dset_range PR_get_range( THD_3dim_dataset * dset )
{
THD_dataxes * daxes ;
THD_fvec3 fv1 , fv2 , fv3 ;
THD_ivec3 iv ;
float tf ;
dset_range dr ;
#define FSWAP(x,y) (tf=(x),(x)=(y),(y)=tf)
daxes = dset->daxes ;
LOAD_FVEC3(fv1 , daxes->xxorg , daxes->yyorg , daxes->zzorg) ;
fv1 = THD_3dmm_to_dicomm( dset , fv1 ) ;
LOAD_FVEC3(fv2 , daxes->xxorg + (daxes->nxx-1)*daxes->xxdel ,
daxes->yyorg + (daxes->nyy-1)*daxes->yydel ,
daxes->zzorg + (daxes->nzz-1)*daxes->zzdel ) ;
fv2 = THD_3dmm_to_dicomm( dset , fv2 ) ;
if( fv1.xyz[0] > fv2.xyz[0] ) FSWAP( fv1.xyz[0] , fv2.xyz[0] ) ;
if( fv1.xyz[1] > fv2.xyz[1] ) FSWAP( fv1.xyz[1] , fv2.xyz[1] ) ;
if( fv1.xyz[2] > fv2.xyz[2] ) FSWAP( fv1.xyz[2] , fv2.xyz[2] ) ;
dr.xbot = fv1.xyz[0] ; dr.xtop = fv2.xyz[0] ;
dr.ybot = fv1.xyz[1] ; dr.ytop = fv2.xyz[1] ;
dr.zbot = fv1.xyz[2] ; dr.ztop = fv2.xyz[2] ;
return dr ;
}
int THD_dataset_mismatch( THD_3dim_dataset *ds1 , THD_3dim_dataset *ds2 )
{
THD_dataxes * dax1 , * dax2 ;
THD_fvec3 fv1 , fv2 , dv ;
int code ;
float cd,c1,c2 ;
double angle;
ENTRY("THD_dataset_mismatch") ;
if( !ISVALID_DSET(ds1) || !ISVALID_DSET(ds2) ) RETURN(-1) ;
dax1 = ds1->daxes ;
dax2 = ds2->daxes ;
code = 0 ; /* will be return value */
/* check if the number of voxels in each direction is the same */
if( dax1->nxx != dax2->nxx ||
dax1->nyy != dax2->nyy ||
dax1->nzz != dax2->nzz ) code |= MISMATCH_DIMEN ;
/* check if the grid spacings are the same */
if( fabs(dax1->xxdel-dax2->xxdel) > 0.01*fabs(dax1->xxdel) ||
fabs(dax1->yydel-dax2->yydel) > 0.01*fabs(dax1->yydel) ||
fabs(dax1->zzdel-dax2->zzdel) > 0.01*fabs(dax1->zzdel) ) code |= MISMATCH_DELTA ;
/* check if the orientations are the same */
if( dax1->xxorient != dax2->xxorient ||
dax1->yyorient != dax2->yyorient ||
dax1->zzorient != dax2->zzorient ) code |= MISMATCH_ORIENT ;
/* check if they have the same centers */
fv1 = THD_dataset_center( ds1 ) ;
fv2 = THD_dataset_center( ds2 ) ;
dv = SUB_FVEC3(fv1,fv2) ; cd = SIZE_FVEC3(dv) ;
LOAD_FVEC3(fv1,dax1->xxdel,dax1->yydel,dax1->zzdel) ; c1 = SIZE_FVEC3(fv1) ;
LOAD_FVEC3(fv2,dax2->xxdel,dax2->yydel,dax2->zzdel) ; c2 = SIZE_FVEC3(fv1) ;
if( cd > 0.1*(c1+c2) ) code |= MISMATCH_CENTER ;
/* check if the obliquity is the same */
angle = dset_obliquity_angle_diff(ds1, ds2, -1.0);
if (angle > 0.0) code |= MISMATCH_OBLIQ ;
RETURN(code) ;
}
void THD_3mni_to_3tta( float *x , float *y , float *z )
{
THD_fvec3 mv , tv ;
LOAD_FVEC3( mv , *x,*y,*z ) ;
tv = THD_mni_to_tta( mv ) ;
*x = tv.xyz[0] ; *y = tv.xyz[1] ; *z = tv.xyz[2] ; return ;
}
void THD_3tta_to_3mni( float *x , float *y , float *z )
{
THD_fvec3 mv , tv ;
LOAD_FVEC3( tv , *x,*y,*z ) ;
mv = THD_tta_to_mni( tv ) ;
*x = mv.xyz[0] ; *y = mv.xyz[1] ; *z = mv.xyz[2] ; return ;
}
THD_fvec3 THD_tta_to_mni( THD_fvec3 tv )
{
float mx,my,mz , tx,ty,tz ;
THD_fvec3 mv ;
tx = -tv.xyz[0] ; ty = -tv.xyz[1] ; /* flip xy from RAI to LPI */
tz = tv.xyz[2] ;
mx = 1.01010 * tx ;
my = 1.02962 * ty - 0.05154 * tz ;
mz = 0.05434 * ty + 1.08554 * tz ;
if( mz < 0.0 ) mz *= 1.09523 ;
LOAD_FVEC3( mv , mx,my,mz ) ; return mv ;
}
THD_fvec3 THD_mni_to_tta( THD_fvec3 mv )
{
float mx,my,mz , tx,ty,tz ;
THD_fvec3 tv ;
mx = mv.xyz[0] ; my = mv.xyz[1] ; mz = mv.xyz[2] ;
tx = 0.99 * mx ;
if( mz > 0.0 ){
ty = 0.9688 * my + 0.0460 * mz ;
tz = -0.0485 * my + 0.9189 * mz ;
} else {
ty = 0.9688 * my + 0.0420 * mz ;
tz = -0.0485 * my + 0.8390 * mz ;
}
tx = -tx ; ty = -ty ; /* flip x,y from LPI to RAI */
LOAD_FVEC3( tv , tx,ty,tz ) ; return tv ;
}
char * SUMA_BrainVoyager_Read_vmr(char *fnameorig, THD_3dim_dataset *dset, int LoadData,
byte Qxforce, byte bsforce, int viewforce, char *outname)
{
static char FuncName[]={"SUMA_BrainVoyager_Read_vmr"};
int i = 0, nf, iop, dchunk, End, bs, doff, ex,
data_type=SUMA_notypeset, view, endian, dblock;
THD_ivec3 iv3;
unsigned long len;
short qxver;
short nvox[3]; /* values are unsigned, so check for sign for bs... */
THD_mat33 m33;
THD_ivec3 orixyz , nxyz ;
THD_fvec3 dxyz , orgxyz ;
float ep[3], sp[3];
char sview[10], *fname = NULL, *scom=NULL, form[10], swp[10], orstr[10], xfov[100], yfov[100], zfov[100], *prefix = NULL, *dsetheadname = NULL;
FILE *fid = NULL;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
if (!dset || !fnameorig) {
SUMA_SL_Err("NULL fname || NULL dset!");
SUMA_RETURN(NOPE);
}
if (!SUMA_isExtension(fnameorig, ".vmr")) {
SUMA_SL_Err("vmr dset is expected to have .vmr for an extension");
SUMA_RETURN(NOPE);
}
if (!SUMA_filexists(fnameorig)) {
SUMA_SL_Err("file does not exist");
SUMA_RETURN(NOPE);
}
/* make fname be the new name without the extension*/
if (!outname) {
fname = SUMA_Extension(fnameorig,".vmr", YUP);
} else {
fname = SUMA_Extension(outname, ".vmr", YUP);
}
prefix = SUMA_AfniPrefix(fname, NULL, NULL, NULL);
if( !THD_filename_ok(prefix) ) {
SUMA_SL_Err("Bad prefix");
goto CLEAN_EXIT;
}
/* someday, guess format on your own...*/
qxver = 0;
if (Qxforce) {
SUMA_LH("Forcing qxver");
qxver = 1; /* set to 1 if qx format */
}
/* view ? */
SUMA_LHv("Viewforce = %d; [%d %d]\n", viewforce, VIEW_ORIGINAL_TYPE, VIEW_TALAIRACH_TYPE);
if (viewforce >= VIEW_ORIGINAL_TYPE && viewforce <= VIEW_TALAIRACH_TYPE) {
view = viewforce;
} else {
view = VIEW_ORIGINAL_TYPE;
if (SUMA_iswordin_ci(fnameorig, "_tal") == 1) { view = VIEW_TALAIRACH_TYPE; }
else if (SUMA_iswordin_ci(fnameorig, "_acpc") == 1) { view = VIEW_ACPCALIGNED_TYPE; }
else { view = VIEW_ORIGINAL_TYPE; }
}
switch (view) {
case VIEW_ORIGINAL_TYPE:
sprintf(sview,"+orig"); break;
case VIEW_ACPCALIGNED_TYPE:
sprintf(sview,"+acpc"); break;
case VIEW_TALAIRACH_TYPE:
sprintf(sview,"+tlrc"); break;
default:
SUMA_SL_Err("Bad view");
goto CLEAN_EXIT;
}
if (LocalHead) fprintf(SUMA_STDERR,"%s: View %s, %d\n", FuncName, sview, view);
dsetheadname = SUMA_append_replace_string(prefix,".HEAD", sview, 0);
if (SUMA_filexists(dsetheadname)) {
SUMA_S_Errv("Bad prefix, output dset %s exists\n", dsetheadname);
goto CLEAN_EXIT;
}
SUMA_free(dsetheadname); dsetheadname = NULL;
fid = fopen(fnameorig,"r");
if (!fid) {
SUMA_SL_Err("Could not open file for reading");
goto CLEAN_EXIT;
}
if (qxver) {
SUMA_LH("Reading dimensions, 2+ 1st 6 bytes and deciding on swap");
doff = 4*sizeof(short);/* data offset 2 + 6 bytes */
} else {
SUMA_LH("Reading dimensions, 1st 6 bytes and deciding on swap");
doff = 3*sizeof(short);/* data offset */
}
SUMA_WHAT_ENDIAN(endian);
bs = 0;
swp[0] = '\0';
data_type = SUMA_byte; /* voxel data is bytes */
dchunk = sizeof(byte); /* voxel data is bytes */
sprintf(form,"3Db");
if (qxver) { SUMA_READ_NUM(&(qxver), fid, ex, sizeof(short)); if (LocalHead) fprintf(SUMA_STDERR,"%s: QXver = %d\n", FuncName, qxver);}/* is this a QX format?*/
SUMA_READ_NUM(&(nvox[2]), fid, ex, sizeof(short)); /* Z first */
SUMA_READ_NUM(&(nvox[1]), fid, ex, sizeof(short));
SUMA_READ_NUM(&(nvox[0]), fid, ex, sizeof(short));
if ((nvox[0] < 0 || nvox[1] < 0 || nvox[2] < 0 )) {
SUMA_LH("Byte swapping needed");
bs = 1;
}
if (bsforce) {
SUMA_LH("Byte swapping forced");
bs = 1;
}
if (bs) {
if (qxver) SUMA_swap_2(&(qxver));
SUMA_swap_2(&(nvox[0]));
SUMA_swap_2(&(nvox[1]));
SUMA_swap_2(&(nvox[2]));
sprintf(swp,"-2swap");
SUMA_OTHER_ENDIAN(endian);
}
/* 1 1 1???? */
if (nvox[0] == nvox[1] && nvox[1] == nvox[2] && nvox[2] == 1) {
if (LocalHead) { fprintf(SUMA_STDERR,"Warning %s: Voxel nums all 1. Trying from file size\n", FuncName); }
len = THD_filesize( fnameorig ) ;
len -= doff;
len /= dchunk;
nvox[0] = (int)pow((double)len, 1.0/3.0);
if (nvox[0] * nvox[0] * nvox[0] != len) {
fprintf(SUMA_STDERR,"Error %s: Bad voxel numbers and could not infer number from filesize.\n"
"Size of file: %lld, data offset: %d, datum size: %d, data number: %ld\n"
"Inferred nvox:%d\n",
FuncName,
THD_filesize( fnameorig ), doff, dchunk, len,
nvox[0]);
goto CLEAN_EXIT;
}
nvox[2] = nvox[1] = nvox[0];
if (LocalHead) { fprintf(SUMA_STDERR,"Warning %s: Using filesize inferred number of voxels: %d %d %d\n",
FuncName, nvox[0], nvox[1], nvox[2]); }
}
if (LocalHead) fprintf(SUMA_STDERR,"Number of voxels: %d %d %d. qxver %d\n", nvox[0], nvox[1], nvox[2], qxver);
/* check against filesize */
len = THD_filesize( fnameorig ) ;
dblock = nvox[0]*nvox[1]*nvox[2]*dchunk;
if (len != (dblock + doff)) {
if (!qxver) {
fprintf(SUMA_STDERR, "Mismatch between file size %ld\n"
"and expected size %d = (%d*%d*%d*%d+%d) \n",
len, (dblock + doff), nvox[0], nvox[1], nvox[2], dchunk, doff);
goto CLEAN_EXIT;
}else if (len < dblock + doff) {
fprintf(SUMA_STDERR, "Mismatch between file size %ld\n"
