/***************************************************************************** Major portions of this software are copyrighted by the Medical College of Wisconsin, 1994-2000, and are released under the Gnu General Public License, Version 2. See the file README.Copyright for details. ******************************************************************************/ #include "mrilib.h" void Syntax(char * str) { int ii ; if( str != NULL ){ printf("\n*** Fatal error: %s\n\n*** Try '3drefit -help'\n",str) ; exit(1) ; } printf( "Changes some of the information inside a 3D dataset's header.\n" "Note that this program does NOT change the .BRIK file at all;\n" "the main purpose of 3drefit is to fix up errors made when\n" "using to3d.\n" "To see the current values stored in a .HEAD file, use the command\n" "'3dinfo dataset'. Using 3dinfo both before and after 3drefit is\n" "a good idea to make sure the changes have been made correctly!\n\n" ) ; printf( "Usage: 3drefit [options] dataset ...\n" "where the options are\n" " -orient code Sets the orientation of the 3D volume(s) in the .BRIK.\n" " The code must be 3 letters, one each from the\n" " pairs {R,L} {A,P} {I,S}. The first letter gives\n" " the orientation of the x-axis, the second the\n" " orientation of the y-axis, the third the z-axis:\n" " R = right-to-left L = left-to-right\n" " A = anterior-to-posterior P = posterior-to-anterior\n" " I = inferior-to-superior S = superior-to-inferior\n" " ** WARNING: when changing the orientation, you must be sure\n" " to check the origins as well, to make sure that the volume\n" " is positioned correctly in space.\n" "\n" " -xorigin distx Puts the center of the edge voxel off at the given\n" " -yorigin disty distance, for the given axis (x,y,z); distances in mm.\n" " -zorigin distz (x=first axis, y=second axis, z=third axis).\n" " Usually, only -zorigin makes sense. Note that this\n" " distance is in the direction given by the corresponding\n" " letter in the -orient code. For example, '-orient RAI'\n" " would mean that '-zorigin 30' sets the center of the\n" " first slice at 30 mm Inferior. See the to3d manual\n" " for more explanations of axes origins.\n" " ** SPECIAL CASE: you can use the string 'cen' in place of\n" " a distance to force that axis to be re-centered.\n" "\n" " -xorigin_raw xx Puts the center of the edge voxel at the given COORDINATE\n" " -yorigin_raw yy rather than the given DISTANCE. That is, these values\n" " -zorigin_raw zz directly replace the offsets in the dataset header,\n" " without any possible sign changes.\n" "\n" " -duporigin cset Copies the xorigin, yorigin, and zorigin values from\n" " the header of dataset 'cset'.\n" "\n" " -dxorigin dx Adds distance 'dx' (or 'dy', or 'dz') to the center\n" " -dyorigin dy coordinate of the edge voxel. Can be used with the\n" " -dzorigin dz values input to the 'Nudge xyz' plugin.\n" " ** WARNING: you can't use these options at the same\n" " time you use -orient.\n" "\n" " -xdel dimx Makes the size of the voxel the given dimension,\n" " -ydel dimy for the given axis (x,y,z); dimensions in mm.\n" " -zdel dimz ** WARNING: if you change a voxel dimension, you will\n" " probably have to change the origin as well.\n" "\n" " -TR time Changes the TR time to a new value (see 'to3d -help').\n" " -notoff Removes the slice-dependent time-offsets.\n" " -Torg ttt Set the time origin of the dataset to value 'ttt'.\n" " (Time origins are set to 0 in to3d.)\n" " ** WARNING: these 3 options apply only to 3D+time datasets.\n" "\n" " -newid Changes the ID code of this dataset as well.\n" "\n" " -nowarp Removes all warping information from dataset.\n" "\n" " -apar aset Set the dataset's anatomy parent dataset to 'aset'\n" " ** N.B.: The anatomy parent is the dataset from which the\n" " transformation from +orig to +acpc and +tlrc coordinates\n" " is taken. It is appropriate to use -apar when there is\n" " more than 1 anatomical dataset in a directory that has\n" " been transformed. In this way, you can be sure that\n" " AFNI will choose the correct transformation. You would\n" " use this option on all the +orig dataset that are\n" " aligned with 'aset' (i.e., that were acquired in the\n" " same scanning session).\n" " ** N.B.: Special cases of 'aset'\n" " aset = NULL --> remove the anat parent info from the dataset\n" " aset = SELF --> set the anat parent to be the dataset itself\n" "\n" " -clear_bstat Clears the statistics (min and max) stored for each sub-brick\n" " in the dataset. This is useful if you have done something to\n" " modify the contents of the .BRIK file associated with this\n" " dataset.