static int
most_frequent_label(MRI *mri_seg, MRI_SEGMENT *mseg)
{
int label_counts[MAX_CMA_LABELS], i, max_count, max_label, label ;
memset(label_counts, 0, sizeof(label_counts)) ;
for (i = max_count = max_label = 0 ; i < mseg->nvoxels ; i++)
{
label = MRIgetVoxVal(mri_seg,
mseg->voxels[i].x,
mseg->voxels[i].y,
mseg->voxels[i].z, 0) ;
if (IS_WM(label) == 0 && IS_UNKNOWN(label) == 0)
{
label_counts[label]++ ;
}
}
for (i = max_count = max_label = 0 ; i < MAX_CMA_LABELS ; i++)
{
if (label_counts[i] > max_count)
{
max_count = label_counts[i] ;
max_label = i ;
}
}
return(max_label) ;
}
static MRI *
add_interior_points(MRI *mri_src, MRI *mri_vals, float intensity_above,
float intensity_below, MRI_SURFACE *mris_white1,
MRI_SURFACE *mris_white2,
MRI *mri_aseg, MRI *mri_dst)
{
int x, y, z, ctrl, label, i ;
float val ;
MRI *mri_core ;
MRI *mri_interior, *mri_tmp ;
mri_interior = MRIclone(mri_src, NULL) ;
MRISfillInterior(mris_white1, mri_src->xsize, mri_interior) ;
mri_tmp = MRIclone(mri_src, NULL) ;
MRISfillInterior(mris_white2, mri_src->xsize, mri_tmp) ;
MRIcopyLabel(mri_tmp, mri_interior, 1) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_interior, "i.mgz") ;
}
mri_core = MRIerode(mri_interior, NULL) ;
for (i = 1 ; i < nint(1.0/mri_src->xsize) ; i++)
{
MRIcopy(mri_core, mri_tmp) ;
MRIerode(mri_tmp, mri_core) ;
}
MRIfree(&mri_tmp) ;
if (mri_aseg == NULL)
{
for (x = 0 ; x < mri_src->width ; x++)
for (y = 0 ; y < mri_src->height ; y++)
for (z = 0 ; z < mri_src->depth ; z++)
{
if (Gx == x && Gy == y && Gz == z)
{
DiagBreak() ;
}
ctrl = MRIgetVoxVal(mri_core, x, y, z, 0) ;
if (ctrl > 0)
{
MRIsetVoxVal(mri_dst, x, y, z, 0, ctrl) ;
}
}
}
else
{
for (x = 0 ; x < mri_src->width ; x++)
for (y = 0 ; y < mri_src->height ; y++)
for (z = 0 ; z < mri_src->depth ; z++)
{
if (Gx == x && Gy == y && Gz == z)
{
DiagBreak() ;
}
ctrl = MRIgetVoxVal(mri_src, x, y, z, 0) ;
if (ctrl == 0) // add in some missed ones that are inside the surface
{
label = MRIgetVoxVal(mri_aseg, x, y, z, 0) ;
if (IS_GM(label) || IS_WM(label))
{
val = MRIgetVoxVal(mri_vals, x, y, z, 0) ;
if ((val >= 110-intensity_below && val <= 110 + intensity_above)&&
MRIgetVoxVal(mri_core, x, y, z, 0) > 0)
{
ctrl = 1 ;
}
}
}
MRIsetVoxVal(mri_dst, x, y, z, 0, ctrl) ;
}
}
MRIfree(&mri_core) ;
return(mri_dst) ;
}
MRI *
MRImarkTemporalWM(MRI *mri_seg, MRI *mri_dst) {
int x, y, z, yi, found_other, found_gray, nchanged, label, i,
width, height, depth, left ;
MRI *mri_tmp ;
width = mri_seg->width ;
height = mri_seg->height ;
depth = mri_seg->depth ;
if (!mri_dst)
mri_dst = MRIclone(mri_seg, NULL) ;
mri_tmp = MRIcopy(mri_dst, NULL) ;
for (z = 0 ; z < depth ; z++) {
for (y = 0 ; y < height ; y++) {
for (x = 0 ; x < width ; x++) {
if (x == Gx && y == Gy && z== Gz)
DiagBreak() ;
label = MRIvox(mri_seg, x, y, z) ;
if (!IS_WM(label))
continue ;
left =
(label == Left_Cerebral_White_Matter) ||
(label == Left_Temporal_Cerebral_White_Matter) ;
for (found_other = found_gray = 0, i = 1 ; i <= 3 ; i++) {
yi = mri_seg->yi[y+i] ;
label = MRIvox(mri_seg, x, yi, z) ;
if (IS_CORTEX(label))
found_gray = 1 ; /* gray matter inferior */
yi = mri_seg->yi[y-i] ;
label = MRIvox(mri_seg, x, yi, z) ;
if (IS_HIPPO(label) || IS_AMYGDALA(label))
found_other = 1 ;
}
if (found_other && found_gray) {
MRIvox(mri_dst, x, y, z) = left ?
Left_Cerebral_White_Matter:
Right_Cerebral_White_Matter ;
MRIvox(mri_seg, x, y, z) = left ?
Left_Temporal_Cerebral_White_Matter:
Right_Temporal_Cerebral_White_Matter ;
}
}
}
}
do {
nchanged = 0 ;
for (z = 0 ; z < depth ; z++) {
for (y = 0 ; y < height ; y++) {
for (x = 0 ; x < width ; x++) {
if (x == Gx && y == Gy && z== Gz)
DiagBreak() ;
if (MRIvox(mri_dst, x, y, z) > 0)
continue ;
label = MRIvox(mri_seg, x, y, z) ;
if (!IS_WM(label))
continue ;
left =
(label == Left_Cerebral_White_Matter) ||
(label == Left_Temporal_Cerebral_White_Matter) ;
for (found_other = found_gray = 0, i = 1 ; i <= 3 ; i++) {
yi = mri_seg->yi[y+i] ;
label = MRIvox(mri_seg, x, yi, z) ;
if (IS_CORTEX(label))
found_gray = 1 ; /* gray matter inferior */
yi = mri_seg->yi[y-i] ; /* lateral ventricle superior */
label = MRIvox(mri_seg, x, yi, z) ;
if (IS_LAT_VENT(label))
found_other = 1 ;
}
if (found_other && found_gray && MRIneighborsOn(mri_dst, x, y,z,1)>0) {
nchanged++ ;
MRIvox(mri_dst, x, y, z) = left ?
