int
main(int argc, char *argv[]) {
char **av ;
int ac, nargs ;
MRI *mri_src, *mri_dst ;
char *in_fname, *out_fname ;
int label, nvox ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_copy_values.c,v 1.5 2011/03/02 00:04:14 nicks Exp $", "$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 2)
ErrorExit(ERROR_BADPARM, "%s: no input name specified", Progname) ;
in_fname = argv[1] ;
if (argc < 3)
ErrorExit(ERROR_BADPARM, "%s: no value specified", Progname) ;
label = atoi(argv[2]) ;
if (argc < 4)
ErrorExit(ERROR_BADPARM, "%s: no output name specified", Progname) ;
out_fname = argv[3] ;
fprintf(stderr, "reading from %s...\n", in_fname) ;
mri_src = MRIread(in_fname) ;
if (!mri_src)
ErrorExit(ERROR_NOFILE, "%s: could not read input volume %s",
Progname, in_fname) ;
mri_dst = MRIread(out_fname) ;
if (!mri_dst)
ErrorExit(ERROR_NOFILE, "%s: could not read destination volume %s",
Progname, out_fname) ;
nvox = MRIcopyLabel(mri_src, mri_dst, label) ;
fprintf(stderr, "%d voxels copied from input to output volume...\n", nvox);
fprintf(stderr, "writing to %s...\n", out_fname) ;
MRIwrite(mri_dst, out_fname) ;
MRIfree(&mri_dst) ;
MRIfree(&mri_src) ;
exit(0) ;
return(0) ;
}
static int
extract_labeled_image(MRI *mri_src,
TRANSFORM *transform,
int label,
MRI *mri_dst)
{
MRI *mri_binarized, *mri_tmp ;
mri_binarized = MRIclone(mri_src, NULL) ;
nvoxels += MRIcopyLabel(mri_src, mri_binarized, label) ;
MRIbinarize(mri_binarized, mri_binarized, 1, 0, UNIT_VOLUME) ;
if (transform)
mri_tmp = TransformCreateDensityMap(transform, mri_binarized, NULL) ;
else
mri_tmp = MRIcopy(mri_binarized,NULL) ;
MRIadd(mri_tmp, mri_dst, mri_dst) ;
MRIfree(&mri_binarized) ;
MRIfree(&mri_tmp) ;
return(NO_ERROR) ;
}
int
main(int argc, char *argv[]) {
char **av, *hemi, *subject_name, *cp, fname[STRLEN];
char *parc_name, *annot_name ;
int ac, nargs, vno, i ;
MRI_SURFACE *mris ;
MRI *mri_parc ;
VERTEX *v ;
double d ;
Real x, y, z, xw, yw, zw ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv,
"$Id: mris_sample_parc.c,v 1.31 2016/12/11 14:33:38 fischl Exp $", "$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 4)
usage_exit() ;
subject_name = argv[1] ;
hemi = argv[2] ;
parc_name = argv[3] ;
annot_name = argv[4] ;
if (strlen(sdir) == 0) /* if not specified explicitly as option */
{
cp = getenv("SUBJECTS_DIR") ;
if (!cp)
ErrorExit(ERROR_BADPARM,
"%s: SUBJECTS_DIR not defined in environment.\n", Progname) ;
strcpy(sdir, cp) ;
}
if (parc_name[0] == '/') // full path specified
strcpy(fname, parc_name) ;
else
sprintf(fname, "%s/%s/mri/%s", sdir, subject_name, parc_name) ;
printf("reading parcellation volume from %s...\n", fname) ;
mri_parc = MRIread(fname) ;
if (!mri_parc)
ErrorExit(ERROR_NOFILE, "%s: could not read input volume %s",
Progname, fname) ;
if (mask_fname) {
MRI *mri_mask, *mri_tmp ;
mri_tmp = MRIread(mask_fname) ;
if (mri_tmp == NULL)
ErrorExit(ERROR_BADPARM, "%s: could not load mask volume %s", Progname, mask_fname) ;
mri_mask = MRIclone(mri_tmp, NULL) ;
MRIcopyLabel(mri_tmp, mri_mask, mask_val) ;
MRIdilate(mri_mask, mri_mask) ;
MRIdilate(mri_mask, mri_mask) ;
MRIdilate(mri_mask, mri_mask) ;
MRIdilate(mri_mask, mri_mask) ;
MRIfree(&mri_tmp) ;
mri_tmp = MRIclone(mri_parc, NULL) ;
MRIcopyLabeledVoxels(mri_parc, mri_mask, mri_tmp, mask_val) ;
MRIfree(&mri_parc) ;
mri_parc = mri_tmp ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
MRIwrite(mri_parc, "p.mgz") ;
MRIfree(&mri_mask) ;
}
for (i = 0 ; i < ntrans ; i++) {
MRIreplaceValues(mri_parc, mri_parc, trans_in[i], trans_out[i]) ;
}
sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject_name, hemi, surf_name) ;
printf("reading input surface %s...\n", fname) ;
mris = MRISread(fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, fname) ;
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
MRIScomputeMetricProperties(mris) ;
if (avgs > 0)
MRISaverageVertexPositions(mris, avgs) ;
if (FZERO(proj_mm)) {
if (MRISreadCurvatureFile(mris, thickness_name) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read thickness file %s",
Progname, thickness_name) ;
}
if (color_table_fname) {
mris->ct = CTABreadASCII(color_table_fname) ;
if (mris->ct == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read color file %s",
Progname, color_table_fname) ;
}
if (sample_from_vol_to_surf) // sample from volume to surface */
{
MRIsampleParcellationToSurface(mris, mri_parc) ;
} else /* sample from surface to volume */
{
for (vno = 0 ; vno < mris->nvertices ; vno++) {
v = &mris->vertices[vno] ;
if (v->ripflag)
continue ;
if (vno == Gdiag_no)
DiagBreak() ;
if (!FZERO(proj_mm))
d = proj_mm ;
else
d = v->curv*proj_frac ; /* halfway out */
x = v->x+d*v->nx ;
y = v->y+d*v->ny ;
z = v->z+d*v->nz ;
MRIsurfaceRASToVoxel(mri_parc, x, y, z, &xw, &yw, &zw) ;
v->annotation = v->val =
MRIfindNearestNonzero(mri_parc, wsize, xw, yw, zw, ((float)wsize-1)/2) ;
if (v->val == 0xffffffff)
DiagBreak() ;
}
}
if (replace_label)
replace_vertices_with_label(mris, mri_parc, replace_label, proj_mm);
if (unknown_label >= 0) {
LABEL **labels, *label ;
int nlabels, i, biggest_label, most_vertices, nzero ;
#define TMP_LABEL 1000
for (nzero = vno = 0 ; vno < mris->nvertices ; vno++) {
v = &mris->vertices[vno] ;
if (v->annotation == 0) {
v->annotation = TMP_LABEL;
nzero++ ;
}
}
printf("%d unknown vertices found\n", nzero) ;
MRISsegmentAnnotated(mris, &labels, &nlabels, 10) ;
most_vertices = 0 ;
biggest_label = -1 ;
for (i = 0 ; i < nlabels ; i++) {
label = labels[i] ;
if (mris->vertices[label->lv[0].vno].annotation == TMP_LABEL) {
if (label->n_points > most_vertices) {
biggest_label = i ;
most_vertices = label->n_points ;
}
}
}
if (biggest_label >= 0) {
label = labels[biggest_label] ;
printf("replacing label # %d with %d vertices "
"(vno=%d) with label %d\n",
biggest_label,
label->n_points,
label->lv[0].vno,
unknown_label) ;
for (i = 0 ; i < label->n_points ; i++) {
v = &mris->vertices[label->lv[i].vno] ;
v->annotation = v->val = unknown_label ;
}
}
for (nzero = vno = 0 ; vno < mris->nvertices ; vno++) {
v = &mris->vertices[vno] ;
if (v->annotation == TMP_LABEL) {
v->annotation = 0;
nzero++ ;
}
}
printf("after replacement, %d unknown vertices found\n", nzero) ;
MRISmodeFilterZeroVals(mris) ; /* get rid of the rest
of the unknowns by mode filtering */
for (i = 0 ; i < nlabels ; i++)
LabelFree(&labels[i]) ;
free(labels) ;
}
MRIScopyValsToAnnotations(mris) ;
if (fix_topology != 0)
fix_label_topology(mris, fix_topology) ;
if (mode_filter) {
printf("mode filtering sample labels...\n") ;
#if 0
MRISmodeFilterZeroVals(mris) ;
#else
MRISmodeFilterVals(mris, mode_filter) ;
#endif
for (vno = 0 ; vno < mris->nvertices ; vno++) {
v = &mris->vertices[vno] ;
if (v->ripflag)
continue ;
v->annotation = v->val ;
}
}
/* this will fill in the v->annotation field from the v->val ones */
translate_indices_to_annotations(mris, translation_fname) ;
if (label_index >= 0)
{
int index ;
LABEL *area ;
printf("writing label to %s...\n", annot_name) ;
MRISclearMarks(mris) ;
for (vno = 0 ; vno < mris->nvertices ; vno++)
{
if (vno == Gdiag_no)
DiagBreak() ;
v = &mris->vertices[vno] ;
if (v->annotation > 0)
DiagBreak() ;
CTABfindAnnotation(mris->ct, v->annotation, &index);