"and minimum expected size %d = (%d*%d*%d*%d+%d) \n",
len, (dblock + doff), nvox[0], nvox[1], nvox[2], dchunk, doff);
goto CLEAN_EXIT;
}else {
SUMA_LH("Proceeding");
}
}
if (LocalHead) fprintf(SUMA_STDERR,"File size passes test\n");
/* orientation */
orixyz.ijk[0] = ORI_A2P_TYPE;
orixyz.ijk[1] = ORI_S2I_TYPE;
orixyz.ijk[2] = ORI_R2L_TYPE;
/* load number of voxels */
LOAD_IVEC3( nxyz , nvox[0] , nvox[1] , nvox[2] ) ;
/* form the command */
SUMA_LH("Forming command");
{
float delta[3]={1.0, 1.0, 1.0};
float origin[3]={0.0, 0.0, 0.0};
/* set origin of 0th voxel*/
origin[0] = (float)((nvox[0]*delta[0]))/2.0; /* ZSS: Changed from 0 0 0 Nov 1 07 */
origin[1] = (float)((nvox[1]*delta[1]))/2.0;
origin[2] = (float)((nvox[2]*delta[2]))/2.0;
/* dimensions, same for vmr*/
LOAD_FVEC3( dxyz , delta[0], delta[1], delta[2] ) ;
SUMA_sizeto3d_2_deltaHEAD(orixyz, &dxyz);
/* origin */
LOAD_FVEC3( orgxyz , origin[0], origin[1], origin[2] ) ;
SUMA_originto3d_2_originHEAD(orixyz, &orgxyz);
}
/* start point (edge of origin voxel) and end point (opposite to start ) */
sp[0] = orgxyz.xyz[0] + SUMA_ABS(dxyz.xyz[0]) / 2.0;
sp[1] = orgxyz.xyz[1] + SUMA_ABS(dxyz.xyz[1]) / 2.0;
sp[2] = orgxyz.xyz[2] + SUMA_ABS(dxyz.xyz[2]) / 2.0;
ep[0] = orgxyz.xyz[0] + (nxyz.ijk[0] - 0.5) * SUMA_ABS(dxyz.xyz[0]);
ep[1] = orgxyz.xyz[1] + (nxyz.ijk[1] - 0.5) * SUMA_ABS(dxyz.xyz[1]);
ep[2] = orgxyz.xyz[2] + (nxyz.ijk[2] - 0.5) * SUMA_ABS(dxyz.xyz[2]);
SUMA_orcode_to_orstring (orixyz.ijk[0], orixyz.ijk[1], orixyz.ijk[2], orstr);
sprintf(xfov," -xFOV %.2f%c-%.2f%c", sp[0], orstr[0], ep[0], orstr[3]);
sprintf(yfov," -yFOV %.2f%c-%.2f%c", sp[1], orstr[1], ep[1], orstr[4]);
sprintf(zfov," -zFOV %.2f%c-%.2f%c", sp[2], orstr[2], ep[2], orstr[5]);
scom = (char *)SUMA_calloc((strlen(fnameorig)+500), sizeof(char));
sprintf(scom,"to3d %s %s %s %s -prefix %s %s:%d:0:%d:%d:%d:%s ",
swp, xfov, yfov, zfov, prefix, form, doff,
nvox[0], nvox[1], nvox[0], fnameorig);
SUMA_LH("HERE");
if (dset) { /* form the dset header */
int nvals_read = 0;
SUMA_LH("Filling header");
EDIT_dset_items( dset ,
ADN_prefix , prefix ,
ADN_datum_all , data_type ,
ADN_nxyz , nxyz ,
ADN_xyzdel , dxyz ,
ADN_xyzorg , orgxyz ,
ADN_xyzorient , orixyz ,
ADN_malloc_type , DATABLOCK_MEM_MALLOC ,
ADN_view_type , view ,
ADN_type , HEAD_ANAT_TYPE ,
ADN_func_type , ANAT_BUCK_TYPE ,
ADN_none ) ;
if (LoadData) {
void *vec=NULL;
SUMA_LH("Loading data");
if (!(vec = SUMA_BinarySuck(fnameorig, data_type, endian, 3*sizeof(short), -1, &nvals_read))) {
SUMA_SL_Err("Failed to read data file"); goto CLEAN_EXIT;
}
if (qxver) {
if (nvals_read < nvox[0]*nvox[1]*nvox[2]) {
SUMA_SL_Warn("Failed to read expected number of voxels\n proceeding...");
}
} else {
if (nvals_read != nvox[0]*nvox[1]*nvox[2]) {
SUMA_SL_Warn("Failed to read the appropriate number of voxels\n proceeding...");
}
}
EDIT_substitute_brick( dset , 0 , data_type , vec) ;
if (LocalHead) fprintf(SUMA_STDERR,"%s: Read %d values from file.\n", FuncName, nvals_read);
/* DSET_write(dset) ; */
}
}
CLEAN_EXIT:
if (prefix) SUMA_free(prefix); prefix = NULL;
if (fname) SUMA_free(fname); fname = NULL;
if (fid) fclose(fid); fid = NULL;
SUMA_RETURN(scom);
}
char * THD_dataset_info( THD_3dim_dataset *dset , int verbose )
{
THD_dataxes *daxes ;
THD_fvec3 fv1 , fv2 , fv3 ;
int ival , ntimes , nval_per , n1,n2,n3 , kv,npar ;
float tf, angle=0.0;
long long tb ;
static char *RR="[R]" , *LL="[L]" ,
*PP="[P]" , *AA="[A]" ,
*SS="[S]" , *II="[I]" , *ZZ=" " ;
char *xlbot , *xltop , *ylbot , *yltop , *zlbot , *zltop , *cpt ;
char str[1024], soblq[1024] ;
int nstr , obliquity;
char *outbuf = NULL ; /* output buffer */
ENTRY("THD_dataset_info") ;
if( ! ISVALID_3DIM_DATASET(dset) ) RETURN(NULL) ;
daxes = dset->daxes ;
if( DSET_IS_BRIK(dset) )
outbuf = THD_zzprintf(outbuf,"Dataset File: %s\n" , DSET_FILECODE(dset) ) ;
else
outbuf = THD_zzprintf(outbuf,"Dataset File: %s\n" , DSET_BRIKNAME(dset) ) ;
outbuf = THD_zzprintf(outbuf,"Identifier Code: %s Creation Date: %s\n" ,
dset->idcode.str , dset->idcode.date ) ;
outbuf = THD_zzprintf(outbuf, "Template Space: %s\n", dset->atlas_space);
if( ISANAT(dset) ){
outbuf = THD_zzprintf(outbuf,"Dataset Type: %s (-%s)\n",
ANAT_typestr[dset->func_type] , ANAT_prefixstr[dset->func_type] ) ;
} else {
outbuf = THD_zzprintf(outbuf,"Dataset Type: %s (-%s)\n",
FUNC_typestr[dset->func_type] , FUNC_prefixstr[dset->func_type] ) ;
}
/* 25 April 1998: do byte order stuff */
switch( DSET_BYTEORDER(dset) ){
case LSB_FIRST:
outbuf = THD_zzprintf(outbuf,"Byte Order: %s" , LSB_FIRST_STRING) ;
break ;
case MSB_FIRST:
outbuf = THD_zzprintf(outbuf,"Byte Order: %s" , MSB_FIRST_STRING) ;
break ;
}
if( THD_find_string_atr(dset->dblk,ATRNAME_BYTEORDER) == NULL ) /* 19 Sep 1999 */
outbuf = THD_zzprintf(outbuf," {assumed}") ;
kv = mri_short_order() ;
switch( kv ){
case LSB_FIRST:
outbuf = THD_zzprintf(outbuf," [this CPU native = %s]\n" , LSB_FIRST_STRING) ;
break ;
case MSB_FIRST:
outbuf = THD_zzprintf(outbuf," [this CPU native = %s]\n" , MSB_FIRST_STRING) ;
break ;
}
/*-- 21 Jun 2002: print storage mode --*/
if( dset->dblk->diskptr != NULL ){
outbuf = THD_zzprintf(outbuf,"Storage Mode: %s\n",
storage_mode_str(dset->dblk->diskptr->storage_mode));
}
tb = dset->dblk->total_bytes ;
if( tb > 0 )
outbuf = THD_zzprintf(outbuf,"Storage Space: %s (%s) bytes\n",
commaized_integer_string(dset->dblk->total_bytes) ,
approximate_number_string(dset->dblk->total_bytes) ) ;
/*-- keywords --*/
if( verbose >= 0 ){
cpt = DSET_KEYWORDS(dset) ;
if( cpt != NULL && cpt[0] != '\0' ){
int j = strlen(cpt) ;
if( j < 99 ){
outbuf = THD_zzprintf(outbuf,"Keywords: %s\n" , cpt ) ;
} else {
int k ;
outbuf = THD_zzprintf(outbuf,"\n----- KEYWORDS -----\n") ;
for( k=0 ; k < j ; k += ZMAX )
outbuf = THD_zzprintf(outbuf,SZMAX,cpt+k) ;
outbuf = THD_zzprintf(outbuf,"\n") ;
}
}
}
/*-- idcodes --*/
if( verbose >= 0 ){
if( ! ISZERO_IDCODE(dset->anat_parent_idcode) )
outbuf = THD_zzprintf(outbuf,"Anatomy Parent: %s [%s]\n" ,
dset->anat_parent_name , dset->anat_parent_idcode.str ) ;
else if( strlen(dset->anat_parent_name) > 0 )
outbuf = THD_zzprintf(outbuf,"Anatomy Parent: %s\n" , dset->anat_parent_name ) ;
if( ! ISZERO_IDCODE(dset->warp_parent_idcode) )
outbuf = THD_zzprintf(outbuf,"Warp Parent: %s [%s]\n" ,
dset->warp_parent_name , dset->warp_parent_idcode.str) ;
else if( strlen(dset->warp_parent_name) > 0 )
outbuf = THD_zzprintf(outbuf,"Warp Parent: %s\n" , dset->warp_parent_name ) ;
}
/*-- tagset --*/
if( verbose > 0 && dset->tagset != NULL && dset->tagset->num > 0 ){
int ii , ns=0 ;
for( ii=0 ; ii < dset->tagset->num ; ii++ )
if( dset->tagset->tag[ii].set ) ns++ ;
outbuf = THD_zzprintf(outbuf,"Tagset: %d set [out of %d total]\n",
ns , dset->tagset->num ) ;
}
/* are we oblique ? */
if((obliquity = dset_obliquity(dset, &angle)) >= 0) {
if(angle>0.0) {
sprintf (soblq,
"Data Axes Tilt: Oblique (%.3f deg. from plumb)\n"
"Data Axes Approximate Orientation:",
angle);
} else {
sprintf (soblq,
"Data Axes Tilt: Plumb\n"
"Data Axes Orientation:");
}
{ char *gstr = EDIT_get_geometry_string(dset) ;
if( gstr != NULL && *gstr != '\0' )
outbuf = THD_zzprintf(outbuf,"Geometry String: \"%s\"\n",gstr) ;
}
} else {
sprintf (soblq,
"Data Axes Tilt: Unspecified, assumed plumb\n"
"Data Axes Orientation:");
}
outbuf = THD_zzprintf(outbuf,
"%s\n"
" first (x) = %s\n"
" second (y) = %s\n"
" third (z) = %s [-orient %c%c%c]\n" ,
soblq,
ORIENT_typestr[daxes->xxorient] ,
ORIENT_typestr[daxes->yyorient] ,
ORIENT_typestr[daxes->zzorient] ,
ORIENT_typestr[daxes->xxorient][0] ,
ORIENT_typestr[daxes->yyorient][0] ,
ORIENT_typestr[daxes->zzorient][0] ) ;
LOAD_FVEC3(fv1 , daxes->xxorg , daxes->yyorg , daxes->zzorg) ;
fv1 = THD_3dmm_to_dicomm( dset , fv1 ) ;
LOAD_FVEC3(fv2 , daxes->xxorg + (daxes->nxx-1)*daxes->xxdel ,
daxes->yyorg + (daxes->nyy-1)*daxes->yydel ,
daxes->zzorg + (daxes->nzz-1)*daxes->zzdel ) ;
fv2 = THD_3dmm_to_dicomm( dset , fv2 ) ;
if( fv1.xyz[0] > fv2.xyz[0] ) FSWAP( fv1.xyz[0] , fv2.xyz[0] ) ;
if( fv1.xyz[1] > fv2.xyz[1] ) FSWAP( fv1.xyz[1] , fv2.xyz[1] ) ;
if( fv1.xyz[2] > fv2.xyz[2] ) FSWAP( fv1.xyz[2] , fv2.xyz[2] ) ;
LOAD_FVEC3(fv3 , daxes->xxdel , daxes->yydel , daxes->zzdel) ;
fv3 = THD_3dmm_to_dicomm( dset , fv3 ) ;
XLAB(xlbot,fv1.xyz[0]) ; YLAB(ylbot,fv1.xyz[1]) ; ZLAB(zlbot,fv1.xyz[2]) ;
XLAB(xltop,fv2.xyz[0]) ; YLAB(yltop,fv2.xyz[1]) ; ZLAB(zltop,fv2.xyz[2]) ;
n1 = DAXES_NUM(daxes,ORI_R2L_TYPE) ;
n2 = DAXES_NUM(daxes,ORI_A2P_TYPE) ;
