoadDavidsTable(statfile, &lutindex, &log10p);
    }
    if (DoSue) {
        printf("Loading Sue's stat file\n");
        nitems = LoadSuesTable(statfile, datcol1, log10flag, &lutindex, &log10p);
    }
    if (nitems == 0) {
        printf("ERROR: could not find any items in %s\n",statfile);
        exit(1);
    }

    if (annot == NULL) {
        seg = MRIread(segfile);
        if (seg == NULL) exit(1);
    } else {
        printf("Constructing seg from annotation\n");
        sprintf(tmpstr,"%s/%s/surf/%s.white",SUBJECTS_DIR,subject,hemi);
        mris = MRISread(tmpstr);
        if (mris==NULL) exit(1);
        sprintf(tmpstr,"%s/%s/label/%s.%s.annot",SUBJECTS_DIR,subject,hemi,annot);
        err = MRISreadAnnotation(mris, tmpstr);
        if (err) exit(1);
        seg = MRISannotIndex2Seg(mris);
    }

    out = MRIallocSequence(seg->width,seg->height,seg->depth,MRI_FLOAT,1);
    MRIcopyHeader(seg,out);

    for (c=0; c < seg->width; c++) {
        //printf("%3d ",c);
        //if(c%20 == 19) printf("\n");
        fflush(stdout);
        for (r=0; r < seg->height; r++) {
            for (s=0; s < seg->depth; s++) {
                segid = MRIgetVoxVal(seg,c,r,s,0);
                val = 0;
                if (segid != 0) {
                    if (annot != NULL) {
                        if (strcmp(hemi,"lh")==0) segid = segid + 1000;
                        if (strcmp(hemi,"rh")==0) segid = segid + 2000;
                        MRIsetVoxVal(seg,c,r,s,0,segid);
                    }
                    for (n=0; n < nitems; n++) {
                        if (lutindex[n] == segid) {
                            val = log10p[n];
                            break;
                        }
                    }
                }
                MRIsetVoxVal(out,c,r,s,0,val);
            }
        }
    }
    printf("\n");
    MRIwrite(out,outfile);
    MRIwrite(seg,"segtmp.mgh");

    printf("mri_stats2seg done\n");
    return 0;
}