if (index == label_index)
v->marked = 1 ;
}
area = LabelFromMarkedSurface(mris) ;
if (nclose > 0)
{
LabelDilate(area, mris, nclose, CURRENT_VERTICES) ;
LabelErode(area, mris, nclose) ;
}
LabelWrite(area, annot_name) ;
}
else
{
printf("writing annotation to %s...\n", annot_name) ;
MRISwriteAnnotation(mris, annot_name) ;
}
/* MRISreadAnnotation(mris, fname) ;*/
exit(0) ;
return(0) ; /* for ansi */
}
static MRI *
MRIcomputeSurfaceDistanceIntensities(MRI_SURFACE *mris, MRI *mri_ribbon, MRI *mri_aparc, MRI *mri, MRI *mri_aseg, int whalf)
{
MRI *mri_features, *mri_binary, *mri_white_dist, *mri_pial_dist ;
int vno, ngm, outside_of_ribbon, label0, label, ohemi_label, xi, yi, zi, xk, yk, zk, x0, y0, z0, hemi_label, assignable ;
double xv, yv, zv, step_size, dist, thickness, wdist, pdist, snx, sny, snz, nx, ny, nz, xl, yl, zl, x, y, z, dot, angle ;
VERTEX *v ;
mri_features = MRIallocSequence(mris->nvertices, 1, 1, MRI_FLOAT, 1) ; // one samples inwards, one in ribbon, and one outside
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") ;
if (mris->hemisphere == LEFT_HEMISPHERE)
{
ohemi_label = Right_Cerebral_Cortex ;
hemi_label = Left_Cerebral_Cortex ;
}
else
{
hemi_label = Right_Cerebral_Cortex ;
ohemi_label = Left_Cerebral_Cortex ;
}
step_size = mri->xsize/2 ;
for (vno = 0 ; vno < mris->nvertices ; vno++)
{
v = &mris->vertices[vno] ;
if (vno == Gdiag_no)
DiagBreak() ;
if (v->ripflag)
continue ; // not cortex
nx = v->pialx - v->whitex ; ny = v->pialy - v->whitey ; nz = v->pialz - v->whitez ;
thickness = sqrt(nx*nx + ny*ny + nz*nz) ;
if (FZERO(thickness))
continue ; // no cortex here
x = (v->pialx + v->whitex)/2 ; y = (v->pialy + v->whitey)/2 ; z = (v->pialz + v->whitez)/2 ; // halfway between white and pial is x0
MRISsurfaceRASToVoxelCached(mris, mri_aseg, x, y, z, &xl, &yl, &zl) ;
x0 = nint(xl); y0 = nint(yl) ; z0 = nint(zl) ;
label0 = MRIgetVoxVal(mri_aparc, x0, y0, z0,0) ;
// compute surface normal in voxel coords
MRISsurfaceRASToVoxelCached(mris, mri_aseg, x+v->nx, y+v->ny, z+v->nz, &snx, &sny, &snz) ;
snx -= xl ; sny -= yl ; snz -= zl ;
for (ngm = 0, xk = -whalf ; xk <= whalf ; xk++)
{
xi = mri_aseg->xi[x0+xk] ;
for (yk = -whalf ; yk <= whalf ; yk++)
{
yi = mri_aseg->yi[y0+yk] ;
for (zk = -whalf ; zk <= whalf ; zk++)
{
zi = mri_aseg->zi[z0+zk] ;
label = MRIgetVoxVal(mri_aseg, xi, yi, zi,0) ;
if (xi == Gx && yi == Gy && zi == Gz)
DiagBreak() ;
if (label != hemi_label)
continue ;
label = MRIgetVoxVal(mri_aparc, xi, yi, zi,0) ;
if (label && label != label0) // if outside the ribbon it won't be assigned to a parcel
continue ; // constrain it to be in the same cortical parcel
// search along vector connecting x0 to this point to make sure it is we don't perforate wm or leave and re-enter cortex
nx = xi-x0 ; ny = yi-y0 ; nz = zi-z0 ;
thickness = sqrt(nx*nx + ny*ny + nz*nz) ;
assignable = 1 ; // assume this point should be counted
if (thickness > 0)
{
nx /= thickness ; ny /= thickness ; nz /= thickness ;
dot = nx*snx + ny*sny + nz*snz ; angle = acos(dot) ;
if (FABS(angle) > angle_threshold)
assignable = 0 ;
outside_of_ribbon = 0 ;
for (dist = 0 ; assignable && dist <= thickness ; dist += step_size)
{
xv = x0+nx*dist ; yv = y0+ny*dist ; zv = z0+nz*dist ;
if (nint(xv) == Gx && nint(yv) == Gy && nint(zv) == Gz)
DiagBreak() ;
MRIsampleVolume(mri_pial_dist, xv, yv, zv, &pdist) ;
MRIsampleVolume(mri_white_dist, xv, yv, zv, &wdist) ;
label = MRIgetVoxVal(mri_aseg, xi, yi, zi,0) ;
if (SKIP_LABEL(label) || label == ohemi_label)
assignable = 0 ;
if (wdist < 0) // entered wm - not assignable
assignable = 0 ;
else
{
if (pdist > 0) // outside pial surface
outside_of_ribbon = 1 ;
else
{
if (outside_of_ribbon) // left ribbon and reentered
assignable = 0 ;
}
}
}
} // close of thickness > 0
if (assignable)
ngm++ ;
else
DiagBreak() ;
}
}
}
MRIsetVoxVal(mri_features, vno, 0, 0, 0, ngm) ;
}
MRIfree(&mri_white_dist) ; MRIfree(&mri_pial_dist) ; MRIfree(&mri_binary) ;
return(mri_features) ;
}
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) ;
}
int
main(int argc, char *argv[])
{
char **av ;
int ac, nargs, n ;
MRI *mri_src, *mri_dst = NULL, *mri_bias, *mri_orig, *mri_aseg = NULL ;
char *in_fname, *out_fname ;
int msec, minutes, seconds ;
struct timeb start ;
char cmdline[CMD_LINE_LEN] ;
make_cmd_version_string
(argc, argv,
"$Id: mri_normalize.c,v 1.80 2012/10/16 21:38:35 nicks Exp $",
"$Name: $",
cmdline);
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mri_normalize.c,v 1.80 2012/10/16 21:38:35 nicks Exp $",
"$Name: $");
if (nargs && argc - nargs == 1)
{
exit (0);
}
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
mni.max_gradient = MAX_GRADIENT ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
{
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 3)
{
usage_exit(0) ;
}
if (argc < 1)
{
ErrorExit(ERROR_BADPARM, "%s: no input name specified", Progname) ;
}
in_fname = argv[1] ;
if (argc < 2)
{
ErrorExit(ERROR_BADPARM, "%s: no output name specified", Progname) ;
}
out_fname = argv[2] ;
if(verbose)
{
printf( "reading from %s...\n", in_fname) ;
}
mri_src = MRIread(in_fname) ;
if (!mri_src)
ErrorExit(ERROR_NO_FILE, "%s: could not open source file %s",
Progname, in_fname) ;
MRIaddCommandLine(mri_src, cmdline) ;
if(nsurfs > 0)
{
MRI_SURFACE *mris ;
MRI *mri_dist=NULL, *mri_dist_sup=NULL, *mri_ctrl, *mri_dist_one ;
LTA *lta= NULL ;
int i ;
TRANSFORM *surface_xform ;
if (control_point_fname) // do one pass with only file control points first
{
MRI3dUseFileControlPoints(mri_src, control_point_fname) ;
mri_dst =
MRI3dGentleNormalize(mri_src,
NULL,
DEFAULT_DESIRED_WHITE_MATTER_VALUE,
NULL,
intensity_above,
intensity_below/2,1,
bias_sigma, mri_not_control);
}
else
{
mri_dst = MRIcopy(mri_src, NULL) ;
}
for (i = 0 ; i < nsurfs ; i++)
{
mris = MRISread(surface_fnames[i]) ;
if (mris == NULL)
ErrorExit(ERROR_NOFILE,"%s: could not surface %s",
Progname,surface_fnames[i]);
surface_xform = surface_xforms[i] ;
TransformInvert(surface_xform, NULL) ;
if (surface_xform->type == MNI_TRANSFORM_TYPE ||
surface_xform->type == TRANSFORM_ARRAY_TYPE ||
surface_xform->type == REGISTER_DAT)
{
lta = (LTA *)(surface_xform->xform) ;
#if 0
if (invert)
{
VOL_GEOM vgtmp;
LT *lt;
MATRIX *m_tmp = lta->xforms[0].m_L ;
lta->xforms[0].m_L = MatrixInverse(lta->xforms[0].m_L, NULL) ;
MatrixFree(&m_tmp) ;
lt = <a->xforms[0];
if (lt->dst.valid == 0 || lt->src.valid == 0)
{
printf( "WARNING:***************************************************************\n");
printf( "WARNING:dst volume infor is invalid. Most likely produce wrong inverse.\n");
printf( "WARNING:***************************************************************\n");
}
copyVolGeom(<->dst, &vgtmp);
copyVolGeom(<->src, <->dst);
copyVolGeom(&vgtmp, <->src);
}
#endif
}
if (stricmp(surface_xform_fnames[i], "identity.nofile") != 0)
{
MRIStransform(mris, NULL, surface_xform, NULL) ;
}
mri_dist_one = MRIcloneDifferentType(mri_dst, MRI_FLOAT) ;
printf("computing distance transform\n") ;
MRIScomputeDistanceToSurface(mris, mri_dist_one, mri_dist_one->xsize) ;
if (i == 0)
{
mri_dist = MRIcopy(mri_dist_one, NULL) ;
}
else
{
MRIcombineDistanceTransforms(mri_dist_one, mri_dist, mri_dist) ;
}