n3 = DAXES_NUM(daxes,ORI_I2S_TYPE) ;
outbuf = THD_zzprintf(outbuf,
"R-to-L extent: %9.3f %s -to- %9.3f %s -step- %9.3f mm [%3d voxels]\n"
"A-to-P extent: %9.3f %s -to- %9.3f %s -step- %9.3f mm [%3d voxels]\n"
"I-to-S extent: %9.3f %s -to- %9.3f %s -step- %9.3f mm [%3d voxels]\n" ,
fv1.xyz[0],xlbot , fv2.xyz[0],xltop , fabs(fv3.xyz[0]) , n1 ,
fv1.xyz[1],ylbot , fv2.xyz[1],yltop , fabs(fv3.xyz[1]) , n2 ,
fv1.xyz[2],zlbot , fv2.xyz[2],zltop , fabs(fv3.xyz[2]) , n3 ) ;
/*-- 01 Feb 2001: print the center of the dataset as well --*/
if( verbose > 0 ){
fv1.xyz[0] = 0.5*(fv1.xyz[0]+fv2.xyz[0]) ; XLAB(xlbot,fv1.xyz[0]) ;
fv1.xyz[1] = 0.5*(fv1.xyz[1]+fv2.xyz[1]) ; YLAB(ylbot,fv1.xyz[1]) ;
fv1.xyz[2] = 0.5*(fv1.xyz[2]+fv2.xyz[2]) ; ZLAB(zlbot,fv1.xyz[2]) ;
outbuf = THD_zzprintf(outbuf,
"R-to-L center: %9.3f %s\n"
"A-to-P center: %9.3f %s\n"
"I-to-S center: %9.3f %s\n" ,
fv1.xyz[0],xlbot ,
fv1.xyz[1],ylbot ,
fv1.xyz[2],zlbot ) ;
}
ntimes = DSET_NUM_TIMES(dset) ;
nval_per = DSET_NVALS_PER_TIME(dset) ;
if( ntimes > 1 ){
outbuf = THD_zzprintf(outbuf,
"Number of time steps = %d" , ntimes ) ;
STATUS("timestep") ;
outbuf = THD_zzprintf(outbuf, " Time step = %.5f%s Origin = %.5f%s" ,
dset->taxis->ttdel ,
UNITS_TYPE_LABEL(dset->taxis->units_type) ,
dset->taxis->ttorg ,
UNITS_TYPE_LABEL(dset->taxis->units_type) ) ;
if( dset->taxis->nsl > 0 )
outbuf = THD_zzprintf(outbuf," Number time-offset slices = %d Thickness = %.3f",
dset->taxis->nsl , fabs(dset->taxis->dz_sl) ) ;
outbuf = THD_zzprintf(outbuf,"\n") ;
STATUS("nsl done") ;
if( verbose > 0 && dset->taxis->nsl > 0 && dset->taxis->toff_sl != NULL ){
outbuf = THD_zzprintf(outbuf,"Time-offsets per slice:") ;
for( ival=0 ; ival < dset->taxis->nsl ; ival++ )
outbuf = THD_zzprintf(outbuf, " %.3f" , dset->taxis->toff_sl[ival] ) ;
outbuf = THD_zzprintf(outbuf,"\n") ;
}
} else {
outbuf = THD_zzprintf(outbuf,
"Number of values stored at each pixel = %d\n" , nval_per ) ;
}
#if 0
if( verbose > 0 && ntimes > 1 ) nval_per = dset->dblk->nvals ;
else nval_per = 1 ; /* 12 Feb 2002 */
#else
nval_per = dset->dblk->nvals ;
if( verbose < 0 && nval_per > 5 ) nval_per = 3 ;
#endif
/* print out stuff for each sub-brick */
for( ival=0 ; ival < nval_per ; ival++ ){
STATUS("ival a") ;
sprintf( str ,
" -- At sub-brick #%d '%s' datum type is %s" ,
ival , DSET_BRICK_LAB(dset,ival) ,
MRI_TYPE_name[DSET_BRICK_TYPE(dset,ival)] ) ;
nstr = strlen(str) ;
tf = DSET_BRICK_FACTOR(dset,ival) ;
if( ISVALID_STATISTIC(dset->stats) ){
if( tf != 0.0 ){
sprintf( str+nstr ,
":%13.6g to %13.6g [internal]\n"
"%*s[*%13.6g] %13.6g to %13.6g [scaled]\n" ,
dset->stats->bstat[ival].min/tf ,
dset->stats->bstat[ival].max/tf ,
nstr-16," " , tf ,
dset->stats->bstat[ival].min , dset->stats->bstat[ival].max ) ;
} else {
sprintf( str+nstr , ":%13.6g to %13.6g\n" ,
dset->stats->bstat[ival].min , dset->stats->bstat[ival].max ) ;
}
} else if( tf != 0.0 ){
sprintf( str+nstr , " [*%g]\n",tf) ;
} else {
sprintf( str+nstr , "\n") ;
}
STATUS("ival b") ;
outbuf = THD_zzprintf(outbuf,"%s",str) ;
/** 30 Nov 1997: print sub-brick stat params **/
kv = DSET_BRICK_STATCODE(dset,ival) ;
if( FUNC_IS_STAT(kv) ){
STATUS("ival c") ;
outbuf = THD_zzprintf(outbuf," statcode = %s",FUNC_prefixstr[kv] ) ;
npar = FUNC_need_stat_aux[kv] ;
if( npar > 0 ){
outbuf = THD_zzprintf(outbuf,"; statpar =") ;
for( kv=0 ; kv < npar ; kv++ )
outbuf = THD_zzprintf(outbuf," %g",DSET_BRICK_STATPAR(dset,ival,kv)) ;
}
outbuf = THD_zzprintf(outbuf,"\n") ;
STATUS("ival d") ;
}
cpt = DSET_BRICK_KEYWORDS(dset,ival) ;
if( cpt != NULL && cpt[0] != '\0' ){
outbuf = THD_zzprintf(outbuf," keywords = %.66s\n",cpt) ;
}
STATUS("ival z") ;
}
if( verbose < 0 && nval_per < dset->dblk->nvals ) /* 21 Sep 2007 */
outbuf = THD_zzprintf(outbuf,
"** For info on all %d sub-bricks, use '3dinfo -verb' **\n",
dset->dblk->nvals) ;
/** print out dataset global statistical parameters **/
if( ISFUNC(dset) && FUNC_need_stat_aux[dset->func_type] > 0 ){
outbuf = THD_zzprintf(outbuf,"Auxiliary functional statistical parameters:\n %s\n",
FUNC_label_stat_aux[dset->func_type] ) ;
for( ival=0 ; ival < FUNC_need_stat_aux[dset->func_type] ; ival++ )
outbuf = THD_zzprintf(outbuf," %g",dset->stat_aux[ival]) ;
outbuf = THD_zzprintf(outbuf,"\n") ;
}
/** If present, print out History **/
{ char *chn ; int j,k ;
chn = tross_Get_History(dset) ;
if( chn != NULL ){
j = strlen(chn) ;
outbuf = THD_zzprintf(outbuf,"\n----- HISTORY -----\n") ;
for( k=0 ; k < j ; k += ZMAX )
outbuf = THD_zzprintf(outbuf,SZMAX,chn+k) ;
free(chn) ;
outbuf = THD_zzprintf(outbuf,"\n") ;
}
}
/** If present, print out Notes **/
if( verbose >= 0 ){
ATR_int *notecount;
int num_notes, i, j, mmm ;
char *chn , *chd ;
notecount = THD_find_int_atr(dset->dblk, "NOTES_COUNT");
if( notecount != NULL ){
num_notes = notecount->in[0] ;
if( verbose == 0 && num_notes > 5 ) num_notes = 5 ;
mmm = (verbose > 0) ? ZMAX : 1200 ; /* 400 it was!
Come on Bob, have a heart! -ZSS */
for (i=1; i<= num_notes; i++) {
chn = tross_Get_Note( dset , i ) ;
if( chn != NULL ){
j = strlen(chn) ; if( j > mmm ) chn[mmm] = '\0' ;
chd = tross_Get_Notedate(dset,i) ;
if( chd == NULL ){ chd = AFMALL(char,16) ; strcpy(chd,"no date") ; }
outbuf = THD_zzprintf(outbuf,"\n----- NOTE %d [%s] -----\n%s\n",i,chd,chn) ;
free(chn) ; free(chd) ;
}
int main( int argc , char *argv[] )
{
MRI_IMAGE *imin, *imout , *imout_orig;
THD_3dim_dataset *iset, *oset , *ooset;
char *prefix = "SpatNorm", *bottom_cuts = NULL;
int iarg , verb=0, OrigSpace = 0 , specie = HUMAN;
float SpatNormDxyz= 0.0, iset_scaled=1.0;
THD_ivec3 orixyz , nxyz ;
THD_fvec3 dxyz , orgxyz, originRAIfv, fv2;
mainENTRY("3dSpatNorm main") ; machdep() ;
if (argc == 1) { usage_3dSpatNorm(1); exit(0); }
/*--- options ---*/
iarg = 1 ;
OrigSpace = 0;
while( iarg < argc && argv[iarg][0] == '-' ){
if (strcmp(argv[iarg],"-h") == 0 || strcmp(argv[iarg],"-help") == 0 ) {
usage_3dSpatNorm(strlen(argv[iarg]) > 3 ? 2:1);
exit(0);
}
/* -prefix */
if( strcmp(argv[iarg],"-prefix") == 0 ){
if( ++iarg >= argc ){
fprintf(stderr,"**ERROR: -prefix requires another argument!\n") ;
exit(1) ;
}
prefix = strdup(argv[iarg]) ;
if( !THD_filename_ok(prefix) ){
fprintf(stderr,"**ERROR: -prefix value contains forbidden characters!\n") ;
exit(1) ;
}
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-dxyz") == 0 ){
if( ++iarg >= argc ){
fprintf(stderr,"**ERROR: -dxyz requires another argument!\n") ;
exit(1) ;
}
SpatNormDxyz = atof(argv[iarg]) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-bottom_cuts") == 0 ){
if( ++iarg >= argc ){
fprintf(stderr,"**ERROR: -bottom_cuts requires another argument!\n") ;
exit(1) ;
}
bottom_cuts = argv[iarg] ;
iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-verb",5) == 0 ){
verb++ ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-human",5) == 0 ){
specie = HUMAN ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-monkey",5) == 0 ){
specie = MONKEY ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-marmoset",5) == 0 ){
specie = MARMOSET ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-rat",5) == 0 ){
specie = RAT ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-orig_space",10) == 0 ){
OrigSpace = 1 ; iarg++ ; continue ;
}
fprintf(stderr,"**ERROR: %s is unknown option!\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1) ;
}
if( iarg >= argc ){
fprintf(stderr,"**ERROR: no input dataset name on command line?!\n") ;
exit(1) ;
}
/*--- read dataset ---*/
iset = THD_open_dataset( argv[iarg] ) ;
if( !ISVALID_DSET(iset) ){
fprintf(stderr,"**ERROR: can't open dataset %s\n",argv[iarg]) ;
exit(1) ;
}
/*--- get median brick --*/
if( verb ) fprintf(stderr,"++3dSpatNorm: loading dataset\n") ;
if (specie == MARMOSET) {
iset_scaled = 2.5;
THD_volDXYZscale(iset->daxes, iset_scaled, 0);
specie = MONKEY;
}
imin = THD_median_brick( iset ) ;
if( imin == NULL ){
fprintf(stderr,"**ERROR: can't load dataset %s\n",argv[iarg]) ;
exit(1) ;
}
imin->dx = fabs(iset->daxes->xxdel) ;
imin->dy = fabs(iset->daxes->yydel) ;
imin->dz = fabs(iset->daxes->zzdel) ;
mri_speciebusiness(specie);
mri_brain_normalize_cuts(bottom_cuts);
if (SpatNormDxyz) {
if (verb) fprintf(stderr,"Overriding default resampling\n");
mri_brainormalize_initialize(SpatNormDxyz, SpatNormDxyz, SpatNormDxyz);
} else {
float xxdel, yydel, zzdel, minres;
if (specie == MONKEY) minres = 0.5;
else if (specie == MARMOSET) minres = 0.2;
else if (specie == RAT) minres = 0.1;
else minres = 0.5;
/* don't allow for too low a resolution, please */