\n" "\n" " -statpar v ... Changes the statistical parameters stored in this\n" " dataset. See 'to3d -help' for more details.\n" "\n" " -markers Adds an empty set of AC-PC markers to the dataset,\n" " if it can handle them (is anatomical, is in the +orig\n" " view, and isn't 3D+time).\n" " ** WARNING: this will erase any markers that already exist!\n" "\n" " -view code Changes the 'view' to be 'code', where the string 'code'\n" " is one of 'orig', 'acpc', or 'tlrc'.\n" " ** WARNING: The program will also change the .HEAD and .BRIK\n" " filenames to match. If the dataset filenames already\n" " exist in the '+code' view, then this option will fail.\n" " You will have to rename the dataset files before trying\n" " to use '-view'. If you COPY the files and then use\n" " '-view', don't forget to use '-newid' as well!\n" "\n" " -label2 llll Set the 'label2' field in a dataset .HEAD file to the\n" " string 'llll'. (Can be used as in AFNI window titlebars.)\n" "\n" " -byteorder bbb Sets the byte order string in the header.\n" " Allowable values for 'bbb' are:\n" " LSB_FIRST MSB_FIRST NATIVE_ORDER\n" " Note that this does not change the .BRIK file!\n" " This is done by programs 2swap and 4swap.\n" "\n" " -appkey ll Appends the string 'll' to the keyword list for the\n" " whole dataset.\n" " -repkey ll Replaces the keyword list for the dataset with the\n" " string 'll'.\n" " -empkey Destroys the keyword list for the dataset.\n" ) ; printf( "\n" " -'type' Changes the type of data that is declared for this\n" " dataset, where 'type' is chosen from the following:\n" ) ; printf(" ANATOMICAL TYPES\n") ; for( ii=FIRST_ANAT_TYPE ; ii <= LAST_ANAT_TYPE ; ii++ ){ printf(" %8s == %-16.16s",ANAT_prefixstr[ii],ANAT_typestr[ii] ) ; if( (ii-FIRST_ANAT_TYPE)%2 == 1 ) printf("\n") ; } if( (ii-FIRST_ANAT_TYPE)%2 == 1 ) printf("\n") ; printf(" FUNCTIONAL TYPES\n") ; for( ii=FIRST_FUNC_TYPE ; ii <= LAST_FUNC_TYPE ; ii++ ){ printf(" %8s == %-16.16s",FUNC_prefixstr[ii],FUNC_typestr[ii] ) ; if( (ii-FIRST_ANAT_TYPE)%2 == 1 ) printf("\n") ; } if( (ii-FIRST_ANAT_TYPE)%2 == 1 ) printf("\n") ; printf( /* 08 Jun 2004 */ "-copyaux auxset Copies the 'auxiliary' data from dataset 'auxset'\n" " over the auxiliary data for the dataset being\n" " modified. Auxiliary data comprises sub-brick labels,\n" " keywords, and statistics codes.\n" " '-copyaux' occurs BEFORE the '-sub' operations below,\n" " so you can use those to alter the auxiliary data\n" " that is copied from auxset.\n" "\n" ) ; printf( "The options below allow you to attach auxiliary data to sub-bricks\n" "in the dataset. Each option may be used more than once so that\n" "multiple sub-bricks can be modified in a single run of 3drefit.\n" "\n" " -sublabel n ll Attach to sub-brick #n the label string 'll'.\n" " -subappkey n ll Add to sub-brick #n the keyword string 'll'.\n" " -subrepkey n ll Replace sub-brick #n's keyword string with 'll'.\n" " -subempkey n Empty out sub-brick #n' keyword string\n" "\n" " -substatpar n type v ...\n" " Attach to sub-brick #n the statistical type and\n" " the auxiliary parameters given by values 'v ...',\n" " where 'type' is one of the following:\n" ) ; printf(" type Description PARAMETERS\n" " ---- ----------- ----------------------------------------\n" ) ; for( ii=FIRST_FUNC_TYPE ; ii <= LAST_FUNC_TYPE ; ii++ ){ if( FUNC_IS_STAT(ii) ) printf(" %4s %-11.11s %s\n", FUNC_prefixstr[ii] , FUNC_typestr[ii]+6 , FUNC_label_stat_aux[ii] ) ; } printf( "\n" "The following options allow you to modify VOLREG fields:\n" " -vr_mat ... Use these twelve values for VOLREG_MATVEC_index.\n" " [-vr_mat_ind ] Index of VOLREG_MATVEC_index field to be modified. Optional, default index is 0.\n" " Note: You can only modify one VOLREG_MATVEC_index at a time.\n" " -vr_center_old Use these 3 values for VOLREG_CENTER_OLD.\n" " -vr_center_base Use these 3 values for VOLREG_CENTER_BASE.\n" "\n" ); printf("\t\tLast modified: Oct 04/02.