// MRIminAbs(mri_dist_one, mri_dist, mri_dist) ;
MRIfree(&mri_dist_one) ;
}
MRIscalarMul(mri_dist, mri_dist, -1) ;
if (nonmax_suppress)
{
printf("computing nonmaximum suppression\n") ;
mri_dist_sup = MRInonMaxSuppress(mri_dist, NULL, 0, 1) ;
mri_ctrl = MRIcloneDifferentType(mri_dist_sup, MRI_UCHAR) ;
MRIbinarize(mri_dist_sup, mri_ctrl, min_dist, CONTROL_NONE, CONTROL_MARKED) ;
}
else if (erode)
{
int i ;
mri_ctrl = MRIcloneDifferentType(mri_dist, MRI_UCHAR) ;
MRIbinarize(mri_dist, mri_ctrl, min_dist, CONTROL_NONE, CONTROL_MARKED) ;
for (i = 0 ; i < erode ; i++)
{
MRIerode(mri_ctrl, mri_ctrl) ;
}
}
else
{
mri_ctrl = MRIcloneDifferentType(mri_dist, MRI_UCHAR) ;
MRIbinarize(mri_dist, mri_ctrl, min_dist, CONTROL_NONE, CONTROL_MARKED) ;
}
if (control_point_fname)
{
MRInormAddFileControlPoints(mri_ctrl, CONTROL_MARKED) ;
}
if (mask_sigma > 0)
{
MRI *mri_smooth, *mri_mag, *mri_grad ;
mri_smooth = MRIgaussianSmooth(mri_dst, mask_sigma, 1, NULL) ;
mri_mag = MRIcloneDifferentType(mri_dst, MRI_FLOAT) ;
mri_grad = MRIsobel(mri_smooth, NULL, mri_mag) ;
MRIbinarize(mri_mag, mri_mag, mask_thresh, 1, 0) ;
MRImask(mri_ctrl, mri_mag, mri_ctrl, 0, CONTROL_NONE) ;
MRIfree(&mri_grad) ;
MRIfree(&mri_mag) ;
MRIfree(&mri_smooth) ;
}
if (mask_orig_fname)
{
MRI *mri_orig ;
mri_orig = MRIread(mask_orig_fname) ;
MRIbinarize(mri_orig, mri_orig, mask_orig_thresh, 0, 1) ;
MRImask(mri_ctrl, mri_orig, mri_ctrl, 0, CONTROL_NONE) ;
MRIfree(&mri_orig) ;
}
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_dist, "d.mgz");
MRIwrite(mri_dist_sup, "dm.mgz");
MRIwrite(mri_ctrl, "c.mgz");
}
MRIeraseBorderPlanes(mri_ctrl, 4) ;
if (aseg_fname)
{
mri_aseg = MRIread(aseg_fname) ;
if (mri_aseg == NULL)
{
ErrorExit(ERROR_NOFILE,
"%s: could not load aseg from %s", Progname, aseg_fname) ;
}
remove_nonwm_voxels(mri_ctrl, mri_aseg, mri_ctrl) ;
MRIfree(&mri_aseg) ;
}
else
{
remove_surface_outliers(mri_ctrl, mri_dist, mri_dst, mri_ctrl) ;
}
mri_bias = MRIbuildBiasImage(mri_dst, mri_ctrl, NULL, 0.0) ;
if (mri_dist)
{
MRIfree(&mri_dist) ;
}
if (mri_dist_sup)
{
MRIfree(&mri_dist_sup) ;
}
if (bias_sigma> 0)
{
MRI *mri_kernel = MRIgaussian1d(bias_sigma, -1) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_bias, "b.mgz") ;
}
printf("smoothing bias field\n") ;
MRIconvolveGaussian(mri_bias, mri_bias, mri_kernel) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_bias, "bs.mgz") ;
}
MRIfree(&mri_kernel);
}
MRIfree(&mri_ctrl) ;
mri_dst = MRIapplyBiasCorrectionSameGeometry
(mri_dst, mri_bias, mri_dst,
DEFAULT_DESIRED_WHITE_MATTER_VALUE) ;
printf("writing normalized volume to %s\n", out_fname) ;
MRIwrite(mri_dst, out_fname) ;
exit(0) ;
} // end if(surface_fname)
if (!mriConformed(mri_src) && conform > 0)
{
printf("unconformed source detected - conforming...\n") ;
mri_src = MRIconform(mri_src) ;
}
if (mask_fname)
{
MRI *mri_mask ;
mri_mask = MRIread(mask_fname) ;
if (!mri_mask)
ErrorExit(ERROR_NOFILE, "%s: could not open mask volume %s.\n",
Progname, mask_fname) ;
MRImask(mri_src, mri_mask, mri_src, 0, 0) ;
MRIfree(&mri_mask) ;
}
if (read_flag)
{
MRI *mri_ctrl ;
double scale ;
mri_bias = MRIread(bias_volume_fname) ;
if (!mri_bias)
ErrorExit
(ERROR_BADPARM,
"%s: could not read bias volume %s", Progname, bias_volume_fname) ;
mri_ctrl = MRIread(control_volume_fname) ;
if (!mri_ctrl)
ErrorExit
(ERROR_BADPARM,
"%s: could not read control volume %s",
Progname, control_volume_fname) ;
MRIbinarize(mri_ctrl, mri_ctrl, 1, 0, 128) ;
mri_dst = MRImultiply(mri_bias, mri_src, NULL) ;
scale = MRImeanInLabel(mri_dst, mri_ctrl, 128) ;
printf("mean in wm is %2.0f, scaling by %2.2f\n", scale, 110/scale) ;
scale = 110/scale ;
MRIscalarMul(mri_dst, mri_dst, scale) ;
MRIwrite(mri_dst, out_fname) ;
exit(0) ;
}
if(long_flag)
{
MRI *mri_ctrl ;
double scale ;
mri_bias = MRIread(long_bias_volume_fname) ;
if (!mri_bias)
ErrorExit
(ERROR_BADPARM,
"%s: could not read bias volume %s", Progname, long_bias_volume_fname) ;
mri_ctrl = MRIread(long_control_volume_fname) ;
if (!mri_ctrl)
ErrorExit
(ERROR_BADPARM,
"%s: could not read control volume %s",
Progname, long_control_volume_fname) ;
MRIbinarize(mri_ctrl, mri_ctrl, 1, 0, CONTROL_MARKED) ;
if (mri_ctrl->type != MRI_UCHAR)
{
MRI *mri_tmp ;
mri_tmp = MRIchangeType(mri_ctrl, MRI_UCHAR, 0, 1,1);
MRIfree(&mri_ctrl) ;
mri_ctrl = mri_tmp ;
}
scale = MRImeanInLabel(mri_src, mri_ctrl, CONTROL_MARKED) ;
printf("mean in wm is %2.0f, scaling by %2.2f\n", scale, 110/scale) ;
scale = DEFAULT_DESIRED_WHITE_MATTER_VALUE/scale ;
mri_dst = MRIscalarMul(mri_src, NULL, scale) ;
MRIremoveWMOutliers(mri_dst, mri_ctrl, mri_ctrl, intensity_below/2) ;
mri_bias = MRIbuildBiasImage(mri_dst, mri_ctrl, NULL, 0.0) ;
MRIsoapBubble(mri_bias, mri_ctrl, mri_bias, 50, 1) ;
MRIapplyBiasCorrectionSameGeometry(mri_dst, mri_bias, mri_dst,
DEFAULT_DESIRED_WHITE_MATTER_VALUE);
// MRIwrite(mri_dst, out_fname) ;
// exit(0) ;
} // end if(long_flag)
if (grad_thresh > 0)
{
float thresh ;
MRI *mri_mag, *mri_grad, *mri_smooth ;
MRI *mri_kernel = MRIgaussian1d(.5, -1) ;
mri_not_control = MRIcloneDifferentType(mri_src, MRI_UCHAR) ;
switch (scan_type)
{
case MRI_MGH_MPRAGE:
thresh = 15 ;
break ;
case MRI_WASHU_MPRAGE:
thresh = 20 ;
break ;
case MRI_UNKNOWN:
default:
thresh = 12 ;
break ;
}
mri_smooth = MRIconvolveGaussian(mri_src, NULL, mri_kernel) ;
thresh = grad_thresh ;
mri_mag = MRIcloneDifferentType(mri_src, MRI_FLOAT) ;
mri_grad = MRIsobel(mri_smooth, NULL, mri_mag) ;
MRIwrite(mri_mag, "m.mgz") ;
MRIbinarize(mri_mag, mri_not_control, thresh, 0, 1) ;
MRIwrite(mri_not_control, "nc.mgz") ;
MRIfree(&mri_mag) ;
MRIfree(&mri_grad) ;
MRIfree(&mri_smooth) ;
MRIfree(&mri_kernel) ;
}
#if 0
#if 0
if ((mri_src->type != MRI_UCHAR) ||
(!(mri_src->xsize == 1 && mri_src->ysize == 1 && mri_src->zsize == 1)))
#else
if (conform || (mri_src->type != MRI_UCHAR && conform > 0))
#endif
{
MRI *mri_tmp ;
fprintf
(stderr,
"downsampling to 8 bits and scaling to isotropic voxels...\n") ;
mri_tmp = MRIconform(mri_src) ;
mri_src = mri_tmp ;
}
#endif
if(aseg_fname)
{
printf("Reading aseg %s\n",aseg_fname);
mri_aseg = MRIread(aseg_fname) ;
if (mri_aseg == NULL)
ErrorExit
(ERROR_NOFILE,
"%s: could not read aseg from file %s", Progname, aseg_fname) ;
if (!mriConformed(mri_aseg))
{
ErrorExit(ERROR_UNSUPPORTED, "%s: aseg volume %s must be conformed",
Progname, aseg_fname) ;
}
}
else
{
mri_aseg = NULL ;
}
if(verbose)
{
printf( "normalizing image...\n") ;
}
fflush(stdout);
fflush(stderr);
TimerStart(&start) ;
if (control_point_fname)
{
MRI3dUseFileControlPoints(mri_src, control_point_fname) ;
}
// this just setup writing control-point volume saving
if(control_volume_fname)
{
MRI3dWriteControlPoints(control_volume_fname) ;
}
/* first do a gentle normalization to get
things in the right intensity range */
if(long_flag == 0) // if long, then this will already have been done with base control points
{
if(control_point_fname != NULL) /* do one pass with only
file control points first */
mri_dst =
MRI3dGentleNormalize(mri_src,
NULL,
DEFAULT_DESIRED_WHITE_MATTER_VALUE,
NULL,
intensity_above,
intensity_below/2,1,
bias_sigma, mri_not_control);
else
{
mri_dst = MRIcopy(mri_src, NULL) ;
}
}
fflush(stdout);
fflush(stderr);
if(mri_aseg)
{