if (imin->dx < minres) xxdel = minres;
else xxdel = imin->dx;
if (imin->dy < minres) yydel = minres;
else yydel = imin->dy;
if (imin->dz < minres) zzdel = minres;
else zzdel = imin->dz;
if (verb) {
fprintf(stderr,
"%s:\n"
" Original resolution %f, %f, %f\n"
" SpatNorm resolution %f, %f, %f\n",
"3dSpatnorm", imin->dx, imin->dy, imin->dz,
xxdel, yydel, zzdel);
}
mri_brainormalize_initialize(xxdel, yydel, zzdel);
}
/* To get around the #define for voxel counts and dimensions */
mri_brainormalize_initialize(imin->dz, imin->dy, imin->dz);
/* me needs the origin of this dset in RAI world */
LOAD_FVEC3( originRAIfv ,
iset->daxes->xxorg , iset->daxes->yyorg , iset->daxes->zzorg) ;
originRAIfv = THD_3dmm_to_dicomm( iset , originRAIfv ) ;
LOAD_FVEC3(fv2, iset->daxes->xxorg + (iset->daxes->nxx-1)*iset->daxes->xxdel ,
iset->daxes->yyorg + (iset->daxes->nyy-1)*iset->daxes->yydel ,
iset->daxes->zzorg + (iset->daxes->nzz-1)*iset->daxes->zzdel);
fv2 = THD_3dmm_to_dicomm( iset , fv2 ) ;
if( originRAIfv.xyz[0] > fv2.xyz[0] ) {
float tf; tf = originRAIfv.xyz[0];
originRAIfv.xyz[0] = fv2.xyz[0]; fv2.xyz[0] = tf; }
if( originRAIfv.xyz[1] > fv2.xyz[1] ) {
float tf; tf = originRAIfv.xyz[1];
originRAIfv.xyz[1] = fv2.xyz[1]; fv2.xyz[1] = tf; }
if( originRAIfv.xyz[2] > fv2.xyz[2] ) {
float tf; tf = originRAIfv.xyz[2];
originRAIfv.xyz[2] = fv2.xyz[2]; fv2.xyz[2] = tf; }
if (verb) {
fprintf(stderr,"++3dSpatNorm (ZSS): RAI origin info: %f %f %f\n",
originRAIfv.xyz[0], originRAIfv.xyz[1], originRAIfv.xyz[2]);
}
DSET_unload( iset ) ; /* don't need this data no more */
/*-- convert image to shorts, if appropriate --*/
if( DSET_BRICK_TYPE(iset,0) == MRI_short ||
DSET_BRICK_TYPE(iset,0) == MRI_byte ){
imout = mri_to_short(0.0,imin) ; /* ZSS Oct 2012: Let function set scaling*/
mri_free(imin) ; imin = imout ;
}
/*--- normalize image spatially ---*/
mri_brainormalize_verbose( verb ) ;
if (OrigSpace) {
imout = mri_brainormalize( imin , iset->daxes->xxorient,
iset->daxes->yyorient,
iset->daxes->zzorient , &imout_orig, NULL) ;
} else {
imout = mri_brainormalize( imin , iset->daxes->xxorient,
iset->daxes->yyorient,
iset->daxes->zzorient , NULL, NULL) ;
}
mri_free( imin ) ;
if( imout == NULL ){
fprintf(stderr,"**ERROR: normalization fails!?\n"); exit(1);
}
if (OrigSpace) {
if( verb ) fprintf(stderr,"++3dSpatNorm: Output in Orignal space\n") ;
mri_free( imout ) ;
imout = imout_orig;
imout->xo = originRAIfv.xyz[0];
imout->yo = originRAIfv.xyz[1];
imout->zo = originRAIfv.xyz[2];
imout_orig = NULL;
} else {
if( verb ) fprintf(stderr,"++3dSpatNorm: Output in SpatNorm space\n") ;
}
#if 0
if( AFNI_yesenv("WATERSHED") ){
imin = mri_watershedize( imout , 0.10 ) ;
if( imin != NULL ){ mri_free(imout); imout = imin; }
}
#endif
/*--- create output dataset ---*/
if( verb )
fprintf(stderr,"++3dSpatNorm: Creating output dset\n") ;
oset = EDIT_empty_copy( NULL ) ;
tross_Copy_History( iset , oset ) ;
tross_Make_History( "3dSpatNorm" , argc,argv , oset ) ;
LOAD_IVEC3( nxyz , imout->nx , imout->ny , imout->nz ) ;
LOAD_FVEC3( dxyz , imout->dx , imout->dy , imout->dz ) ;
LOAD_FVEC3( orgxyz , imout->xo , imout->yo , imout->zo ) ;
LOAD_IVEC3( orixyz , ORI_R2L_TYPE , ORI_A2P_TYPE , ORI_I2S_TYPE ) ;
if( verb )
fprintf(stderr,"++3dSpatNorm: EDIT_dset_items\n") ;
EDIT_dset_items( oset ,
ADN_prefix , prefix ,
ADN_datum_all , imout->kind ,
ADN_nxyz , nxyz ,
ADN_xyzdel , dxyz ,
ADN_xyzorg , orgxyz ,
ADN_xyzorient , orixyz ,
ADN_malloc_type , DATABLOCK_MEM_MALLOC ,
ADN_view_type , VIEW_ORIGINAL_TYPE ,
ADN_type , HEAD_ANAT_TYPE ,
ADN_func_type , ANAT_BUCK_TYPE ,
ADN_none ) ;
if( verb )
fprintf(stderr,"++3dSpatNorm: EDIT_substitute_brick\n") ;
EDIT_substitute_brick( oset , 0 , imout->kind , mri_data_pointer(imout) ) ;
if (OrigSpace) {
if( verb )
fprintf(stderr,"++3dSpatNorm: Changing orientation from RAI\n") ;
ooset = r_new_resam_dset ( oset, iset, 0, 0, 0, NULL, MRI_NN, NULL, 1, 0);
if (!ooset) {
fprintf(stderr,"**ERROR: Failed to reslice!?\n"); exit(1);
}
/* put prefix back, r_new_resam_dset puts dummy prefix */
EDIT_dset_items( ooset ,
ADN_prefix , prefix,
ADN_none ) ;
DSET_delete(oset); oset = ooset; ooset = NULL;
}
if (iset_scaled != 1.0f)
THD_volDXYZscale(oset->daxes,
1/iset_scaled, 0);
DSET_write(oset) ;
if( verb )
fprintf(stderr,"++3dSpatNorm: wrote dataset %s\n",DSET_BRIKNAME(oset)) ;
exit(0) ;
}
void AFNI_lock_carryout( Three_D_View *im3d )
{
Three_D_View *qq3d ;
int ii,jj,kk , cc , glock ;
THD_fvec3 old_fv , fv ;
THD_ivec3 iv ;
THD_dataxes *qaxes , *daxes ;
static int busy = 0 ; /* !=0 if this routine is "busy" */
ENTRY("AFNI_lock_carryout") ;
/* first, determine if there is anything to do */
glock = GLOBAL_library.controller_lock ;
if( busy ) EXRETURN ; /* routine already busy */
if( glock == 0 ) EXRETURN ; /* nothing to do */
if( !IM3D_OPEN(im3d) ) EXRETURN ; /* bad input */
if( GLOBAL_library.ignore_lock ) EXRETURN ; /* ordered not to do anything */
ii = AFNI_controller_index(im3d) ; /* which one am I? */
if( ii < 0 ) EXRETURN ; /* nobody? bad input! */
if( ((1<<ii) & glock) == 0 ) EXRETURN ; /* input not locked */
/* something to do? */
busy = 1 ; /* don't let this routine be called recursively */
/* load Dicom location of current point of view in this controller */
LOAD_FVEC3( old_fv , im3d->vinfo->xi, im3d->vinfo->yj, im3d->vinfo->zk ) ;
LOAD_ANAT_VIEW(im3d) ; /* prepare coordinates */
daxes = CURRENT_DAXES(im3d->anat_now) ;
/* loop through other controllers:
for those that ARE open, ARE NOT the current one,
and ARE locked, transform the above vector to the
controller's dataset, and then jump to that point */
for( cc=0 ; cc < MAX_CONTROLLERS ; cc++ ){
qq3d = GLOBAL_library.controllers[cc] ; /* controller */
if( IM3D_OPEN(qq3d) && qq3d != im3d && ((1<<cc) & glock) != 0 ){
LOAD_ANAT_VIEW(qq3d) ; /* prepare coordinates */
qaxes = CURRENT_DAXES(qq3d->anat_now) ;
if( !GLOBAL_library.ijk_lock ){ /* xyz coord lock */
fv = AFNI_transform_vector( im3d->anat_now, old_fv, qq3d->anat_now ) ;
fv = THD_dicomm_to_3dmm( qq3d->anat_now , fv ) ;
iv = THD_3dmm_to_3dind ( qq3d->anat_now , fv ) ;
ii = iv.ijk[0] ; jj = iv.ijk[1] ; kk = iv.ijk[2] ;
} else { /* 11 Sep 2000: ijk index lock */
ii = im3d->vinfo->i1 * qaxes->nxx / daxes->nxx ;
jj = im3d->vinfo->j2 * qaxes->nyy / daxes->nyy ;
kk = im3d->vinfo->k3 * qaxes->nzz / daxes->nzz ;
}
/* if have good new ijk coords, jump to them */
if( ii >= 0 && ii < qaxes->nxx &&
jj >= 0 && jj < qaxes->nyy && kk >= 0 && kk < qaxes->nzz ){
SAVE_VPT(qq3d) ;
AFNI_set_viewpoint( qq3d , ii,jj,kk , REDISPLAY_ALL ) ; /* jump */
}
}
}
busy = 0 ; /* OK, let this routine be activated again */
EXRETURN ;
}
RHDD_array * RHDD_array_create( int nx , int ny , int nz ,
float dx , float dy , float dz ,
float asiz , byte *mask )
{
int pb,pt , qb,qt , rb,rt , pp,qq,rr , np,nq,nr,npq,npqr , nmax,ngood ;
float ah=0.5f*asiz , xt,yt,zt ;
THD_mat33 latmat , invlatmat ; THD_fvec3 pqr , xyz ;
RHDD_plist *rpl ; RHDD_array *rar ;
ENTRY("RHDD_array_create") ;
if( nx < 9 || ny < 9 || nz < 9 ) RETURN(NULL) ;
if( dx <= 0.0f ) dx = 1.0f ;
if( dy <= 0.0f ) dy = 1.0f ;
if( dz <= 0.0f ) dz = 1.0f ;
xt = MAX(dx,dy) ; xt = MAX(xt,dz) ;
if( asiz < 3.0f*xt ) RETURN(NULL) ;
/* find range of (p,q,r) indexes needed to cover volume,
by checking out all 7 corners besides (0,0,0) (where p=q=r=0) */
LOAD_MAT( latmat , -ah,ah,ah , ah,-ah,ah , ah,ah,-ah ) ;
invlatmat = MAT_INV(latmat) ;
xt = (nx-1)*dx ; yt = (ny-1)*dy ; zt = (nz-1)*dz ;
pb = pt = qb = qt = rb = rt = 0 ; /* initialize (p,q,r) bot, top values */
LOAD_FVEC3(xyz , xt,0.0f,0.0f ); pqr = MATVEC( invlatmat , xyz ) ;
pp = (int)floorf( pqr.xyz[0] ) ; pb = MIN(pb,pp) ; pp++ ; pt = MAX(pt,pp) ;
qq = (int)floorf( pqr.xyz[1] ) ; qb = MIN(qb,qq) ; qq++ ; qt = MAX(qt,qq) ;
rr = (int)floorf( pqr.xyz[2] ) ; rb = MIN(rb,rr) ; rr++ ; rt = MAX(rt,rr) ;
LOAD_FVEC3(xyz , xt,yt,0.0f ) ; pqr = MATVEC( invlatmat , xyz ) ;
pp = (int)floorf( pqr.xyz[0] ) ; pb = MIN(pb,pp) ; pp++ ; pt = MAX(pt,pp) ;
qq = (int)floorf( pqr.xyz[1] ) ; qb = MIN(qb,qq) ; qq++ ; qt = MAX(qt,qq) ;
rr = (int)floorf( pqr.xyz[2] ) ; rb = MIN(rb,rr) ; rr++ ; rt = MAX(rt,rr) ;
LOAD_FVEC3(xyz , xt,0.0f,zt ) ; pqr = MATVEC( invlatmat , xyz ) ;
pp = (int)floorf( pqr.xyz[0] ) ; pb = MIN(pb,pp) ; pp++ ; pt = MAX(pt,pp) ;
qq = (int)floorf( pqr.xyz[1] ) ; qb = MIN(qb,qq) ; qq++ ; qt = MAX(qt,qq) ;
rr = (int)floorf( pqr.xyz[2] ) ; rb = MIN(rb,rr) ; rr++ ; rt = MAX(rt,rr) ;
LOAD_FVEC3(xyz , xt,yt,zt ) ; pqr = MATVEC( invlatmat , xyz ) ;