Left_Cerebral_White_Matter :
Right_Cerebral_White_Matter ;
MRIvox(mri_seg, x, y, z) = left ?
Left_Temporal_Cerebral_White_Matter :
Right_Temporal_Cerebral_White_Matter ;
}
}
}
}
} while (nchanged > 0) ;
for (i = 0 ; i < 3 ; i++) {
MRIcopy(mri_dst, mri_tmp) ;
for (z = 0 ; z < depth ; z++) {
for (y = 0 ; y < height ; y++) {
for (x = 0 ; x < width ; x++) {
if (x == Gx && y == Gy && z== Gz)
DiagBreak() ;
label = MRIvox(mri_seg, x, y, z) ;
if (!IS_WM(label) || (MRIvox(mri_dst, x, y, z) > 0))
continue ;
left =
(label == Left_Cerebral_White_Matter) ||
(label == Left_Temporal_Cerebral_White_Matter) ;
if (MRIneighborsOn(mri_dst, x, y,z, 1)>= 2) {
nchanged++ ;
MRIvox(mri_tmp, x, y, z) = left ?
Left_Cerebral_White_Matter :
Right_Cerebral_White_Matter ;
MRIvox(mri_seg, x, y, z) = left ?
Left_Temporal_Cerebral_White_Matter :
Right_Temporal_Cerebral_White_Matter ;
}
}
}
}
MRIcopy(mri_tmp, mri_dst) ;
}
/* now dilate twice to get stray voxels and a bit of main temporal lobe */
for (i = 0 ; i < 2 ; i++) {
MRIcopy(mri_dst, mri_tmp) ;
for (z = 0 ; z < depth ; z++) {
for (y = 0 ; y < height ; y++) {
for (x = 0 ; x < width ; x++) {
if (x == Gx && y == Gy && z== Gz)
DiagBreak() ;
label = MRIvox(mri_seg, x, y, z) ;
if (!IS_WM(label) || (MRIvox(mri_dst, x, y, z) > 0))
continue ;
left =
(label == Left_Cerebral_White_Matter) ||
(label == Left_Temporal_Cerebral_White_Matter) ;
if (MRIneighborsOn(mri_dst, x, y,z, 1)>= 1) {
nchanged++ ;
MRIvox(mri_tmp, x, y, z) = left ?
Left_Cerebral_White_Matter :
Right_Cerebral_White_Matter ;
MRIvox(mri_seg, x, y, z) = left ?
Left_Temporal_Cerebral_White_Matter :
Right_Temporal_Cerebral_White_Matter ;
}
}
}
}
MRIcopy(mri_tmp, mri_dst) ;
}
MRIfree(&mri_tmp) ;
return(mri_dst) ;
}
int
FCDcomputeThicknessLabels(FCD_DATA *fcd,
double thickness_thresh,
double sigma,
int size_thresh)
{
MRI *mri_lh, *mri_rh, *mri_lh_diff, *mri_rh_diff ;
int niter, vno, s ;
MRI_SEGMENTATION *mriseg ;
fcdFreeLabels(fcd) ; // free old ones if they exist
niter = SIGMA_TO_SURFACE_SMOOTH_STEPS(sigma) ;
// do LH
mri_lh = MRIclone(fcd->lh_thickness_on_lh, NULL) ;
mri_rh = MRIclone(fcd->lh_thickness_on_lh, NULL) ;
exec_progress_callback(1, 8, 0, 1) ;
MRISwriteFrameToValues(fcd->mris_lh, fcd->lh_thickness_on_lh, 0) ;
MRISaverageVals(fcd->mris_lh, niter) ;
MRISreadFrameFromValues(fcd->mris_lh, mri_lh, 0) ;
exec_progress_callback(2, 8, 0, 1) ;
MRISwriteFrameToValues(fcd->mris_lh, fcd->rh_thickness_on_lh, 0) ;
MRISaverageVals(fcd->mris_lh, niter) ;
MRISreadFrameFromValues(fcd->mris_lh, mri_rh, 0) ;
mri_lh_diff = MRIsubtract(mri_lh, mri_rh, NULL) ; // lh minus rh on lh
MRIfree(&mri_lh);
MRIfree(&mri_rh) ;
// do RH
mri_lh = MRIclone(fcd->lh_thickness_on_rh, NULL) ;
mri_rh = MRIclone(fcd->lh_thickness_on_rh, NULL) ;
exec_progress_callback(3, 8, 0, 1) ;
MRISwriteFrameToValues(fcd->mris_rh, fcd->lh_thickness_on_rh, 0) ;
MRISaverageVals(fcd->mris_rh, niter) ;
MRISreadFrameFromValues(fcd->mris_rh, mri_lh, 0) ;
exec_progress_callback(4, 8, 0, 1) ;
MRISwriteFrameToValues(fcd->mris_rh, fcd->rh_thickness_on_rh, 0) ;
MRISaverageVals(fcd->mris_rh, niter) ;
MRISreadFrameFromValues(fcd->mris_rh, mri_rh, 0) ;
mri_rh_diff = MRIsubtract(mri_rh, mri_lh, NULL) ; // lh minus rh on rh
MRIfree(&mri_lh);
MRIfree(&mri_rh) ;
MRIclear(fcd->mri_thickness_increase) ;
MRIclear(fcd->mri_thickness_decrease) ;
exec_progress_callback(5, 8, 0, 1) ;
// process left hemisphere
#if 1
#ifdef HAVE_OPENMP
#pragma omp parallel for shared(fcd, mri_lh_diff, Gdiag_no, thickness_thresh) schedule(static,1)
#endif
#endif
for (vno = 0 ; vno < fcd->mris_lh->nvertices ; vno++)
{
double d ;
float val, val2, thickness;
int base_label ;
VERTEX *v ;
v = &fcd->mris_lh->vertices[vno] ;
if (v->ripflag)
{
continue ;
}
thickness = MRIgetVoxVal(fcd->lh_thickness_on_lh, vno, 0, 0, 0) ;
if (vno == Gdiag_no)
{
DiagBreak() ;
}
val = MRIgetVoxVal(mri_lh_diff, vno, 0, 0, 0) ;
