MRI *
MRIfindBrightNonWM(MRI *mri_T1, MRI *mri_wm)
{
int width, height, depth, x, y, z, nlabeled, nwhite,
xk, yk, zk, xi, yi, zi;
BUFTYPE val, wm ;
MRI *mri_labeled, *mri_tmp ;
mri_labeled = MRIclone(mri_T1, NULL) ;
width = mri_T1->width ;
height = mri_T1->height ;
depth = mri_T1->depth ;
for (z = 0 ; z < depth ; z++)
{
for (y = 0 ; y < height ; y++)
{
for (x = 0 ; x < width ; x++)
{
val = MRIgetVoxVal(mri_T1, x, y, z, 0) ;
wm = MRIgetVoxVal(mri_wm, x, y, z, 0) ;
if (x == 110 && y == 125 && z == 172) /* T1=148 */
{
DiagBreak() ;
}
/* not white matter and bright (e.g. eye sockets) */
if ((wm < WM_MIN_VAL) && (val > 125))
{
nwhite = 0 ;
for (xk = -1 ; xk <= 1 ; xk++)
{
xi = mri_T1->xi[x+xk] ;
for (yk = -1 ; yk <= 1 ; yk++)
{
yi = mri_T1->yi[y+yk] ;
for (zk = -1 ; zk <= 1 ; zk++)
{
zi = mri_T1->zi[z+zk] ;
if (MRIgetVoxVal(mri_wm, xi, yi, zi, 0) >= WM_MIN_VAL)
{
nwhite++ ;
}
}
}
}
#define MIN_WHITE ((3*3*3-1)/2)
if (nwhite < MIN_WHITE)
{
MRIsetVoxVal(mri_labeled, x, y, z, 0, BRIGHT_LABEL) ;
}
}
}
}
}
/* find all connected voxels that are above 115 */
MRIdilateThreshLabel(mri_labeled, mri_T1, NULL, BRIGHT_LABEL, 10,115);
MRIclose(mri_labeled, mri_labeled) ;
/* expand once more to all neighboring voxels that are bright. At
worst we will erase one voxel of white matter.
*/
mri_tmp =
MRIdilateThreshLabel(mri_labeled, mri_T1, NULL, BRIGHT_LABEL,1,100);
MRIxor(mri_labeled, mri_tmp, mri_tmp, 1, 255) ;
MRIreplaceValues(mri_tmp, mri_tmp, 1, BRIGHT_BORDER_LABEL) ;
MRIunion(mri_tmp, mri_labeled, mri_labeled) ;
#if 0
fprintf(stderr, "selectively smoothing volume....\n") ;
MRIsoapBubbleLabel(mri_T1, mri_labeled, mri_T1, BRIGHT_LABEL, 200) ;
#endif
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_labeled, "label.mgh") ;
}
/* MRIwrite(mri_tmp, "tmp.mgh") ;*/
nlabeled = MRIvoxelsInLabel(mri_labeled, BRIGHT_LABEL) ;
fprintf(stderr, "%d bright non-wm voxels segmented.\n", nlabeled) ;
MRIfree(&mri_tmp) ;
return(mri_labeled) ;
}
MRI *
MRIfillBasalGanglia(MRI *mri_src, MRI *mri_dst)
{
float low_thresh, hi_thresh ;
int total_filled, depth, height, width, x, y, z,
xi, yi, zi, xk, yk, zk, fill, val0, val, i ;
MRI *mri_bg ;
Real tx, ty, tz ;
MRI_SEGMENTATION *mriseg ;
MRI_SEGMENT *mseg ;
float dx_left, dx_right, dy, dz, dist_left, dist_right ;
if (!mri_dst)
{
mri_dst = MRIcopy(mri_src, NULL) ;
}
mri_bg = MRIclone(mri_src, NULL) ;
width = mri_src->width ;
height = mri_src->height ;
depth = mri_src->depth ;
low_thresh = 85 ;
hi_thresh = 105 ;
total_filled = 0 ;
for (z = 0 ; z < depth ; z++)