pp = (int)floorf( pqr.xyz[0] ) ; pb = MIN(pb,pp) ; pp++ ; pt = MAX(pt,pp) ;
qq = (int)floorf( pqr.xyz[1] ) ; qb = MIN(qb,qq) ; qq++ ; qt = MAX(qt,qq) ;
rr = (int)floorf( pqr.xyz[2] ) ; rb = MIN(rb,rr) ; rr++ ; rt = MAX(rt,rr) ;
LOAD_FVEC3(xyz , 0.0f,yt,0.0f ); pqr = MATVEC( invlatmat , xyz ) ;
pp = (int)floorf( pqr.xyz[0] ) ; pb = MIN(pb,pp) ; pp++ ; pt = MAX(pt,pp) ;
qq = (int)floorf( pqr.xyz[1] ) ; qb = MIN(qb,qq) ; qq++ ; qt = MAX(qt,qq) ;
rr = (int)floorf( pqr.xyz[2] ) ; rb = MIN(rb,rr) ; rr++ ; rt = MAX(rt,rr) ;
LOAD_FVEC3(xyz , 0.0f,0.0f,zt ); pqr = MATVEC( invlatmat , xyz ) ;
pp = (int)floorf( pqr.xyz[0] ) ; pb = MIN(pb,pp) ; pp++ ; pt = MAX(pt,pp) ;
qq = (int)floorf( pqr.xyz[1] ) ; qb = MIN(qb,qq) ; qq++ ; qt = MAX(qt,qq) ;
rr = (int)floorf( pqr.xyz[2] ) ; rb = MIN(rb,rr) ; rr++ ; rt = MAX(rt,rr) ;
LOAD_FVEC3(xyz , 0.0f,yt,zt ) ; pqr = MATVEC( invlatmat , xyz ) ;
pp = (int)floorf( pqr.xyz[0] ) ; pb = MIN(pb,pp) ; pp++ ; pt = MAX(pt,pp) ;
qq = (int)floorf( pqr.xyz[1] ) ; qb = MIN(qb,qq) ; qq++ ; qt = MAX(qt,qq) ;
rr = (int)floorf( pqr.xyz[2] ) ; rb = MIN(rb,rr) ; rr++ ; rt = MAX(rt,rr) ;
pb-- ; qb-- ; rb-- ; /* push outwards, for luck */
pt++ ; qt++ ; rt++ ;
/* Lattice index range is (p,q,r) = (pb..pt,qb..qt,rb..rt) inclusive */
np = pt-pb+1 ; /* number of p values to consider */
nq = qt-qb+1 ; npq = np*nq ;
nr = rt-rb+1 ; npqr = npq*nr ;
rar = (RHDD_array *)calloc(1,sizeof(RHDD_array)) ;
rar->asiz = asiz ;
rar->num_rhdd = npqr ;
rar->rhdd = (RHDD_plist **)calloc(npqr,sizeof(RHDD_plist *)) ;
for( nmax=0,rr=rb ; rr <= rt ; rr++ ){
for( qq=qb ; qq <= qt ; qq++ ){
for( pp=pb ; pp <= pt ; pp++ ){
LOAD_FVEC3(pqr,pp,qq,rr) ; xyz = MATVEC(latmat,pqr) ;
rar->rhdd[(pp-pb)+(qq-qb)*np+(rr-rb)*npq] = rpl =
RHDD_plist_create( nx,ny,nz , dx,dy,dz , asiz ,
xyz.xyz[0] , xyz.xyz[1] , xyz.xyz[2] , mask ) ;
if( rpl != NULL && rpl->num_in_mask > nmax ) nmax = rpl->num_in_mask ;
}}}
if( nmax <= 9 ){
for( pp=0 ; pp < npqr ; pp++ ){
if( rar->rhdd[pp] != NULL ) DESTROY_RHDD_plist(rar->rhdd[pp]) ;
}
DESTROY_RHDD_array(rar) ; RETURN(NULL) ;
}
nmax = (int)(0.3456789f*nmax) ;
for( ngood=pp=0 ; pp < npqr ; pp++ ){
if( rar->rhdd[pp] != NULL ){
if( rar->rhdd[pp]->num_in_mask < nmax ){
DESTROY_RHDD_plist(rar->rhdd[pp]) ; rar->rhdd[pp] = NULL ;
} else {
ngood++ ;
}
}
}
if( ngood < npqr ){
RHDD_array *qar ;
qar = (RHDD_array *)calloc(1,sizeof(RHDD_array)) ;
qar->asiz = asiz ;
qar->num_rhdd = ngood ;
qar->rhdd = (RHDD_plist **)calloc(ngood,sizeof(RHDD_plist *)) ;
for( pp=qq=0 ; pp < npqr ; pp++ ){
if( rar->rhdd[pp] != NULL ) qar->rhdd[qq++] = rar->rhdd[pp] ;
}
DESTROY_RHDD_array(rar) ; rar = qar ;
}
RETURN(rar) ;
}
THD_3dim_dataset * THD_open_nifti( char *pathname )
{
THD_3dim_dataset *dset=NULL ;
nifti_image *nim ;
int ntt , nbuc , nvals ;
int use_qform = 0 , use_sform = 0, form_code = 0 ;
int statcode = 0 , datum , iview , ibr ;
int scale_data = 0 ; /* flag based on scl_slope and inter 20 Jun 2008 */
int xform_data = 0;
THD_ivec3 orixyz , nxyz ;
THD_fvec3 dxyz , orgxyz ;
THD_mat33 R ;
mat44 ijk_to_dicom44 ;
char *ppp , prefix[THD_MAX_PREFIX] ;
char form_priority = 'S' ; /* 23 Mar 2006 */
static int n_xform_warn=0;
ENTRY("THD_open_nifti") ;
/*-- open input file --*/
{ /* set the nifti_io debug level 8 Apr 2005 [rickr] */
char * ept = my_getenv("AFNI_NIFTI_DEBUG");
if( ept != NULL ) nifti_set_debug_level(atoi(ept));
}
nifti_set_alter_cifti(1) ; /* if CIFTI, shift dims 23 Jul 2015 [rickr] */
nim = nifti_image_read( pathname, 0 ) ;
if( nim == NULL || nim->nifti_type == 0 ) RETURN(NULL) ;
/*-- extract some useful AFNI-ish information from the nim struct --*/
/* we must have at least 2 spatial dimensions */
/* this should be okay 11 Jun 2007 */
/* if( nim->nx < 2 || nim->ny < 2 ) RETURN(NULL) ; */
/* 4th dimension = time; 5th dimension = bucket:
these are mutually exclusive in AFNI at present */
ntt = nim->nt ; nbuc = nim->nu ;
/* nt and nu might be 0 now (see irritating niftilib 1.17 update) */
/* so ensure that ntt and nbuc are positive 02 Mar 2006 [rickr] */
if( ntt <= 0 ) ntt = 1;
if( nbuc <= 0 ) nbuc = 1;
if( nim->nz <= 0 ) nim->nz = 1 ; /* 03 Mar 2006: RWCox */
if( ntt > 1 && nbuc > 1 ){
fprintf(stderr,
"** AFNI can't deal with 5 dimensional NIfTI(%s)\n",
pathname ) ;
RETURN(NULL) ;
}
nvals = MAX(ntt,nbuc) ;
/* collapse higher-dimensional datasets 23 Jul 2015 [rickr] */
/* (this includes CIFTI) */
if( nim->nv > 1 ) nvals *= nim->nv;
if( nim->nw > 1 ) nvals *= nim->nw;
if( ntt > 1 ) ntt = nvals;
else nbuc = nvals;
/* determine type of dataset values:
if we are scaling, or if the data type in the NIfTI file
is something AFNI can't handle, then the result will be floats */
/* do not scale if slope is 0 or if slope is 1 and inter is 0 */
if( !isfinite(nim->scl_slope) || !isfinite(nim->scl_inter) ){
fprintf(stderr,"** bad scl_slope and inter = %f, %f, ignoring...\n",
nim->scl_slope, nim->scl_inter);
} else {
scale_data = nim->scl_slope != 0.0 &&
(nim->scl_slope != 1.0 || nim->scl_inter != 0.0) ;
}
{ char *eee = getenv("AFNI_NIFTI_SCALE") ;
if( eee != NULL && toupper(*eee) == 'N' ) scale_data = 0 ;
}
switch( nim->datatype ){
default:
fprintf(stderr,
"** AFNI can't handle NIFTI datatype=%d (%s) in file %s\n",
nim->datatype, nifti_datatype_string(nim->datatype), pathname );
RETURN(NULL) ;
break ;
case DT_UINT8: datum = scale_data ? MRI_float : MRI_byte ;
xform_data = scale_data;
break ;
case DT_INT16: datum = scale_data ? MRI_float : MRI_short ;
xform_data = scale_data;
break ;
case DT_FLOAT32: datum = MRI_float ; break ;
case DT_COMPLEX64: datum = MRI_complex ; break ;
case DT_RGB24: datum = MRI_rgb ; break ;
case DT_INT8: /* NIfTI-1 data types that AFNI can't handle directly */
case DT_UINT16:
case DT_INT32:
case DT_UINT32:
case DT_FLOAT64: datum = MRI_float ; xform_data = 1 ; break ;
#if 0
case DT_COMPLEX128: /* this case would be too much like real work */
fprintf(stderr,
"** AFNI convert NIFTI_datatype=%d (%s) in file %s to COMPLEX64\n",
nim->datatype, nifti_datatype_string(nim->datatype), pathname );
datum = MRI_complex ;
break ;
#endif
}
if( xform_data && !AFNI_noenv("AFNI_NIFTI_TYPE_WARN")) {
if (!n_xform_warn || AFNI_yesenv("AFNI_NIFTI_TYPE_WARN")) {/* ZSS 04/11 */
fprintf(stderr,
"** AFNI converts NIFTI_datatype=%d (%s) in file %s to FLOAT32\n",
nim->datatype, nifti_datatype_string(nim->datatype), pathname );
if (!AFNI_yesenv("AFNI_NIFTI_TYPE_WARN")) {
fprintf(stderr,
" Warnings of this type will be muted for this session.\n"
" Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.\n");
}
}
++n_xform_warn;
}
/* check for statistics code */
if( nim->intent_code >= NIFTI_FIRST_STATCODE &&
nim->intent_code <= NIFTI_LAST_STATCODE ){
if( nim->intent_code > FUNC_PT_TYPE ){
fprintf(stderr,
"** AFNI doesn't understand NIFTI statistic type %d (%s) in file %s\n",
nim->intent_code , nifti_intent_string(nim->intent_code) , pathname ) ;
} else {
statcode = nim->intent_code ;
if( nbuc > 1 ){
fprintf(stderr,
"** AFNI doesn't support NIFTI voxel-dependent statistic parameters"
" in file %s\n" , pathname ) ;
statcode = 0 ;
}
}
}
/* 23 Mar 2006: set qform or sform as having priority -- RWCox */
ppp = my_getenv("NIFTI_FORM_PRIORITY") ;
if( ppp == NULL ) ppp = getenv("AFNI_FORM_PRIORITY") ;
if( ppp == NULL ) ppp = getenv("AFNI_NIFTI_PRIORITY") ;
if( ppp == NULL ) ppp = getenv("AFNI_NIFTI_FORM") ;
if( ppp == NULL ) ppp = getenv("AFNI_NIFTI_FORM_PRIORITY") ;
if( ppp != NULL ){
char fp = toupper(*ppp) ;
if( fp == 'S' || fp == 'Q' ) form_priority = fp ;
else WARNING_message("Illegal NIFTI_FORM_PRIORITY='%s'",ppp) ;
}
/** 24 Mar 2006: check determs of qform and sform, if have both **/
if( nim->qform_code > 0 && nim->sform_code > 0 ){
float qdet , sdet ;
LOAD_MAT(R, nim->qto_xyz.m[0][0] ,
nim->qto_xyz.m[0][1] ,
nim->qto_xyz.m[0][2] ,
nim->qto_xyz.m[1][0] ,
nim->qto_xyz.m[1][1] ,
nim->qto_xyz.m[1][2] ,
nim->qto_xyz.m[2][0] ,
nim->qto_xyz.m[2][1] ,
nim->qto_xyz.m[2][2] ) ; qdet = MAT_DET(R) ;
LOAD_MAT(R, nim->sto_xyz.m[0][0] ,
nim->sto_xyz.m[0][1] ,
nim->sto_xyz.m[0][2] ,
nim->sto_xyz.m[1][0] ,
nim->sto_xyz.m[1][1] ,
nim->sto_xyz.m[1][2] ,
nim->sto_xyz.m[2][0] ,
nim->sto_xyz.m[2][1] ,
nim->sto_xyz.m[2][2] ) ; sdet = MAT_DET(R) ;
if( qdet*sdet < 0.0f )
WARNING_message("NIfTI('%s'): Qform/Sform handedness differ; %c wins!",
pathname , form_priority ) ;
}
/* KRH 07/11/05 -- adding ability to choose spatial transform
from the options of qform, sform, bothform, or noform.