\n"); exit(0) ; } #define ASET_NULL 1 #define ASET_SELF 2 int main( int argc , char * argv[] ) { THD_3dim_dataset * dset , * aset = NULL ; int aset_code = 0 ; /* 14 Dec 1999 */ THD_dataxes * daxes ; int new_stuff = 0 ; int new_orient = 0 ; char orient_code[4] ; int xxor,yyor,zzor ; int new_xorg = 0 ; float xorg ; int cxorg=0, dxorg=0 , duporg=0 ; int new_yorg = 0 ; float yorg ; int cyorg=0, dyorg=0 ; int new_zorg = 0 ; float zorg ; int czorg=0, dzorg=0 ; int new_xdel = 0 ; float xdel ; int new_ydel = 0 ; float ydel ; int new_zdel = 0 ; float zdel ; int new_TR = 0 ; float TR ; int new_Torg = 0 ; float Torg ; /* 29 Jan 2003 */ int new_tunits = 0 ; int tunits ; int new_idcode = 0 ; int new_nowarp = 0 ; int new_stataux= 0 ; float stataux[MAX_STAT_AUX] ; int new_type = 0 ; int dtype , ftype , nvals ; int new_markers= 0 ; int new_view = 0 ; int vtype ; int new_key = 0 ; char * key ; int new_byte_order = 0 ; /* 25 Apr 1998 */ int new_toff_sl = 0 ; /* 12 Feb 2001 */ int clear_bstat = 0 ; /* 28 May 2002 */ int copyaux = 0 ; /* 08 Jun 2004 */ THD_3dim_dataset *auxset=NULL ; /* 08 Jun 2004 */ char *new_label2 = NULL ; /* 21 Dec 2004 */ char str[256] ; int iarg , ii ; typedef struct { int iv ; char lab[32] ; } SUBlabel ; typedef struct { int iv ; float par[MAX_STAT_AUX+2] ; } SUBstatpar ; typedef struct { int iv , code ; char * keyword ; } SUBkeyword ; int nsublab = 0 ; SUBlabel * sublab = NULL ; int nsubstatpar = 0 ; SUBstatpar * substatpar = NULL ; int nsubkeyword = 0 ; SUBkeyword * subkeyword = NULL ; char * cpt ; int iv ; float volreg_mat[12]; float center_old[3]; float center_base[3]; int Do_volreg_mat = 0, Do_center_old = 0, Do_center_base = 0, volreg_matind = 0, icnt = 0; char *lcpt=NULL; /*--- help me if you can? ---*/ if( argc < 2 || strncmp(argv[1],"-help",4) == 0 ) Syntax(NULL) ; iarg = 1 ; /*-- 20 Apr 2001: addto the arglist, if user wants to [RWCox] --*/ mainENTRY("3drefit main"); machdep() ; { int new_argc ; char ** new_argv ; addto_args( argc , argv , &new_argc , &new_argv ) ; if( new_argv != NULL ){ argc = new_argc ; argv = new_argv ; } } AFNI_logger("3drefit",argc,argv) ; while( iarg < argc && argv[iarg][0] == '-' ){ #if 0 if( strncmp(argv[iarg],"-v",5) == 0 ){ verbose = 1 ; iarg++ ; continue ; } #endif /*----- -copyaux auxset [08 Jun 2004] -----*/ if( strcmp(argv[iarg],"-copyaux") == 0 ){ if( iarg+1 >= argc ) Syntax("need 1 argument after -copyaux!") ; if( auxset != NULL ) Syntax("can't have more than one -copyaux option!") ; iarg++ ; copyaux = 1 ; if( strcmp(argv[iarg],"NULL") == 0 ){ /* special case */ auxset = NULL ; } else { auxset = THD_open_one_dataset( argv[iarg] ) ; if( auxset == NULL ) Syntax("can't open -copyaux dataset!") ; } new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /*----- -apar aset [14 Oct 1999] -----*/ if( strcmp(argv[iarg],"-apar") == 0 || strcmp(argv[iarg],"-anatparent") == 0 || strcmp(argv[iarg],"-aset") == 0 ){ if( iarg+1 >= argc ) Syntax("need 1 argument after -apar!") ; if( aset != NULL || aset_code != 0 ) /* 13-14 Dec 1999 */ Syntax("can't have more than one -apar option!"); iarg++ ; if( strcmp(argv[iarg],"NULL") == 0 ){ /* 14 Dec 1999: special cases */ aset_code = ASET_NULL ; } else if( strcmp(argv[iarg],"SELF") == 0 ){ aset_code = ASET_SELF ; } else { aset = THD_open_one_dataset( argv[iarg] ) ; if( aset == NULL ) Syntax("can't open -apar dataset!") ; } new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /*----- -clear_bstat option [28 May 2002] -----*/ if( strcmp(argv[iarg],"-clear_bstat") == 0 ){ clear_bstat = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /*----- -byteorder option [25 April 1998] -----*/ if( strncmp(argv[iarg],"-byteorder",7) == 0 ){ if( iarg+1 >= argc ) Syntax("need 1 argument after -byteorder!") ; iarg++ ; if( strcmp(argv[iarg],LSB_FIRST_STRING) == 0 ) new_byte_order = LSB_FIRST ; else if( strcmp(argv[iarg],MSB_FIRST_STRING) == 0 ) new_byte_order = MSB_FIRST ; else if( strcmp(argv[iarg],NATIVE_STRING) == 0 ) new_byte_order = mri_short_order() ; else Syntax("illegal argument after -byteorder!") ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /*----- -sublabel option -----*/ if( strncmp(argv[iarg],"-sublabel",7) == 0 ){ if( iarg+2 >= argc ) Syntax("need 2 arguments after -sublabel!") ; iv = strtol( argv[++iarg] , &cpt , 10 ) ; if( iv < 0 || iv == 0 && cpt == argv[iarg] ) Syntax("illegal sub-brick index after -sublabel!") ; sublab = (SUBlabel *) XtRealloc( (char *)sublab , sizeof(SUBlabel) * (nsublab+1) ) ; sublab[nsublab].iv = iv ; MCW_strncpy( sublab[nsublab].lab , argv[++iarg] , 32 ) ; nsublab++ ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /*----- -subkeyword options -----*/ if( strncmp(argv[iarg],"-subappkey",7) == 0 || strncmp(argv[iarg],"-subrepkey",7) == 0 || strncmp(argv[iarg],"-subempkey",7) == 0 ){ int code , npl ; if( strncmp(argv[iarg],"-subappkey",7) == 0 ) code = 1 ; else if( strncmp(argv[iarg],"-subrepkey",7) == 0 ) code = 2 ; else code = 3 ; npl = (code == 3) ? 