/***************************************************************************** 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" #undef TTDEBUG #undef USE_PTHRESH /*-------------------------- global data --------------------------*/ /** inputs **/ static EDIT_options TT_edopt ; static int TT_paired = 0 ; static int TT_pooled = 1 ; static float TT_pthresh = 0.0 ; static int TT_use_bval = 0 ; static float TT_bval = 0.0 ; static int TT_use_editor = 0 ; static int TT_be_quiet = 0 ; static int TT_workmem = 12 ; /* default = 12 Megabytes */ #define MEGA 1048576 /* 2^20 */ static THD_string_array * TT_set1 = NULL ; /* sets of dataset names */ static THD_string_array * TT_set2 = NULL ; static char TT_session[THD_MAX_NAME] = "./" ; static char TT_prefix[THD_MAX_PREFIX] = "tdif" ; static char TT_label[THD_MAX_LABEL] = "\0" ; static int TT_datum = ILLEGAL_TYPE ; static char TT_dof_prefix[THD_MAX_PREFIX] = "\0" ; /* 27 Dec 2002 */ /*--------------------------- prototypes ---------------------------*/ void TT_read_opts( int , char ** ) ; void TT_syntax(char *) ; /*-------------------------------------------------------------------- read the arguments, and load the global variables ----------------------------------------------------------------------*/ #ifdef TTDEBUG # define DUMP1 fprintf(stderr,"ARG: %s\n",argv[nopt]) # define DUMP2 fprintf(stderr,"ARG: %s %s\n",argv[nopt],argv[nopt+1]) # define DUMP3 fprintf(stderr,"ARG: %s %s %s\n",argv[nopt],argv[nopt+1],argv[nopt+2]) #else # define DUMP1 # define DUMP2 # define DUMP3 #endif void TT_read_opts( int argc , char * argv[] ) { int nopt = 1 ; float val ; int ival , kk ; INIT_EDOPT( &TT_edopt ) ; while( nopt < argc && argv[nopt][0] == '-' ){ /**** editing option? ****/ ival = EDIT_check_argv( argc , argv , nopt , &TT_edopt ) ; if( ival > 0 ){ TT_use_editor = 1 ; nopt += ival ; continue ; } /**** -quiet ****/ if( strncmp(argv[nopt],"-quiet",6) == 0 ){ DUMP1 ; TT_be_quiet = 1 ; nopt++ ; continue ; } /**** -workmem megabytes ****/ if( strncmp(argv[nopt],"-workmem",6) == 0 ){ nopt++ ; if( nopt >= argc ) TT_syntax("need argument after -workmem!") ; ival = strtol( argv[nopt] , NULL , 10 ) ; if( ival <= 0 ) TT_syntax("illegal argument after -workmem!") ; TT_workmem = ival ; nopt++ ; continue ; } /**** -datum type ****/ if( strncmp(argv[nopt],"-datum",6) == 0 ){ if( ++nopt >= argc ) TT_syntax("need an argument after -datum!") ; if( strcmp(argv[nopt],"short") == 0 ){ TT_datum = MRI_short ; } else if( strcmp(argv[nopt],"float") == 0 ){ TT_datum = MRI_float ; } else { char buf[256] ; sprintf(buf,"-datum of type '%s' is not supported in 3dttest!", argv[nopt] ) ; TT_syntax(buf) ; } nopt++ ; continue ; /* go to next arg */ } /**** -session dirname ****/ if( strncmp(argv[nopt],"-session",6) == 0 ){ DUMP2 ; nopt++ ; if( nopt >= argc ) TT_syntax("need argument after -session!") ; MCW_strncpy( TT_session , argv[nopt++] , THD_MAX_NAME ) ; continue ; } /**** -prefix prefix ****/ if( strncmp(argv[nopt],"-prefix",6) == 0 ){ DUMP2 ; nopt++ ; if( nopt >= argc ) TT_syntax("need argument after -prefix!") ; MCW_strncpy( TT_prefix , argv[nopt++] , THD_MAX_PREFIX ) ; continue ; } #if 0 /**** -label string ****/ if( strncmp(argv[nopt],"-label",6) == 0 ){ DUMP2 ; nopt++ ; if( nopt >= argc ) TT_syntax("need argument after -label!") ; MCW_strncpy( TT_label , argv[nopt++] , THD_MAX_LABEL ) ; continue ; } #endif /** -paired **/ if( strncmp(argv[nopt],"-paired",6) == 0 ){ TT_paired = 1 ; nopt++ ; continue ; /* skip to next arg */ } /** -unpooled **/ if( strncmp(argv[nopt],"-unpooled",6) == 0 ){ TT_pooled = 0 ; nopt++ ; continue ; /* skip to