If qform is present, it will be used.
If qform is absent, but sform present, then the sform
will be modified to be an orthogonal rotation and used.
If both qform and sform are absent, then we will have
an error.
Previously assumed qform present. */
/* 23 Mar 2006: use form_priority to choose between them */
if ((nim->qform_code > 0) && (nim->sform_code > 0) ) {
if( form_priority == 'Q' ) { use_qform = 1 ; use_sform = 0 ; }
else { use_qform = 0 ; use_sform = 1 ; }
} else if (nim->qform_code > 0){ use_qform = 1 ; use_sform = 0 ; }
else if (nim->sform_code > 0){ use_qform = 0 ; use_sform = 1 ; }
else {
use_qform = 0 ; use_sform = 0 ;
WARNING_message(
"NO spatial transform (neither qform nor sform), in NIfTI file '%s'" ,
pathname ) ;
}
/** now take NIfTI-1.1 coords and transform to AFNI codes **/
if (use_qform) {
float orgx, orgy, orgz ;
form_code = nim->qform_code;
/* determine orientation from the qto_xyz matrix,
which transforms (i,j,k) voxel indexes to (x,y,z) LPI coordinates */
LOAD_MAT(R, -nim->qto_xyz.m[0][0] , /* negate x and y */
-nim->qto_xyz.m[0][1] , /* coefficients, */
-nim->qto_xyz.m[0][2] , /* since AFNI works */
-nim->qto_xyz.m[1][0] , /* with RAI coords, */
-nim->qto_xyz.m[1][1] , /* but NIFTI uses */
-nim->qto_xyz.m[1][2] , /* LPI coordinates. */
nim->qto_xyz.m[2][0] , /* [Which is my own] */
nim->qto_xyz.m[2][1] , /* [damn fault!!!!!] */
nim->qto_xyz.m[2][2] ) ;
LOAD_MAT44(ijk_to_dicom44,
-nim->qto_xyz.m[0][0] , /* negate x and y */
-nim->qto_xyz.m[0][1] , /* coefficients, */
-nim->qto_xyz.m[0][2] , /* since AFNI works */
-nim->qto_xyz.m[0][3] ,
-nim->qto_xyz.m[1][0] , /* with RAI coords, */
-nim->qto_xyz.m[1][1] , /* but NIFTI uses */
-nim->qto_xyz.m[1][2] , /* LPI coordinates. */
-nim->qto_xyz.m[1][3] ,
nim->qto_xyz.m[2][0] , /* [Which is my own] */
nim->qto_xyz.m[2][1] , /* [damn fault!!!!!] */
nim->qto_xyz.m[2][2] ,
nim->qto_xyz.m[2][3] ) ;
orixyz = THD_matrix_to_orientation( R ) ; /* compute orientation codes */
iview = NIFTI_code_to_view(nim->qform_code);
/* load the offsets and the grid spacings */
if (ORIENT_xyz[orixyz.ijk[0]] == 'z' ) {
orgx = nim->qto_xyz.m[ORIENT_xyzint[orixyz.ijk[0]] - 1][3] ;
} else {
orgx = - nim->qto_xyz.m[ORIENT_xyzint[orixyz.ijk[0]] - 1][3] ;
}
if (ORIENT_xyz[orixyz.ijk[1]] == 'z' ) {
orgy = nim->qto_xyz.m[ORIENT_xyzint[orixyz.ijk[1]] - 1][3] ;
} else {
orgy = - nim->qto_xyz.m[ORIENT_xyzint[orixyz.ijk[1]] - 1][3] ;
}
if (ORIENT_xyz[orixyz.ijk[2]] == 'z' ) {
orgz = nim->qto_xyz.m[ORIENT_xyzint[orixyz.ijk[2]] - 1][3] ;
} else {
orgz = - nim->qto_xyz.m[ORIENT_xyzint[orixyz.ijk[2]] - 1][3] ;
}
LOAD_FVEC3( orgxyz , orgx ,
orgy ,
orgz ) ;
#if 0
LOAD_FVEC3( orgxyz , -nim->qto_xyz.m[0][3] , /* again, negate */
-nim->qto_xyz.m[1][3] , /* x and y coords */
nim->qto_xyz.m[2][3] ) ;
#endif
/* AFNI space units are always mm */
if( nim->xyz_units == NIFTI_UNITS_METER ){
nim->dx *= 1000.0 ; nim->dy *= 1000.0 ; nim->dz *= 1000.0 ;
} else if( nim->xyz_units == NIFTI_UNITS_MICRON ){
nim->dx *= 0.001 ; nim->dy *= 0.001 ; nim->dz *= 0.001 ;
}
LOAD_FVEC3( dxyz , (ORIENT_sign[orixyz.ijk[0]]=='+') ? nim->dx : -nim->dx ,
(ORIENT_sign[orixyz.ijk[1]]=='+') ? nim->dy : -nim->dy ,
(ORIENT_sign[orixyz.ijk[2]]=='+') ? nim->dz : -nim->dz ) ;
} else if (use_sform) {
int orimap[7] = { 6 , 1 , 0 , 2 , 3 , 4 , 5 } ;
int oritmp[3] ;
float dxtmp, dytmp, dztmp ;
float xmax, ymax, zmax ;
float orgx, orgy, orgz ;
float fig_merit, ang_merit ;
form_code = nim->sform_code;
/* convert sform to nifti orientation codes */
/* n2 10 Jul, 2015 [rickr] */
nifti_dmat44_to_orientation(nim->sto_xyz,
&oritmp[0], &oritmp[1], &oritmp[2] ) ;
/* convert nifti orientation codes to AFNI codes and store in vector */
LOAD_IVEC3( orixyz , orimap[oritmp[0]] ,
orimap[oritmp[1]] ,
orimap[oritmp[2]] ) ;
/* assume original view if there's no talairach id present */
iview = NIFTI_code_to_view(nim->sform_code);
/* load the offsets and the grid spacings */
if (ORIENT_xyz[orixyz.ijk[0]] == 'z' ) {
orgx = nim->sto_xyz.m[ORIENT_xyzint[orixyz.ijk[0]] - 1][3] ;
} else {
orgx = - nim->sto_xyz.m[ORIENT_xyzint[orixyz.ijk[0]] - 1][3] ;
}
if (ORIENT_xyz[orixyz.ijk[1]] == 'z' ) {
orgy = nim->sto_xyz.m[ORIENT_xyzint[orixyz.ijk[1]] - 1][3] ;
} else {
orgy = - nim->sto_xyz.m[ORIENT_xyzint[orixyz.ijk[1]] - 1][3] ;
}
if (ORIENT_xyz[orixyz.ijk[2]] == 'z' ) {
orgz = nim->sto_xyz.m[ORIENT_xyzint[orixyz.ijk[2]] - 1][3] ;
} else {
orgz = - nim->sto_xyz.m[ORIENT_xyzint[orixyz.ijk[2]] - 1][3] ;
}
LOAD_FVEC3( orgxyz , orgx ,
orgy ,
orgz ) ;
#if 0
LOAD_FVEC3( orgxyz , -nim->sto_xyz.m[0][3] , /* again, negate */
-nim->sto_xyz.m[1][3] , /* x and y coords */
nim->sto_xyz.m[2][3] ) ;
#endif
#define MAXNUM(a,b) ( (a) > (b) ? (a):(b))
#define MAX3(a,b,c) ( (MAXNUM(a,b)) > (MAXNUM(a,c)) ? (MAXNUM(a,b)):(MAXNUM(a,c)))
#define MINNUM(a,b) ( (a) < (b) ? (a):(b))
#define MIN3(a,b,c) ( (MINNUM(a,b)) < (MINNUM(a,c)) ? (MINNUM(a,b)):(MINNUM(a,c)))
dxtmp = sqrt ( nim->sto_xyz.m[0][0] * nim->sto_xyz.m[0][0] +
nim->sto_xyz.m[1][0] * nim->sto_xyz.m[1][0] +
nim->sto_xyz.m[2][0] * nim->sto_xyz.m[2][0] ) ;
xmax = MAX3(fabs(nim->sto_xyz.m[0][0]),fabs(nim->sto_xyz.m[1][0]),fabs(nim->sto_xyz.m[2][0])) / dxtmp ;
dytmp = sqrt ( nim->sto_xyz.m[0][1] * nim->sto_xyz.m[0][1] +
nim->sto_xyz.m[1][1] * nim->sto_xyz.m[1][1] +
nim->sto_xyz.m[2][1] * nim->sto_xyz.m[2][1] ) ;
ymax = MAX3(fabs(nim->sto_xyz.m[0][1]),fabs(nim->sto_xyz.m[1][1]),fabs(nim->sto_xyz.m[2][1])) / dytmp ;
dztmp = sqrt ( nim->sto_xyz.m[0][2] * nim->sto_xyz.m[0][2] +
nim->sto_xyz.m[1][2] * nim->sto_xyz.m[1][2] +
nim->sto_xyz.m[2][2] * nim->sto_xyz.m[2][2] ) ;
zmax = MAX3(fabs(nim->sto_xyz.m[0][2]),fabs(nim->sto_xyz.m[1][2]),fabs(nim->sto_xyz.m[2][2])) / dztmp ;
fig_merit = MIN3(xmax,ymax,zmax) ;
ang_merit = acos (fig_merit) * 180.0 / 3.141592653 ;
#if 0
if (fabs(ang_merit) > .01) {
WARNING_message (
"qform not present in:\n"
" '%s'\n"
" oblique sform used, and the worst axis is\n"
" %f degrees from plumb.\n"
" If you are performing spatial transformations on this dset, \n"
" or viewing/combining it with volumes of differing obliquity,\n"
" you should consider running: \n"
" 3dWarp -deoblique \n"
" on this and other oblique datasets in the same session.\n"
,pathname, ang_merit ) ;
}
#endif
if( nim->xyz_units == NIFTI_UNITS_METER ){
dxtmp *= 1000.0 ; dytmp *= 1000.0 ; dztmp *= 1000.0 ;
} else if( nim->xyz_units == NIFTI_UNITS_MICRON ){
dxtmp *= 0.001 ; dytmp *= 0.001 ; dztmp *= 0.001 ;
}
LOAD_FVEC3( dxyz , (ORIENT_sign[orixyz.ijk[0]]=='+') ? dxtmp : -dxtmp ,
(ORIENT_sign[orixyz.ijk[1]]=='+') ? dytmp : -dytmp ,
(ORIENT_sign[orixyz.ijk[2]]=='+') ? dztmp : -dztmp ) ;
LOAD_MAT44(ijk_to_dicom44, -nim->sto_xyz.m[0][0] , /* negate x and y */
-nim->sto_xyz.m[0][1] , /* coefficients, */
-nim->sto_xyz.m[0][2] , /* since AFNI works */
-nim->sto_xyz.m[0][3] ,
-nim->sto_xyz.m[1][0] , /* with RAI coords, */
-nim->sto_xyz.m[1][1] , /* but NIFTI uses */
-nim->sto_xyz.m[1][2] , /* LPI coordinates. */
-nim->sto_xyz.m[1][3] ,
nim->sto_xyz.m[2][0] , /* [Which is my own] */
nim->sto_xyz.m[2][1] , /* [damn fault!!!!!] */
nim->sto_xyz.m[2][2] ,
nim->sto_xyz.m[2][3] ) ;
} else { /* NO SPATIAL XFORM. BAD BAD BAD BAD BAD BAD. */
float dxtmp, dytmp, dztmp ;
/* if pixdim data are present, use them in order to set pixel
dimensions. otherwise, set the dimensions to 1 unit. */
dxtmp = ((nim->pixdim[1] > 0) ? nim->pixdim[1] : 1) ;
dytmp = ((nim->pixdim[2] > 0) ? nim->pixdim[2] : 1) ;
dztmp = ((nim->pixdim[3] > 0) ? nim->pixdim[3] : 1) ;
if( nim->xyz_units == NIFTI_UNITS_METER ){
dxtmp *= 1000.0 ; dytmp *= 1000.0 ; dztmp *= 1000.0 ;
} else if( nim->xyz_units == NIFTI_UNITS_MICRON ){
dxtmp *= 0.001 ; dytmp *= 0.001 ; dztmp *= 0.001 ;
}
/* set orientation to LPI by default */
LOAD_IVEC3( orixyz , 1 ,
2 ,
4 ) ;
LOAD_FVEC3( dxyz , (ORIENT_sign[orixyz.ijk[0]]=='+') ? dxtmp : -dxtmp ,
(ORIENT_sign[orixyz.ijk[1]]=='+') ? dytmp : -dytmp ,
(ORIENT_sign[orixyz.ijk[2]]=='+') ? dztmp : -dztmp ) ;
iview = NIFTI_default_view();
/* set origin to 0,0,0 */
LOAD_FVEC3( orgxyz , 0 ,
0 ,
0 ) ;
/* put scaled identity matrix by default */
LOAD_MAT44(ijk_to_dicom44, dxtmp, 0.0, 0.0, 0.0,
0.0, dytmp, 0.0, 0.0,
0.0, 0.0, dztmp, 0.0 );
}
/*-- make an AFNI dataset! --*/
dset = EDIT_empty_copy(NULL) ;
ppp = THD_trailname(pathname,0) ; /* strip directory */
MCW_strncpy( prefix , ppp , THD_MAX_PREFIX ) ; /* to make prefix */
/* You need to set the path too
before, if you loaded ~/tmp/joe.nii the path appeared
to be ./joe.nii, troubling in multiple instances.