if (fabs(val) < thickness_thresh)
{
continue ;
}
for (d = 0, base_label = 0 ; d < thickness ; d += 0.25)
{
double xv, yv, zv;
double xs = v->x+d*v->nx ;
double ys = v->y+d*v->ny ;
double zs = v->z+d*v->nz ;
MRISsurfaceRASToVoxel(fcd->mris_lh,
fcd->mri_thickness_increase,
xs, ys, zs,
&xv, &yv, &zv) ;
int xvi = nint(xv) ;
int yvi = nint(yv) ;
int zvi = nint(zv) ;
int label = MRIgetVoxVal(fcd->mri_aparc, xvi, yvi, zvi, 0) ;
if (IS_WM(label) == 0 &&
label >= MIN_CORTICAL_PARCELLATION &&
label != ctx_lh_unknown)
{
if (label != base_label)
{
if (base_label)
{
break ;
}
}
else
{
base_label = label ;
}
if (val >= 0)
{
val2 = MRIgetVoxVal(fcd->mri_thickness_increase, xvi, yvi, zvi, 0) ;
// check another thread already populated this voxel
if (val > val2)
{
MRIsetVoxVal(fcd->mri_thickness_increase, xvi, yvi, zvi, 0, val) ;
}
}
else
{
val2 = MRIgetVoxVal(fcd->mri_thickness_decrease, xvi, yvi, zvi, 0) ;
// check if another thread already populated this voxel
if (val < val2)
{
MRIsetVoxVal(fcd->mri_thickness_decrease, xvi, yvi, zvi, 0, val) ;
}
}
}
}
}
exec_progress_callback(6, 8, 0, 1) ;
// now do right hemisphere
#if 1
#ifdef HAVE_OPENMP
#pragma omp parallel for shared(fcd, mri_rh_diff, Gdiag_no, thickness_thresh) schedule(static,1)
#endif
#endif
for (vno = 0 ; vno < fcd->mris_rh->nvertices ; vno++)
{
double d ;
float val, val2, thickness;
int base_label ;
VERTEX *v ;
v = &fcd->mris_rh->vertices[vno] ;
if (v->ripflag)
{
continue ;
}
if (vno == Gdiag_no)
{
DiagBreak() ;
}
val = MRIgetVoxVal(mri_rh_diff, vno, 0, 0, 0) ;
if (fabs(val) < thickness_thresh)
{
continue ;
}
thickness = MRIgetVoxVal(fcd->rh_thickness_on_rh, vno, 0, 0, 0) ;
for (d = 0, base_label = 0; d < thickness ; d += 0.25)
{
double xv, yv, zv;
double xs = v->x+d*v->nx ;
double ys = v->y+d*v->ny ;
double zs = v->z+d*v->nz ;
MRISsurfaceRASToVoxel(fcd->mris_rh,
fcd->mri_thickness_increase,
xs, ys, zs,
&xv, &yv, &zv) ;
int xvi = nint(xv) ;
int yvi = nint(yv) ;
int zvi = nint(zv) ;
int label = MRIgetVoxVal(fcd->mri_aparc, xvi, yvi, zvi, 0) ;
if (IS_WM(label) == 0 &&
label >= MIN_CORTICAL_PARCELLATION &&
label != ctx_rh_unknown)
{
if (label != base_label)
{
if (base_label)
{
break ;
}
}
else
{
base_label = label ;
}
if (val >= 0)
{
val2 = MRIgetVoxVal(fcd->mri_thickness_increase, xvi, yvi, zvi, 0) ;
if (val > val2)
{
MRIsetVoxVal(fcd->mri_thickness_increase, xvi, yvi, zvi, 0, val) ;
}
}
else
{
val2 = MRIgetVoxVal(fcd->mri_thickness_decrease, xvi, yvi, zvi, 0) ;
if (val < val2)
{
MRIsetVoxVal(fcd->mri_thickness_decrease, xvi, yvi, zvi, 0, val) ;
}
}
}
}
}
exec_progress_callback(7, 8, 0, 1) ;
mriseg = MRIsegment(fcd->mri_thickness_increase, thickness_thresh, 1e10) ;
MRIeraseSmallSegments(mriseg, fcd->mri_thickness_increase, thickness_thresh) ;
MRIsegmentFree(&mriseg) ;
MRIclose(fcd->mri_thickness_increase, fcd->mri_thickness_increase) ;
mriseg = MRIsegment(fcd->mri_thickness_increase, thickness_thresh, 1e10) ;
MRIremoveSmallSegments(mriseg, size_thresh) ;
printf("segmenting volume at threshold %2.1f with %d "
"smoothing iters yields %d segments\n",
thickness_thresh, niter,mriseg->nsegments) ;
fflush(stdout) ;
exec_progress_callback(8, 8, 0, 1) ;
fcd->nlabels = mriseg->nsegments ;
for (s = 0 ; s < mriseg->nsegments ; s++)
{
int label ;
fcd->labels[s] = MRIsegmentToLabel(mriseg, fcd->mri_thickness_increase, s) ;
label = most_frequent_label(fcd->mri_aparc, &mriseg->segments[s]) ;
strcpy(fcd->labels[s]->name, cma_label_to_name(label)) ;
}
sort_labels(fcd) ;
MRIadd(fcd->mri_thickness_increase, fcd->mri_thickness_decrease, fcd->mri_thickness_difference);
for (s = 0 ; s < mriseg->nsegments ; s++)
{
printf("%s: %2.3fmm\n", fcd->label_names[s], fcd->labels[s]->avg_stat) ;
fflush(stdout) ;
}
MRIfree(&mri_lh_diff) ;
MRIfree(&mri_rh_diff) ;
MRIsegmentFree(&mriseg) ;
return(fcd->nlabels) ;
}
static MRI *