1 : 2 ; if( iarg+npl >= argc ) Syntax("need arguments after -sub...key!") ; iv = strtol( argv[++iarg] , &cpt , 10 ) ; if( iv < 0 || iv == 0 && cpt == argv[iarg] ) Syntax("illegal sub-brick index after -sub...key!") ; subkeyword = (SUBkeyword *) XtRealloc( (char *)subkeyword , sizeof(SUBkeyword)*(nsubkeyword+1) ) ; subkeyword[nsubkeyword].iv = iv ; subkeyword[nsubkeyword].code = code ; if( code != 3 ) subkeyword[nsubkeyword].keyword = argv[++iarg] ; nsubkeyword++ ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /*----- -keywords options -----*/ if( strncmp(argv[iarg],"-appkey",4) == 0 || strncmp(argv[iarg],"-repkey",4) == 0 || strncmp(argv[iarg],"-empkey",4) == 0 ){ int code , npl ; if( strncmp(argv[iarg],"-appkey",4) == 0 ) code = 1 ; else if( strncmp(argv[iarg],"-repkey",4) == 0 ) code = 2 ; else code = 3 ; npl = (code == 3) ? 0 : 1 ; if( iarg+code >= argc ) Syntax("need arguments after -...key!") ; new_key = code ; if( code != 3 ) key = argv[++iarg] ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /*----- -substatpar option -----*/ if( strncmp(argv[iarg],"-substatpar",7) == 0 ){ int fc ; float val ; if( iarg+2 >= argc ) Syntax("need at least 2 arguments after -substatpar!") ; iv = strtol( argv[++iarg] , &cpt , 10 ) ; if( iv < 0 || iv == 0 && cpt == argv[iarg] ) Syntax("illegal sub-brick index after -substatpar!") ; iarg++ ; if( strlen(argv[iarg]) < 3 ) Syntax("illegal type code after -substatpar!") ; fc = (argv[iarg][0] == '-') ? 1 : 0 ; for( ii=FIRST_FUNC_TYPE ; ii <= LAST_FUNC_TYPE ; ii++ ){ if( ! FUNC_IS_STAT(ii) ) continue ; if( strncmp( &(argv[iarg][fc]) , FUNC_prefixstr[ii] , THD_MAX_PREFIX ) == 0 ) break ; } if( ii > LAST_FUNC_TYPE ) Syntax("unknown type code after -substatpar!") ; substatpar = (SUBstatpar *) XtRealloc( (char *)substatpar , sizeof(SUBstatpar) * (nsubstatpar+1) ) ; substatpar[nsubstatpar].iv = iv ; substatpar[nsubstatpar].par[0] = ii ; substatpar[nsubstatpar].par[1] = MAX_STAT_AUX ; for( ii=0 ; ii < MAX_STAT_AUX ; ii++ ) substatpar[nsubstatpar].par[ii+2] = 0.0 ; ii = 2 ; iarg++ ; do{ val = strtod( argv[iarg] , &cpt ) ; if( *cpt != '\0' ) break ; substatpar[nsubstatpar].par[ii++] = val ; iarg++ ; } while( iarg < argc ) ; nsubstatpar++ ; new_stuff++ ; continue ; /* go to next arg */ } /*----- -orient code option -----*/ #define ORCODE(aa) \ ( (aa)=='R' ? ORI_R2L_TYPE : (aa)=='L' ? ORI_L2R_TYPE : \ (aa)=='P' ? ORI_P2A_TYPE : (aa)=='A' ? ORI_A2P_TYPE : \ (aa)=='I' ? ORI_I2S_TYPE : (aa)=='S' ? ORI_S2I_TYPE : ILLEGAL_TYPE ) #define OR3OK(x,y,z) ( ((x)&6) + ((y)&6) + ((z)&6) == 6 ) if( strncmp(argv[iarg],"-orient",4) == 0 ){ char acod ; if( iarg+1 >= argc ) Syntax("need an argument after -orient!"); MCW_strncpy(orient_code,argv[++iarg],4) ; if( strlen(orient_code) != 3 ) Syntax("Illegal -orient code") ; acod = toupper(orient_code[0]) ; xxor = ORCODE(acod) ; acod = toupper(orient_code[1]) ; yyor = ORCODE(acod) ; acod = toupper(orient_code[2]) ; zzor = ORCODE(acod) ; if( xxor<0 || yyor<0 || zzor<0 || ! OR3OK(xxor,yyor,zzor) ) Syntax("Unusable -orient code!") ; new_orient = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /** -?origin dist **/ if( strcmp(argv[iarg],"-xorigin") == 0 ){ if( ++iarg >= argc ) Syntax("need an argument after -xorigin!"); if( strncmp(argv[iarg],"cen",3) == 0 ) cxorg = 1 ; else xorg = strtod(argv[iarg],NULL) ; dxorg = 0 ; new_xorg = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } if( strcmp(argv[iarg],"-yorigin") == 0 ){ if( ++iarg >= argc ) Syntax("need an argument after -yorigin!"); if( strncmp(argv[iarg],"cen",3) == 0 ) cyorg = 1 ; else yorg = strtod(argv[iarg],NULL) ; dyorg = 0 ; new_yorg = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } if( strcmp(argv[iarg],"-zorigin") == 0 ){ if( ++iarg >= argc ) Syntax("need an argument after -zorigin!"); if( strncmp(argv[iarg],"cen",3) == 0 ) czorg = 1 ; else zorg = strtod(argv[iarg],NULL) ; dzorg = 0 ; new_zorg = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /* 13 Sep 2000: -duporigin */ if( strcmp(argv[iarg],"-duporigin") == 0 ){ THD_3dim_dataset * cset ; if( ++iarg >= argc ) Syntax("need an argument after -duporigin!"); cset = THD_open_dataset( argv[iarg] ) ; if( cset == NULL ) Syntax("couldn't open -duporigin dataset!"); daxes = cset->daxes ; xorg = daxes->xxorg ; yorg = daxes->yyorg ; zorg = daxes->zzorg ; cxorg = cyorg = czorg = dxorg = dyorg = dzorg = 0 ; new_xorg = new_yorg = new_zorg = duporg = 1 ; new_stuff++ ; DSET_delete(cset) ; iarg++ ; continue ; /* go to next arg */ } /* 02 Mar 2000: -d?origin stuff, to go with plug_nudge.c */ if( strncmp(argv[iarg],"-dxorigin",4) == 0 ){ if( ++iarg >= argc ) Syntax("need an argument after -dxorigin!"); xorg = strtod(argv[iarg],NULL) ; dxorg = 1 ; cxorg = 0 ; new_xorg = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } if( strncmp(argv[iarg],"-dyorigin",4) == 0 ){ if( ++iarg >= argc ) Syntax("need an argument after -dyorigin!"); yorg = strtod(argv[iarg],NULL) ; dyorg = 1 ; cyorg = 0 ; new_yorg = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } if( strncmp(argv[iarg],"-dzorigin",4) == 0 ){ if( ++iarg >= argc ) Syntax("need an argument after -dzorigin!"); zorg = strtod(argv[iarg],NULL) ; dzorg = 1 ; czorg = 0 ; new_zorg = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /** 04 Oct 2002: _raw origins **/ if( strcmp(argv[iarg],"-xorigin_raw") == 0 ){ if( ++iarg >= argc ) Syntax("need an argument after -xorigin_raw!"); xorg = strtod(argv[iarg],NULL) ; cxorg = dxorg = 0 ; new_xorg = 2 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } if( strcmp(argv[iarg],"-yorigin_raw") == 0 ){ if( ++iarg >= argc ) Syntax("need an argument after -yorigin_raw!"); yorg = strtod(argv[iarg],NULL) ; cyorg = dyorg = 0 ; new_yorg = 2 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } if( strcmp(argv[iarg],"-zorigin_raw") == 0 ){ if( ++iarg >= argc ) Syntax("need an argument after -zorigin_raw!"); zorg = strtod(argv[iarg],NULL) ; czorg = dzorg = 0 ; new_zorg = 2 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /** 04 Oct 2002: zadd VOLREG fields **/ if( strcmp(argv[iarg],"-vr_mat") == 0 ){ if( iarg+12 >= argc ) Syntax("need 12 arguments after -vr_mat!"); icnt = 0; while (icnt < 12) { ++iarg; volreg_mat[icnt] = strtod(argv[iarg], &lcpt) ; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!"); ++icnt; } Do_volreg_mat = 1; new_stuff++ ; ++iarg; continue ; /* go to next arg */ } if( strcmp(argv[iarg],"-vr_mat_ind") == 0) { if (++iarg >= argc) Syntax("need 1 argument after -vr_mat_ind!"); volreg_matind = (int)strtol(argv[iarg], &lcpt, 10); if (*lcpt != '\0') Syntax("Bad syntax in number argument!"); ++iarg; continue ; /* go to next arg */ } if( strcmp(argv[iarg],"-vr_cen_old") == 0) { if (iarg+3 >= argc) Syntax("need 3 arguments after -vr_cen_old"); ++iarg; center_old[0] = strtod(argv[iarg],&lcpt) ; ++iarg; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!"); center_old[1] = strtod(argv[iarg],&lcpt) ; ++iarg; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!"); center_old[2] = strtod(argv[iarg],&lcpt) ; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!"); Do_center_old = 1; new_stuff++ ; ++iarg; continue ; /* go to next arg */ } if( strcmp(argv[iarg],"-vr_cen_base") == 0) { if (iarg+3 >= argc) Syntax("need 3 arguments after -vr_cen_base"); ++iarg; center_base[0] = strtod(argv[iarg],&lcpt) ; ++iarg; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!"); center_base[1] = strtod(argv[iarg],&lcpt) ; ++iarg; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!"); center_base[2] = strtod(argv[iarg],&lcpt) ; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!"); Do_center_base = 1; new_stuff++ ; ++iarg; continue ; /* go to next arg */ } /** -?del dim **/ if( strncmp(argv[iarg],"-xdel",4) == 0 ){ if( iarg+1 >= argc ) Syntax("need an argument after -xdel!"); xdel = strtod( argv[++iarg] , NULL ) ; if( xdel <= 0.0 ) Syntax("argument after -xdel must be positive!") ; new_xdel = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } if( strncmp(argv[iarg],"-ydel",4) == 0 ){ if( iarg+1 >= argc ) Syntax("need an argument after -ydel!"); ydel = strtod( argv[++iarg] , NULL ) ; if( ydel <= 0.0 ) Syntax("argument after -ydel must be positive!") ; new_ydel = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } if( strncmp(argv[iarg],"-zdel",4) == 0 ){ if( iarg+1 >= argc ) Syntax("need an argument after -zdel!"); zdel = strtod( argv[++iarg] , NULL ) ; if( zdel <= 0.0 ) Syntax("argument after -zdel must be positive!") ; new_zdel = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /** -TR **/ if( strncmp(argv[iarg],"-TR",3) == 0 ){ char * eptr ; if( iarg+1 >= argc ) Syntax("need an argument after -TR!"); TR = strtod( argv[++iarg] , &eptr ) ; if( TR <= 0.0 ) Syntax("argument after -TR must be positive!") ; if( strcmp(eptr,"ms")==0 || strcmp(eptr,"msec")==0 ){ new_tunits = 1 ; tunits = UNITS_MSEC_TYPE ; } else if( strcmp(eptr,"s")==0 || strcmp(eptr,"sec")==0 ){ new_tunits = 1 ; tunits = UNITS_SEC_TYPE ; } else if( strcmp(eptr,"Hz")==0 || strcmp(eptr,"Hertz")==0 ){ new_tunits = 1 ; tunits = UNITS_HZ_TYPE ; } new_TR = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /** -notoff (12 Feb 2001) **/ if( strncmp(argv[iarg],"-notoff",7) == 0 ){ new_toff_sl = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /** -Torg (29 Jan 2003) **/ if( strncmp(argv[iarg],"-Torg",5) == 0 ){ char *eptr ; if( iarg+1 >= argc ) Syntax("need an argument after -Torg!"); Torg = strtod( argv[++iarg] , &eptr ) ; if( *eptr != '\0' ) fprintf(stderr,"** -Torg %s ends in unexpected character\n",argv[iarg]) ; new_Torg = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /** -newid **/ if( strncmp(argv[iarg],"-newid",4) == 0 ){ new_idcode = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /** -nowarp **/ if( strncmp(argv[iarg],"-nowarp",6) == 0 ){ new_nowarp = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /** -statpar x x x **/ if( strncmp(argv[iarg],"-statpar",4) == 0 ){ float val ; char * ptr ; if( ++iarg >= argc ) Syntax("need an argument after -statpar!") ; for( ii=0 ; ii < MAX_STAT_AUX ; ii++ ) stataux[ii] = 0.0 ; ii = 0 ; do{ val = strtod( argv[iarg] , &ptr ) ; if( *ptr != '\0' ) break ; stataux[ii++] = val ; iarg++ ; } while( iarg < argc ) ; if( ii == 0 ) Syntax("No numbers given after -statpar?") ; new_stataux = 1 ; new_stuff++ ; continue ; } /** -markers **/ if( strncmp(argv[iarg],"-markers",4) == 0 ){ new_markers = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /** -label2 [21 Dec 2004] **/ if( strcmp(argv[iarg],"-label2") == 0 ){ new_label2 = argv[++iarg] ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /** -view code **/ if( strncmp(argv[iarg],"-view",4) == 0 ){ char * code ; if( iarg+1 >= argc ) Syntax("need an argument after -view!") ; code = argv[++iarg] ; if( code[0] == '+' ) code++ ; for( vtype=0 ; vtype <= LAST_VIEW_TYPE ; vtype++ ) if( strcmp(code,VIEW_codestr[vtype]) == 0 ) break ; if( vtype > LAST_VIEW_TYPE ) Syntax("argument after -view is illegal!") ; new_view = 1 ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */ } /** anything else must be a -type **/ /* try the anatomy prefixes */ for( ii=FIRST_ANAT_TYPE ; ii <= LAST_ANAT_TYPE ; ii++ ) if( strncmp( &(argv[iarg][1]) , ANAT_prefixstr[ii] , THD_MAX_PREFIX ) == 0 ) break ; if( ii <= LAST_ANAT_TYPE ){ ftype = ii ; dtype = HEAD_ANAT_TYPE ; nvals = ANAT_nvals[ftype] ; new_type = 1 ; new_stuff++ ; iarg++ ; continue ; } /* try the function prefixes */ for( ii=FIRST_FUNC_TYPE ; ii <= LAST_FUNC_TYPE ; ii++ ) if( strncmp( &(argv[iarg][1]) , FUNC_prefixstr[ii] , THD_MAX_PREFIX ) == 0 ) break ; if( ii <= LAST_FUNC_TYPE ){ ftype = ii ; dtype = HEAD_FUNC_TYPE ; nvals = FUNC_nvals[ftype] ; new_type = 1 ; new_stuff++ ; iarg++ ; continue ; } /** error **/ { char str[256] ; sprintf(str,"Unknown option %s",argv[iarg]) ; Syntax(str) ; } } /* end of loop over switches */ if( new_stuff == 0 ) Syntax("No options given!?") ; if( iarg >= argc ) Syntax("No datasets given!?") ; if( new_orient && (dxorg || dyorg || dzorg) ) /* 02 Mar 2000 */ Syntax("Can't use -orient with -d?origin!?") ; /*--- process datasets ---*/ for( ; iarg < argc ; iarg++ ){ dset = THD_open_one_dataset( argv[iarg] ) ; if( dset == NULL ){ fprintf(stderr,"** 3drefit: Can't open dataset %s\n",argv[iarg]) ; continue ; } if( DSET_IS_MINC(dset) ){ fprintf(stderr,"** 3drefit: Can't process MINC dataset %s\n",argv[iarg]); continue ; } if( DSET_IS_ANALYZE(dset) ){ fprintf(stderr,"** 3drefit: Can't process ANALYZE dataset %s\n",argv[iarg]); continue ; } if( DSET_IS_1D(dset) ){ fprintf(stderr,"** 3drefit: Can't process 1D dataset %s\n",argv[iarg]); continue ; } if( DSET_IS_CTFMRI(dset) || DSET_IS_CTFSAM(dset) ){ fprintf(stderr,"** 3drefit: Can't process CTF dataset %s\n",argv[iarg]); continue ; } if( DSET_IS_NIFTI(dset) ){ fprintf(stderr,"** 3drefit: Can't process NIFTI dataset %s\n",argv[iarg]); continue ; } if( DSET_IS_MPEG(dset) ){ fprintf(stderr,"** 3drefit: Can't process MPEG dataset %s\n",argv[iarg]); continue ; } fprintf(stderr,"++ 3drefit: Processing AFNI dataset %s\n",argv[iarg]) ; tross_Make_History( "3drefit" , argc,argv, dset ) ; /* 21 Dec 2004: -label2 option */ if( new_label2 != NULL ) EDIT_dset_items( dset , ADN_label2 , new_label2 , ADN_none ) ; /* 14 Oct 1999: change anat parent */ /* 14 Dec 1999: allow special cases: SELF and NULL */ if( aset != NULL ){ EDIT_dset_items( dset , ADN_anat_parent , aset , ADN_none ) ; } else if( aset_code == ASET_SELF ){ EDIT_dset_items( dset , ADN_anat_parent , dset , ADN_none ) ; } else if( aset_code == ASET_NULL ){ EDIT_ZERO_ANATOMY_PARENT_ID( dset ) ; dset->anat_parent_name[0] = '\0' ; } /* Oct 04/02: zmodify volreg fields */ if (Do_volreg_mat) { sprintf(str,"VOLREG_MATVEC_%06d", volreg_matind) ; fprintf (stderr," Modifying %s ...