MRI *mri_ctrl, *mri_bias ;
int i ;
printf("processing with aseg\n");
mri_ctrl = MRIclone(mri_aseg, NULL) ;
for (i = 0 ; i < NWM_LABELS ; i++)
{
MRIcopyLabel(mri_aseg, mri_ctrl, aseg_wm_labels[i]) ;
}
printf("removing outliers in the aseg WM...\n") ;
MRIremoveWMOutliersAndRetainMedialSurface(mri_dst,
mri_ctrl,
mri_ctrl,
intensity_below) ;
MRIbinarize(mri_ctrl, mri_ctrl, 1, CONTROL_NONE, CONTROL_MARKED) ;
MRInormAddFileControlPoints(mri_ctrl, CONTROL_MARKED) ;
if (interior_fname1)
{
MRIS *mris_interior1, *mris_interior2 ;
mris_interior1 = MRISread(interior_fname1) ;
if (mris_interior1 == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not read white matter surface from %s\n",
Progname, interior_fname1) ;
mris_interior2 = MRISread(interior_fname2) ;
if (mris_interior2 == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not read white matter surface from %s\n",
Progname, interior_fname2) ;
add_interior_points(mri_ctrl,
mri_dst,
intensity_above,
1.25*intensity_below,
mris_interior1,
mris_interior2,
mri_aseg,
mri_ctrl) ;
MRISfree(&mris_interior1) ;
MRISfree(&mris_interior2) ;
}
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_ctrl, "norm_ctrl.mgz") ;
}
printf("Building bias image\n");
fflush(stdout);
fflush(stderr);
mri_bias = MRIbuildBiasImage(mri_dst, mri_ctrl, NULL, 0.0) ;
fflush(stdout);
fflush(stderr);
if (bias_sigma> 0)
{
printf("Smoothing with sigma %g\n",bias_sigma);
MRI *mri_kernel = MRIgaussian1d(bias_sigma, -1) ;
MRIconvolveGaussian(mri_bias, mri_bias, mri_kernel) ;
MRIfree(&mri_kernel);
fflush(stdout);
fflush(stderr);
}
MRIfree(&mri_ctrl) ;
MRIfree(&mri_aseg) ;
printf("Applying bias correction\n");
mri_dst = MRIapplyBiasCorrectionSameGeometry
(mri_dst, mri_bias, mri_dst,
DEFAULT_DESIRED_WHITE_MATTER_VALUE) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_dst, "norm_1.mgz") ;
}
fflush(stdout);
fflush(stderr);
} // if(mri_aseg)
else
{
printf("processing without aseg, no1d=%d\n",no1d);
if (!no1d)
{
printf("MRInormInit(): \n");
MRInormInit(mri_src, &mni, 0, 0, 0, 0, 0.0f) ;
printf("MRInormalize(): \n");
mri_dst = MRInormalize(mri_src, NULL, &mni) ;
if (!mri_dst)
{
no1d = 1 ;
printf("1d normalization failed - trying no1d...\n") ;
// ErrorExit(ERROR_BADPARM, "%s: normalization failed", Progname) ;
}
}
if(no1d)
{
if ((file_only && nosnr) ||
((gentle_flag != 0) && (control_point_fname != NULL)))
{
if (mri_dst == NULL)
{
mri_dst = MRIcopy(mri_src, NULL) ;
}
}
else
{
if (nosnr)
{
if (interior_fname1)
{
MRIS *mris_interior1, *mris_interior2 ;
MRI *mri_ctrl ;
printf("computing initial normalization using surface interiors\n");
mri_ctrl = MRIcloneDifferentType(mri_src, MRI_UCHAR) ;
mris_interior1 = MRISread(interior_fname1) ;
if (mris_interior1 == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not read white matter surface from %s\n",
Progname, interior_fname1) ;
mris_interior2 = MRISread(interior_fname2) ;
if (mris_interior2 == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not read white matter surface from %s\n",
Progname, interior_fname2) ;
add_interior_points(mri_ctrl,
mri_dst,
intensity_above,
1.25*intensity_below,
mris_interior1,
mris_interior2,
mri_aseg,
mri_ctrl) ;
MRISfree(&mris_interior1) ;
MRISfree(&mris_interior2) ;
mri_bias = MRIbuildBiasImage(mri_dst, mri_ctrl, NULL, 0.0) ;
if (bias_sigma> 0)
{
MRI *mri_kernel = MRIgaussian1d(bias_sigma, -1) ;
MRIconvolveGaussian(mri_bias, mri_bias, mri_kernel) ;
MRIfree(&mri_kernel);
}
mri_dst = MRIapplyBiasCorrectionSameGeometry
(mri_src,
mri_bias,
mri_dst,
DEFAULT_DESIRED_WHITE_MATTER_VALUE) ;
MRIfree(&mri_ctrl) ;
}
else if (long_flag == 0) // no initial normalization specified
{
mri_dst = MRIcopy(mri_src, NULL) ;
}
}
else
{
printf("computing initial normalization using SNR...\n") ;
mri_dst = MRInormalizeHighSignalLowStd
(mri_src, mri_dst, bias_sigma,
DEFAULT_DESIRED_WHITE_MATTER_VALUE) ;
}
}
if (!mri_dst)
ErrorExit
(ERROR_BADPARM, "%s: could not allocate volume", Progname) ;
}
} // else (not using aseg)
fflush(stdout);
fflush(stderr);
if (file_only == 0)
MRI3dGentleNormalize(mri_dst, NULL, DEFAULT_DESIRED_WHITE_MATTER_VALUE,
mri_dst,
intensity_above, intensity_below/2,
file_only, bias_sigma, mri_not_control);
mri_orig = MRIcopy(mri_dst, NULL) ;
printf("\n");
printf("Iterating %d times\n",num_3d_iter);
for (n = 0 ; n < num_3d_iter ; n++)
{
if(file_only)
{
break ;
}
printf( "---------------------------------\n");
printf( "3d normalization pass %d of %d\n", n+1, num_3d_iter) ;
if (gentle_flag)
MRI3dGentleNormalize(mri_dst, NULL, DEFAULT_DESIRED_WHITE_MATTER_VALUE,
mri_dst,
intensity_above/2, intensity_below/2,
file_only, bias_sigma, mri_not_control);
else
MRI3dNormalize(mri_orig, mri_dst, DEFAULT_DESIRED_WHITE_MATTER_VALUE,
mri_dst,
intensity_above, intensity_below,
file_only, prune, bias_sigma, scan_type, mri_not_control);
}
printf( "Done iterating ---------------------------------\n");
// this just setup writing control-point volume saving
if(control_volume_fname)
{
MRI3dWriteControlPoints(control_volume_fname) ;
}
if(bias_volume_fname)
{
mri_bias = compute_bias(mri_src, mri_dst, NULL) ;
printf("writing bias field to %s....\n", bias_volume_fname) ;
MRIwrite(mri_bias, bias_volume_fname) ;
MRIfree(&mri_bias) ;
}
if (verbose)
{
printf("writing output to %s\n", out_fname) ;
}
MRIwrite(mri_dst, out_fname) ;
msec = TimerStop(&start) ;
MRIfree(&mri_src);
MRIfree(&mri_dst);
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
printf( "3D bias adjustment took %d minutes and %d seconds.\n",
minutes, seconds) ;
exit(0) ;
return(0) ;
}
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) ;
}
int
main(int argc, char *argv[]) {
char **av, *label_name, *vol_name, *out_name ;
int ac, nargs ;
int msec, minutes, seconds, i ;
LABEL *area ;
struct timeb start ;
MRI *mri, *mri_seg ;
Real xw, yw, zw, xv, yv, zv, val;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_label_vals.c,v 1.16 2015/08/24 18:22:05 fischl Exp $", "$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
TimerStart(&start) ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 3)
usage_exit(1) ;
vol_name = argv[1] ;
label_name = argv[2] ;
out_name = argv[3] ;
mri = MRIread(vol_name) ;
if (!mri)
ErrorExit(ERROR_NOFILE, "%s: could not read volume from %s",Progname, vol_name) ;
if (scaleup_flag) {
float scale, fov_x, fov_y, fov_z ;
scale = 1.0/MIN(MIN(mri->xsize, mri->ysize),mri->zsize) ;
fprintf(stderr, "scaling voxel sizes up by %2.2f\n", scale) ;
mri->xsize *= scale ;
mri->ysize *= scale ;
mri->zsize *= scale ;
fov_x = mri->xsize * mri->width;
fov_y = mri->ysize * mri->height;
fov_z = mri->zsize * mri->depth;
mri->xend = fov_x / 2.0;
mri->xstart = -mri->xend;
mri->yend = fov_y / 2.0;
mri->ystart = -mri->yend;
mri->zend = fov_z / 2.0;
mri->zstart = -mri->zend;
mri->fov = (fov_x > fov_y ? (fov_x > fov_z ? fov_x : fov_z) : (fov_y > fov_z ? fov_y : fov_z) );
}
if (segmentation_flag >= 0) {
int x, y, z ;
VECTOR *v_seg, *v_mri ;
MATRIX *m_seg_to_mri ;
v_seg = VectorAlloc(4, MATRIX_REAL) ;
v_mri = VectorAlloc(4, MATRIX_REAL) ;
VECTOR_ELT(v_seg, 4) = 1.0 ;
VECTOR_ELT(v_mri, 4) = 1.0 ;
mri_seg = MRIread(argv[2]) ;
if (!mri_seg)
ErrorExit(ERROR_NOFILE, "%s: could not read volume from %s",Progname, argv[2]) ;
