"\n******** Please use results with caution! ********"  \
                  "\n******** Brain anatomy is quite variable! ********"  \
                  "\n******** The database may contain errors! ********"

00421 {
00422   float x, y, z;
00423   char *string, *fstring;
00424   int output = 0;
00425   int first = 1, num = 0;
00426   int a;
00427   int iarg, dicom = 1, i, nakedarg, arglen;
00428 
00429    dicom = 1;
00430    output = 0;
00431    iarg = 1 ; nakedarg = 0;
00432    while( iarg < argc ){
00433       arglen = strlen(argv[iarg]);
00434       if(argv[iarg][0] == '-' && arglen > 1 && zischar(argv[iarg][1])) {
00435          for (i=1;i<arglen; ++i) argv[iarg][i] = tolower(argv[iarg][i]);
00436          if (strcmp(argv[iarg],"-spm") == 0 || strcmp(argv[iarg],"-lpi") == 0) dicom = 0;
00437          else if (strcmp(argv[iarg],"-dicom") == 0 || strcmp(argv[iarg],"-rai") == 0) dicom = 1;
00438          else {
00439             fprintf(stderr,"** bad option %s\n", argv[iarg]);
00440             return 1;
00441          }
00442       } else {
00443          /* xyz format */
00444          if (nakedarg == 0) x = atof(argv[iarg]);
00445          else if (nakedarg == 1) y = atof(argv[iarg]);
00446          else if (nakedarg == 2) z = atof(argv[iarg]);
00447          else if (nakedarg == 3) output = atoi(argv[iarg]);
00448          ++nakedarg;
00449       }
00450       ++iarg;
00451    }
00452   
00453   
00454   if (nakedarg < 3) {
00455       printf("Usage: whereami [-lpi/-spm] x y z [output format]\n");
00456       printf("x y z coordinates are assumed to be in RAI or DICOM format\n");
00457       printf("unless you use -lpi or -spm to indicate otherwise.\n");
00458       printf("Output format: 0 - standard AFNI 'Where am I?' format [default]\n");
00459       printf("               1 - Blank separated list\n");
00460       return 1;
00461   }
00462   
00463   if (!dicom) {
00464    /* go from lpi to rai */
00465    x = -x;
00466    y = -y; 
00467   }
00468 
00469   string = TT_whereami(x,y,z);
00470   if (string == NULL ) {                              /* 30 Apr 2005 [rickr] */
00471     fprintf(stderr,"** whereami lookup failure: is TTatlas+tlrc/TTatlas.nii.gz available?\n");
00472     fprintf(stderr,"   (the TTatlas+tlrc or TTatlas.nii.gz dataset must be in your PATH)\n");
00473     return 1;
00474   }
00475 
00476   if (output == 1) {
00477     fstring = malloc(sizeof(string));
00478     strncpy(fstring, "Focus point", 11);
00479     num = 11;
00480     for(a = 0; string[a] != '\0'; a++) {
00481       /* remove header info up to Focus point:
00482           remove newlines as you go; once you hit a *, stop */
00483       if ((string[a] != ':') && (first == 1)) {
00484         continue;
00485       }
00486       first = 0;
00487       if ((string[a] == ' ') && (string[a-1] == ' ')) {
00488         continue;
00489       }
00490       if ((string[a] == '*')) {
00491         fstring[num] = '\0';
00492         printf("%s\n", fstring);
00493         break;
00494       }
00495       if ((string[a] != '\n')) {
00496         if (string[a] == 'W') {
00497           fstring[num++] = '\t';
00498         }
00499         fstring[num++] = string[a];
00500       } else {
00501         fstring[num++] = ' ';
00502       }
00503     }
00504       free(fstring);
00505   } else {
00506     printf("%s\n", string);
00507   }
00508 
00509 return 0;
00510 }

00051 {
00052    char *epath, *elocal, ename[THD_MAX_NAME], dname[THD_MAX_NAME], *eee ;
00053    int epos , ll , ii , id ;
00054 