\n", str); THD_set_float_atr( dset->dblk , str , 12 , volreg_mat ) ; } if (Do_center_old) { fprintf (stderr," Modifying VOLREG_CENTER_OLD ...\n"); THD_set_float_atr( dset->dblk , "VOLREG_CENTER_OLD" , 3 , center_old ) ; } if (Do_center_base) { fprintf (stderr," Modifying VOLREG_CENTER_BASE ...\n"); THD_set_float_atr( dset->dblk , "VOLREG_CENTER_BASE" , 3 , center_base ) ; } /* 28 May 2002: clear brick stats */ if( clear_bstat ){ if( !ISVALID_STATISTIC(dset->stats) ){ fprintf(stderr,"++ -clear_bstat: dataset has no brick statistics\n") ; } else { KILL_STATISTIC(dset->stats) ; REMOVEFROM_KILL( dset->kl , dset->stats ) ; REMOVEFROM_KILL( dset->kl , dset->stats->bstat ) ; dset->stats = NULL ; } } /* 25 April 1998 */ if( new_byte_order > 0 ) dset->dblk->diskptr->byte_order = new_byte_order ; daxes = dset->daxes ; if( new_orient ){ daxes->xxorient = xxor ; daxes->yyorient = yyor ; daxes->zzorient = zzor ; } if( !new_xorg ) xorg = fabs(daxes->xxorg) ; if( !new_yorg ) yorg = fabs(daxes->yyorg) ; if( !new_zorg ) zorg = fabs(daxes->zzorg) ; if( !new_xdel ) xdel = fabs(daxes->xxdel) ; if( !new_ydel ) ydel = fabs(daxes->yydel) ; if( !new_zdel ) zdel = fabs(daxes->zzdel) ; if( cxorg ) xorg = 0.5 * (daxes->nxx - 1) * xdel ; if( cyorg ) yorg = 0.5 * (daxes->nyy - 1) * ydel ; if( czorg ) zorg = 0.5 * (daxes->nzz - 1) * zdel ; if( dxorg ) daxes->xxorg += xorg ; else if( duporg || new_xorg==2 ) daxes->xxorg = xorg ; else if( new_xorg==1 || new_orient ) daxes->xxorg = (ORIENT_sign[daxes->xxorient] == '+') ? (-xorg) : (xorg) ; if( dyorg ) daxes->yyorg += yorg ; else if( duporg || new_yorg==2 ) daxes->yyorg = yorg ; else if( new_yorg==1 || new_orient ) daxes->yyorg = (ORIENT_sign[daxes->yyorient] == '+') ? (-yorg) : (yorg) ; if( dzorg ) daxes->zzorg += zorg ; else if( duporg || new_zorg==2 ) daxes->zzorg = zorg ; else if( new_zorg==1 || new_orient ) daxes->zzorg = (ORIENT_sign[daxes->zzorient] == '+') ? (-zorg) : (zorg) ; if( new_xdel || new_orient ) daxes->xxdel = (ORIENT_sign[daxes->xxorient] == '+') ? (xdel) : (-xdel) ; if( new_ydel || new_orient ) daxes->yydel = (ORIENT_sign[daxes->yyorient] == '+') ? (ydel) : (-ydel) ; if( new_zdel || new_orient ) daxes->zzdel = (ORIENT_sign[daxes->zzorient] == '+') ? (zdel) : (-zdel) ; if( new_TR ){ if( dset->taxis == NULL ){ fprintf(stderr," ** can't process -TR for this dataset!\n") ; } else { float frac = TR / dset->taxis->ttdel ; int ii ; dset->taxis->ttdel = TR ; if( new_tunits ) dset->taxis->units_type = tunits ; if( dset->taxis->nsl > 0 ){ for( ii=0 ; ii < dset->taxis->nsl ; ii++ ) dset->taxis->toff_sl[ii] *= frac ; } } } if( new_Torg ){ /* 29 Jan 2003 */ if( dset->taxis == NULL ){ fprintf(stderr," ** can't process -Torg for this dataset!\n") ; } else { dset->taxis->ttorg = Torg ; } } if( new_toff_sl ){ /* 12 Feb 2001 */ if( dset->taxis == NULL ){ fprintf(stderr," ** -notoff: dataset has no time axis to clear!\n") ; } else if( dset->taxis->nsl <= 0 ){ fprintf(stderr," ** -notoff: dataset has no time-offsets to clear!\n") ; } else { EDIT_dset_items( dset , ADN_nsl,0 , ADN_none ) ; } } if( (new_orient || new_zorg) && dset->taxis != NULL && dset->taxis->nsl > 0 ){ dset->taxis->zorg_sl = daxes->zzorg ; } if( (new_orient || new_zdel) && dset->taxis != NULL && dset->taxis->nsl > 0 ){ dset->taxis->dz_sl = daxes->zzdel ; } if( new_idcode ) dset->idcode = MCW_new_idcode() ; if( new_nowarp ){ ZERO_IDCODE( dset->warp_parent_idcode ) ; dset->warp_parent_name[0] = '\0' ; dset->warp = NULL ; } if( new_type ){ if( nvals > 1 && dset->taxis != NULL ){ fprintf(stderr," ** can't change 3D+time dataset to new type:\n") ; fprintf(stderr," new type has more than one value per voxel!\n") ; } else if( dset->taxis == NULL && nvals != dset->dblk->nvals && ((dtype==HEAD_FUNC_TYPE && ftype!=FUNC_BUCK_TYPE)|| (dtype==HEAD_ANAT_TYPE && ftype!