static MRI *
MRIcomputeSurfaceDistanceProbabilities(MRI_SURFACE *mris, MRI *mri_ribbon, MRI *mri, MRI *mri_aseg)
{
MRI *mri_features, *mri_binary, *mri_white_dist, *mri_pial_dist, *mri_mask ;
int nwhite_bins, npial_bins, x, y, z, label, i ;
HISTOGRAM2D *hw, *hp ;
float pdist, wdist, val ;
double wval, pval ;
mri_features = MRIallocSequence(mri->width, mri->height, mri->depth, MRI_FLOAT, 2) ;
MRIcopyHeader(mri, mri_features) ;
mri_binary = MRIcopy(mri_ribbon, NULL) ;
mri_binary = MRIbinarize(mri_ribbon, NULL, 1, 0, 1) ;
mri_pial_dist = MRIdistanceTransform(mri_binary, NULL, 1, max_pial_dist+1, DTRANS_MODE_SIGNED,NULL);
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
MRIwrite(mri_pial_dist, "pd.mgz") ;
MRIclear(mri_binary) ;
MRIcopyLabel(mri_ribbon, mri_binary, Left_Cerebral_White_Matter) ;
MRIcopyLabel(mri_ribbon, mri_binary, Right_Cerebral_White_Matter) ;
MRIbinarize(mri_binary, mri_binary, 1, 0, 1) ;
mri_white_dist = MRIdistanceTransform(mri_binary, NULL, 1, max_white_dist+1, DTRANS_MODE_SIGNED,NULL);
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
MRIwrite(mri_white_dist, "wd.mgz") ;
nwhite_bins = ceil((max_white_dist - min_white_dist) / white_bin_size)+1 ;
npial_bins = ceil((max_pial_dist - min_pial_dist) / pial_bin_size)+1 ;
hw = HISTO2Dalloc(NBINS, nwhite_bins) ;
hp = HISTO2Dalloc(NBINS, npial_bins) ;
HISTO2Dinit(hw, NBINS, nwhite_bins, 0, NBINS-1, min_white_dist, max_white_dist) ;
HISTO2Dinit(hp, NBINS, npial_bins, 0, NBINS-1, min_pial_dist, max_pial_dist) ;
for (x = 0 ; x < mri->width ; x++)
for (y = 0 ; y < mri->height ; y++)
for (z = 0 ; z < mri->depth ; z++)
{
label = MRIgetVoxVal(mri_aseg, x, y, z, 0) ;
if (IS_CEREBELLUM(label) || IS_VENTRICLE(label) || label == Brain_Stem || IS_CC(label))
continue ;
pdist = MRIgetVoxVal(mri_pial_dist, x, y, z, 0) ;
wdist = MRIgetVoxVal(mri_pial_dist, x, y, z, 0) ;
val = MRIgetVoxVal(mri, x, y, z, 0) ;
if (pdist >= min_pial_dist && pdist <= max_pial_dist)
HISTO2DaddSample(hp, val, pdist, 0, 0, 0, 0) ;
if (wdist >= min_white_dist && wdist <= max_white_dist)
HISTO2DaddSample(hw, val, wdist, 0, 0, 0, 0) ;
}
HISTO2DmakePDF(hp, hp) ;
HISTO2DmakePDF(hw, hw) ;
for (x = 0 ; x < mri->width ; x++)
for (y = 0 ; y < mri->height ; y++)
for (z = 0 ; z < mri->depth ; z++)
{
label = MRIgetVoxVal(mri_aseg, x, y, z, 0) ;
if (IS_CEREBELLUM(label) || IS_VENTRICLE(label) || label == Brain_Stem || IS_CC(label))
continue ;
pdist = MRIgetVoxVal(mri_pial_dist, x, y, z, 0) ;
wdist = MRIgetVoxVal(mri_pial_dist, x, y, z, 0) ;
val = MRIgetVoxVal(mri, x, y, z, 0) ;
wval = HISTO2DgetCount(hw, val, wdist);
if (DZERO(wval) == 0)
MRIsetVoxVal(mri_features, x, y, z, 1, -log10(wval)) ;
pval = HISTO2DgetCount(hp, val, pdist);
if (DZERO(pval) == 0)