edit_ventricular_unknowns(MRI *mri_in_labeled, MRI *mri_T1, MRI *mri_out_labeled) {
int label, x, y, z, xm1, xp1, ym1, yp1, zm1, zp1, lxp1, lxm1, lyp1, lym1, lzp1, lzm1, nchanged,
l1 = 0, l2 = 0, change, i, total_changed, dwm, dhypo, dven, left ;
MRI *mri_in ;
mri_in = MRIcopy(mri_in_labeled, NULL) ;
mri_out_labeled = MRIcopy(mri_in_labeled, mri_out_labeled) ;
total_changed = 0 ;
/* first change unknowns near hypointensities to wm or hypo */
do {
nchanged = 0 ;
for (x = 0 ; x < mri_T1->width ; x++) {
for (y = 0 ; y < mri_T1->height ; y++) {
for (z = 0 ; z < mri_T1->depth ; z++) {
if (x == Gx && y == Gy && z == Gz)
DiagBreak() ;
change = 0 ;
left = 0 ;
label = MRIvox(mri_in, x, y, z) ;
if ((IS_GM(label) == 0) && (IS_UNKNOWN(label) == 0))
continue ;
dhypo = distance_to_label(mri_in, WM_hypointensities, x, y, z, 0, 1, 0, 2) ; /* look inferior */
if (dhypo > 2)
dhypo = distance_to_label(mri_in, WM_hypointensities, x, y, z, 0, 0, -1, 2) ; /* look inferior */
if (dhypo > 2)
dhypo = distance_to_label(mri_in, WM_hypointensities, x, y, z, 0, 0, 1, 2) ; /* look anterior */
if (dhypo > 2)
dhypo = distance_to_label(mri_in, WM_hypointensities, x, y, z, 0, 0, -1, 2) ; /* look inferior */
if (dhypo > 2)
continue ;
#define WM_DIST 4
dwm = distance_to_label(mri_in, Left_Cerebral_White_Matter, x, y, z, 0, -1, 0, WM_DIST) ; /* superior */
if (dwm > WM_DIST) {
dwm = distance_to_label(mri_in, Right_Cerebral_White_Matter, x, y, z, 0, -1, 0, WM_DIST) ;
} else
left = 1 ;
if (dwm > WM_DIST) /* not superior, look anterior */
{
dwm = distance_to_label(mri_in, Right_Cerebral_White_Matter, x, y, z, 0, 0, 1, WM_DIST) ;
if (dwm > WM_DIST) {
dwm = distance_to_label(mri_in, Left_Cerebral_White_Matter, x, y, z, 0, 0, 1, WM_DIST) ;
if (dwm <= WM_DIST)
left = 1 ;
}
}
if (dwm > WM_DIST) /* not superior, or anterior look posterior */
{
dwm = distance_to_label(mri_in, Right_Cerebral_White_Matter, x, y, z, 0, 0, -1, WM_DIST) ;
if (dwm > WM_DIST) {
dwm = distance_to_label(mri_in, Left_Cerebral_White_Matter, x, y, z, 0, 0, -1, WM_DIST) ;
if (dwm <= WM_DIST)
left = 1 ;
}
}
if (dwm > WM_DIST) /* couldn't find wm anywhere (didn't look inferior), check for region of hypos */
{
dwm = distance_to_label(mri_in, WM_hypointensities, x, y, z, 0, -1, 0, WM_DIST) ;
if (distance_to_label(mri_in, Left_Cerebral_White_Matter, x, y, z, 0, -1, 0, 30) <= 30)
left = 1 ;
}
if (dwm > WM_DIST)
continue ;
dven = distance_to_label(mri_in, left ? Left_Lateral_Ventricle : Right_Lateral_Ventricle, x, y, z, 0, 1, 0, 15) ;
if (dven > 15) {
dven = distance_to_label(mri_in, left ? Left_Lateral_Ventricle : Right_Lateral_Ventricle, x, y, z, 0, 0, -1, 3) ;
if (dven > 3)
distance_to_label(mri_in, left ? Left_Lateral_Ventricle : Right_Lateral_Ventricle, x, y, z, 0, 0, 1, 3) ;
if (dven > 3)
continue ;
}
nchanged++ ;
mle_label(mri_T1, mri_out_labeled, x, y, z, 15, left ? Left_Cerebral_White_Matter : Right_Cerebral_White_Matter,
WM_hypointensities) ;
}
}
}
total_changed += nchanged ;
MRIcopy(mri_out_labeled, mri_in) ;
} while (nchanged > 0) ;
for (i = 0 ; i < 2 ; i++) {
for ( nchanged = x = 0 ; x < mri_T1->width ; x++) {
for (y = 0 ; y < mri_T1->height ; y++) {
for (z = 0 ; z < mri_T1->depth ; z++) {
if (x == Gx && y == Gy && z == Gz)
DiagBreak() ;
change = 0 ;
label = MRIvox(mri_in, x, y, z) ;
if (IS_UNKNOWN(label) == 0)
continue ;
xm1 = mri_T1->xi[x-1] ;
xp1 = mri_T1->xi[x+1] ;
ym1 = mri_T1->yi[y-1] ;
yp1 = mri_T1->yi[y+1] ;
zm1 = mri_T1->zi[z-1] ;
zp1 = mri_T1->zi[z+1] ;
lxp1 = MRIvox(mri_in, xp1, y, z) ;
lxm1 = MRIvox(mri_in, xm1, y, z) ;
lyp1 = MRIvox(mri_in, x, yp1, z) ;
lym1 = MRIvox(mri_in, x, ym1, z) ;
lzp1 = MRIvox(mri_in, x, y, zp1) ;
lzm1 = MRIvox(mri_in, x, y, zm1) ;
/* if it has ventricle on one side and wm on the other, change it to wm or ventricle
these are caused by slight discrepencies between the FreeSurfer ribbon and the
CMA subcortical segs.
