static int
discard_unlikely_control_points(GCA *gca, GCA_SAMPLE *gcas, int nsamples,
MRI *mri_in, TRANSFORM *transform, char *name)
{
int i, xv, yv, zv, n, peak, start, end, num ;
HISTO *h, *hsmooth ;
float fmin, fmax ;
Real val, mean_ratio ;
if (nsamples == 0)
return(NO_ERROR) ;
for (num = n = 0 ; n < mri_in->nframes ; n++)
{
int niter = 0 ;
MRIvalRangeFrame(mri_in, &fmin, &fmax, n) ;
h = HISTOalloc(nint(fmax-fmin)+1) ;
h->bin_size = (fmax-fmin)/(float)h->nbins ;
for (i = 0 ; i < h->nbins ; i++)
h->bins[i] = (i+1)*h->bin_size+fmin ;
for (i = 0 ; i < nsamples ; i++)
{
xv = gcas[i].x ; yv = gcas[i].y ; zv = gcas[i].z ;
if (xv == Gx && yv == Gy && zv == Gz)
DiagBreak() ;
MRIsampleVolumeFrame(mri_in, gcas[i].x,gcas[i].y,gcas[i].z, n, &val) ;
if (FZERO(val))
DiagBreak() ;
h->counts[nint(val-fmin)]++ ;
}
/* check to see if peak is unlikely */
hsmooth = HISTOsmooth(h, NULL, 2) ;
do
{
if (gca->ninputs == 1) /* find brightest peak as
for n=1 it is T1 weighted */
peak = HISTOfindLastPeak(hsmooth, HISTO_WINDOW_SIZE,MIN_HISTO_PCT);
else
peak = HISTOfindHighestPeakInRegion(hsmooth, 0, h->nbins-1) ;
end = HISTOfindEndOfPeak(hsmooth, peak, 0.01) ;
start = HISTOfindStartOfPeak(hsmooth, peak, 0.01) ;
for (mean_ratio = 0.0, i = 0 ; i < nsamples ; i++)
{
mean_ratio += hsmooth->bins[peak] / gcas[i].means[0];
}
mean_ratio /= (Real)nsamples ;
HISTOclearBins
(hsmooth, hsmooth, hsmooth->bins[start], hsmooth->bins[end]) ;
if (niter++ > 5)
break ;
if (niter > 1)
DiagBreak() ;
} while (mean_ratio < 0.5 || mean_ratio > 2.0) ;
printf("%s: limiting intensities to %2.1f --> %2.1f\n",
name, fmin+start, fmin+end) ;
for (i = 0 ; i < nsamples ; i++)
{
xv = gcas[i].x ; yv = gcas[i].y ; zv = gcas[i].z ;
if (xv == Gx && yv == Gy && zv == Gz)
DiagBreak() ;
MRIsampleVolumeFrame(mri_in,gcas[i].x,gcas[i].y,gcas[i].z,n,&val) ;
if (val-fmin < start || val-fmin > end)
{
num++ ; gcas[i].label = 0 ;
}
}
HISTOfree(&h) ; HISTOfree(&hsmooth) ;
}
printf("%d of %d (%2.1f%%) samples deleted\n",
num, nsamples, 100.0f*(float)num/(float)nsamples) ;
return(NO_ERROR) ;
}
MRI *
MRIsynthesizeWeightedVolume(MRI *mri_T1, MRI *mri_PD, float w5, float TR5,
float w30, float TR30, float target_wm, float TE) {
MRI *mri_dst ;
int x, y, z, width, height, depth ;
MRI *mri30, *mri5 ;
Real val30, val5, val, min_val ;
#if 0
int mri_peak, n, min_real_bin ;
double mean_PD ;
MRI_REGION box ;
HISTOGRAM *h_mri, *h_smooth ;
float x0, y0, z0, min_real_val ;
#endif
width = mri_T1->width ;