if (erode) {
MRI *mri_tmp ;
mri_tmp = MRIclone(mri_seg, NULL) ;
MRIcopyLabel(mri_seg, mri_tmp, segmentation_flag) ;
while (erode-- > 0)
MRIerode(mri_tmp, mri_tmp) ;
MRIcopy(mri_tmp, mri_seg) ;
MRIfree(&mri_tmp) ;
}
m_seg_to_mri = MRIgetVoxelToVoxelXform(mri_seg, mri) ;
for (x = 0 ; x < mri_seg->width ; x++) {
V3_X(v_seg) = x ;
for (y = 0 ; y < mri_seg->height ; y++) {
V3_Y(v_seg) = y ;
for (z = 0 ; z < mri_seg->depth ; z++) {
V3_Z(v_seg) = z ;
if (MRIvox(mri_seg, x, y, z) == segmentation_flag) {
MatrixMultiply(m_seg_to_mri, v_seg, v_mri) ;
xv = V3_X(v_mri) ;
yv = V3_Y(v_mri) ;
zv = V3_Z(v_mri) ;
MRIsampleVolumeType(mri, xv, yv, zv, &val, SAMPLE_NEAREST);
#if 0
if (val < .000001) {
val *= 1000000;
printf("%f*0.000001\n", val);
} else
#endif
if (coords)
printf("%2.1f %2.1f %2.1f %f\n", xv, yv, zv, val);
else
printf("%f\n", val);
}
}
}
}
MatrixFree(&m_seg_to_mri) ;
VectorFree(&v_seg) ;
VectorFree(&v_mri) ;
} else {
if (cras == 1)
fprintf(stderr,"using the label coordinates to be c_(r,a,s) != 0.\n");
if (surface_dir) {
MRI_SURFACE *mris ;
char fname[STRLEN] ;
sprintf(fname, "%s/%s.white", surface_dir, hemi) ;
mris = MRISread(fname) ;
if (mris == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s...\n", Progname,fname) ;
sprintf(fname, "%s/%s.thickness", surface_dir, hemi) ;
if (MRISreadCurvatureFile(mris, fname) != NO_ERROR)
ErrorExit(ERROR_BADPARM, "%s: could not read thickness file %s...\n", Progname,fname) ;
if (annot_prefix) /* read an annotation in and print vals in it */
{
#define MAX_ANNOT 10000
int vno, annot_counts[MAX_ANNOT], index ;
VERTEX *v ;
Real xw, yw, zw, xv, yv, zv, val ;
float annot_means[MAX_ANNOT] ;
FILE *fp ;
memset(annot_means, 0, sizeof(annot_means)) ;
memset(annot_counts, 0, sizeof(annot_counts)) ;
if (MRISreadAnnotation(mris, label_name) != NO_ERROR)
ErrorExit(ERROR_BADPARM, "%s: could not read annotation file %s...\n", Progname,fname) ;
if (mris->ct == NULL)
ErrorExit(ERROR_BADPARM, "%s: annot file does not contain a color table, specifiy one with -t ", Progname);
for (vno = 0 ; vno < mris->nvertices ; vno++) {
v = &mris->vertices[vno] ;
if (v->ripflag)
continue ;
CTABfindAnnotation(mris->ct, v->annotation, &index) ;
if (index >= 0 && index < mris->ct->nentries) {
annot_counts[index]++ ;
xw = v->x + v->curv*.5*v->nx ;
yw = v->y + v->curv*.5*v->ny ;
zw = v->z + v->curv*.5*v->nz ;
if (cras == 1)
MRIworldToVoxel(mri, xw, yw, zw, &xv, &yv, &zv) ;
else
MRIsurfaceRASToVoxel(mri, xw, yw, zw, &xv, &yv, &zv);
MRIsampleVolume(mri, xv, yv, zv, &val) ;
annot_means[index] += val ;
sprintf(fname, "%s-%s-%s.dat", annot_prefix, hemi, mris->ct->entries[index]->name) ;
fp = fopen(fname, "a") ;
fprintf(fp, "%f\n", val) ;
fclose(fp) ;
}
}
}
else /* read label in and print vals in it */
{
area = LabelRead(NULL, label_name) ;
if (!area)
ErrorExit(ERROR_NOFILE, "%s: could not read label from %s",Progname, label_name) ;
}
} else {
area = LabelRead(NULL, label_name) ;
if (!area)
ErrorExit(ERROR_NOFILE, "%s: could not read label from %s",Progname, label_name) ;
for (i = 0 ; i < area->n_points ; i++) {
xw = area->lv[i].x ;
yw = area->lv[i].y ;
zw = area->lv[i].z ;
if (cras == 1)
MRIworldToVoxel(mri, xw, yw, zw, &xv, &yv, &zv) ;
else
MRIsurfaceRASToVoxel(mri, xw, yw, zw, &xv, &yv, &zv);
MRIsampleVolumeType(mri, xv, yv, zv, &val, SAMPLE_NEAREST);
#if 0
if (val < .000001) {
val *= 1000000;
printf("%f*0.000001\n", val);
} else
#endif
printf("%f\n", val);
}
}
}
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
if (DIAG_VERBOSE_ON)
fprintf(stderr, "label value extractiong took %d minutes and %d seconds.\n",
minutes, seconds) ;
exit(0) ;
return(0) ;
}
int
main(int argc, char *argv[]) {
char **av, fname[STRLEN], *out_fname, *subject_name, *cp ;
int ac, nargs, i, n, noint = 0, options ;
int msec, minutes, seconds, nsubjects, input ;
struct timeb start ;
GCA *gca ;
MRI *mri_seg, *mri_tmp, *mri_inputs ;
TRANSFORM *transform ;
LTA *lta;
GCA_BOUNDARY *gcab ;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
TimerStart(&start) ;
parms.use_gradient = 0 ;
spacing = 8 ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mri_gcab_train.c,v 1.4 2011/03/16 20:23:33 fischl Exp $",
"$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
// parse command line args
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
printf("reading gca from %s\n", argv[1]) ;
gca = GCAread(argv[1]) ;
if (!gca)
exit(Gerror) ;
if (!strlen(subjects_dir)) /* hasn't been set on command line */
{
cp = getenv("SUBJECTS_DIR") ;
if (!cp)
ErrorExit(ERROR_BADPARM, "%s: SUBJECTS_DIR not defined in environment",
Progname);
strcpy(subjects_dir, cp) ;
if (argc < 4)
usage_exit(1) ;
}
// options parsed. subjects and gca name remaining
out_fname = argv[argc-1] ;
nsubjects = argc-3 ;
for (options = i = 0 ; i < nsubjects ; i++) {
if (argv[i+1][0] == '-') {
nsubjects-- ;
options++ ;
}
}
printf("training on %d subject and writing results to %s\n",
nsubjects, out_fname) ;
n = 0 ;
gcab = GCABalloc(gca, 8, 0, 30, 10, target_label);
strcpy(gcab->gca_fname, argv[1]) ;
// going through the subject one at a time
for (nargs = i = 0 ; i < nsubjects+options ; i++) {
subject_name = argv[i+2] ;
//////////////////////////////////////////////////////////////
printf("***************************************"
"************************************\n");
printf("processing subject %s, %d of %d...\n", subject_name,i+1-nargs,
nsubjects);
if (stricmp(subject_name, "-NOINT") == 0) {
printf("not using intensity information for subsequent subjects...\n");
noint = 1 ;
nargs++ ;
continue ;
} else if (stricmp(subject_name, "-INT") == 0) {
printf("using intensity information for subsequent subjects...\n");
noint = 0 ;
nargs++ ;
continue ;
}
// reading this subject segmentation
sprintf(fname, "%s/%s/mri/%s", subjects_dir, subject_name, seg_dir) ;
if (Gdiag & DIAG_SHOW && DIAG_VERBOSE_ON)
fprintf(stderr, "Reading segmentation from %s...\n", fname) ;
mri_seg = MRIread(fname) ;
if (!mri_seg)
ErrorExit(ERROR_NOFILE, "%s: could not read segmentation file %s",
Progname, fname) ;
if ((mri_seg->type != MRI_UCHAR) && (mri_seg->type != MRI_FLOAT)) {
ErrorExit
(ERROR_NOFILE,
"%s: segmentation file %s is not type UCHAR or FLOAT",
Progname, fname) ;
}
if (binarize) {
int j ;
for (j = 0 ; j < 256 ; j++) {
if (j == binarize_in)
MRIreplaceValues(mri_seg, mri_seg, j, binarize_out) ;
else
MRIreplaceValues(mri_seg, mri_seg, j, 0) ;
}
}
if (insert_fname) {
MRI *mri_insert ;
sprintf(fname, "%s/%s/mri/%s",
subjects_dir, subject_name, insert_fname) ;
mri_insert = MRIread(fname) ;
if (mri_insert == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not read volume from %s for insertion",
Progname, insert_fname) ;
MRIbinarize(mri_insert, mri_insert, 1, 0, insert_label) ;
MRIcopyLabel(mri_insert, mri_seg, insert_label) ;
MRIfree(&mri_insert) ;
}
replaceLabels(mri_seg) ;
MRIeraseBorderPlanes(mri_seg, 1) ;
for (input = 0 ; input < gca->ninputs ; input++) {
//////////// set the gca type //////////////////////////////
// is this T1/PD training?
// how can we allow flash data training ???????
// currently checks the TE, TR, FA to be the same for all inputs
// thus we cannot allow flash data training.