*/
if ((IS_WMH(lxm1) && IS_LAT_VENT(lxp1)) ||
(IS_WMH(lxp1) && IS_LAT_VENT(lxm1))) {
change = 1 ;
l1 = lxm1 ;
l2 = lxp1 ;
}
if ((IS_WMH(lym1) && IS_LAT_VENT(lyp1)) ||
(IS_WMH(lyp1) && IS_LAT_VENT(lym1))) {
change = 1 ;
l1 = lym1 ;
l2 = lyp1 ;
}
if ((IS_WMH(lzm1) && IS_LAT_VENT(lzp1)) ||
(IS_WMH(lzp1) && IS_LAT_VENT(lzm1))) {
change = 1 ;
l1 = lzm1 ;
l2 = lzp1 ;
}
if (change) {
nchanged++ ;
mle_label(mri_T1, mri_out_labeled, x, y, z, 15, l1, l2) ;
} else /* could be two unknowns in a row */
{
int yi, olabel, wm, un, ven ;
#define WLEN 4
ven = un = wm = 0 ;
change = 0 ;
for (yi = y-1 ; yi >= MAX(0,y-WLEN) ; yi--) {
olabel = MRIvox(mri_in, x, yi, z) ;
/* should be only white matter and unkowns above it */
if (IS_WMH(olabel)) {
if (IS_WM(olabel))
l1 = olabel ;
wm++ ;
} else if (IS_UNKNOWN(olabel))
un++ ;
else
change = -1 ; /* something else there - don't change */
}
/* if there is some wm above and no other labels */
if ((wm >= WLEN/2) && ((wm+un) >= (WLEN-1)) && change >= 0) {
un = 0 ;
for (yi = y+1 ; yi <= MIN(mri_in->height-1,y+WLEN) ; yi++) {
olabel = MRIvox(mri_in, x, yi, z) ;
/* should be only ventricle and unkowns below it */
if (IS_LAT_VENT(olabel)) {
ven++ ;
l2 = olabel ;
} else if (IS_UNKNOWN(olabel))
un++ ;
else
change = -1 ;
}
if (change >= 0 && ((ven+un) >= WLEN) && (ven >= WLEN/2))
change = 1 ;
if (change > 0) {
nchanged++ ;
mle_label(mri_T1, mri_out_labeled, x, y, z, 15, l1, l2) ;
}
}
if (change <= 0) /* look in posterior/anterior direction. If everthing is wm and ven change it */
{
int zi ;
change = wm = ven = un = 0 ;
for (zi = z-WLEN ; zi <= z+WLEN ; zi++) {
if (zi < 0 || zi >= mri_in->depth)
continue ;
olabel = MRIvox(mri_in, x, y, zi) ;
/* should be only white matter and unkowns above it */
if (IS_WMH(olabel)) {
if (IS_WM(olabel))
l1 = olabel ;
wm++ ;
} else if (IS_UNKNOWN(olabel))
un++ ;
else if (IS_LAT_VENT(olabel))
ven++ ;
else
change = -1 ; /* something else there - don't change */
}
if (change >= 0 && ((ven+wm) >= WLEN) && (ven >= WLEN/2) && (wm >= WLEN/2))
change = 1 ;
if (change > 0) {
nchanged++ ;
mle_label(mri_T1, mri_out_labeled, x, y, z, 15, l1, l2) ;
}
}
if (change <= 0) /* look in medial/lateral direction. If everthing is wm and ven change it */
{
int xi ;
change = wm = ven = un = 0 ;
for (xi = x-WLEN ; xi <= x+WLEN ; xi++) {
if (xi < 0 || xi >= mri_in->width)
continue ;
olabel = MRIvox(mri_in, xi, y, z) ;
/* should be only white matter and unkowns above it */
if (IS_WMH(olabel)) {
if (IS_WM(olabel))
l1 = olabel ;
wm++ ;
} else if (IS_UNKNOWN(olabel))
un++ ;
else if (IS_LAT_VENT(olabel)) {
ven++ ;
l2 = olabel ;
} else
change = -1 ; /* something else there - don't change */
}
if (change >= 0 && ((ven+wm) >= WLEN) && (ven >= WLEN/2) && (wm >= WLEN/2))
change = 1 ;
if (change > 0) {
nchanged++ ;
mle_label(mri_T1, mri_out_labeled, x, y, z, 15, l1, l2) ;
}
}
}
}
}
}
/* now relabel cortex that is between WM and hypointensity */
for (x = 0 ; x < mri_T1->width ; x++) {
for (y = 0 ; y < mri_T1->height ; y++) {
for (z = 0 ; z < mri_T1->depth ; z++) {
if (x == Gx && y == Gy && z == Gz)
DiagBreak() ;
change = 0 ;
label = MRIvox(mri_in, x, y, z) ;
if (IS_GM(label) == 0 && (IS_UNKNOWN(label) == 0))
continue ;
xm1 = mri_T1->xi[x-1] ;
xp1 = mri_T1->xi[x+1] ;
ym1 = mri_T1->yi[y-1] ;
yp1 = mri_T1->yi[y+1] ;
zm1 = mri_T1->zi[z-1] ;
zp1 = mri_T1->zi[z+1] ;
lxp1 = MRIvox(mri_in, xp1, y, z) ;
lxm1 = MRIvox(mri_in, xm1, y, z) ;
lyp1 = MRIvox(mri_in, x, yp1, z) ;
lym1 = MRIvox(mri_in, x, ym1, z) ;
lzp1 = MRIvox(mri_in, x, y, zp1) ;
lzm1 = MRIvox(mri_in, x, y, zm1) ;
if ((IS_WM(lxm1) && IS_HYPO(lxp1)) ||
(IS_WM(lxp1) && IS_HYPO(lxm1))) {
change = 1 ;
l1 = lxm1 ;
l2 = lxp1 ;
}
if ((IS_WM(lym1) && IS_HYPO(lyp1)) ||
(IS_WM(lyp1) && IS_HYPO(lym1))) {
change = 1 ;
l1 = lym1 ;
l2 = lyp1 ;
}
if ((IS_WM(lzm1) && IS_HYPO(lzp1)) ||
(IS_WM(lzp1) && IS_HYPO(lzm1))) {
change = 1 ;
l1 = lzm1 ;
l2 = lzp1 ;
}
if ((IS_HYPO(lxm1) && IS_HYPO(lxp1)) ||
(IS_HYPO(lxp1) && IS_HYPO(lxm1))) {
change = 1 ;
l1 = lxm1 ;
l2 = lxp1 ;
}
if ((IS_HYPO(lym1) && IS_HYPO(lyp1)) ||
(IS_HYPO(lyp1) && IS_HYPO(lym1))) {
change = 1 ;
l1 = lym1 ;
l2 = lyp1 ;
}
if ((IS_HYPO(lzm1) && IS_HYPO(lzp1)) ||
(IS_HYPO(lzp1) && IS_HYPO(lzm1))) {
change = 1 ;
l1 = lzm1 ;
l2 = lzp1 ;
}
if (change) {
nchanged++ ;
mle_label(mri_T1, mri_out_labeled, x, y, z, 15, l1, l2) ;
}
}
}
}
MRIcopy(mri_out_labeled, mri_in) ;
total_changed += nchanged ;