00055 ENTRY("TT_load_atlas") ;
00056 
00057    if( have_dseTT >= 0 ) RETURN(have_dseTT) ;  /* for later calls */
00058 
00059    have_dseTT = 0 ;  /* don't have it yet */
00060 
00061    /*----- 20 Aug 2001: see if user specified alternate database -----*/
00062 
00063    epath = my_getenv("AFNI_TTATLAS_DATASET") ;
00064    if( epath != NULL ){
00065       dseTT = THD_open_one_dataset( epath ) ;  /* try to open it */
00066       if( dseTT != NULL ){                     /* got it!!! */
00067          have_dseTT = 1; RETURN(1);
00068       }
00069    }
00070 
00071    /*----- get path to search -----*/
00072 
00073                        epath = getenv("AFNI_PLUGINPATH") ;
00074    if( epath == NULL ) epath = getenv("AFNI_PLUGIN_PATH") ;
00075    if( epath == NULL ) epath = getenv("PATH") ;
00076    if( epath == NULL ) RETURN(0) ;
00077 
00078    /*----- copy path list into local memory -----*/
00079 
00080    ll = strlen(epath) ;
00081    elocal = AFMALL(char, sizeof(char) * (ll+2) ) ;
00082 
00083    /*----- put a blank at the end -----*/
00084 
00085    strcpy( elocal , epath ) ; elocal[ll] = ' ' ; elocal[ll+1] = '\0' ;
00086 
00087    /*----- replace colons with blanks -----*/
00088 
00089    for( ii=0 ; ii < ll ; ii++ )
00090       if( elocal[ii] == ':' ) elocal[ii] = ' ' ;
00091 
00092    /*----- extract blank delimited strings;
00093            use as directory names to look for atlas -----*/
00094 
00095    epos = 0 ;
00096 
00097    do{
00098       ii = sscanf( elocal+epos , "%s%n" , ename , &id ); /* next substring */
00099       if( ii < 1 ) break ;                               /* none -> done   */
00100 
00101       epos += id ;                                 /* char after last scanned */
00102 
00103       ii = strlen(ename) ;                         /* make sure name has   */
00104       if( ename[ii-1] != '/' ){                    /* a trailing '/' on it */
00105           ename[ii]  = '/' ; ename[ii+1] = '\0' ;
00106       }
00107       strcpy(dname,ename) ;
00108       strcat(dname,"TTatlas+tlrc") ;               /* add dataset name */
00109 
00110       dseTT = THD_open_one_dataset( dname ) ;      /* try to open it */
00111 
00112       if( dseTT != NULL ){                         /* got it!!! */
00113          free(elocal); have_dseTT = 1; RETURN(1);
00114       }
00115 
00116       strcpy(dname,ename) ; strcat(dname,"TTatlas.nii.gz") ;
00117       dseTT = THD_open_one_dataset( dname ) ;
00118       if( dseTT != NULL ){ free(elocal); have_dseTT = 1; RETURN(1); }
00119 
00120    } while( epos < ll ) ;  /* scan until 'epos' is after end of epath */
00121 
00122    free(elocal) ; RETURN(0) ; /* got here -> didn't find it */
00123 }

00130 {
00131   PURGE_DSET(dseTT) ; return ;
00132 }

00135 {
00136    if( dseTT_big != NULL ){ DSET_delete(dseTT_big) ; dseTT_big = NULL ; }
00137    return ;
00138 }

00021 {
00022    if( have_dseTT < 0 ) TT_load_atlas() ;
00023    return dseTT ;                         /* might be NULL */
00024 }

00029 {
00030    if( dseTT_big != NULL ) return dseTT_big ;
00031    if( have_dseTT < 0    ) TT_load_atlas() ;
00032    if( dseTT == NULL     ) return NULL ;
00033    dseTT_big = THD_zeropad( dseTT , 10,0,0,0,0,0 , "TTatlas_big" , 0 ) ;
00034    DSET_unload( dseTT ) ; /* probably won't need again */
00035    return dseTT_big ;
00036 }

00041 {
00042    if( dseTT_big != NULL ) return dseTT_big ;
00043    if( dseTT     != NULL ) return dseTT     ;
00044    if( have_dseTT < 0    ) TT_load_atlas()  ;
00045    return dseTT ;
00046 }