////////////////////////////////////////////////////////////
sprintf(fname, "%s/%s/mri/%s",
subjects_dir, subject_name,input_names[input]);
if (DIAG_VERBOSE_ON)
printf("reading co-registered input from %s...\n", fname) ;
fprintf(stderr, " reading input %d: %s\n", input, fname);
mri_tmp = MRIread(fname) ;
if (!mri_tmp)
ErrorExit
(ERROR_NOFILE,
"%s: could not read image from file %s", Progname, fname) ;
// input check 1
if (getSliceDirection(mri_tmp) != MRI_CORONAL) {
ErrorExit
(ERROR_BADPARM,
"%s: must be in coronal direction, but it is not\n",
fname);
}
// input check 2
if (mri_tmp->xsize != 1 || mri_tmp->ysize != 1 || mri_tmp->zsize != 1) {
ErrorExit
(ERROR_BADPARM,
"%s: must have 1mm voxel size, but have (%f, %f, %f)\n",
fname, mri_tmp->xsize, mri_tmp->ysize, mri_tmp->ysize);
}
// input check 3 is removed. now we can handle c_(ras) != 0 case
// input check 4
if (i == 0) {
TRs[input] = mri_tmp->tr ;
FAs[input] = mri_tmp->flip_angle ;
TEs[input] = mri_tmp->te ;
} else if (!FEQUAL(TRs[input],mri_tmp->tr) ||
!FEQUAL(FAs[input],mri_tmp->flip_angle) ||
!FEQUAL(TEs[input], mri_tmp->te))
ErrorExit
(ERROR_BADPARM,
"%s: subject %s input volume %s: sequence parameters "
"(%2.1f, %2.1f, %2.1f)"
"don't match other inputs (%2.1f, %2.1f, %2.1f)",
Progname, subject_name, fname,
mri_tmp->tr, DEGREES(mri_tmp->flip_angle), mri_tmp->te,
TRs[input], DEGREES(FAs[input]), TEs[input]) ;
// first time do the following
if (input == 0) {
int nframes = gca->ninputs ;
///////////////////////////////////////////////////////////
mri_inputs =
MRIallocSequence(mri_tmp->width, mri_tmp->height, mri_tmp->depth,
mri_tmp->type, nframes) ;
if (!mri_inputs)
ErrorExit
(ERROR_NOMEMORY,
"%s: could not allocate input volume %dx%dx%dx%d",
mri_tmp->width, mri_tmp->height, mri_tmp->depth,nframes) ;
MRIcopyHeader(mri_tmp, mri_inputs) ;
}
// -mask option ////////////////////////////////////////////
if (mask_fname)
{
MRI *mri_mask ;
sprintf(fname, "%s/%s/mri/%s",
subjects_dir, subject_name, mask_fname);
printf("reading volume %s for masking...\n", fname) ;
mri_mask = MRIread(fname) ;
if (!mri_mask)
ErrorExit(ERROR_NOFILE, "%s: could not open mask volume %s.\n",
Progname, fname) ;
MRImask(mri_tmp, mri_mask, mri_tmp, 0, 0) ;
MRIfree(&mri_mask) ;
}
MRIcopyFrame(mri_tmp, mri_inputs, 0, input) ;
MRIfree(&mri_tmp) ;
}// end of inputs per subject
/////////////////////////////////////////////////////////
// xform_name is given, then we can use the consistent c_(r,a,s) for gca
/////////////////////////////////////////////////////////
if (xform_name)
{
// we read talairach.xfm which is a RAS-to-RAS
sprintf(fname, "%s/%s/mri/transforms/%s",
subjects_dir, subject_name, xform_name) ;
if (Gdiag & DIAG_SHOW && DIAG_VERBOSE_ON)
printf("INFO: reading transform file %s...\n", fname);
if (!FileExists(fname))
{
fprintf(stderr,"ERROR: cannot find transform file %s\n",fname);
exit(1);
}
transform = TransformRead(fname);
if (!transform)
ErrorExit(ERROR_NOFILE, "%s: could not read transform from file %s",
Progname, fname);
modify_transform(transform, mri_inputs, gca);
// Here we do 2 things
// 1. modify gca direction cosines to
// that of the transform destination (both linear and non-linear)
// 2. if ras-to-ras transform,
// then change it to vox-to-vox transform (linear case)
// modify transform to store inverse also
TransformInvert(transform, mri_inputs) ;
// verify inverse
lta = (LTA *) transform->xform;
}
else
{
GCAreinit(mri_inputs, gca);
// just use the input value, since dst = src volume
transform = TransformAlloc(LINEAR_VOXEL_TO_VOXEL, NULL) ;
}
////////////////////////////////////////////////////////////////////
// train gca
////////////////////////////////////////////////////////////////////
// segmentation is seg volume
// inputs is the volumes of all inputs
// transform is for this subject
// noint is whether to use intensity information or not
GCABtrain(gcab, mri_inputs, mri_seg, transform, target_label) ;
MRIfree(&mri_seg) ;
MRIfree(&mri_inputs) ;
TransformFree(&transform) ;
}
GCABcompleteTraining(gcab) ;
if (smooth > 0) {
printf("regularizing conditional densities with smooth=%2.2f\n", smooth) ;
GCAregularizeConditionalDensities(gca, smooth) ;
}
if (navgs) {
printf("applying mean filter %d times to conditional densities\n", navgs) ;
GCAmeanFilterConditionalDensities(gca, navgs) ;
}
printf("writing trained GCAB to %s...\n", out_fname) ;
if (GCABwrite(gcab, out_fname) != NO_ERROR)
ErrorExit
(ERROR_BADFILE, "%s: could not write gca to %s", Progname, out_fname) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRI *mri ;
mri = GCAbuildMostLikelyVolume(gca, NULL) ;
MRIwrite(mri, "m.mgz") ;
MRIfree(&mri) ;
}
if (histo_fname) {
FILE *fp ;
int histo_counts[10000], xn, yn, zn, max_count ;
GCA_NODE *gcan ;
memset(histo_counts, 0, sizeof(histo_counts)) ;
fp = fopen(histo_fname, "w") ;
if (!fp)
ErrorExit(ERROR_BADFILE, "%s: could not open histo file %s",
Progname, histo_fname) ;
max_count = 0 ;
for (xn = 0 ; xn < gca->node_width; xn++) {
for (yn = 0 ; yn < gca->node_height ; yn++) {
for (zn = 0 ; zn < gca->node_depth ; zn++) {
gcan = &gca->nodes[xn][yn][zn] ;
if (gcan->nlabels < 1)
continue ;
if (gcan->nlabels == 1 && IS_UNKNOWN(gcan->labels[0]))
continue ;
histo_counts[gcan->nlabels]++ ;
if (gcan->nlabels > max_count)
max_count = gcan->nlabels ;
}
}
}
max_count = 20 ;
for (xn = 1 ; xn < max_count ; xn++)
fprintf(fp, "%d %d\n", xn, histo_counts[xn]) ;
fclose(fp) ;
}
GCAfree(&gca) ;
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
printf("classifier array training took %d minutes"
" and %d seconds.\n", minutes, seconds) ;
exit(0) ;
return(0) ;
}
int main(int argc, char *argv[]) {
MRIS *mris;
char *in_orig_fname=NULL, *in_seg_fname=NULL,*out_fname=NULL;
MRI *mri_orig=NULL,*mri_seg=NULL,*mri_out=NULL;
int nargs,n;
char fname[512];
Progname=argv[0];
fprintf(stderr,"\n");
MRI_TOPOLOGY_PARMSdefault(&parms);
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (parms.tesselation_mode==-1)
parms.tesselation_mode=parms.connectivity;
if (argc<4) {
fprintf(stderr, "\nUsage: %s options input_orig_file input_segmented_file output_folder\n", Progname);
exit(1);
};
in_orig_fname=argv[argc-3];
in_seg_fname = argv[argc-2];
out_fname = argv[argc-1];
fprintf(stderr,"************************************************************"
"\nThe input orig volume is %s"
"\nThe input segmented volume is %s"
"\nThe output volume is %s"
"\nIf this is incorrect, please exit quickly the program (Ctl-C)\n",in_orig_fname,in_seg_fname,out_fname);
for (n=0;n<parms.nlabels;n++)
fprintf(stderr,"label = %d: %s \n",parms.labels[n],cma_label_to_name(parms.labels[n]));
if (parms.using_gca_maps)
fprintf(stderr,"mixing parameters: alpha=%1.3f , beta=%1.3f \n",parms.alpha,parms.beta);
else {
parms.beta=1.0f;
parms.alpha=1.0f;
}
fprintf(stderr,"connectivity = %d\n",parms.connectivity);
mri_orig=MRIread(in_orig_fname);
if (!mri_orig && parms.using_gca_maps)
Error("orig volume: orig volume could not be read\n");
mri_seg=MRIread(in_seg_fname);
if (!mri_seg)
Error("segmented volume: segmented volume could not be read\n");
//check euler characteristic of initial surface
if (parms.initial_surface_file) {
int i,j,k,val,euler,pnvertices, pnfaces, pnedges;
MRI *mri_tmp;
mri_tmp=MRIclone(mri_seg,NULL);
for (k=0;k<mri_seg->depth;k++)
for (j=0;j<mri_seg->height;j++)
for (i=0;i<mri_seg->width;i++)
for (n=0;n<parms.nlabels;n++) {
val=MRIgetVoxVal(mri_seg,i,j,k, 0);
if (val==parms.labels[n]) {
MRIsetVoxVal(mri_tmp,i,j,k,0,1);
break;
}
}
mris=MRIScreateSurfaceFromVolume(mri_tmp,1,parms.connectivity);