}
printf("%d unknown voxels changed to wm or ventricle\n", total_changed) ;
MRIfree(&mri_in) ;
return(mri_out_labeled) ;
}
static MRI *
edit_hippocampus(MRI *mri_in_labeled, MRI *mri_T1, MRI *mri_out_labeled) {
int width, height, depth, x, y, z, nchanged, dleft, label,
dright, dpos, dant, dup, ddown, i, left, dgray, dhippo, dwhite, olabel ;
MRI *mri_tmp ;
nchanged = 0 ;
width = mri_T1->width ;
height = mri_T1->height ;
depth = mri_T1->depth ;
mri_out_labeled = MRIcopy(mri_in_labeled, mri_out_labeled) ;
/* change all gm within 2 mm of ventricle to wm */
for (z = 0 ; z < depth ; z++) {
for (y = 0 ; y < height ; y++) {
for (x = 0 ; x < width ; x++) {
if (x == Gx && y == Gy && z == Gz)
DiagBreak() ;
label = MRIvox(mri_out_labeled, x, y, z) ;
if (IS_GM(label) == 0)
continue ;
left = label == Left_Cerebral_Cortex ;
olabel = left ? Left_Lateral_Ventricle : Right_Lateral_Ventricle;
if (MRIneighborsInWindow(mri_out_labeled, x, y, z, 5, olabel) >= 1) {
nchanged++ ;
MRIvox(mri_out_labeled, x, y, z) = left ? Left_Cerebral_White_Matter : Right_Cerebral_White_Matter;
}
}
}
}
mri_tmp = MRIcopy(mri_out_labeled, NULL) ;
/* change gray to hippocampus based on wm */
for (i = 0 ; i < 3 ; i++) {
for (z = 0 ; z < depth ; z++) {
for (y = 0 ; y < height ; y++) {
for (x = 0 ; x < width ; x++) {
if (x == Gx && y == Gy && z == Gz)
DiagBreak() ;
label = MRIvox(mri_tmp, x, y, z) ;
if (x == 160 && y == 127 && z == 118)
DiagBreak() ;
left = 0 ;
switch (label) {
case Left_Cerebral_White_Matter:
left = 1 ;
case Right_Cerebral_White_Matter:
dgray = distance_to_label(mri_out_labeled,
left ? Left_Cerebral_Cortex :
Right_Cerebral_Cortex,
x,y,z,0,1,0,3);
dwhite = distance_to_label(mri_out_labeled,
left ? Left_Cerebral_White_Matter :
Right_Cerebral_White_Matter,
x,y,z,0,-1,0,1);
dhippo = distance_to_label(mri_out_labeled,
left ? Left_Hippocampus :
Right_Hippocampus,
x,y,z,0,-1,0,3);
/* change bright hippocampus that borders white matter to white matter */
if (dgray <= 2 && dwhite <= 1 && dhippo <= 3) {
mle_label(mri_T1, mri_tmp, x, y, z, 9,
left ? Left_Cerebral_Cortex : Right_Cerebral_Cortex,
left ? Left_Cerebral_White_Matter : Right_Cerebral_White_Matter) ;
}
case Left_Hippocampus:
left = 1 ;
case Right_Hippocampus:
dgray = distance_to_label(mri_out_labeled,
left ? Left_Cerebral_Cortex :
Right_Cerebral_Cortex,
x,y,z,0,1,0,3);
dwhite = distance_to_label(mri_out_labeled,
left ? Left_Cerebral_White_Matter :
Right_Cerebral_White_Matter,
x,y,z,0,1,0,1);
dhippo = distance_to_label(mri_out_labeled,
left ? Left_Hippocampus :
Right_Hippocampus,
x,y,z,0,-1,0,1);
/* change bright hippocampus that borders white matter to white matter */
if (dgray <= 3 && dwhite <= 1 && dhippo <= 1) {
change_label(mri_T1, mri_tmp, x, y, z, 9, left) ;
}
break ;
case Unknown: {
int dhippo, dl, dr, dgray, dwhite ;
if (x == 160 && y == 129 && z == 121)
DiagBreak() ;
/*
if the current label is unknown, and there is white matter above
and hippocampus above and gray matter below, change to gray matter.
*/
dl = distance_to_label(mri_out_labeled,
Left_Hippocampus,
x,y,z,0,-1,0,4);
dr = distance_to_label(mri_out_labeled,
Right_Hippocampus,
x,y,z,0,-1,0,4);
if (dl > 4 && dr > 4) /* could be inferior to inf-lat-ven also */
{
dl = distance_to_label(mri_out_labeled,
Left_Inf_Lat_Vent,
x,y,z,0,-1,0,4);
dr = distance_to_label(mri_out_labeled,
Right_Inf_Lat_Vent,
x,y,z,0,-1,0,4);
}
if (dl < dr) {
left = 1 ;
dhippo = dl ;
dgray = distance_to_label(mri_out_labeled,
Left_Cerebral_Cortex,
x,y,z,0,1,0,2);
dwhite = distance_to_label(mri_out_labeled,
Left_Cerebral_White_Matter,
x,y,z,0,-1,0,2);
} else {
left = 0 ;
dhippo = dr ;
dwhite = distance_to_label(mri_out_labeled,
Right_Cerebral_White_Matter,
x,y,z,0,-1,0,2);
dgray = distance_to_label(mri_out_labeled,
Right_Cerebral_Cortex,
x,y,z,0,1,0,2);
}
if (dhippo <= 4 && dwhite <= 2 && dgray <= 2) {
MRIvox(mri_tmp, x, y, z) =
left ? Left_Cerebral_Cortex : Right_Cerebral_Cortex ;
nchanged++ ;
continue ;
}
break ;
}
case Left_Cerebral_Cortex:
left = 1 ;
case Right_Cerebral_Cortex:
dup = distance_to_label(mri_out_labeled,
left ? Left_Hippocampus :
Right_Hippocampus,x,y,z,0,-1,0,2);
if (dup <= 1) {
label = left ?
Left_Cerebral_White_Matter : Right_Cerebral_White_Matter;
MRIvox(mri_tmp, x, y, z) = label ;
nchanged++ ;
continue ;
}
/*
if the current label is gray, and there is white matter below
and hippocampus above, change to hippocampus.