00150 {
00151    int ii,kk , ix,jy,kz , nx,ny,nz,nxy , aa,bb,cc , ff,b2f,b4f,rff ;
00152    THD_ivec3 ijk ;
00153    byte *b2 , *b4 ;
00154    THD_string_array *sar ;
00155    char *b2lab , *b4lab ;
00156    char lbuf[256] , *rbuf ;
00157    int nfind, b2_find[MAX_FIND], b4_find[MAX_FIND], rr_find[MAX_FIND] ;
00158 
00159    THD_3dim_dataset * dset ; /* 01 Aug 2001 */
00160 
00161 ENTRY("TT_whereami") ;
00162 
00163    /*-- setup stuff: load atlas dataset, prepare search mask --*/
00164 
00165    if( dseTT == NULL ){
00166       ii = TT_load_atlas() ; if( ii == 0 ) RETURN(NULL) ;
00167    }
00168 
00169    /* 01 Aug 2001: maybe use big dataset (so don't need both in memory) */
00170 
00171    dset = (dseTT_big != NULL) ? dseTT_big : dseTT ;
00172 
00173 #if 0
00174 if( dset == dseTT_big ) fprintf(stderr,"TT_whereami using dseTT_big\n") ;
00175 else                    fprintf(stderr,"TT_whereami using dseTT\n") ;
00176 #endif
00177 
00178    DSET_load(dset) ;
00179    b2 = DSET_BRICK_ARRAY(dset,0) ; if( b2 == NULL ) RETURN(NULL) ;
00180    b4 = DSET_BRICK_ARRAY(dset,1) ; if( b4 == NULL ) RETURN(NULL) ;
00181 
00182    if( wamiclust == NULL ){
00183       wamiclust = MCW_build_mask( 0,0,0 , 1.0,1.0,1.0 , WAMIRAD ) ;
00184       if( wamiclust == NULL ) RETURN(NULL) ;  /* should not happen! */
00185 
00186       for( ii=0 ; ii < wamiclust->num_pt ; ii++ )       /* load radius */
00187          wamiclust->mag[ii] = (int)rint(sqrt((double)(
00188                                          wamiclust->i[ii]*wamiclust->i[ii]
00189                                         +wamiclust->j[ii]*wamiclust->j[ii]
00190                                         +wamiclust->k[ii]*wamiclust->k[ii]))) ;
00191 
00192       MCW_sort_cluster( wamiclust ) ;  /* sort by radius */
00193    }
00194 
00195    /*-- find locations near the given one that are in the Atlas --*/
00196 
00197    ijk = THD_3dmm_to_3dind( dset , TEMP_FVEC3(xx,yy,zz) ) ;  /* get indexes */
00198    UNLOAD_IVEC3(ijk,ix,jy,kz) ;                               /* from coords */
00199 
00200    nx = DSET_NX(dset) ;               /* size of TT atlas dataset axes */
00201    ny = DSET_NY(dset) ;
00202    nz = DSET_NZ(dset) ; nxy = nx*ny ;
00203 
00204    nfind = 0 ;
00205 
00206    /*-- check the exact input location --*/
00207 
00208    kk = ix + jy*nx + kz*nxy ;        /* index into brick arrays */
00209    if( b2[kk] != 0 || b4[kk] != 0 ){
00210       b2_find[0] = b2[kk] ;
00211       b4_find[0] = b4[kk] ;
00212       rr_find[0] = 0      ; nfind++ ;
00213    }
00214 
00215    /*-- check locations near it --*/
00216 
00217    for( ii=0 ; ii < wamiclust->num_pt ; ii++ ){
00218 
00219       /* compute index of nearby location, skipping if outside atlas */
00220 
00221       aa = ix + wamiclust->i[ii] ; if( aa < 0 || aa >= nx ) continue ;
00222       bb = jy + wamiclust->j[ii] ; if( bb < 0 || bb >= ny ) continue ;
00223       cc = kz + wamiclust->k[ii] ; if( cc < 0 || cc >= nz ) continue ;
00224 
00225       kk  = aa + bb*nx + cc*nxy ;   /* index into bricks */
00226       b2f = b2[kk] ; b4f = b4[kk] ; /* TT structures markers there */
00227 
00228       if( b2f == 0 && b4f == 0 )                            continue ;
00229 
00230       for( ff=0 ; ff < nfind ; ff++ ){       /* cast out         */
00231          if( b2f == b2_find[ff] ) b2f = 0 ;  /* duplicate labels */
00232          if( b4f == b4_find[ff] ) b4f = 0 ;  /* we already found */
00233       }
00234       if( b2f == 0 && b4f == 0 )                            continue ;