height = mri_T1->height ;
depth = mri_T1->depth ;
mri_dst = MRIalloc(width, height, depth, MRI_FLOAT) ;
MRIcopyHeader(mri_T1, mri_dst) ;
mri30 = MRIsynthesize(mri_T1, mri_PD, NULL, NULL, TR30, RADIANS(30), TE) ;
mri5 = MRIsynthesize(mri_T1, mri_PD, NULL, NULL, TR5, RADIANS(5), TE) ;
#if 0
mean_PD = MRImeanFrame(mri_PD, 0) ;
/* MRIscalarMul(mri_PD, mri_PD, 1000.0f/mean_PD) ;*/
h_mri = MRIhistogram(mri30, 100) ;
h_smooth = HISTOsmooth(h_mri, NULL, 2) ;
mri_peak = HISTOfindHighestPeakInRegion(h_smooth, 0, h_smooth->nbins) ;
min_real_bin = HISTOfindNextValley(h_smooth, mri_peak) ;
min_real_val = h_smooth->bins[min_real_bin] ;
MRIfindApproximateSkullBoundingBox(mri30, min_real_val, &box) ;
x0 = box.x+box.dx/3 ;
y0 = box.y+box.dy/3 ;
z0 = box.z+box.dz/2 ;
printf("using (%.0f, %.0f, %.0f) as brain centroid...\n",x0, y0, z0) ;
box.dx /= 4 ;
box.x = x0 - box.dx/2;
box.dy /= 4 ;
box.y = y0 - box.dy/2;
box.dz /= 4 ;
box.z = z0 - box.dz/2;
printf("using box (%d,%d,%d) --> (%d, %d,%d) "
"to find MRI wm\n", box.x, box.y, box.z,
box.x+box.dx-1,box.y+box.dy-1, box.z+box.dz-1) ;
h_mri = MRIhistogramRegion(mri30, 0, NULL, &box) ;
for (n = 0 ; n < h_mri->nbins-1 ; n++)
if (h_mri->bins[n+1] > min_real_val)
break ;
HISTOclearBins(h_mri, h_mri, 0, n) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
HISTOplot(h_mri, "mri.histo") ;
mri_peak = HISTOfindLastPeak(h_mri, HISTO_WINDOW_SIZE,MIN_HISTO_PCT);
mri_peak = h_mri->bins[mri_peak] ;
printf("before smoothing, mri peak at %d\n", mri_peak) ;
h_smooth = HISTOsmooth(h_mri, NULL, 2) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
HISTOplot(h_smooth, "mri_smooth.histo") ;
mri_peak = HISTOfindLastPeak(h_smooth, HISTO_WINDOW_SIZE,MIN_HISTO_PCT);
mri_peak = h_mri->bins[mri_peak] ;
printf("after smoothing, mri peak at %d\n", mri_peak) ;
HISTOfree(&h_smooth) ;
HISTOfree(&h_mri) ;
#endif
min_val = 0 ;
for (x = 0 ; x < width ; x++) {
for (y = 0 ; y < height ; y++) {
for (z = 0 ; z < depth ; z++) {
if (x == Gx && y == Gy && z == Gz)
DiagBreak() ;
MRIsampleVolumeType(mri30, x, y, z, &val30, SAMPLE_NEAREST) ;
MRIsampleVolumeType(mri5, x, y, z, &val5, SAMPLE_NEAREST) ;
val = w30*val30 + w5*val5 ;
MRIFvox(mri_dst, x, y, z) = val ;
if (val < min_val)
min_val = val ;
}
}
}
for (x = 0 ; x < width ; x++) {
for (y = 0 ; y < height ; y++) {
for (z = 0 ; z < depth ; z++) {
if (x == Gx && y == Gy && z == Gz)
DiagBreak() ;
MRIFvox(mri_dst, x, y, z) += min_val ;
}
}
}
MRIfree(&mri30) ;
MRIfree(&mri5) ;
return(mri_dst) ;
}