*/
ddown = distance_to_label(mri_out_labeled,
left ? Left_Cerebral_White_Matter :
Right_Cerebral_White_Matter,
x,y,z,0,1,0,3);
dup = distance_to_label(mri_out_labeled,
left ? Left_Hippocampus :
Right_Hippocampus,x,y,z,0,-1,0,2);
if (dup <= 2 && ddown <= 2) {
change_label(mri_T1, mri_tmp, x, y, z, 9, left) ;
nchanged++ ;
continue ;
}
/*
if the current label is gray, and there is white matter above
and hippocampus below, change to hippocampus.
*/
ddown = distance_to_label(mri_out_labeled,
left ? Left_Hippocampus :
Right_Hippocampus,
x,y,z,0,1,0,3);
dup = distance_to_label(mri_out_labeled,
left ? Left_Cerebral_White_Matter :
Right_Cerebral_White_Matter,
x,y,z,0,-1,0,2);
if (dup <= 2 && ddown <= 2) {
change_label(mri_T1, mri_tmp, x, y, z, 9, left) ;
nchanged++ ;
continue ;
}
ddown = distance_to_label(mri_out_labeled,
left ? Left_Hippocampus :
Right_Hippocampus,
x,y,z,0,1,0,3);
dup = distance_to_label(mri_out_labeled,
left ? Left_Hippocampus :
Right_Hippocampus,
x,y,z,0,-1,0,2);
if (dup <= 2 && ddown <= 2) {
change_label(mri_T1, mri_tmp, x, y, z, 9, left) ;
nchanged++ ;
continue ;
}
dleft = distance_to_label(mri_out_labeled, left ?
Left_Cerebral_White_Matter :
Right_Cerebral_White_Matter,
x,y,z,-1,0,0,3);
dright = distance_to_label(mri_out_labeled, left ?
Left_Cerebral_White_Matter :
Right_Cerebral_White_Matter,
x,y,z,1,0,0,3);
dup = distance_to_label(mri_out_labeled,
left ? Left_Hippocampus :
Right_Hippocampus,x,y,z,0,-1,0,2);
if (dleft <= 2 && dright <= 2 && dup <= 1) {
label = left ?
Left_Cerebral_White_Matter : Right_Cerebral_White_Matter;
MRIvox(mri_tmp, x, y, z) = label ;
nchanged++ ;
continue ;
}
dright = distance_to_label(mri_out_labeled, left ?
Left_Cerebral_White_Matter :
Right_Cerebral_White_Matter,
x,y,z,1,0,0,3);
dleft = distance_to_label(mri_out_labeled, left ?
Left_Hippocampus :
Right_Hippocampus,
x,y,z,-1,0,0,3);
if (dleft <= 1 && dright <= 1) {
change_label(mri_T1, mri_tmp, x, y, z, 9, left) ;
nchanged++ ;
continue ;
}
dleft = distance_to_label(mri_out_labeled, left ?
Left_Cerebral_White_Matter :
Right_Cerebral_White_Matter,
x,y,z,-1,0,0,3);
dright = distance_to_label(mri_out_labeled, left ?
Left_Hippocampus :
Right_Hippocampus,
x,y,z,1,0,0,3);
if (dleft <= 1 && dright <= 1) {
change_label(mri_T1, mri_tmp, x, y, z, 9, left) ;
nchanged++ ;
continue ;
}
dright = distance_to_label(mri_out_labeled, left ?
Left_Hippocampus :
Right_Hippocampus,
x,y,z,1,0,0,3);
dleft = distance_to_label(mri_out_labeled, left ?
Left_Hippocampus :
Right_Hippocampus,
x,y,z,-1,0,0,3);
if (dleft <= 1 && dright <= 1) {
label = left ?
Left_Hippocampus : Right_Hippocampus;
MRIvox(mri_tmp, x, y, z) = label ;
nchanged++ ;
continue ;
}
dpos = distance_to_label(mri_out_labeled,
Right_Cerebral_White_Matter,x,y,z,0,0,-1,3);
dant = distance_to_label(mri_out_labeled,
Right_Cerebral_White_Matter,x,y,z,0,0,1,3);
/* if the current label is gray and the is white matter directly above,
and hippocampus within 3 mm, then change label to MLE of either gray or
white
*/
if (x == 156 && y == 128 && z == 115)
DiagBreak() ;
dgray = distance_to_label(mri_out_labeled,
left ? Left_Cerebral_Cortex :
Right_Cerebral_Cortex,
x,y,z,0,1,0,1);
dwhite = distance_to_label(mri_out_labeled,
left ? Left_Cerebral_White_Matter :
Right_Cerebral_White_Matter,
x,y,z,0,-1,0,1);
dhippo = distance_to_label(mri_out_labeled,
left ? Left_Hippocampus :
Right_Hippocampus,
x,y,z,0,-1,0,3);
/* change bright hippocampus that borders white matter to white matter */
if (dgray <= 1 && dwhite <= 1 && dhippo <= 3) {
mle_label(mri_T1, mri_tmp, x, y, z, 9,
left ? Left_Cerebral_Cortex : Right_Cerebral_Cortex,
left ? Left_Cerebral_White_Matter : Right_Cerebral_White_Matter) ;
}
break ;
default:
break ;
}
}
}
}
MRIcopy(mri_tmp, mri_out_labeled) ;
}
/* make gray matter that is superior to hippocampus into hippocampus */
for (z = 0 ; z < depth ; z++) {
for (y = 0 ; y < height ; y++) {
for (x = 0 ; x < width ; x++) {
int yi ;
if (x == Gx && y == Gy && z == Gz)
DiagBreak() ;
label = MRIvox(mri_out_labeled, x, y, z) ;
if (!IS_HIPPO(label))
continue ;
left = label == Left_Hippocampus ;
/* search for first non-hippocampal voxel */
for (yi = y-1 ; yi >= 0 ; yi--) {
label = MRIvox(mri_out_labeled, x, yi, z) ;
if (!IS_HIPPO(label))
break ;