00235 
00236       b2_find[nfind] = b2f ;  /* save what we found */
00237       b4_find[nfind] = b4f ;
00238       rr_find[nfind] = (int) wamiclust->mag[ii] ;
00239       nfind++ ;
00240 
00241       if( nfind == MAX_FIND ) break ;  /* don't find TOO much */
00242    }
00243 
00244    /*-- assemble output string(s) --*/
00245 
00246 #define WAMI_HEAD "+++++++ nearby Talairach Daemon structures +++++++\n"
00247 #define WAMI_TAIL "\n******** Please use results with caution! ********"  \
00248                   "\n******** Brain anatomy is quite variable! ********"  \
00249                   "\n******** The database may contain errors! ********"
00250 
00251    if( nfind == 0 ){
00252       char xlab[24], ylab[24] , zlab[24] ;
00253       THD_fvec3 tv , mv ;
00254       float mx,my,mz ;
00255       char mxlab[24], mylab[24] , mzlab[24] ;
00256 
00257       sprintf(xlab,"%4.0f mm [%c]",-xx,(xx<0.0)?'R':'L') ;
00258       sprintf(ylab,"%4.0f mm [%c]",-yy,(yy<0.0)?'A':'P') ;
00259       sprintf(zlab,"%4.0f mm [%c]", zz,(zz<0.0)?'I':'S') ;
00260 
00261       LOAD_FVEC3(tv,xx,yy,zz);
00262       mv = THD_tta_to_mni(tv); UNLOAD_FVEC3(mv,mx,my,mz);
00263       sprintf(mxlab,"%4.0f mm [%c]",mx,(mx>=0.0)?'R':'L') ;
00264       sprintf(mylab,"%4.0f mm [%c]",my,(my>=0.0)?'A':'P') ;
00265       sprintf(mzlab,"%4.0f mm [%c]",mz,(mz< 0.0)?'I':'S') ;
00266 
00267       rbuf = AFMALL(char, 500) ;
00268       sprintf(rbuf,"%s\n"
00269                    "Focus point=%s,%s,%s {T-T Atlas}\n"
00270                    "           =%s,%s,%s {MNI Brain}\n"
00271                    "\n"
00272                    "***** Not near any region stored in database *****\n" ,
00273               WAMI_HEAD , xlab,ylab,zlab , mxlab,mylab,mzlab ) ;
00274       RETURN(rbuf) ;
00275    }
00276 
00277    /*-- bubble-sort what we found, by radius --*/
00278 
00279    if( nfind > 1 ){  /* don't have to sort only 1 result */
00280      int swap, tmp ;
00281      do{
00282         swap=0 ;
00283         for( ii=1 ; ii < nfind ; ii++ ){
00284            if( rr_find[ii-1] > rr_find[ii] ){
00285              tmp = rr_find[ii-1]; rr_find[ii-1] = rr_find[ii]; rr_find[ii] = tmp;
00286              tmp = b2_find[ii-1]; b2_find[ii-1] = b2_find[ii]; b2_find[ii] = tmp;
00287              tmp = b4_find[ii-1]; b4_find[ii-1] = b4_find[ii]; b4_find[ii] = tmp;
00288              swap++ ;
00289            }
00290         }
00291      } while(swap) ;
00292    }
00293 
00294    /*-- find anatomical label for each found marker, make result string --*/
00295 
00296    INIT_SARR(sar) ; ADDTO_SARR(sar,WAMI_HEAD) ;
00297 
00298    /* 04 Apr 2002: print coordinates (LPI) as well (the HH-PB addition) */
00299 
00300    { char lbuf[128], xlab[24], ylab[24] , zlab[24] ;
00301      sprintf(xlab,"%4.0f mm [%c]",-xx,(xx<0.0)?'R':'L') ;
00302      sprintf(ylab,"%4.0f mm [%c]",-yy,(yy<0.0)?'A':'P') ;
00303      sprintf(zlab,"%4.0f mm [%c]", zz,(zz<0.0)?'I':'S') ;
00304      sprintf(lbuf,"Focus point=%s,%s,%s {T-T Atlas}",xlab,ylab,zlab) ;
00305      ADDTO_SARR(sar,lbuf) ;
00306    }
00307 
00308    /* 29 Apr 2002: print MNI coords as well */
00309 
00310    { THD_fvec3 tv , mv ;
00311      float mx,my,mz ;
00312      char mxlab[24], mylab[24] , mzlab[24] , lbuf[128] ;
00313      LOAD_FVEC3(tv,xx,yy,zz);
00314      mv = THD_tta_to_mni(tv); UNLOAD_FVEC3(mv,mx,my,mz);
00315      sprintf(mxlab,"%4.0f mm [%c]",mx,(mx>=0.0)?'R':'L') ;
00316      sprintf(mylab,"%4.0f mm [%c]",my,(my>=0.0)?'A':'P') ;
00317      sprintf(mzlab,"%4.0f mm [%c]",mz,(mz< 0.0)?'I':'S') ;
