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3dSpatNorm.c File Reference
#include "mrilib.h"#include "rickr/r_new_resam_dset.h"Go to the source code of this file.
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| int | main (int argc, char *argv[]) |
Function Documentation
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---------- Adapted from 3dZeropad.c by RWCox - 08 Aug 2001 ----------* Definition at line 4 of file 3dSpatNorm.c. References ADN_datum_all, ADN_func_type, ADN_malloc_type, ADN_none, ADN_nxyz, ADN_prefix, ADN_type, ADN_view_type, ADN_xyzdel, ADN_xyzorg, ADN_xyzorient, AFNI_yesenv(), ANAT_BUCK_TYPE, argc, DATABLOCK_MEM_MALLOC, THD_3dim_dataset::daxes, DSET_BRICK_TYPE, DSET_BRIKNAME, DSET_delete, DSET_unload, DSET_write, MRI_IMAGE::dx, MRI_IMAGE::dy, MRI_IMAGE::dz, EDIT_dset_items(), EDIT_empty_copy(), EDIT_substitute_brick(), HEAD_ANAT_TYPE, ISVALID_DSET, MRI_IMAGE::kind, LOAD_FVEC3, LOAD_IVEC3, mri_brainormalize(), mri_brainormalize_initialize(), mri_brainormalize_verbose(), mri_free(), MRI_NN, mri_to_short(), mri_watershedize(), MRI_IMAGE::nx, THD_dataxes::nxx, MRI_IMAGE::ny, THD_dataxes::nyy, MRI_IMAGE::nz, THD_dataxes::nzz, ORI_A2P_TYPE, ORI_I2S_TYPE, ORI_R2L_TYPE, r_new_resam_dset(), THD_3dmm_to_dicomm(), THD_filename_ok(), THD_median_brick(), THD_open_dataset(), tross_Copy_History(), tross_Make_History(), VIEW_ORIGINAL_TYPE, MRI_IMAGE::xo, THD_dataxes::xxdel, THD_dataxes::xxorg, THD_dataxes::xxorient, THD_fvec3::xyz, MRI_IMAGE::yo, THD_dataxes::yydel, THD_dataxes::yyorg, THD_dataxes::yyorient, MRI_IMAGE::zo, THD_dataxes::zzdel, THD_dataxes::zzorg, and THD_dataxes::zzorient.
00005 {
00006 MRI_IMAGE *imin, *imout , *imout_orig;
00007 THD_3dim_dataset *iset, *oset , *ooset;
00008 char *prefix = "SpatNorm" ;
00009 int iarg , verb=0, OrigSpace = 0 ;
00010 THD_ivec3 orixyz , nxyz ;
00011 THD_fvec3 dxyz , orgxyz, originRAIfv, fv2;
00012
00013
00014 /*--- get help here or get help somewhere ---*/
00015
00016 if( argc < 2 ){
00017 printf("Usage: 3dSpatNorm [options] dataset\n"
00018 "\n"
00019 "Options:\n"
00020 " -prefix ppp = Write output dataset using 'ppp' for the prefix.\n"
00021 " -orig_space = Write output dataset using the same grid as dataset.\n"
00022 " -verb = Write out progress reports\n"
00023 ) ;
00024 exit(0) ;
00025 }
00026
00027 /*--- options ---*/
00028
00029 iarg = 1 ;
00030 OrigSpace = 0;
00031 while( iarg < argc && argv[iarg][0] == '-' ){
00032
00033 /* -prefix */
00034
00035 if( strcmp(argv[iarg],"-prefix") == 0 ){
00036 if( ++iarg >= argc ){
00037 fprintf(stderr,"**ERROR: -prefix requires another argument!\n") ;
00038 exit(1) ;
00039 }
00040 prefix = strdup(argv[iarg]) ;
00041 if( !THD_filename_ok(prefix) ){
00042 fprintf(stderr,"**ERROR: -prefix value contains forbidden characters!\n") ;