ZSS Dec 2011 */
THD_init_diskptr_names( dset->dblk->diskptr ,
THD_filepath(pathname) ,
NULL , prefix ,
dset->view_type , True );
nxyz.ijk[0] = nim->nx ; /* grid dimensions */
nxyz.ijk[1] = nim->ny ;
nxyz.ijk[2] = nim->nz ;
dset->idcode.str[0] = 'N' ; /* overwrite 1st 3 bytes with something special */
dset->idcode.str[1] = 'I' ;
dset->idcode.str[2] = 'I' ;
MCW_hash_idcode( pathname , dset ) ; /* 06 May 2005 */
EDIT_dset_items( dset ,
ADN_prefix , prefix ,
ADN_datum_all , datum ,
ADN_nxyz , nxyz ,
ADN_xyzdel , dxyz ,
ADN_xyzorg , orgxyz ,
ADN_xyzorient , orixyz ,
ADN_malloc_type , DATABLOCK_MEM_MALLOC ,
ADN_view_type , iview ,
ADN_type , (statcode != 0) ? HEAD_FUNC_TYPE
: HEAD_ANAT_TYPE ,
ADN_none ) ;
/* copy transformation matrix to dataset structure */
/* moved after setting grid 4 Apr 2014 [rickr,drg] */
dset->daxes->ijk_to_dicom_real = ijk_to_dicom44;
/* not a time dependent dataset */
if( ntt < 2 ){
EDIT_dset_items( dset ,
ADN_nvals , nbuc ,
ADN_datum_all , datum ,
ADN_func_type , (statcode != 0) ? FUNC_BUCK_TYPE
: ANAT_BUCK_TYPE ,
ADN_none ) ;
} else { /* is a time dependent dataset */
if( nim->time_units == NIFTI_UNITS_MSEC ){
nim->dt *= 0.001 ;
nim->toffset *= 0.001 ;
} else if( nim->time_units == NIFTI_UNITS_USEC ){
nim->dt *= 1.e-6 ;
nim->toffset *= 1.e-6 ;
}
EDIT_dset_items( dset ,
ADN_nvals , ntt ,
ADN_ntt , ntt ,
ADN_datum_all , datum ,
ADN_ttorg , nim->toffset , /* 12 Oct 2007 [rickr] */
ADN_ttdel , nim->dt ,
ADN_ttdur , 0.0 ,
ADN_tunits , UNITS_SEC_TYPE ,
ADN_func_type , (statcode != 0) ? FUNC_FIM_TYPE
: ANAT_EPI_TYPE ,
ADN_none ) ;
/* if present, add stuff about the slice-timing offsets */
if( nim->slice_dim == 3 && /* AFNI can only deal with */
nim->slice_code > 0 && /* slice timing offsets */
nim->slice_duration > 0.0 && /* along the k-axis of */
nim->slice_start >= 0 && /* the dataset volume */
nim->slice_start < nim->nz &&
nim->slice_end > nim->slice_start &&
nim->slice_end < nim->nz ){
float *toff=(float *)calloc(sizeof(float),nim->nz) , tsl ;
int kk ;
if( nim->time_units == NIFTI_UNITS_MSEC ) nim->slice_duration *= 0.001;
else if( nim->time_units == NIFTI_UNITS_USEC ) nim->slice_duration *= 1.e-6;
/* set up slice time offsets in the divers orders */
switch( nim->slice_code ){
case NIFTI_SLICE_SEQ_INC:
tsl = 0.0 ;
for( kk=nim->slice_start ; kk <= nim->slice_end ; kk++ ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
break ;
case NIFTI_SLICE_SEQ_DEC:
tsl = 0.0 ;
for( kk=nim->slice_end ; kk >= nim->slice_end ; kk-- ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
break ;
case NIFTI_SLICE_ALT_INC:
tsl = 0.0 ;
for( kk=nim->slice_start ; kk <= nim->slice_end ; kk+=2 ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
for( kk=nim->slice_start+1 ; kk <= nim->slice_end ; kk+=2 ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
break ;
case NIFTI_SLICE_ALT_INC2:
tsl = 0.0 ;
for( kk=nim->slice_start+1 ; kk <= nim->slice_end ; kk+=2 ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
for( kk=nim->slice_start ; kk <= nim->slice_end ; kk+=2 ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
break ;
case NIFTI_SLICE_ALT_DEC:
tsl = 0.0 ;
for( kk=nim->slice_end ; kk >= nim->slice_start ; kk-=2 ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
for( kk=nim->slice_end-1 ; kk >= nim->slice_start ; kk-=2 ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
break ;
case NIFTI_SLICE_ALT_DEC2:
tsl = 0.0 ;
for( kk=nim->slice_end-1 ; kk >= nim->slice_start ; kk-=2 ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
for( kk=nim->slice_end ; kk >= nim->slice_start ; kk-=2 ){
toff[kk] = tsl ; tsl += nim->slice_duration ;
}
break ;
}
EDIT_dset_items( dset ,
ADN_nsl , nim->nz ,
ADN_zorg_sl , orgxyz.xyz[2] ,
ADN_dz_sl , dxyz.xyz[2] ,
ADN_toff_sl , toff ,
ADN_none ) ;
free(toff) ;
} /* end of slice timing stuff */
} /* end of 3D+time dataset stuff */
/* set atlas space based on NIFTI s/qform code */
NIFTI_code_to_space(form_code,dset);
/* add statistics, if present */
if( statcode != 0 ){
for( ibr=0 ; ibr < nvals ; ibr++ )
EDIT_STATAUX4(dset,ibr,statcode,nim->intent_p1,nim->intent_p2,nim->intent_p3,0) ;
}
/*-- flag to read data from disk using NIFTI functions --*/
dset->dblk->diskptr->storage_mode = STORAGE_BY_NIFTI ;
strcpy( dset->dblk->diskptr->brick_name , pathname ) ;
dset->dblk->diskptr->byte_order = nim->byteorder ;
#if 0
for( ibr=0 ; ibr < nvals ; ibr++ ){ /* make sub-brick labels */
sprintf(prefix,"%s[%d]",tname,ibr) ;
EDIT_BRICK_LABEL( dset , ibr , prefix ) ;
}
#endif
/** 10 May 2005: see if there is an AFNI extension;
if so, load attributes from it and
then edit the dataset appropriately **/
{ int ee ; /* extension index */
/* scan extension list to find the first AFNI extension */
for( ee=0 ; ee < nim->num_ext ; ee++ )
if( nim->ext_list[ee].ecode == NIFTI_ECODE_AFNI &&
nim->ext_list[ee].esize > 32 &&
nim->ext_list[ee].edata != NULL ) break ;
/* if found an AFNI extension ... */
if( ee < nim->num_ext ){
char *buf = nim->ext_list[ee].edata , *rhs , *cpt ;
int nbuf = nim->ext_list[ee].esize - 8 ;
NI_stream ns ;
void *nini ;
NI_group *ngr , *nngr ;
/* if have data, it's long enough, and starts properly, then ... */
if( buf != NULL && nbuf > 32 && strncmp(buf,"<?xml",5)==0 ){
if( buf[nbuf-1] != '\0' ) buf[nbuf-1] = '\0' ; /* for safety */
cpt = strstr(buf,"?>") ; /* find XML prolog close */
if( cpt != NULL ){ /* if found it, then ... */
ns = NI_stream_open( "str:" , "r" ) ;
NI_stream_setbuf( ns , cpt+2 ) ; /* start just after prolog */
nini = NI_read_element(ns,1) ; /* get root element */
NI_stream_close(ns) ;
if( NI_element_type(nini) == NI_GROUP_TYPE ){ /* must be a group */
ngr = (NI_group *)nini ;
if( strcmp(ngr->name,"AFNI_attributes") == 0 ){ /* root is OK */
nngr = ngr ;
} else { /* search in group for proper element */
int nn ; void **nnini ;
nn = NI_search_group_deep( ngr , "AFNI_attributes" , &nnini ) ;
if( nn <= 0 ) nngr = NULL ;
else { nngr = (NI_group *)nnini[0]; NI_free(nnini); }
}
if( NI_element_type(nngr) == NI_GROUP_TYPE ){ /* have good name */
rhs = NI_get_attribute( nngr , "self_idcode" ) ;
if( rhs == NULL )
rhs = NI_get_attribute( nngr , "AFNI_idcode" ) ;
if( rhs != NULL ) /* set dataset ID code from XML attribute */
MCW_strncpy( dset->idcode.str , rhs , MCW_IDSIZE ) ;
rhs = NI_get_attribute( nngr , "NIfTI_nums" ) ; /* check if */
if( rhs != NULL ){ /* dataset dimensions */
char buf[128] ; /* were altered */
sprintf(buf,"%ld,%ld,%ld,%ld,%ld,%d" , /* 12 May 2005 */
nim->nx, nim->ny, nim->nz, nim->nt, nim->nu, nim->datatype );
if( strcmp(buf,rhs) != 0 ){
static int nnn=0 ;
if(nnn==0){fprintf(stderr,"\n"); nnn=1;}
fprintf(stderr,
"** WARNING: NIfTI file %s dimensions altered since "
"AFNI extension was added\n",pathname ) ;
}
}
THD_dblkatr_from_niml( nngr , dset->dblk ); /* load attributes */
THD_datablock_apply_atr( dset ) ; /* apply to dataset struct */
}
NI_free_element( ngr ) ; /* get rid of the root element */
} /* end of if found a group element at the root */
} /* end of if extension data array had an XML prolog close */
} /* end of if had a good extension data array */
} /* end of if had an AFNI extension */
} /* end of processing extensions */
/* return unpopulated dataset */
nifti_image_free(nim) ; RETURN(dset) ;
}
byte * THD_boxballmask( THD_3dim_dataset *dset ,
int boxball_num , float *boxball_dat )
{
int nx,ny,nz , nxy,nxyz , ii,jj,kk ;
byte *bmask ;
int bb, ibot,itop, jbot,jtop, kbot,ktop , btyp ;
float xbot,xtop, ybot,ytop, zbot,ztop ;
float xcen,ycen,zcen , icen,jcen,kcen ;
float xmin,xmax , ymin,ymax , zmin,zmax , rad,dist , xx,yy,zz ;
THD_fvec3 dv,xv ;
ENTRY("THD_boxballmask") ;
if( !ISVALID_DSET(dset) || boxball_num <= 0 || boxball_dat == NULL ) RETURN(NULL) ;
xmin=dset->daxes->xxmin ; xmax=dset->daxes->xxmax ;
ymin=dset->daxes->yymin ; ymax=dset->daxes->yymax ;
zmin=dset->daxes->zzmin ; zmax=dset->daxes->zzmax ;
nx = DSET_NX(dset) ;
ny = DSET_NY(dset) ; nxy = nx*ny ;
nz = DSET_NZ(dset) ; nxyz = nxy*nz ;
bmask = (byte *)calloc(sizeof(byte),nxyz) ;
for( bb=0 ; bb < boxball_num ; bb++ ){
btyp = boxball_dat[0+BOXLEN*bb] ;
if( btyp < BALL_XYZ ){ /*---- box ----*/
xbot = boxball_dat[1+BOXLEN*bb]; xtop = boxball_dat[2+BOXLEN*bb];
ybot = boxball_dat[3+BOXLEN*bb]; ytop = boxball_dat[4+BOXLEN*bb];
zbot = boxball_dat[5+BOXLEN*bb]; ztop = boxball_dat[6+BOXLEN*bb];
if( btyp != BOX_IJK ){ /* convert coords to indexes */
if( btyp == BOX_NEU ){ /* coords from Neuroscience to DICOM */
xbot = -xbot; xtop = -xtop; ybot = -ybot; ytop = -ytop; btyp = BOX_DIC;
}
if( btyp == BOX_DIC ){ /* coords from DICOM to dataset */
LOAD_FVEC3(dv,xbot,ybot,zbot) ;
xv = THD_dicomm_to_3dmm( dset , dv ) ;
UNLOAD_FVEC3(xv,xbot,ybot,zbot) ;
LOAD_FVEC3(dv,xtop,ytop,ztop) ;
xv = THD_dicomm_to_3dmm( dset , dv ) ;
UNLOAD_FVEC3(xv,xtop,ytop,ztop) ;
}