euler=MRIScomputeEulerNumber(mris,&pnvertices,&pnfaces,&pnedges);
fprintf(stderr,"\ninitial euler characteristic = %d, %d vertices, %d faces, %d edges"
,euler,pnvertices,pnfaces,pnedges);
MRISwrite(mris,parms.initial_surface_file);
MRISfree(&mris);
MRIfree(&mri_tmp);
}
mri_out=MRIcorrectTopology(mri_orig,mri_seg,NULL,&parms);
if (parms.nlabels == 1) {
MRI *mri_tmp ;
// turn off all voxels that are going to be on in the output
MRImask(mri_seg, mri_out, mri_seg, 1, 0) ;
/* whatever ones are left are now incorrect and should be labeled
something else
*/
resegment_erased_voxels(mri_orig, mri_seg, mri_seg, parms.labels[0]) ;
MRIreplaceValues(mri_out, mri_out, 1, parms.labels[0]) ;
mri_tmp = MRIcopy(mri_seg, NULL) ;
MRIcopyLabel(mri_out, mri_tmp, parms.labels[0]) ;
MRIfree(&mri_out) ;
mri_out = mri_tmp ;
// check_volume(mri_save, mri_out, parms.labels[0]) ;
}
MRIwrite(mri_out,out_fname);
////TEMPORARY VALIDATION STUFF //////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////////////////////////
#if 0
//validation of the algo
{
FILE *f;
MRIS *mristb[20],*mrisr;
int n,i,j,k,depth,height,width,count,count2;
int tab[20]={4,43,51,12,52,13,54,18,53,17,49,10,50,11};//,6,7,10,11,12,13,17,18,43,44,45,46,49,50,51,52,53,54};
MRI *mri_val=MRIclone(parms.mri_seg,NULL);
parms.nlabels=1;
depth=parms.mri_seg->depth;
height=parms.mri_seg->height;
width=parms.mri_seg->width;
for (n=0;n<14;n++) {
MRIfree(&parms.mri_output);
MRIfree(&parms.mri_bin);
MRIfree(&parms.mri_dist);
MRIfree(&parms.mri_fcost);
MRIfree(&parms.mri_bcost);
MRIfree(&parms.mri_fprior);
MRIfree(&parms.mri_bprior);
MRIfree(&parms.mri_labeled);
segmentationFree(&parms.F_Bseg);
segmentationFree(&parms.F_Rseg);
segmentationFree(&parms.B_Bseg);
segmentationFree(&parms.B_Rseg);
CCSfree(&parms.F_Bccs);
CCSfree(&parms.F_Rccs);
CCSfree(&parms.B_Bccs);
CCSfree(&parms.B_Rccs);
parms.labels[0]=tab[n];
MRIcorrectTopology(parms.mri_orig,parms.mri_seg,&parms.mri_output,mris
,parms.labels,parms.nblabels,parms.f_c,parms);
MRISwrite(*mris,"./tmp");
mristb[n]=MRISread("./tmp");
#if 0
count=0;
count2=0;
for (k=0;k<depth;k++)
for (j=0;j<height;j++)
for (i=0;i<width;i++) {
if (MRIvox(parms.mri_seg,i,j,k)==parms.labels[0])
count2++;
if (MRIvox(parms.mri_output,i,j,k)==1) {
MRIvox(mri_val,i,j,k)++;
if (MRIvox(parms.mri_seg,i,j,k)!=parms.labels[0])
count++;
} else if (MRIvox(parms.mri_seg,i,j,k)==parms.labels[0])
count++;
}
fprintf(stderr,"\n yeh %d %d %f \n",count,count2,100.*count/count2);
sprintf(fname,"./label%d",tab[n]);
f=fopen(fname,"a+");
fprintf(f,"\n %d %d %f ",count,count2,(float)100.*count/count2);
fclose(f);
#endif
#if 0
sprintf(fname,"./surf%d",n);
MRISwrite(mristb[n],fname);
MRISsmoothSurface2(mristb[n],5,0.5,0);
MRISsmoothSurface2(mristb[n],5,0.25,2);
MRISsmoothSurface2(mristb[n],10,0.05,5);
sprintf(fname,"./surfsmooth%d",n);
mristb[n]->type=MRIS_TRIANGULAR_SURFACE;//MRIS_BINARY_QUADRANGLE_FILE;
MRISwrite(mristb[n],fname);
MRISsetNeighborhoodSize(mristb[n],3) ;
MRIScomputeMetricProperties(mristb[n]) ;
MRIScomputeSecondFundamentalForm(mristb[n]) ;
MRISuseMeanCurvature(mristb[n]);
MRISaverageCurvatures(mristb[n],2) ;
MRISnormalizeCurvature(mristb[n], NORM_MEAN) ;
sprintf(fname,"./curv%d",n);
MRISwriteCurvature(mristb[n],fname);
#endif
}
#if 0
mrisr=MRISconcatenateQuadSurfaces(n,mristb);
mrisr->type=MRIS_TRIANGULAR_SURFACE;
MRISwrite(mrisr,"./lh.ZURFACE");
// for(k=0;k<mrisr->nvertices;k++)
// mrisr->vertices[k].curv=0.3;
//MRISnormalizeCurvature(mrisr, NORM_MEAN) ;
MRISwriteCurvature(mrisr,"./ZURFACE_CURVATURE");
for (k=0;k<mrisr->nvertices;k++)
mrisr->vertices[k].curv=mrisr->vertices[k].val;
MRISwriteCurvature(mrisr,"./ZURFACE_VAL");
#endif
n=0;
count=0;
for (k=0;k<depth;k++)
for (j=0;j<height;j++)
for (i=0;i<width;i++) {
if (MRIgetVoxVal(mri_val,i,j,k,0)>=1) {
n++;
if (MRIsetVoxVal(mri_val,i,j,k,0)>1)
count++;
}
}
// sprintf(fname,"./labeltotal");
/// f=fopen(fname,"a+");
//fprintf(f,"\n %s %d %d %f ",in_seg_fname,count,n,(float)100.*count/n);
//fclose(f);
#if 0
MRIwrite(mri_val,"/tmp/tmp");
#endif
fprintf(stderr,"\n WE HAVE %d %d %f \n",count,n,100.*count/n);
}
#endif
//////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
if (parms.final_surface_file) {
int euler,pnvertices, pnfaces, pnedges;
mris=MRIScreateSurfaceFromVolume(mri_out,1,parms.connectivity);
euler=MRIScomputeEulerNumber(mris,&pnvertices,&pnfaces,&pnedges);
fprintf(stderr,"\nfinal euler characteristic = %d, %d vertices, %d faces, %d edges"
,euler,pnvertices,pnfaces,pnedges);
sprintf(fname,"%s",parms.final_surface_file);
MRISwrite(mris,fname);
#if 0
MRISsmoothSurface(mris,7,0.2);
strcat(fname,"_smooth");
MRISwrite(mris,fname);
if (parms.fit) {
sprintf(fname,parms.surfname);
strcat(fname,"_fit");
MRISmatchSurfaceToLabel(parms.mris,parms.mri_output,1,NULL,NULL,parms.f_c);
MRISwrite(parms.mris,fname);
}
#endif
MRISfree(&mris);
}
if (mri_out)
MRIfree(&mri_out);
if (mri_orig)
MRIfree(&mri_orig);
if (mri_seg)
MRIfree(&mri_seg);
fprintf(stderr,"\n");
return NO_ERROR;
}
int
main(int argc, char *argv[]) {
char **av, fname[STRLEN] ;
int ac, nargs ;
char *reg_fname, *in_fname, *out_stem, *cp ;
int msec, minutes, seconds, nvox, float2int ;
struct timeb start ;
MRI_SURFACE *mris_lh_white, *mris_rh_white, *mris_lh_pial, *mris_rh_pial ;
MRI *mri_aseg, *mri_seg, *mri_pial, *mri_tmp, *mri_ribbon, *mri_in, *mri_cortex,
*mri_subcort_gm, *mri_wm, *mri_csf ;
MATRIX *m_regdat ;
float intensity, betplaneres, inplaneres ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_compute_volume_fractions.c,v 1.9 2012/11/07 18:58:02 greve Exp $", "$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 4)
usage_exit(1) ;
if (!strlen(sdir)) {
cp = getenv("SUBJECTS_DIR") ;
if (!cp)
ErrorExit(ERROR_BADPARM,
"%s: SUBJECTS_DIR not defined in environment.\n", Progname) ;
strcpy(sdir, cp) ;
}
reg_fname = argv[1] ; in_fname = argv[2] ;
out_stem = argv[3] ; Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
TimerStart(&start) ;
if (stricmp(reg_fname, "identity.nofile") == 0)
{
printf("using identity transform\n") ;
m_regdat = NULL ;
inplaneres = betplaneres = intensity = 1 ;
float2int = 0 ;
if (subject == NULL)
subject = "unknown" ;
}
else
{
char *saved_subject = subject ;
printf("reading registration file %s\n", reg_fname) ;
regio_read_register(reg_fname, &subject, &inplaneres,
&betplaneres, &intensity, &m_regdat,
&float2int);
if (saved_subject) // specified on cmdline
subject = saved_subject ;
m_regdat = regio_read_registermat(reg_fname) ;
if (m_regdat == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not load registration file from %s", Progname,reg_fname) ;
}
printf("Format is %s\n",fmt);
sprintf(fname, "%s/%s/surf/lh.white", sdir, subject) ;
printf("reading surface %s\n", fname) ;
mris_lh_white = MRISread(fname) ;
if (mris_lh_white == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not load lh white surface from %s", Progname,fname) ;
sprintf(fname, "%s/%s/surf/rh.white", sdir, subject) ;
printf("reading surface %s\n", fname) ;
mris_rh_white = MRISread(fname) ;
if (mris_rh_white == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not load rh white surface from %s", Progname,fname) ;
sprintf(fname, "%s/%s/surf/lh.pial", sdir, subject) ;
printf("reading surface %s\n", fname) ;
mris_lh_pial = MRISread(fname) ;
if (mris_lh_pial == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not load lh pial surface from %s", Progname,fname) ;
sprintf(fname, "%s/%s/surf/rh.pial", sdir, subject) ;
printf("reading surface %s\n", fname) ;
mris_rh_pial = MRISread(fname) ;