next arg */ } /** -dof_prefix **/ if( strncmp(argv[nopt],"-dof_prefix",6) == 0 ){ /* 27 Dec 2002 */ DUMP2 ; nopt++ ; if( nopt >= argc ) TT_syntax("need argument after -dof_prefix!") ; MCW_strncpy( TT_dof_prefix , argv[nopt++] , THD_MAX_PREFIX ) ; continue ; } #ifdef USE_PTHRESH /** -pthresh pval **/ if( strncmp(argv[nopt],"-pthresh",6) == 0 ){ char * ch ; if( ++nopt >= argc ) TT_syntax("-pthresh needs a value!"); TT_pthresh = strtod( argv[nopt] , &ch ) ; if( *ch != '\0' || TT_pthresh <= 0.0 || TT_pthresh > 0.99999 ) TT_syntax("value after -pthresh is illegal!") ; fprintf(stderr, "*** -pthresh not implemented yet, will ignore!\n" ) ; TT_pthresh = 0.0 ; nopt++ ; continue ; /* skip to next arg */ } #endif /**** after this point, the options are no longer 'free floating' ****/ /** -base1 bval **/ if( strncmp(argv[nopt],"-base1",6) == 0 ){ char * ch ; if( ++nopt >= argc ) TT_syntax("-base1 needs a value!"); if( TT_use_bval == -1 ) TT_syntax("-base1 with -set1 illegal!"); TT_bval = strtod( argv[nopt] , &ch ) ; if( *ch != '\0' ) TT_syntax("value after -base1 is illegal!") ; TT_use_bval = 1 ; nopt++ ; continue ; /* skip to next arg */ } /** -set1 file file ... **/ if( strncmp(argv[nopt],"-set1",6) == 0 ){ if( TT_use_bval == 1 ) TT_syntax("-set1 with -base1 illegal!"); TT_use_bval = -1 ; INIT_SARR( TT_set1 ) ; for( kk=nopt+1 ; kk < argc ; kk++ ){ if( strncmp(argv[kk],"-set2",6) == 0 ) break ; ADDTO_SARR( TT_set1 , argv[kk] ) ; } if( kk >= argc ) TT_syntax("-set1 not followed by -set2") ; if( kk-1-nopt <= 0 ) TT_syntax("-set1 has no datasets after it") ; if( TT_set1->num < 2 ) TT_syntax("-set1 doesn't have enough datasets") ; nopt = kk ; continue ; /* skip to arg that matched -set2 */ } /** -set2 file file ... */ if( strncmp(argv[nopt],"-set2",6) == 0 ){ INIT_SARR( TT_set2 ) ; for( kk=nopt+1 ; kk < argc ; kk++ ){ ADDTO_SARR( TT_set2 , argv[kk] ) ; } if( TT_set2->num < 2 ) TT_syntax("-set2 doesn't have enough datasets") ; break ; /* end of possible inputs */ } /**** unknown switch ****/ fprintf(stderr,"*** unrecognized option %s\n",argv[nopt]) ; exit(1) ; } /* end of loop over options */ if( strlen(TT_label) == 0 ){ MCW_strncpy(TT_label,TT_prefix,THD_MAX_LABEL) ; } /*--- check arguments for consistency ---*/ if( TT_use_bval == 0 ) TT_syntax("neither -base1 nor -set1 is present!") ; if( TT_use_bval == -1 && ( TT_set1 == NULL || TT_set1->num < 2 ) ) TT_syntax("-set1 has too few datasets in it!") ; if( TT_set2 == NULL || TT_set2->num < 2 ) TT_syntax("-set2 has too few datasets in it!") ; if( TT_use_bval == 1 && TT_paired == 1 ) TT_syntax("-paired and -base1 are mutually exclusive!") ; if( TT_paired == 1 && TT_set1 == NULL ) TT_syntax("-paired requires presence of -set1!") ; if( TT_paired == 1 && TT_set1->num != TT_set2->num ){ char str[256] ; sprintf(str,"-paired requires equal size dataset collections,\n" "but -set1 has %d datasets and -set2 has %d datasets" , TT_set1->num , TT_set2->num ) ; TT_syntax(str) ; } if( TT_pooled == 0 && TT_paired == 1 ) TT_syntax("-paired and -unpooled are mutually exclusive!") ; if( TT_pooled == 0 && TT_use_bval == 1 ) TT_syntax("-base1 and -unpooled are mutually exclusive!") ; if( TT_pooled == 1 && TT_dof_prefix[0] != '\0' ) /* 27 Dec 2002 */ fprintf(stderr,"** WARNING: -dof_prefix is used only with -unpooled!\n"); #ifdef TTDEBUG printf("*** finished with options\n") ; #endif return ; } /*------------------------------------------------------------------*/ void TT_syntax(char * msg) { if( msg != NULL ){ fprintf(stderr,"*** %s\n",msg) ; exit(1) ; } printf( "Gosset (Student) t-test sets of 3D datasets\n" "Usage 1: 3dttest [options] -set1 datasets ... -set2 datasets ...