}
i = 0 ;
while (IS_GM(label) && yi >= 0) {
nchanged++ ;
MRIvox(mri_out_labeled, x, yi, z) = left ? Left_Hippocampus : Right_Hippocampus;
yi-- ;
label = MRIvox(mri_out_labeled, x, yi, z) ;
if (++i >= 4)
break ; /* don't let it go too far */
}
}
}
}
/* go through and change wm labels that have hippo both above and below them to hippo */
for (z = 0 ; z < depth ; z++) {
for (y = 0 ; y < height ; y++) {
for (x = 0 ; x < width ; x++) {
if (x == Gx && y == Gy && z == Gz)
DiagBreak() ;
label = MRIvox(mri_tmp, x, y, z) ;
if (x == 160 && y == 127 && z == 118)
DiagBreak() ;
if (!IS_WM(label))
continue ;
left = label == Left_Cerebral_White_Matter ;
if (IS_HIPPO(MRIvox(mri_out_labeled, x, mri_out_labeled->yi[y-1], z)) &&
IS_HIPPO(MRIvox(mri_out_labeled, x, mri_out_labeled->yi[y+1], z))) {
nchanged++ ;
MRIvox(mri_out_labeled, x, y, z) = left ? Left_Hippocampus : Right_Hippocampus;
}
}
}
}
MRIfree(&mri_tmp) ;
printf("%d hippocampal voxels changed.\n", nchanged) ;
return(mri_out_labeled) ;
}
static MRI *
edit_border_voxels(MRI *mri_in_labeled, MRI *mri_T1, MRI *mri_out_labeled) {
int label, x, y, z, xm1, xp1, ym1, yp1, zm1, zp1, lxp1, lxm1, lyp1, lym1, lzp1, lzm1, nchanged,
change, olabel ;
float means[MAX_CMA_LABELS], xp1d, xm1d, yp1d, ym1d, zp1d, zm1d, val, ld ;
MRI *mri_tmp ;
if (mri_in_labeled == mri_out_labeled) {
mri_tmp = MRIcopy(mri_in_labeled, NULL) ;
mri_in_labeled = mri_tmp;
} else
mri_tmp = NULL ;
mri_out_labeled = MRIcopy(mri_in_labeled, mri_out_labeled) ;
for (nchanged = x = 0 ; x < mri_T1->width ; x++) {
for (y = 0 ; y < mri_T1->height ; y++) {
for (z = 0 ; z < mri_T1->depth ; z++) {
if (x == Gx && y == Gy && z == Gz)
DiagBreak() ;
change = 0 ;
olabel = label = MRIvox(mri_in_labeled, x, y, z) ;
if (IS_UNKNOWN(label))
continue ;
xm1 = mri_T1->xi[x-1] ;
xp1 = mri_T1->xi[x+1] ;
ym1 = mri_T1->yi[y-1] ;
yp1 = mri_T1->yi[y+1] ;
zm1 = mri_T1->zi[z-1] ;
zp1 = mri_T1->zi[z+1] ;
lxp1 = MRIvox(mri_in_labeled, xp1, y, z) ;
lxm1 = MRIvox(mri_in_labeled, xm1, y, z) ;
lyp1 = MRIvox(mri_in_labeled, x, yp1, z) ;
lym1 = MRIvox(mri_in_labeled, x, ym1, z) ;
lzp1 = MRIvox(mri_in_labeled, x, y, zp1) ;
lzm1 = MRIvox(mri_in_labeled, x, y, zm1) ;
if (label == lxm1 &&
label == lxp1 &&
label == lym1 &&
label == lyp1 &&
label == lzm1 &&
label == lzp1)
continue ; /* it's not a border label */
if (!(IS_WM(label) || IS_HIPPO(label) || IS_GM(label) || IS_UNKNOWN(label) || IS_LAT_VENT(label)))
continue ;
val = MRIgetVoxVal(mri_T1, x, y, z, 0) ;
means[label] = label_mean(mri_T1, mri_in_labeled, x, y, z, 15, label) ;
ld = fabs(means[label] - val) ;
if (ld/means[label] < 0.1)
continue ;
ld *= 0.5 ; /* bias towards keeping same label */
if (lxm1 != label)
means[lxm1] = label_mean(mri_T1, mri_in_labeled, x, y, z, 15, lxm1) ;
if (lxp1 != label)
means[lxp1] = label_mean(mri_T1, mri_in_labeled, x, y, z, 15, lxp1) ;
if (lym1 != label)
means[lym1] = label_mean(mri_T1, mri_in_labeled, x, y, z, 15, lym1) ;
if (lyp1 != label)
means[lyp1] = label_mean(mri_T1, mri_in_labeled, x, y, z, 15, lyp1) ;
if (lzm1 != label)
means[lzm1] = label_mean(mri_T1, mri_in_labeled, x, y, z, 15, lzm1) ;
if (lzp1 != label)
means[lzp1] = label_mean(mri_T1, mri_in_labeled, x, y, z, 15, lzp1) ;
xp1d = fabs(means[lxp1] - val) ;
if (xp1d < ld) {
ld = xp1d ;
olabel = lxp1 ;
}
xm1d = fabs(means[lxm1] - val) ;
if (xm1d < ld) {
ld = xm1d ;
olabel = lxm1 ;
}
yp1d = fabs(means[lyp1] - val) ;
if (yp1d < ld) {
olabel = lyp1 ;
ld = yp1d ;
}
ym1d = fabs(means[lym1] - val) ;
if (ym1d < ld) {
olabel = lym1 ;
ld = ym1d ;
}
zp1d = fabs(means[lzp1] - val) ;
if (zp1d < ld) {
olabel = lzp1 ;
ld = zp1d ;
}
zm1d = fabs(means[lzm1] - val) ;
if (zp1d < ld) {
olabel = lzp1 ;
ld = zp1d ;
}
/* only let certain labels change */
if (!(IS_WM(olabel) || IS_HIPPO(olabel) || IS_GM(olabel) || IS_UNKNOWN(olabel) || IS_LAT_VENT(olabel)))
continue ;
if ((IS_GM(label) && IS_HIPPO(olabel)) ||
(IS_GM(olabel) && IS_HIPPO(label)))
continue ; /* don't change hippo to gm based on intensity - too similar */
if ((label != olabel) && MRIneighborsInWindow(mri_in_labeled, x, y, z, 3, olabel) > 5) {
nchanged++ ;
MRIvox(mri_out_labeled, x, y, z) = olabel ;
}
}
}
}
if (mri_tmp)
MRIfree(&mri_tmp) ;
printf("%d border voxels changed\n", nchanged) ;
return(mri_out_labeled) ;
}