{
for (y = 0 ; y < height ; y++)
{
for (x = 0 ; x < width ; x++)
{
if (x == 152 && y == 117 && z == 132) /* 93 */
{
DiagBreak() ;
}
val0 = MRIgetVoxVal(mri_src, x, y, z, 0) ;
#if 0
if (val0 >= low_thresh && val0 <= hi_thresh &&
MRIvox(mri_dst,x,y,z) < WM_MIN_VAL)
#else
if (val0 >= 85 && val0 <= 105)
#endif
{
#undef WHALF
#undef WSIZE
#define WSIZE 7
#define WHALF ((WSIZE-1)/2)
fill = 1 ;
for (zk = -WHALF ; fill && zk <= WHALF ; zk++)
{
zi = mri_src->zi[z+zk] ;
for (yk = -WHALF ; fill && yk <= WHALF ; yk++)
{
yi = mri_src->yi[y+yk] ;
for (xk = -WHALF ; fill && xk <= WHALF ; xk++)
{
xi = mri_src->xi[x+xk] ;
val = MRIgetVoxVal(mri_src, xi, yi, zi, 0) ;
if (val < 85 || val > 110)
{
fill = 0 ; /* not homogeneous enough */
}
}
}
}
}
else
{
fill = 0 ;
}
if (fill)
{
total_filled++ ;
}
if (fill)
{
MRIsetVoxVal(mri_bg, x, y, z, 0, BASAL_GANGLIA_FILL) ;
}
}
}
}
MRIclose(mri_bg, mri_bg) ; /* remove small holes */
/* segment into connected components */
mriseg = MRIsegment(mri_bg, 1, 255) ;
fprintf(stderr, "segmenting thick gray regions: %d %d mm segments found\n",
mriseg->nsegments, WSIZE) ;
/* dilate into regions that are not on */
for (i = 0 ; i < 2*WSIZE ; i++)
{
MRIsegmentDilateThreshold(mriseg, mri_src, mri_src, 80, 100) ;
}
/* fill basal ganglia components */
MRIclear(mri_bg) ;
for (total_filled = i = 0 ; i < mriseg->nsegments ; i++)
{
#define TAL_BG_LEFT_X -30
#define TAL_BG_RIGHT_X 30
#define TAL_BG_Y 5
#define TAL_BG_Z 5
#define MAX_DIST 25
mseg = &mriseg->segments[i] ;
MRIvoxelToTalairach(mri_src, mseg->cx, mseg->cy, mseg->cz,&tx, &ty,&tz);
dx_left = tx - TAL_BG_LEFT_X ;
dx_right = tx - TAL_BG_RIGHT_X ;
dy = ty - TAL_BG_Y ;
dz = tz - TAL_BG_Z ;
dist_left = sqrt(dx_left*dx_left+dy*dy+dz*dz) ;
dist_right = sqrt(dx_right*dx_right+dy*dy+dz*dz) ;
if (dist_left > MAX_DIST && dist_right > MAX_DIST)
{
continue ;
}
fprintf(stderr, "filling segment %d with %d voxels\n\tc = "
"(%2.1f,%2.1f,%2.1f) tal (%2.1f,%2.1f,%2.1f), dist %2.1f,%2.1f\n",
i, mseg->nvoxels, mseg->cx, mseg->cy, mseg->cz,
tx, ty, tz, dist_left, dist_right) ;
MRIsegmentToImage(mri_src, mri_bg, mriseg, i) ;
total_filled += mseg->nvoxels ;
}
#if 1
/* MRIremoveIslands(mri_bg, mri_bg, 3, .56) ;*/
MRIbinarize(mri_bg, mri_bg, WM_MIN_VAL, 0, BASAL_GANGLIA_FILL) ;
#endif
MRIsegmentFree(&mriseg) ;
MRIunion(mri_dst, mri_bg, mri_dst) ;
MRIfree(&mri_bg) ;
if (Gdiag & DIAG_SHOW)
{
fprintf(stderr, "%d basal ganglia points filled\n", total_filled);
}
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) ;
}