00043 exit(1) ;
00044 }
00045 iarg++ ; continue ;
00046 }
00047
00048 /* -verb */
00049
00050 if( strncmp(argv[iarg],"-verb",5) == 0 ){
00051 verb++ ; iarg++ ; continue ;
00052 }
00053
00054 if( strncmp(argv[iarg],"-orig_space",10) == 0 ){
00055 OrigSpace = 1 ; iarg++ ; continue ;
00056 }
00057
00058 fprintf(stderr,"**ERROR: %s is unknown option!\n",argv[iarg]) ;
00059 exit(1) ;
00060 }
00061
00062 if( iarg >= argc ){
00063 fprintf(stderr,"**ERROR: no input dataset name on command line?!\n") ;
00064 exit(1) ;
00065 }
00066
00067 /*--- read dataset ---*/
00068
00069 iset = THD_open_dataset( argv[iarg] ) ;
00070 if( !ISVALID_DSET(iset) ){
00071 fprintf(stderr,"**ERROR: can't open dataset %s\n",argv[iarg]) ;
00072 exit(1) ;
00073 }
00074
00075 /*--- get median brick --*/
00076
00077 if( verb ) fprintf(stderr,"++3dSpatNorm: loading dataset\n") ;
00078
00079 imin = THD_median_brick( iset ) ;
00080 if( imin == NULL ){
00081 fprintf(stderr,"**ERROR: can't load dataset %s\n",argv[iarg]) ;
00082 exit(1) ;
00083 }
00084 imin->dx = fabs(iset->daxes->xxdel) ;
00085 imin->dy = fabs(iset->daxes->yydel) ;
00086 imin->dz = fabs(iset->daxes->zzdel) ;
00087
00088 mri_brainormalize_initialize(imin->dz, imin->dy, imin->dz); /* To get around the #define for voxel counts and dimensions */
00089
00090 /* me needs the origin of this dset in RAI world */
00091 LOAD_FVEC3(originRAIfv , iset->daxes->xxorg , iset->daxes->yyorg , iset->daxes->zzorg) ;
00092 originRAIfv = THD_3dmm_to_dicomm( iset , originRAIfv ) ;
00093
00094 LOAD_FVEC3(fv2 , iset->daxes->xxorg + (iset->daxes->nxx-1)*iset->daxes->xxdel ,
00095 iset->daxes->yyorg + (iset->daxes->nyy-1)*iset->daxes->yydel ,
00096 iset->daxes->zzorg + (iset->daxes->nzz-1)*iset->daxes->zzdel ) ;
00097 fv2 = THD_3dmm_to_dicomm( iset , fv2 ) ;
00098
00099 if( originRAIfv.xyz[0] > fv2.xyz[0] ) { float tf; tf = originRAIfv.xyz[0]; originRAIfv.xyz[0] = fv2.xyz[0]; fv2.xyz[0] = tf; }
00100 if( originRAIfv.xyz[1] > fv2.xyz[1] ) { float tf; tf = originRAIfv.xyz[1]; originRAIfv.xyz[1] = fv2.xyz[1]; fv2.xyz[1] = tf; }
00101 if( originRAIfv.xyz[2] > fv2.xyz[2] ) { float tf; tf = originRAIfv.xyz[2]; originRAIfv.xyz[2] = fv2.xyz[2]; fv2.xyz[2] = tf; }
00102
00103 if (1 && verb) {
00104 fprintf(stderr,"++3dSpatNorm (ZSS): RAI origin info: %f %f %f\n", originRAIfv.xyz[0], originRAIfv.xyz[1], originRAIfv.xyz[2]);
00105 }
00106
00107
00108 DSET_unload( iset ) ; /* don't need this data no more */
00109
00110 /*-- convert image to shorts, if appropriate --*/
00111
00112 if( DSET_BRICK_TYPE(iset,0) == MRI_short ||
00113 DSET_BRICK_TYPE(iset,0) == MRI_byte ){
00114
00115 imout = mri_to_short(1.0,imin) ;
00116 mri_free(imin) ; imin = imout ;
00117 }
00118
00119 /*--- normalize image spatially ---*/
00120
00121 mri_brainormalize_verbose( verb ) ;