00318      sprintf(lbuf,"Focus point=%s,%s,%s {MNI Brain}\n",mxlab,mylab,mzlab) ;
00319      ADDTO_SARR(sar,lbuf) ;
00320    }
00321 
00322    rff = -1 ;  /* rff = radius of last found label */
00323 
00324    for( ff=0 ; ff < nfind ; ff++ ){
00325       b2f = b2_find[ff] ; b4f = b4_find[ff] ; b2lab = NULL ; b4lab = NULL ;
00326 
00327       if( b2f != 0 ){                               /* find label     */
00328          for( ii=0 ; ii < TTO_COUNT ; ii++ )        /* in AFNI's list */
00329             if( b2f == TTO_list[ii].tdval ) break ;
00330          if( ii < TTO_COUNT )                       /* always true? */
00331             b2lab = TTO_list[ii].name ;
00332 
00333          if( b2lab != NULL && xx < 0 && strstr(b2lab,"Left") != NULL ) /* maybe is Right */
00334             b2lab = TTO_list[ii+1].name ;
00335       }
00336 
00337       if( b4f != 0 ){
00338          for( ii=0 ; ii < TTO_COUNT ; ii++ )
00339             if( b4f == TTO_list[ii].tdval ) break ;
00340          if( ii < TTO_COUNT )
00341             b4lab = TTO_list[ii].name ;
00342          if( b4lab != NULL && xx < 0 && strstr(b4lab,"Left") != NULL )
00343             b4lab = TTO_list[ii+1].name ;
00344       }
00345 
00346       if( b2lab == NULL && b4lab == NULL ) continue ;  /* no labels? */
00347 
00348       /* make output label into lbuf */
00349 
00350       lbuf[0] = '\0' ;
00351       if( b2lab != NULL ){
00352          if( rr_find[ff] != rff ){
00353             if( rr_find[ff] > 0 )
00354               sprintf( lbuf , "Within %d mm: %s" , rr_find[ff] , b2lab ) ;
00355             else
00356               sprintf( lbuf , "Focus point: %s" , b2lab ) ;
00357          } else {
00358             sprintf( lbuf , "             %s" , b2lab ) ;
00359          }
00360 
00361          for( kk=strlen(lbuf)-1 ; kk > 0 && lbuf[kk] == '.' ; kk-- )
00362             lbuf[kk] = '\0' ;                  /* trim trailing .'s */
00363       }
00364 
00365       if( b4lab != NULL ){
00366          kk = strlen(lbuf) ;
00367          if( kk > 0 ){
00368             sprintf( lbuf+kk , " -AND- %s" , b4lab ) ;
00369          } else if( rr_find[ff] != rff ){
00370             if( rr_find[ff] > 0 )
00371               sprintf( lbuf , "Within %d mm: %s" , rr_find[ff] , b4lab ) ;
00372             else
00373               sprintf( lbuf , "Focus point: %s" , b4lab ) ;
00374          } else {
00375             sprintf( lbuf , "             %s" , b4lab ) ;
00376          }
00377 
00378          for( kk=strlen(lbuf)-1 ; kk > 0 && lbuf[kk] == '.' ; kk-- )
00379             lbuf[kk] = '\0' ;
00380       }
00381 
00382       ADDTO_SARR(sar,lbuf) ;  /* make a list of labels */
00383 
00384       rff = rr_find[ff] ;  /* save for next time around */
00385    }
00386 
00387    /*- if didn't make any label, must produce something -*/
00388 
00389    if( sar->num == 1 ){    /* shouldn't ever happen */
00390       sprintf(lbuf,"Found %d marked but unlabeled regions???\n",nfind) ;
00391       ADDTO_SARR(sar,lbuf) ;
00392    } else {
00393       ADDTO_SARR(sar,WAMI_TAIL) ;  /* cautionary tail */
00394    }
00395 
00396    /*- convert list of labels into one big multi-line string -*/
00397 
00398    for( nfind=ii=0 ; ii < sar->num ; ii++ ) nfind += strlen(sar->ar[ii]) ;
00399    rbuf = AFMALL(char, nfind + 2*sar->num + 32 ) ; rbuf[0] = '\0' ;
00400    for( ii=0 ; ii < sar->num ; ii++ ){
00401       strcat(rbuf,sar->ar[ii]) ; strcat(rbuf,"\n") ;
00402    }
00403 
00404    DESTROY_SARR(sar) ; RETURN(rbuf) ;
00405 }