=ANAT_BUCK_TYPE) ) ){ fprintf(stderr," ** can't change dataset to new type:\n") ; fprintf(stderr," mismatch in number of sub-bricks!\n") ; } else { dset->type = dtype ; dset->func_type = ftype ; if( ISBUCKET(dset) && dset->taxis != NULL ){ /* 29 April 1998 */ fprintf(stderr," ** Warning: changing 3D+time dataset to bucket\n") ; EDIT_dset_items( dset , ADN_ntt , 0 , ADN_none ) ; } } } if( new_stataux ){ for( ii=0 ; ii < MAX_STAT_AUX ; ii++ ){ dset->stat_aux[ii] = stataux[ii] ; } } if( new_view && dset->view_type != vtype ){ int old_vtype = dset->view_type ; char old_head[THD_MAX_NAME] , old_brik[THD_MAX_NAME] ; char new_head[THD_MAX_NAME] , new_brik[THD_MAX_NAME] ; int brick_ccode = COMPRESS_filecode( DSET_BRIKNAME(dset) ) ; strcpy(old_head,DSET_HEADNAME(dset)) ; strcpy(old_brik,DSET_BRIKNAME(dset)) ; dset->view_type = vtype ; THD_init_diskptr_names( dset->dblk->diskptr , NULL , NULL , NULL , vtype , True ) ; strcpy(new_head,DSET_DIRNAME(dset)) ; strcat(new_head,DSET_HEADNAME(dset)) ; strcpy(new_brik,DSET_DIRNAME(dset)) ; strcat(new_brik,DSET_BRIKNAME(dset)) ; if( THD_is_file(new_head) ){ dset->view_type = old_vtype ; THD_init_diskptr_names( dset->dblk->diskptr , NULL , NULL , NULL , old_vtype , True ) ; fprintf(stderr, " ** Can't change view: would overwrite existing files!\n") ; } else { rename( old_head , new_head ) ; { char * fff = COMPRESS_filename(old_brik) ; if( fff != NULL ){ char * ggg = malloc( sizeof(char) * (strlen(fff)+32) ) ; strcpy(ggg,new_brik) ; if( brick_ccode >= 0 ) strcat(ggg,COMPRESS_suffix[brick_ccode]) ; rename( fff , ggg ) ; free(fff) ; free(ggg) ; } } fprintf(stderr," -- Changed dataset view type and filenames.\n") ; } } if( new_markers && dset->type == HEAD_ANAT_TYPE && dset->view_type == VIEW_ORIGINAL_TYPE && DSET_NUM_TIMES(dset) == 1 ){ /* code copied from to3d.c */ THD_marker_set * markers ; int ii , jj ; markers = dset->markers = myXtNew( THD_marker_set ) ; markers->numdef = 0 ; for( ii=0 ; ii < MARKS_MAXNUM ; ii++ ){ /* null all data out */ markers->valid[ii] = 0 ; for( jj=0 ; jj < MARKS_MAXLAB ; jj++ ) markers->label[ii][jj] = '\0'; for( jj=0 ; jj < MARKS_MAXHELP ; jj++ ) markers->help[ii][jj] = '\0'; } for( ii=0 ; ii < NMARK_ALIGN ; ii++ ){ /* copy strings in */ MCW_strncpy( &(markers->label[ii][0]) , THD_align_label[ii] , MARKS_MAXLAB ) ; MCW_strncpy( &(markers->help[ii][0]) , THD_align_help[ii] , MARKS_MAXHELP ) ; } for( ii=0 ; ii < MARKS_MAXFLAG ; ii++ ) /* copy flags in */ markers->aflags[ii] = THD_align_aflags[ii] ; } else if( new_markers ){ fprintf(stderr," ** can't add markers to this dataset\n") ; } /* end of markers */ /*-- 08 Jun 2004: copyaux? --*/ if( copyaux ){ if( auxset != NULL ){ THD_copy_datablock_auxdata( auxset->dblk , dset->dblk ); INIT_STAT_AUX( dset , MAX_STAT_AUX , auxset->stat_aux ) ; } else { THD_copy_datablock_auxdata( NULL , dset->dblk ); } } /*-- new aux data? --*/ if( nsublab > 0 ){ for( ii=0 ; ii < nsublab ; ii++ ){ iv = sublab[ii].iv ; if( iv < 0 || iv >= DSET_NVALS(dset) ){ fprintf(stderr," ** can't put label on sub-brick %d\n",iv) ; } else { EDIT_dset_items( dset , ADN_brick_label_one + iv , sublab[ii].lab , ADN_none ) ; } } } if( nsubkeyword > 0 ){ int code ; for( ii=0 ; ii < nsubkeyword ; ii++ ){ iv = subkeyword[ii].iv ; code = subkeyword[ii].code ; if( iv < 0 || iv >= DSET_NVALS(dset) ){ fprintf(stderr," ** can't put keyword on sub-brick %d\n",iv) ; } else if( code == 1 ){ EDIT_dset_items( dset , ADN_brick_keywords_append_one + iv , subkeyword[ii].keyword , ADN_none ) ; } else if( code == 2 ){ EDIT_dset_items( dset , ADN_brick_keywords_replace_one + iv , subkeyword[ii].keyword , ADN_none ) ; } else if( code == 3 && dset->dblk->brick_keywords != NULL ){ EDIT_dset_items( dset , ADN_brick_keywords_replace_one + iv , NULL , ADN_none ) ; } } } switch( new_key ){ case 1: EDIT_dset_items(dset, ADN_keywords_append , key , ADN_none); break; case 2: EDIT_dset_items(dset, ADN_keywords_replace, key , ADN_none); break; case 3: EDIT_dset_items(dset, ADN_keywords_replace, NULL, ADN_none); break; } if( nsubstatpar > 0 ){ for( ii=0 ; ii < nsubstatpar ; ii++ ){ iv = substatpar[ii].iv ; if( iv < 0 || iv >= DSET_NVALS(dset) ){ fprintf(stderr," ** can't put statpar on sub-brick %d\n",iv) ; } else { EDIT_dset_items( dset , ADN_brick_stataux_one + iv , substatpar[ii].par , ADN_none ) ; } } } THD_write_3dim_dataset( NULL,NULL , dset , False ) ; THD_delete_3dim_dataset( dset , False ) ; } exit(0) ; }