\n" " for comparing the means of 2 sets of datasets (voxel by voxel).\n" "\n" "Usage 2: 3dttest [options] -base1 bval -set2 datasets ...\n" " for comparing the mean of 1 set of datasets against a constant.\n" "\n" "OUTPUTS:\n" " A single dataset is created that is the voxel-by-voxel difference\n" " of the mean of set2 minus the mean of set1 (or minus 'bval').\n" " The output dataset will be of the intensity+Ttest ('fitt') type.\n" " The t-statistic at each voxel can be used as an interactive\n" " thresholding tool in AFNI.\n" #ifdef USE_PTHRESH " If the -pthresh option (below) is used to threshold for significance,\n" " then the t-values will NOT be stored for each voxel; that is, the output\n" " dataset will be of the intensity-only ('fim') type.\n" #endif "\n" "t-TESTING OPTIONS:\n" " -set1 datasets ... = Specifies the collection of datasets to put into\n" " the first set. The mean of set1 will be tested\n" " with a 2-sample t-test against the mean of set2.\n" " N.B.: -set1 and -base1 are mutually exclusive!\n" " -base1 bval = 'bval' is a numerical value that the mean of set2\n" " will be tested against with a 1-sample t-test.\n" " -set2 datasets ... = Specifies the collection of datasets to put into\n" " the second set. There must be at least 2 datasets\n" " in each of set1 (if used) and set2.\n" " -paired = Specifies the use of a paired-sample t-test to\n" " compare set1 and set2. If this option is used,\n" " set1 and set2 must have the same cardinality.\n" " N.B.: A paired test is intended for use when the set1 and set2\n" " dataset function values may be pairwise correlated.\n" " If they are in fact uncorrelated, this test has less\n" " statistical 'power' than the unpaired (default) t-test.\n" " This loss of power is the price that is paid for\n" " insurance against pairwise correlations.\n" " -unpooled = Specifies that the variance estimates for set1 and\n" " set2 be computed separately (not pooled together).\n" " This only makes sense if -paired is NOT given.\n" " N.B.: If this option is used, the number of degrees\n" " of freedom per voxel is a variable, rather\n" " than a constant.\n" " -dof_prefix ddd = If '-unpooled' is also used, then a dataset with\n" " prefix 'ddd' will be created that contains the\n" " degrees of freedom (DOF) in each voxel.\n" " You can convert the t-value in the -prefix\n" " dataset to a z-score using the -dof_prefix dataset\n" " using commands like so:\n" " 3dcalc -a 'pname+orig[1]' -b ddd+orig \\\n" " -datum float -prefix ddd_zz -expr 'fitt_t2z(a,b)'\n" " 3drefit -substatpar 0 fizt ddd_zz+orig\n" " At present, AFNI is incapable of directly dealing\n" " with datasets whose DOF parameter varies between\n" " voxels. Converting to a z-score (with no parameters)\n" " is one way of getting around this difficulty.\n" #ifdef USE_PTHRESH " -pthresh pval = 'pval' is a probability level (i.e., from 0 to 1)\n" " at which to threshold the output, per voxel.\n" " N.B.: NOT IMPLEMENTED YET!\n" #endif " -workmem mega = 'mega' specifies the number of megabytes of RAM\n" " to use for statistical workspace. It defaults\n" " to 12. The program will run faster if this is\n" " larger (see the NOTES section below).\n" "\n" "The -base1 or -set1 command line switches must follow all other options\n" "(including those described below) except for the -set2 switch.\n" "\n" "INPUT EDITING OPTIONS: The same as are available in 3dmerge.\n" "\n" "OUTPUT OPTIONS: these options control the output files.