00001 /******************************* DTIStudioFibertoSegments.c **************************************/
00002 
00003 #if 0
00004 # format from Hangyi Jiang for DTIStudio fibers
00005 File Header (128 bytes):
00006 char     sFiberFileTag[8] = "FiberDat";
00007 int        nFiberNr;    // number of fibers in this file 
00008 int        nFiberLenMax;        // max-length of fibers 
00009 float     fFiberLenMean;        // mean-length of fibers
00010 int        nImgWidth;           // image dimension 
00011 int        nImgHeight; 
00012 int        nImgSlices;
00013 float   fPixelSizeWidth;        // voxel size 
00014 float   fPixelSizeHeight; 
00015 float   fSliceThickness;
00016 
00017 int     enumSliceOrientation;  // orientation:  0=Coronal, 1=Axial, 
00018 2=Sagittal 
00019 int     enumSliceSequencing;  // sequencing:  0=Normal,  1= 
00020                 
00021 Fiber Data (starts from offset 128 bytes) 
00022 for each fiber: 
00023   int      nLength;    // fiber length; 
00024   int      nReserved; 
00025   int      nFiberStartIndex;   // the start-point of the selected fiber 
00026   int      nFiberEndIndex;     // the end-point of the selected fiber
00027   XYZ_TRIPLE  xyzFiberChain[];  // the fiber data, in x-y-z format.
00028 then, next fiber.. 
00029 #endif
00030 
00031 #include "mrilib.h"
00032 
00033 static char outfname[THD_MAX_PREFIX] = "rawxyzseg.dat";
00034 static char infname[THD_MAX_PREFIX];
00035 
00036 /*! convert DTIStudio fiber format data to SUMA segment data */
00037 int main( int argc , char * argv[] )
00038 {
00039    int nopt;
00040    int i,j;
00041    FILE *fout, *fin;
00042    float fxyz[3];
00043    char fiberheaderstring[32];
00044    int totalpts=0;
00045    int npts, nfibers;
00046    int statcode;
00047 
00048    /*----- Read command line -----*/
00049    if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
00050       printf("Usage: DTIStudioFibertoSegments [options] dataset\n"
00051              "Convert a DTIStudio Fiber file to a SUMA segment file\n"
00052              "Options:\n"
00053              "  -output / -prefix = name of the output file (not an AFNI dataset prefix)\n"
00054              "    the default output name will be rawxyzseg.dat\n\n"
00055              );
00056       exit(0) ;
00057    }
00058    fout = NULL;
00059    mainENTRY("DTIStudioFibertoSegments main"); machdep(); AFNI_logger("DTIStudioFibertoSegments",argc,argv);
00060    nopt = 1;
00061    while( nopt < argc && argv[nopt][0] == '-' ){
00062     if( (strcmp(argv[nopt],"-output") == 0 ) || (strcmp(argv[nopt],"-prefix")==0))
00063       {
00064        if (++nopt >= argc)
00065          {
00066           fprintf (stderr, "*** Error - output / prefix needs an argument!\n");
00067           exit (1);
00068          }
00069        MCW_strncpy (outfname, argv[nopt], THD_MAX_PREFIX);      /* change name from default prefix */
00070        if (!THD_filename_ok (outfname))
00071          {
00072           fprintf (stderr, "*** Error - %s is not a valid output name!\n", outfname);
00073           exit (1);
00074          }
00075        if (THD_is_file(outfname))
00076         {
00077           fprintf (stderr, "*** Error - %s already exists!\n", outfname);
00078           exit (1);
00079          }
00080        nopt++; continue;
00081       }
00082 
00083      fprintf(stderr, "*** Error - unknown option %s\n", argv[nopt]);
00084      exit(1);
00085    }
00086  
00087    fout = fopen (outfname, "w") ;
00088    if( fout == NULL ){
00089      fprintf (stderr, "*** Error - can not create %s for some reason!\n", outfname);
00090      exit (1);
00091    }
00092 
00093 
00094    /* get fiber file as input and check if we can open it */
00095    MCW_strncpy (infname, argv[nopt], THD_MAX_PREFIX);   /* get name of fiber file */
00096    if (!THD_filename_ok (infname))
00097       {
00098        fprintf (stderr, "*** Error - %s is not a valid input name!\n", infname);
00099        exit (1);
00100       }
00101    if (!THD_is_file(infname))
00102       {
00103        fprintf (stderr, "*** Error - %s does not exist!\n", infname);
00104        exit (1);
00105       }
00106    fin = fopen (infname, "r") ;
00107    if( fin == NULL ){
00108       fprintf (stderr, "*** Error - can not open %s for some reason!\n", infname);
00109       exit (1);
00110    }
00111  
00112 
00113 
00114    /* read the header */
00115 
00116    statcode = fread(fiberheaderstring, 8, 1, fin);
00117    if(!strcmp(fiberheaderstring,"FiberDat")) {
00118      fprintf(stderr, "*** Error - file does not have correct header format\n");
00119      fclose(fin);
00120      fclose(fout);
00121      exit(1);
00122    }
00123 
00124    statcode = fread(&nfibers, sizeof(int), 1, fin);
00125    if((statcode<1)||(nfibers<1)) {
00126      fprintf(stderr, "*** Error - file does not have correct header format\n");
00127      fclose(fin);
00128      fclose(fout);
00129      exit(1);
00130    }
00131 
00132    fseek(fin, 128, SEEK_SET);    /* go to start of data - 128 byte header */
00133 
00134    fprintf(stderr, "Number of fibers = %d \n", nfibers);
00135    for(i=0;i<nfibers;i++) {                    /* get all the fibers */
00136       statcode = fread(&npts,sizeof(int),1, fin);
00137       if((statcode<1)||(npts<1)) {
00138          fprintf(stderr, "*** can not read fiber info.\n");
00139          fclose(fin);
00140          fclose(fout);
00141          exit(1);
00142       }
00143 
00144       totalpts += npts;
00145       statcode = fseek(fin, 12,  SEEK_CUR); /* skip unused byte,RGB bytes,Start and End point indices */
00146 
00147       for(j=0;j<npts;j++) {                     /* get each point in each fiber */
00148         statcode = fread(fxyz, sizeof(float),3, fin);      /* xyz floating point triplet */
00149         if(statcode<3) {
00150            fprintf(stderr, "*** can not read fiber data.\n");
00151            fclose(fin);
00152            fclose(fout);
00153            exit(1);
00154         }
00155 
00156         if(j!=0) {     /* after first point put space and write x,y,z, then repeat x,y,z on next line */
00157           statcode = fprintf(fout," %10.3f %10.3f %10.3f\n",fxyz[0],fxyz[1],fxyz[2]);
00158         }
00159         if(j<(npts-1)) {  /* for all but the last point, write point again (first time for 1st pt*/
00160           statcode = fprintf(fout,"%10.3f %10.3f %10.3f",fxyz[0],fxyz[1],fxyz[2]);
00161         }
00162         if(statcode==0) {
00163            fprintf(stderr, "*** Error - writing output file!\n");
00164            fclose(fout);
00165            exit(1);
00166         }
00167      }
00168    }
00169 
00170    fprintf(stderr, "Total number of points = %d \n", totalpts);
00171    fclose(fout);
00172    fclose(fin);
00173    exit(0);
00174 }