if( xbot < xmin && xtop < xmin ) continue ; /* skip box if outside dataset */
if( xbot > xmax && xtop > xmax ) continue ;
if( ybot < ymin && ytop < ymin ) continue ;
if( ybot > ymax && ytop > ymax ) continue ;
if( zbot < zmin && ztop < zmin ) continue ;
if( zbot > zmax && ztop > zmax ) continue ;
LOAD_FVEC3(dv,xbot,ybot,zbot) ;
xv = THD_3dmm_to_3dfind( dset , dv ) ; /* coords from dataset to index */
UNLOAD_FVEC3(xv,xbot,ybot,zbot) ;
LOAD_FVEC3(dv,xtop,ytop,ztop) ;
xv = THD_3dmm_to_3dfind( dset , dv ) ;
UNLOAD_FVEC3(xv,xtop,ytop,ztop) ;
}
ibot = rint(xbot) ; jbot = rint(ybot) ; kbot = rint(zbot) ; /* round */
itop = rint(xtop) ; jtop = rint(ytop) ; ktop = rint(ztop) ;
if( ibot > itop ){ btyp = ibot; ibot = itop; itop = btyp; } /* flip? */
if( jbot > jtop ){ btyp = jbot; jbot = jtop; jtop = btyp; }
if( kbot > ktop ){ btyp = kbot; kbot = ktop; ktop = btyp; }
/* skip box if outside dataset */
if ( itop < 0 || ibot >= nx ) continue;
if ( jtop < 0 || jbot >= ny ) continue;
if ( ktop < 0 || kbot >= nz ) continue;
/* constrain values to dataset dimensions */
if ( ibot < 0 ) ibot = 0; if ( itop >= nx ) itop = nx-1;
if ( jbot < 0 ) jbot = 0; if ( jtop >= ny ) jtop = ny-1;
if ( kbot < 0 ) kbot = 0; if ( ktop >= nz ) ktop = nz-1;
for( kk=kbot ; kk <= ktop ; kk++ )
for( jj=jbot ; jj <= jtop ; jj++ )
for( ii=ibot ; ii <= itop ; ii++ ) bmask[ii+jj*nx+kk*nxy] = 1 ;
} else { /*---- ball ----*/
xcen = boxball_dat[1+BOXLEN*bb] ; ycen = boxball_dat[2+BOXLEN*bb] ;
zcen = boxball_dat[3+BOXLEN*bb] ; rad = boxball_dat[4+BOXLEN*bb] ;
/* convert center coords to dataset indexes */
if( btyp == BALL_NEU ){ /* coords from Neuroscience to DICOM */
xcen = -xcen; ycen = -ycen; btyp = BALL_DIC;
}
if( btyp == BALL_DIC ){ /* coords from DICOM to dataset */
LOAD_FVEC3(dv,xcen,ycen,zcen) ;
xv = THD_dicomm_to_3dmm( dset , dv ) ;
UNLOAD_FVEC3(xv,xcen,ycen,zcen) ;
}
if( xcen < xmin || xcen > xmax ) continue ; /* skip ball if outside */
if( ycen < ymin || ycen > ymax ) continue ;
if( zcen < zmin || zcen > zmax ) continue ;
LOAD_FVEC3(dv,xcen,ycen,zcen) ;
xv = THD_3dmm_to_3dfind( dset , dv ) ; /* coords from dataset to index */
UNLOAD_FVEC3(xv,icen,jcen,kcen) ;
ibot = rint(icen-rad) ; itop = rint(icen+rad) ; /* box around ball */
jbot = rint(jcen-rad) ; jtop = rint(jcen+rad) ;
kbot = rint(kcen-rad) ; ktop = rint(kcen+rad) ;
rad = rad*rad ;
for( kk=kbot ; kk <= ktop ; kk++ ){
for( jj=jbot ; jj <= jtop ; jj++ ){
for( ii=ibot ; ii <= itop ; ii++ ){
LOAD_FVEC3( dv , ii,jj,kk ) ; /* convert to xyz coords */
xv = THD_3dfind_to_3dmm( dset , dv ) ; /* then test distance^2 */
UNLOAD_FVEC3( xv , xx,yy,zz ) ; /* xyz of ball center. */
dist = SQR(xx-xcen) + SQR(yy-ycen) + SQR(zz-zcen) ;
if( dist <= rad ) bmask[ii+jj*nx+kk*nxy] = 1 ;
}}}
}
} /*----- end of loop over box/ball list -----*/
RETURN(bmask) ;
}
int main( int argc , char * argv[] )
{
int narg=1, do_automask=0 , iv , nxyz , do_set=0 ,
*rois=NULL, N_rois=0, all_rois = 0;
THD_3dim_dataset *xset ;
byte *mmm=NULL ; int nmask=0 , nvox_mask=0 ;
THD_fvec3 cmv , setv ;
/*-- read command line arguments --*/
if( argc < 2 || strncmp(argv[1],"-help",5) == 0 ){
printf("Usage: 3dCM [options] dset\n"
"Output = center of mass of dataset, to stdout.\n"
" -mask mset Means to use the dataset 'mset' as a mask:\n"
" Only voxels with nonzero values in 'mset'\n"
" will be averaged from 'dataset'. Note\n"
" that the mask dataset and the input dataset\n"
" must have the same number of voxels.\n"
" -automask Generate the mask automatically.\n"
" -set x y z After computing the CM of the dataset, set the\n"
" origin fields in the header so that the CM\n"
" will be at (x,y,z) in DICOM coords.\n"
" -roi_vals v0 v1 v2 ... : Compute center of mass for each blob\n"
" with voxel value of v0, v1, v2, etc.\n"
" This option is handy for getting ROI \n"
" centers of mass.\n"
" -all_rois Don't bother listing the values of ROIs you want\n"
" the program will find all of them and produce a \n"
" full list.\n"
" NOTE: Masking options are ignored with -roi_vals and -all_rois\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
LOAD_FVEC3(setv,0,0,0) ; /* ZSS: To quiet init. warnings */
narg = 1 ;
while( narg < argc && argv[narg][0] == '-' ){
if( strcmp(argv[narg],"-set") == 0 ){
float xset,yset,zset ;
if( narg+3 >= argc ){
fprintf(stderr,"*** -set need 3 args following!\n") ; exit(1) ;
}
xset = strtod( argv[++narg] , NULL ) ;
yset = strtod( argv[++narg] , NULL ) ;
zset = strtod( argv[++narg] , NULL ) ;
LOAD_FVEC3(setv,xset,yset,zset) ; do_set = 1 ;
THD_set_write_compression(COMPRESS_NONE); /* do not alter compression*/
narg++ ; continue ;
}
if( strncmp(argv[narg],"-mask",5) == 0 ){
THD_3dim_dataset *mask_dset ;
if( mmm != NULL ){
fprintf(stderr,"*** Cannot have two -mask options!\n") ; exit(1) ;
}
if( do_automask ){
fprintf(stderr,"*** Can't have -mask and -automask!\n") ; exit(1) ;
}
if( narg+1 >= argc ){
fprintf(stderr,"*** -mask option requires a following argument!\n");
exit(1) ;
}
mask_dset = THD_open_dataset( argv[++narg] ) ;
CHECK_OPEN_ERROR(mask_dset,argv[narg]) ;
if( DSET_BRICK_TYPE(mask_dset,0) == MRI_complex ){
fprintf(stderr,"*** Cannot deal with complex-valued mask dataset!\n");
exit(1) ;
}
mmm = THD_makemask( mask_dset , 0 , 1.0,0.0 ) ;
nvox_mask = DSET_NVOX(mask_dset) ;
nmask = THD_countmask( nvox_mask , mmm ) ;
if( mmm == NULL || nmask <= 0 ){
fprintf(stderr,"*** Can't make mask from dataset %s\n",argv[narg-1]);
exit(1) ;
}
DSET_delete( mask_dset ) ;
narg++ ; continue ;
}
if( strncmp(argv[narg],"-roi_vals",5) == 0 ){
if( narg+1 >= argc ){
fprintf(stderr,"*** -mask option requires a following argument(s)!\n");
exit(1) ;
}
rois = (int *)calloc(argc, sizeof(int));
N_rois = 0;
++narg;
while (narg < argc-1 && argv[narg][0] != '-') {
rois[N_rois++] = atoi(argv[narg]);
++narg;
}
continue ;
}
if( strncmp(argv[narg],"-all_rois",5) == 0 ){
all_rois = 1;
narg++ ; continue ;
}
if( strcmp(argv[narg],"-automask") == 0 ){
if( mmm != NULL ){
fprintf(stderr,"*** Can't have -mask and -automask!\n") ; exit(1) ;
}
do_automask = 1 ; narg++ ; continue ;
}
fprintf(stderr,"*** Unknown option: %s\n",argv[narg]) ; exit(1) ;
}
/* should have at least 1 more argument */
if( argc <= narg ){
fprintf(stderr,"*** No input dataset!?\n") ; exit(1) ;
}
for( ; narg < argc ; narg++ ){
xset = THD_open_dataset( argv[narg] ) ;
if( xset == NULL ){
fprintf(stderr,"+++ Can't open dataset %s -- skipping\n",argv[narg]);
continue ;
}
DSET_load(xset) ;
if( !DSET_LOADED(xset) ){
fprintf(stderr,"+++ Can't load dataset %s -- skipping\n",argv[narg]);
DSET_delete(xset) ; continue ;
}
if( do_automask ){
if( mmm != NULL ){ free(mmm); mmm = NULL; }
mmm = THD_automask(xset) ;
nvox_mask = DSET_NVOX(xset) ;
nmask = THD_countmask( nvox_mask , mmm ) ;
if( mmm == NULL || nmask <= 0 ){
fprintf( stderr,
"+++ Can't make automask from dataset %s "
"-- skipping\n",argv[narg]) ;
DSET_delete(xset) ; continue ;
}
}
nxyz = DSET_NVOX(xset) ;
if( mmm != NULL && nxyz != nvox_mask ){
fprintf(stderr,"+++ Mask/Dataset grid size mismatch at %s\n -- skipping\n",argv[narg]) ;
DSET_delete(xset) ; continue ;
}
if (all_rois) {
if (!(rois = THD_unique_vals(xset, 0, &N_rois, NULL)) || N_rois == 0) {
ERROR_message("No rois or error in THD_unique_vals"); continue;
}
fprintf(stderr,"#%d distinct ROIs", N_rois);
}
if (!N_rois) {
cmv = THD_cmass( xset , 0 , mmm ) ;
printf("%g %g %g\n",cmv.xyz[0],cmv.xyz[1],cmv.xyz[2]) ;
DSET_unload(xset) ;
if( do_set ){
THD_fvec3 dv , ov ;
if( DSET_IS_MASTERED(xset) ){
fprintf(stderr,"+++ Can't modify CM of dataset %s\n",argv[narg]) ;
} else {
/* lose obliquity */
/* recompute Tc(Cardinal transformation matrix for new grid output */
THD_make_cardinal(xset);
LOAD_FVEC3(ov,DSET_XORG(xset),DSET_YORG(xset),DSET_ZORG(xset)) ;
ov = THD_3dmm_to_dicomm( xset , ov ) ;
dv = SUB_FVEC3(setv,cmv) ;
ov = ADD_FVEC3(dv,ov) ;
ov = THD_dicomm_to_3dmm( xset , ov ) ;
xset->daxes->xxorg = ov.xyz[0] ;
xset->daxes->yyorg = ov.xyz[1] ;
xset->daxes->zzorg = ov.xyz[2] ;
/* allow overwriting header for all types of output data */
putenv("AFNI_DECONFLICT=OVERWRITE") ;
tross_Make_History( "3dCM" , argc,argv , xset );/* ZSS Dec. 09 08 */
if(DSET_IS_BRIK(xset)) {
INFO_message("Rewriting header %s",DSET_HEADNAME(xset)) ;
DSET_overwrite_header( xset ) ;
}
else { /* for other dataset types like NIFTI, rewrite whole dset */
DSET_load( xset ) ;
DSET_overwrite(xset) ;
INFO_message("Wrote new dataset: %s",DSET_BRIKNAME(xset)) ;
}
}
}
} else {
float *xyz;
if ((xyz = THD_roi_cmass(xset , 0 , rois, N_rois))) {
printf("#Dset %s\n",DSET_BRIKNAME(xset));
for (iv=0; iv<N_rois; ++iv) {
printf("#ROI %d\n", rois[iv]);
printf("%g %g %g\n",xyz[3*iv],xyz[3*iv+1],xyz[3*iv+2]) ;
}
free(xyz); free(rois);
} else {
ERROR_message("Failed in THD_roi_cmass"); continue;
}
}
DSET_delete(xset) ;
}
exit(0);
}