00122 if (OrigSpace) {
00123 imout = mri_brainormalize( imin , iset->daxes->xxorient,
00124 iset->daxes->yyorient,
00125 iset->daxes->zzorient , &imout_orig, NULL) ;
00126 } else {
00127 imout = mri_brainormalize( imin , iset->daxes->xxorient,
00128 iset->daxes->yyorient,
00129 iset->daxes->zzorient , NULL, NULL) ;
00130 }
00131 mri_free( imin ) ;
00132
00133 if( imout == NULL ){
00134 fprintf(stderr,"**ERROR: normalization fails!?\n"); exit(1);
00135 }
00136
00137 if (OrigSpace) {
00138 if( verb ) fprintf(stderr,"++3dSpatNorm: Output in Orignal space\n") ;
00139 mri_free( imout ) ;
00140 imout = imout_orig; imout->xo = originRAIfv.xyz[0]; imout->yo = originRAIfv.xyz[1]; imout->zo = originRAIfv.xyz[2];
00141 imout_orig = NULL;
00142 } else {
00143 if( verb ) fprintf(stderr,"++3dSpatNorm: Output in SpatNorm space\n") ;
00144 }
00145
00146 #if 0
00147 if( AFNI_yesenv("WATERSHED") ){
00148 imin = mri_watershedize( imout , 0.10 ) ;
00149 if( imin != NULL ){ mri_free(imout); imout = imin; }
00150 }
00151 #endif
00152
00153 /*--- create output dataset ---*/
00154 if( verb )
00155 fprintf(stderr,"++3dSpatNorm: Creating output dset\n") ;
00156
00157 oset = EDIT_empty_copy( NULL ) ;
00158
00159 tross_Copy_History( iset , oset ) ;
00160 tross_Make_History( "3dSpatNorm" , argc,argv , oset ) ;
00161
00162 LOAD_IVEC3( nxyz , imout->nx , imout->ny , imout->nz ) ;
00163 LOAD_FVEC3( dxyz , imout->dx , imout->dy , imout->dz ) ;
00164 LOAD_FVEC3( orgxyz , imout->xo , imout->yo , imout->zo ) ;
00165 LOAD_IVEC3( orixyz , ORI_R2L_TYPE , ORI_A2P_TYPE , ORI_I2S_TYPE ) ;
00166
00167 if( verb )
00168 fprintf(stderr,"++3dSpatNorm: EDIT_dset_items\n") ;
00169 EDIT_dset_items( oset ,
00170 ADN_prefix , prefix ,
00171 ADN_datum_all , imout->kind ,
00172 ADN_nxyz , nxyz ,
00173 ADN_xyzdel , dxyz ,
00174 ADN_xyzorg , orgxyz ,
00175 ADN_xyzorient , orixyz ,
00176 ADN_malloc_type , DATABLOCK_MEM_MALLOC ,
00177 ADN_view_type , VIEW_ORIGINAL_TYPE ,
00178 ADN_type , HEAD_ANAT_TYPE ,
00179 ADN_func_type , ANAT_BUCK_TYPE ,
00180 ADN_none ) ;
00181
00182 if( verb )
00183 fprintf(stderr,"++3dSpatNorm: EDIT_substitute_brick\n") ;
00184 EDIT_substitute_brick( oset , 0 , imout->kind , mri_data_pointer(imout) ) ;
00185
00186 if (OrigSpace) {
00187 if( verb )
00188 fprintf(stderr,"++3dSpatNorm: Changing orientation from RAI\n") ;
00189 ooset = r_new_resam_dset ( oset, iset, 0, 0, 0, NULL, MRI_NN, NULL);
00190 if (!ooset) {
00191 fprintf(stderr,"**ERROR: Failed to reslice!?\n"); exit(1);
00192 }
00193 DSET_delete(oset); oset = ooset; ooset = NULL;
00194 }
00195
00196 DSET_write(oset) ;
00197 if( verb )
00198 fprintf(stderr,"++3dSpatNorm: wrote dataset %s\n",DSET_BRIKNAME(oset)) ;
00199
00200 exit(0) ;
00201 }
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