\n" " -session dirname = Write output into given directory (default=./)\n" " -prefix pname = Use 'pname' for the output directory prefix\n" " (default=tdif)\n" #if 0 " -label string = Use 'string' for the label in the output\n" " dataset (the label is used for switching\n" " between datasets in AFNI)\n" #endif " -datum type = Use 'type' to store the output difference\n" " in the means; 'type' may be short or float.\n" " How the default is determined is described\n" " in the notes below.\n" "\n" "NOTES:\n" " ** To economize on memory, 3dttest makes multiple passes through\n" " the input datasets. On each pass, the entire editing process\n" " will be carried out again. For efficiency's sake, it is\n" " better to carry out the editing using 3dmerge to produce\n" " temporary datasets, and then run 3dttest on them. This applies\n" " with particular force if a 'blurring' option is used.\n" " Note also that editing a dataset requires that it be read into\n" " memory in its entirety (so that the disk file is not altered).\n" " This will increase the memory needs of the program far beyond\n" " the level set by the -workmem option.\n" " ** The input datasets are specified by their .HEAD files,\n" " but their .BRIK files must exist also! This program cannot\n" " 'warp-on-demand' from other datasets.\n" " ** This program cannot deal with time-dependent or complex-valued datasets!\n" " By default, the output dataset function values will be shorts if the\n" " first input dataset is byte- or short-valued; otherwise they will be\n" " floats. This behavior may be overridden using the -datum option.\n" ) ; printf("\n" MASTER_SHORTHELP_STRING ) ; exit(0) ; } /*------------------------------------------------------------------*/ static float ptable[] = { 0.5 , 0.2 , 0.1 , 0.05 , 0.01 , 0.001 , 0.0001 , 0.00001 } ; int main( int argc , char * argv[] ) { int nx,ny,nz , nxyz , ii,kk , num1,num2 , num_tt=0 , iv , output_type , output_nvals , piece , num_piece , piece_len , fim_offset ; float dx,dy,dz , dxyz , num1_inv , num2_inv , num1m1_inv , num2m1_inv , dof , tthr , dd,tt,q1,q2 , f1,f2 , tt_max=0.0 ; THD_3dim_dataset * dset=NULL , * new_dset=NULL , * qset=NULL ; float * av1 , * av2 , * sd1 , * sd2 , * ffim , * gfim ; void * vsp ; short * tsp , * tsar ; /* output t-statistic */ float * fsp , * fsar ; void * vdif ; /* output mean difference */ short * sdif , * sdar ; /* (in various formats) */ float * fdif , * fdar ; void * vfim ; char cbuf[THD_MAX_NAME] ; float fbuf[MAX_STAT_AUX] , fimfac , fimfacinv ; int output_datum ; int piece_size ; float npiece , memuse ; float *dofbrik=NULL , *dofar=NULL ; THD_3dim_dataset *dof_dset=NULL ; /*-- read command line arguments --*/ if( argc < 2 || strncmp(argv[1],"-help",5) == 0 ) TT_syntax(NULL) ; /*-- 20 Apr 2001: addto the arglist, if user wants to [RWCox] --*/ mainENTRY("3dttest 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("3dttest",argc,argv) ; TT_read_opts( argc , argv ) ; if( ! TT_be_quiet ) printf("3dttest: t-tests of 3D datasets, by RW Cox\n") ; /*-- read first dataset in set2 to get dimensions, etc. --*/ dset = THD_open_dataset( TT_set2->ar[0] ) ; /* 20 Dec 1999 BDW */ if( ! ISVALID_3DIM_DATASET(dset) ){ fprintf(stderr,"*** Unable to open dataset file %s\n",TT_set2->ar[0]); exit(1) ; } nx = dset->daxes->nxx ; ny = dset->daxes->nyy ; nz = dset->daxes->nzz ; nxyz = nx * ny * nz ; dx = fabs(dset->daxes->xxdel) ; dy = fabs(dset->daxes->yydel) ; dz = fabs(dset->daxes->zzdel) ; dxyz = dx * dy * dz ; #ifdef TTDEBUG printf("*** nx=%d ny=%d nz=%d\n",nx,ny,nz) ; #endif /*-- make an empty copy of this dataset, for eventual output --*/ #ifdef TTDEBUG printf("*** making empty dataset\n") ; #endif new_dset = EDIT_empty_copy( dset ) ; tross_Make_History( "3dttest" , argc,argv , new_dset ) ; strcpy( cbuf , dset->self_name ) ; strcat( cbuf , "+TT" ) ; iv = DSET_PRINCIPAL_VALUE(dset) ; if( TT_datum >= 0 ){ output_datum = TT_datum ; } else { output_datum = DSET_BRICK_TYPE(dset,iv) ; if( output_datum == MRI_byte ) output_datum = MRI_short ; } #ifdef TTDEBUG printf(" ** datum = %s\n",MRI_TYPE_name[output_datum]) ; #endif iv = EDIT_dset_items( new_dset , ADN_prefix , TT_prefix , ADN_label1 , TT_prefix , ADN_directory_name , TT_session , ADN_self_name , cbuf , ADN_type , ISHEAD(dset) ? HEAD_FUNC_TYPE : GEN_FUNC_TYPE , ADN_func_type , FUNC_TT_TYPE , ADN_nvals , FUNC_nvals[FUNC_TT_TYPE] , ADN_datum_all , output_datum , ADN_none ) ; if( iv > 0 ){ fprintf(stderr, "*** %d errors in attempting to create output dataset!\n",iv ) ; exit(1) ; } if( THD_is_file(new_dset->dblk->diskptr->header_name) ){ fprintf(stderr, "*** Output dataset file %s already exists--cannot continue!\a\n", new_dset->dblk->diskptr->header_name ) ; exit(1) ; } #ifdef TTDEBUG printf("*** deleting exemplar dataset\n") ; #endif THD_delete_3dim_dataset( dset , False ) ; dset = NULL ; /** macro to test a malloc-ed pointer for validity **/ #define MTEST(ptr) \ if((ptr)==NULL) \ ( fprintf(stderr,"*** Cannot allocate memory for statistics!\n" \ "*** Try using the -workmem option to reduce memory needs,\n" \ "*** or create more swap space in the operating system.\n" \ ), exit(0) ) /*-- make space for the t-test computations --*/ npiece = 3.0 ; /* need at least this many */ if( TT_paired ) npiece += 1.0 ; else if( TT_set1 != NULL ) npiece += 2.0 ; npiece += mri_datum_size(output_datum) / (float) sizeof(float) ; npiece += mri_datum_size(output_datum) / (float) sizeof(float) ; piece_size = TT_workmem * MEGA / ( npiece * sizeof(float) ) ; if( piece_size > nxyz ) piece_size = nxyz ; #ifdef TTDEBUG printf("*** malloc-ing space for statistics: %g float arrays of length %d\n", npiece,piece_size) ; #endif av2 = (float *) malloc( sizeof(float) * piece_size ) ; MTEST(av2) ; sd2 = (float *) malloc( sizeof(float) * piece_size ) ; MTEST(sd2) ; ffim = (float *) malloc( sizeof(float) * piece_size ) ; MTEST(ffim) ; num2 = TT_set2->num ; if( TT_paired ){ av1 = sd1 = NULL ; gfim = (float *) malloc( sizeof(float) * piece_size ) ; MTEST(gfim) ; num1 = num2 ; } else if( TT_set1 != NULL ){ av1 = (float *) malloc( sizeof(float) * piece_size ) ; MTEST(av1) ; sd1 = (float *) malloc( sizeof(float) * piece_size ) ; MTEST(sd1) ; gfim = NULL ; num1 = TT_set1->num ; } else { av1 = sd1 = NULL ; gfim = NULL ; num1 = 0 ; } vdif = (void *) malloc( mri_datum_size(output_datum) * nxyz ) ; MTEST(vdif) ; vsp = (void *) malloc( mri_datum_size(output_datum) * nxyz ) ; MTEST(vsp) ; /* 27 Dec 2002: make DOF dataset (if prefix is given, and unpooled is on) */ if( TT_pooled == 0 && TT_dof_prefix[0] != '\0' ){ dofbrik = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(dofbrik) ; dof_dset = EDIT_empty_copy( new_dset ) ; tross_Make_History( "3dttest" , argc,argv , dof_dset ) ; EDIT_dset_items( dof_dset , ADN_prefix , TT_dof_prefix , ADN_directory_name , TT_session , ADN_type , ISHEAD(dset) ? HEAD_FUNC_TYPE : GEN_FUNC_TYPE, ADN_func_type , FUNC_BUCK_TYPE , ADN_nvals , 1 , ADN_datum_all , MRI_float , ADN_none ) ; if( THD_is_file(dof_dset->dblk->diskptr->header_name) ){ fprintf(stderr, "*** -dof_prefix dataset file %s already exists--cannot continue!