MRIsetVoxVal(mri_features, x, y, z, 0, -log10(pval)) ;
}
MRIclear(mri_binary) ;
MRIbinarize(mri_ribbon, mri_binary, 1, 0, 1) ;
mri_mask = MRIcopy(mri_binary, NULL) ;
for (i = 0 ; i < close_order ; i++)
{
MRIdilate(mri_binary, mri_mask) ;
MRIcopy(mri_mask, mri_binary) ;
}
for (i = 0 ; i < close_order ; i++)
{
MRIerode(mri_binary, mri_mask) ;
MRIcopy(mri_mask, mri_binary) ;
}
MRIwrite(mri_mask, "m.mgz") ;
MRImask(mri_features, mri_mask, mri_features, 0, 0) ;
HISTO2Dfree(&hw) ;
HISTO2Dfree(&hp) ;
MRIfree(&mri_white_dist) ; MRIfree(&mri_pial_dist) ; MRIfree(&mri_binary) ;
return(mri_features) ;
}
static MRI *
build_distance_by_intensity_histo(MRI *mri_norm,
MRI *mri_dist,
MRI *mri_aseg,
double dist_spacing,
double max_dist)
{
HISTOGRAM2D *h_dist_by_int ;
int x, y, z, b1, b2, label ;
float val, dist ;
double total, unlikely, pval ;
MRI *mri_pvals ;
h_dist_by_int = HISTO2Dalloc((int)ceil(max_dist/dist_spacing), 256) ;
HISTO2Dinit(h_dist_by_int,
h_dist_by_int->nbins1,
h_dist_by_int->nbins2,
0,
MAX_DIST,
0,
255) ;
for (x = 0 ; x < mri_dist->width ; x++)
for (y = 0 ; y < mri_dist->height ; y++)
for (z = 0 ; z < mri_dist->depth ; z++)
{
if (x == Gx && y == Gy && z == Gz)
{
DiagBreak() ;
}
dist = MRIgetVoxVal(mri_dist, x, y, z, 0) ;
if (dist < 0 || dist > MAX_DIST) // in interior or too far away
{
continue ;
}
label = MRIgetVoxVal(mri_aseg, x, y, z, 0) ;
if (IS_WHITE_CLASS(label) == 0 &&
IS_CORTEX(label) == 0 &&
label < MIN_CORTICAL_PARCELLATION)
{
continue ;
}
val = MRIgetVoxVal(mri_norm, x, y, z, 0) ;
HISTO2DaddSample(h_dist_by_int, dist, val, 0, max_dist, 0, 255) ;
}
// normalize the counts for each distance
for (b1 = 0 ; b1 < h_dist_by_int->nbins1 ; b1++)
{
for (total = 0.0, b2 = 0 ; b2 < h_dist_by_int->nbins2 ; b2++)
{
total += h_dist_by_int->counts[b1][b2] ;
}
if (total > 0)
{
unlikely = 1.0/(10*total) ;
for (b2 = 0 ; b2 < h_dist_by_int->nbins2 ; b2++)
{
h_dist_by_int->counts[b1][b2]/=total ;
if (DZERO(h_dist_by_int->counts[b1][b2]))
{
h_dist_by_int->counts[b1][b2] = unlikely ;
}
}
}
}
mri_pvals = MRIclone(mri_dist, NULL) ;
for (x = 0 ; x < mri_dist->width ; x++)
for (y = 0 ; y < mri_dist->height ; y++)
for (z = 0 ; z < mri_dist->depth ; z++)
{
if (x == Gx && y == Gy && z == Gz)
{
DiagBreak() ;
}
dist = MRIgetVoxVal(mri_dist, x, y, z, 0) ;
if (dist < 0 || dist > MAX_DIST) // in interior
{
continue ;
}
label = MRIgetVoxVal(mri_aseg, x, y, z, 0) ;
if (IS_WHITE_CLASS(label) == 0 &&
IS_CORTEX(label) == 0 &&
label < MIN_CORTICAL_PARCELLATION)
{
continue ;
}
val = MRIgetVoxVal(mri_norm, x, y, z, 0) ;
pval = HISTO2DgetCount(h_dist_by_int, dist, val) ;
if (pval > 0)
{
pval = -log10(pval) ;
}
else
{
pval = -10000 ;
}
MRIsetVoxVal(mri_pvals, x, y, z, 0, pval) ;
}
HISTO2Dfree(&h_dist_by_int) ;
return(mri_pvals) ;
}