\a\n", dof_dset->dblk->diskptr->header_name ) ; exit(1) ; } EDIT_substitute_brick( dof_dset , 0 , MRI_float , dofbrik ) ; } /* print out memory usage to edify the user */ if( ! TT_be_quiet ){ memuse = sizeof(float) * piece_size * npiece + ( mri_datum_size(output_datum) + sizeof(short) ) * nxyz ; if( dofbrik != NULL ) memuse += sizeof(float) * nxyz ; /* 27 Dec 2002 */ printf("--- allocated %d Megabytes memory for internal use\n",(int)(memuse/MEGA)) ; } mri_fix_data_pointer( vdif , DSET_BRICK(new_dset,0) ) ; /* attach bricks */ mri_fix_data_pointer( vsp , DSET_BRICK(new_dset,1) ) ; /* to new dataset */ switch( output_datum ){ default: fprintf(stderr,"Illegal input data type %d = %s!\n", output_datum , MRI_TYPE_name[output_datum] ) ; exit(1) ; case MRI_short: sdif = (short *) vdif ; tsp = (short *) vsp ; break ; case MRI_float: fdif = (float *) vdif ; fsp = (float *) vsp ; break ; } num2_inv = 1.0 / num2 ; num2m1_inv = 1.0 / (num2-1) ; if( num1 > 0 ){ num1_inv = 1.0 / num1 ; num1m1_inv = 1.0 / (num1-1) ; } /*----- loop over pieces to process the input datasets with -----*/ /** macro to open a dataset and make it ready for processing **/ #define DOPEN(ds,name) \ do{ int pv ; (ds) = THD_open_dataset((name)) ; /* 16 Sep 1999 */ \ if( !ISVALID_3DIM_DATASET((ds)) ){ \ fprintf(stderr,"*** Can't open dataset: %s\n",(name)) ; exit(1) ; } \ if( (ds)->daxes->nxx!=nx || (ds)->daxes->nyy!=ny || (ds)->daxes->nzz!=nz ){ \ fprintf(stderr,"*** Axes mismatch: %s\n",(name)) ; exit(1) ; } \ if( DSET_NUM_TIMES((ds)) > 1 ){ \ fprintf(stderr,"*** Can't use time-dependent data: %s\n",(name));exit(1); } \ if( TT_use_editor ) EDIT_one_dataset( (ds), &TT_edopt ) ; \ else THD_load_datablock( (ds)->dblk ) ; \ pv = DSET_PRINCIPAL_VALUE((ds)) ; \ if( DSET_ARRAY((ds),pv) == NULL ){ \ fprintf(stderr,"*** Can't access data: %s\n",(name)) ; exit(1); } \ if( DSET_BRICK_TYPE((ds),pv) == MRI_complex ){ \ fprintf(stderr,"*** Can't use complex data: %s\n",(name)) ; exit(1); } \ break ; } while (0) /** macro to return pointer to correct location in brick for current processing **/ #define SUB_POINTER(ds,vv,ind,ptr) \ do{ switch( DSET_BRICK_TYPE((ds),(vv)) ){ \ default: fprintf(stderr,"\n*** Illegal datum! ***\n");exit(1); \ case MRI_short:{ short * fim = (short *) DSET_ARRAY((ds),(vv)) ; \ (ptr) = (void *)( fim + (ind) ) ; \ } break ; \ case MRI_byte:{ byte * fim = (byte *) DSET_ARRAY((ds),(vv)) ; \ (ptr) = (void *)( fim + (ind) ) ; \ } break ; \ case MRI_float:{ float * fim = (float *) DSET_ARRAY((ds),(vv)) ; \ (ptr) = (void *)( fim + (ind) ) ; \ } break ; } break ; } while(0) /** number of pieces to process **/ num_piece = (nxyz + piece_size - 1) / piece_size ; nice(2) ; /** lower priority a little **/ for( piece=0 ; piece < num_piece ; piece++ ){ fim_offset = piece * piece_size ; piece_len = (piece < num_piece-1 ) ? piece_size : (nxyz - fim_offset) ; #ifdef TTDEBUG printf("*** start of piece %d: length=%d offset=%d\n",piece,piece_len,fim_offset) ; #else if( ! TT_be_quiet ){ printf("--- starting piece %d/%d (%d voxels) ",piece+1,num_piece,piece_len) ; fflush(stdout) ; } #endif /** process set2 (and set1, if paired) **/ for( ii=0 ; ii < piece_len ; ii++ ) av2[ii] = 0.0 ; for( ii=0 ; ii < piece_len ; ii++ ) sd2[ii] = 0.0 ; for( kk=0 ; kk < num2 ; kk++ ){ /** read in the data **/ DOPEN(dset,TT_set2->ar[kk]) ; iv = DSET_PRINCIPAL_VALUE(dset) ; #ifndef TTDEBUG if( ! TT_be_quiet ){ printf(".") ; fflush(stdout) ; } /* progress */ #else printf(" ** opened dataset file %s\n",TT_set2->ar[kk]); #endif if( piece == 0 && kk == 0 ){ fimfac = DSET_BRICK_FACTOR(dset,iv) ; if( fimfac == 0.0 ) fimfac = 1.0 ; fimfacinv = 1.0 / fimfac ; #ifdef TTDEBUG printf(" ** set fimfac = %g\n",fimfac) ; #endif } /** convert it to floats (in ffim) **/ SUB_POINTER(dset,iv,fim_offset,vfim) ; EDIT_coerce_scale_type( piece_len , DSET_BRICK_FACTOR(dset,iv) , DSET_BRICK_TYPE(dset,iv),vfim , /* input */ MRI_float ,ffim ) ; /* output */ THD_delete_3dim_dataset( dset , False ) ; dset = NULL ; /** get the paired dataset, if present **/ if( TT_paired ){ DOPEN(dset,TT_set1->ar[kk]) ; iv = DSET_PRINCIPAL_VALUE(dset) ; #ifndef TTDEBUG if( ! TT_be_quiet ){ printf(".") ; fflush(stdout) ; } /* progress */ #else printf(" ** opened dataset file %s\n",TT_set1->ar[kk]); #endif SUB_POINTER(dset,iv,fim_offset,vfim) ; EDIT_coerce_scale_type( piece_len , DSET_BRICK_FACTOR(dset,iv) , DSET_BRICK_TYPE(dset,iv),vfim , /* input */ MRI_float ,gfim ) ; /* output */ THD_delete_3dim_dataset( dset , False ) ; dset = NULL ; for( ii=0 ; ii < piece_len ; ii++ ) ffim[ii] -= gfim[ii] ; } #ifdef TTDEBUG printf(" * adding into av2 and sd2\n") ; #endif /* accumulate into av2 and sd2 */ for( ii=0 ; ii < piece_len ; ii++ ){ dd = ffim[ii] ; av2[ii] += dd ; sd2[ii] += dd * dd ; } } /* end of loop over set2 datasets */ /** form the mean and stdev of set2 **/ #ifdef TTDEBUG printf(" ** forming mean and sigma of set2\n") ; #endif for( ii=0 ; ii < piece_len ; ii++ ){ av2[ii] *= num2_inv ; dd = (sd2[ii] - num2*av2[ii]*av2[ii]) ; sd2[ii] = (dd > 0.0) ? sqrt( num2m1_inv * dd ) : 0.0 ; } /** if set1 exists but is not paired with set2, process it now **/ if( ! TT_paired && TT_set1 != NULL ){ for( ii=0 ; ii < piece_len ; ii++ ) av1[ii] = 0.0 ; for( ii=0 ; ii < piece_len ; ii++ ) sd1[ii] = 0.0 ; for( kk=0 ; kk < num1 ; kk++ ){ DOPEN(dset,TT_set1->ar[kk]) ; iv = DSET_PRINCIPAL_VALUE(dset) ; #ifndef TTDEBUG if( ! TT_be_quiet ){ printf(".") ; fflush(stdout) ; } /* progress */ #else printf(" ** opened dataset file %s\n",TT_set1->ar[kk]); #endif SUB_POINTER(dset,iv,fim_offset,vfim) ; EDIT_coerce_scale_type( piece_len , DSET_BRICK_FACTOR(dset,iv) , DSET_BRICK_TYPE(dset,iv),vfim , /* input */ MRI_float ,ffim ) ; /* output */ THD_delete_3dim_dataset( dset , False ) ; dset = NULL ; #ifdef TTDEBUG printf(" * adding into av1 and sd1\n") ; #endif for( ii=0 ; ii < piece_len ; ii++ ){ dd = ffim[ii] ; av1[ii] += dd ; sd1[ii] += dd * dd ; } } /* end of loop over set1 datasets */ /** form the mean and stdev of set1 **/ #ifdef TTDEBUG printf(" ** forming mean and sigma of set1\n") ; #endif for( ii=0 ; ii < piece_len ; ii++ ){ av1[ii] *= num1_inv ; dd = (sd1[ii] - num1*av1[ii]*av1[ii]) ; sd1[ii] = (dd > 0.0) ? sqrt( num1m1_inv * dd ) : 0.0 ; } } /* end of processing set1 by itself */ /***** now form difference and t-statistic *****/ #ifndef TTDEBUG if( ! TT_be_quiet ){ printf("+") ; fflush(stdout) ; } /* progress */ #else printf(" ** computing t-tests next\n") ; #endif switch( output_datum ){ case MRI_short: /* if fim is shorts */ sdar = sdif + fim_offset ; tsar = tsp + fim_offset ; /* pointer into output t-statistic array */ break ; case MRI_float: /* if fim is floats */ fdar = fdif + fim_offset ; fsar = fsp + fim_offset ; break ; } /** macro to assign difference value to correct type of array **/ #define DIFASS switch( output_datum ){ \ case MRI_short: sdar[ii] = (short) (fimfacinv*dd) ; break ; \ case MRI_float: fdar[ii] = (float) dd ; break ; } #define TOP_SS 32700 #define TOP_TT (32700.0/FUNC_TT_SCALE_SHORT) if( TT_paired || TT_use_bval == 1 ){ /** case 1: paired estimate or 1-sample **/ f2 = 1.0 / sqrt( (double) num2 ) ; for( ii=0 ; ii < piece_len ; ii++ ){ dd = av2[ii] - TT_bval ; DIFASS ; if( sd2[ii] > 0.0 ){ num_tt++ ; tt = dd / (f2 * sd2[ii]) ; switch( output_datum ){ case MRI_short: tsar[ii] = (tt>TOP_TT) ? (TOP_SS) : (tt<-TOP_TT) ? (-TOP_SS) : ((short)(FUNC_TT_SCALE_SHORT*tt)) ; break ; case MRI_float: fsar[ii] = tt ; break ; } tt = fabs(tt) ; if( tt > tt_max ) tt_max = tt ; } else { switch( output_datum ){ case MRI_short: tsar[ii] = 0 ; break ; case MRI_float: fsar[ii] = 0 ; break ; } } } #ifdef TTDEBUG printf(" ** paired or bval test: num_tt = %d\n",num_tt) ; #endif } else if( TT_pooled ){ /** case 2: unpaired 2-sample, pooled variance **/ f1 = (num1-1.0) * (1.0/num1 + 1.0/num2) / (num1+num2-2.0) ; f2 = (num2-1.0) * (1.0/num1 + 1.0/num2) / (num1+num2-2.0) ; for( ii=0 ; ii < piece_len ; ii++ ){ dd = av2[ii] - av1[ii] ; DIFASS ; q1 = f1 * sd1[ii]*sd1[ii] + f2 * sd2[ii]*sd2[ii] ; if( q1 > 0.0 ){ num_tt++ ; tt = dd / sqrt(q1) ; switch( output_datum ){ case MRI_short: tsar[ii] = (tt>TOP_TT) ? (TOP_SS) : (tt<-TOP_TT) ? (-TOP_SS) : ((short)(FUNC_TT_SCALE_SHORT*tt)) ; break ; case MRI_float: fsar[ii] = tt ; break ; } tt = fabs(tt) ; if( tt > tt_max ) tt_max = tt ; } else { switch( output_datum ){ case MRI_short: tsar[ii] = 0 ; break ; case MRI_float: fsar[ii] = 0 ; break ; } } } #ifdef TTDEBUG printf(" ** pooled test: num_tt = %d\n",num_tt) ; #endif } else { /** case 3: unpaired 2-sample, unpooled variance **/ /** 27 Dec 2002: modified to save DOF into dofar **/ if( dofbrik != NULL ) dofar = dofbrik + fim_offset ; /* 27 Dec 2002 */ for( ii=0 ; ii < piece_len ; ii++ ){ dd = av2[ii] - av1[ii] ; DIFASS ; q1 = num1_inv * sd1[ii]*sd1[ii] ; q2 = num2_inv * sd2[ii]*sd2[ii] ; if( q1>0.0 && q2>0.0 ){ /* have positive variances? */ num_tt++ ; tt = dd / sqrt(q1+q2) ; switch( output_datum ){ case MRI_short: tsar[ii] = (tt>TOP_TT) ? (TOP_SS) : (tt<-TOP_TT) ? (-TOP_SS) : ((short)(FUNC_TT_SCALE_SHORT*tt)) ; break ; case MRI_float: fsar[ii] = tt ; break ; } tt = fabs(tt) ; if( tt > tt_max ) tt_max = tt ; if( dofar != NULL ) /* 27 Dec 2002 */ dofar[ii] = (q1+q2)*(q1+q2) / (num1m1_inv*q1*q1 + num2m1_inv*q2*q2) ; } else { switch( output_datum ){ case MRI_short: tsar[ii] = 0 ; break ; case MRI_float: fsar[ii] = 0 ; break ; } if( dofar != NULL ) dofar[ii] = 1.0 ; /* 27 Dec 2002 */ } } #ifdef TTDEBUG printf(" ** unpooled test: num_tt = %d\n",num_tt) ; #endif } #ifndef TTDEBUG if( ! TT_be_quiet ){ printf("\n") ; fflush(stdout) ; } #endif } /* end of loop over pieces of the input */ if( TT_paired ){ printf("--- Number of degrees of freedom = %d (paired test)\n",num2-1) ; dof = num2 - 1 ; } else if( TT_use_bval == 1 ){ printf("--- Number of degrees of freedom = %d (1-sample test)\n",num2-1) ; dof = num2 - 1 ; } else { printf("--- Number of degrees of freedom = %d (2-sample test)\n",num1+num2-2) ; dof = num1+num2-2 ; if( ! TT_pooled ) printf(" (For unpooled variance estimate, this is only approximate!)\n") ; } printf("--- Number of t-tests performed = %d out of %d voxels\n",num_tt,nxyz) ; printf("--- Largest |t| value found = %g\n",tt_max) ; kk = sizeof(ptable) / sizeof(float) ; for( ii=0 ; ii < kk ; ii++ ){ tt = student_p2t( ptable[ii] , dof ) ; printf("--- Double sided tail p = %8f at t = %8f\n" , ptable[ii] , tt ) ; } printf("--- Writing combined dataset into %s\n", new_dset->dblk->diskptr->header_name) ; fbuf[0] = dof ; for( ii=1 ; ii < MAX_STAT_AUX ; ii++ ) fbuf[ii] = 0.0 ; (void) EDIT_dset_items( new_dset , ADN_stat_aux , fbuf , ADN_none ) ; fbuf[0] = (output_datum == MRI_short && fimfac != 1.0 ) ? fimfac : 0.0 ; fbuf[1] = (output_datum == MRI_short ) ? 1.0 / FUNC_TT_SCALE_SHORT : 0.0 ; (void) EDIT_dset_items( new_dset , ADN_brick_fac , fbuf , ADN_none ) ; THD_load_statistics( new_dset ) ; THD_write_3dim_dataset( NULL,NULL , new_dset , True ) ; if( dof_dset != NULL ){ /* 27 Dec 2002 */ printf("--- Writing unpooled DOF dataset into %s\n", dof_dset->dblk->diskptr->header_name) ; DSET_write( dof_dset ) ; } exit(0) ; }