if (mris_rh_pial == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not load rh pial surface from %s", Progname,fname) ;
sprintf(fname, "%s/%s/mri/aseg.mgz", sdir, subject) ;
printf("reading volume %s\n", fname) ;
mri_aseg = MRIread(fname) ;
if (mri_aseg == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not load aseg volume from %s", Progname,fname) ;
printf("reading movable volume %s\n", in_fname) ;
mri_in = MRIread(in_fname) ;
if (mri_in == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not load input volume from %s", Progname,in_fname) ;
nvox = (int)ceil(256/resolution);
mri_pial = MRIalloc(nvox, nvox, nvox, MRI_UCHAR) ;
MRIsetResolution(mri_pial, resolution, resolution, resolution) ;
mri_pial->xstart = -resolution*mri_pial->width/2.0 ;
mri_pial->xend = resolution*mri_pial->width/2.0 ;
mri_pial->ystart = -resolution*mri_pial->height/2.0 ;
mri_pial->yend = resolution*mri_pial->height/2.0 ;
mri_pial->zstart = -resolution*mri_pial->depth/2.0 ;
mri_pial->zend = resolution*mri_pial->depth/2 ;
mri_pial->c_r = mri_aseg->c_r ; mri_pial->c_a = mri_aseg->c_a ; mri_pial->c_s = mri_aseg->c_s ;
MRIreInitCache(mri_pial) ;
printf("filling interior of lh pial surface...\n") ;
MRISfillInterior(mris_lh_pial, resolution, mri_pial) ;
mri_seg = MRIclone(mri_pial, NULL) ;
mri_tmp = MRIclone(mri_pial, NULL) ;
printf("filling interior of rh pial surface...\n") ;
MRISfillInterior(mris_rh_pial, resolution, mri_tmp) ;
MRIcopyLabel(mri_tmp, mri_pial, 1) ;
MRIclear(mri_tmp) ;
printf("filling interior of lh white matter surface...\n") ;
MRISfillWhiteMatterInterior(mris_lh_white, mri_aseg, mri_seg, resolution,
WM_VAL, SUBCORT_GM_VAL, CSF_VAL);
printf("filling interior of rh white matter surface...\n") ;
MRISfillWhiteMatterInterior(mris_rh_white, mri_aseg, mri_tmp, resolution,
WM_VAL, SUBCORT_GM_VAL, CSF_VAL);
MRIcopyLabel(mri_tmp, mri_seg, WM_VAL) ;
MRIcopyLabel(mri_tmp, mri_seg, SUBCORT_GM_VAL) ;
MRIcopyLabel(mri_tmp, mri_seg, CSF_VAL) ;
MRIfree(&mri_tmp) ;
mri_ribbon = MRInot(mri_seg, NULL) ;
MRIcopyLabel(mri_seg, mri_pial, CSF_VAL) ;
MRIreplaceValuesOnly(mri_pial, mri_pial, CSF_VAL, 0) ;
MRIand(mri_ribbon, mri_pial, mri_ribbon, 1) ;
MRIbinarize(mri_ribbon, mri_ribbon, 1, 0, GM_VAL) ;
MRIcopyLabel(mri_ribbon, mri_seg, GM_VAL) ;
MRIreplaceValuesOnly(mri_seg, mri_seg, CSF_VAL, 0) ;
add_aseg_structures_outside_ribbon(mri_seg, mri_aseg, mri_seg, WM_VAL, SUBCORT_GM_VAL, CSF_VAL) ;
{
MATRIX *m_conformed_to_epi_vox2vox, *m_seg_to_conformed_vox2vox,
*m_seg_to_epi_vox2vox ;
if (m_regdat == NULL) // assume identity transform
m_seg_to_epi_vox2vox = MRIgetVoxelToVoxelXform(mri_seg, mri_in) ;
else
{
m_conformed_to_epi_vox2vox = MRIvoxToVoxFromTkRegMtx(mri_in, mri_aseg, m_regdat);
m_seg_to_conformed_vox2vox = MRIgetVoxelToVoxelXform(mri_seg, mri_aseg) ;
m_seg_to_epi_vox2vox = MatrixMultiply(m_conformed_to_epi_vox2vox, m_seg_to_conformed_vox2vox, NULL) ;
MatrixFree(&m_regdat) ; MatrixFree(&m_conformed_to_epi_vox2vox) ;
MatrixFree(&m_seg_to_conformed_vox2vox);
}
printf("seg to EPI vox2vox matrix:\n") ;
MatrixPrint(Gstdout, m_seg_to_epi_vox2vox) ;
mri_cortex = MRIalloc(mri_in->width, mri_in->height, mri_in->depth, MRI_FLOAT) ;
MRIcopyHeader(mri_in, mri_cortex) ;
mri_subcort_gm = MRIclone(mri_cortex, NULL) ;
mri_wm = MRIclone(mri_cortex, NULL) ;
mri_csf = MRIclone(mri_cortex, NULL) ;
printf("computing partial volume fractions...\n") ;
MRIcomputePartialVolumeFractions(mri_in, m_seg_to_epi_vox2vox, mri_seg, mri_wm, mri_subcort_gm, mri_cortex, mri_csf,
WM_VAL, SUBCORT_GM_VAL, GM_VAL, 0) ;
}
sprintf(fname, "%s.wm.%s", out_stem,fmt) ;
printf("writing wm %% to %s\n", fname) ;
MRIwrite(mri_wm, fname) ;
sprintf(fname, "%s.subcort_gm.%s", out_stem,fmt) ;
printf("writing subcortical gm %% to %s\n", fname) ;
MRIwrite(mri_subcort_gm, fname) ;
sprintf(fname, "%s.cortex.%s", out_stem, fmt) ;
printf("writing cortical gm %% to %s\n", fname) ;
MRIwrite(mri_cortex, fname) ;
sprintf(fname, "%s.csf.%s", out_stem,fmt) ;
printf("writing csf %% to %s\n", fname) ;
MRIwrite(mri_csf, fname) ;
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
printf("volume fraction calculation took %d minutes"
" and %d seconds.\n", minutes, seconds) ;
exit(0) ;
return(0) ;
}
static int
MRIcheckRemovals(MRI *mri_T1, MRI *mri_dst, MRI *mri_labels, int wsize)
{
int x, y, z, width, depth, height, whalf, ntested, nchanged, on, vertex;
MRI *mri_tmp, *mri_region, *mri_plane, *mri_binary_plane ;
float min_on ;
whalf = (wsize-1)/2 ;
mri_tmp = MRIcopy(mri_dst, NULL) ;
mri_region = MRIalloc(wsize, wsize, wsize, MRI_UCHAR) ;
min_on = .1*wsize*wsize ;
MRIcopyLabel(mri_labels, mri_tmp, 255) ;
MRIbinarize(mri_tmp, mri_tmp, WM_MIN_VAL, 0, 100) ;
width = mri_T1->width ;
height = mri_T1->height ;
depth = mri_T1->depth ;
ntested = nchanged = 0 ;
if (Gdiag == 99)
{
MRIwrite(mri_tmp, "tmp.mgh") ;
}
for (z = 0 ; z < depth ; z++)
{
for (y = 0 ; y < height ; y++)
{
for (x = 0 ; x < width ; x++)
{
if (z == 87 && y == 88 && x == 163) /* test1 cs filled */
{
DiagBreak() ;
}
if (z == 88 && y == 89 && x == 163) /* test1 cs filled */
{
DiagBreak() ;
}
if (z == 101 && y == 133 && x == 152)
{
DiagBreak() ;
}
if (x == 157 && y == 143 && z == 98)
{
DiagBreak() ;
}
if (x == 156 && y == 143 && z == 98)
{
DiagBreak() ;
}
if (x == 154 && y == 167 && z == 128)
{
DiagBreak() ;
}
if (x == 136 && y == 147 && z == 28)
{
DiagBreak() ;
}
if (x == 163 && y == 88 && z == 86)
{
DiagBreak() ;
}
if ((x == 140 && y == 141 && z == 54) ||
(x == 140 && y == 141 && z == 53) ||
(x == 140 && y == 142 && z == 53) ||
(x == 140 && y == 142 && z == 54) ||
(x == 140 && y == 140 && z == 53))
{
DiagBreak() ; /* test4 cerebellum */
}
if (x == 142 && y == 139 && z == 54) /* test4 */
{
DiagBreak() ;
}
if (!MRIgetVoxVal(mri_labels, x, y, z, 0))
{
continue ;
}
ntested++ ;
MRIextract(mri_tmp, mri_region, x-whalf,y-whalf,z-whalf,
wsize, wsize, wsize) ;
vertex =
MRIcountCpolvOnAtVoxel(mri_region, whalf, whalf, whalf, wsize, &on) ;
mri_plane = MRIextractVertexPlane(mri_tmp, NULL, vertex,x,y,z,wsize);
MRIthreshold(mri_plane, mri_plane, 50) ;
MRIremove1dStructures(mri_plane,mri_plane, 10000,2,NULL);
mri_binary_plane = MRIfillFG(mri_plane, NULL, whalf, whalf, 0,
50, 128, &on) ;
if (on > min_on)
{
int xk, yk, i, ntransitions, i_prev ;
/*
now look at the winding # (number of white-black transitions
in a circle around the central point
*/
ntransitions = 0 ;
for (i = 0 ; i < NPTS ; i++)
{
xk = xpts[i] ;
yk = ypts[i] ;
i_prev = i-1 ;
if (i_prev < 0)
{
i_prev = NPTS-1 ;
}
if (MRIgetVoxVal(mri_binary_plane, whalf+xpts[i], whalf+ypts[i], 0, 0) !=
MRIgetVoxVal(mri_binary_plane,whalf+xpts[i_prev],
whalf+ypts[i_prev],0, 0))
{
ntransitions++ ;
}
}
if (ntransitions > 2) /* not planar */
{
nchanged++ ;
MRIsetVoxVal(mri_dst, x, y, z, 0, MRIgetVoxVal(mri_T1, x, y, z, 0)) ;
}
}
if (Gdiag & DIAG_WRITE)
{
MRIwrite(mri_region, "region.mgh") ;
MRIwrite(mri_plane, "plane.mgh") ;
MRIwrite(mri_binary_plane, "binary_plane.mgh") ;
}
MRIfree(&mri_plane) ;
MRIfree(&mri_binary_plane) ;
}
}
}
MRIfree(&mri_tmp) ;
MRIfree(&mri_region) ;
if (Gdiag & DIAG_SHOW)
{
fprintf(stderr, " %8d voxels tested (%2.2f%%)\n",
ntested, 100.0f*(float)ntested/ (float)(width*height*depth));
fprintf(stderr, " %8d voxels restored (%2.2f%%)\n",
nchanged, 100.0f*(float)nchanged/ (float)(width*height*depth));
}
return(NO_ERROR) ;
}
int
main(int argc, char *argv[])
{
MRI *mri_src, *mri_dst, *mri_tmp, *mri_labeled, *mri_labels;
char *input_file_name, *output_file_name ;
int nargs, i, msec ;
struct timeb then ;
float white_mean, white_sigma, gray_mean, gray_sigma ;
char cmdline[CMD_LINE_LEN] ;
TAGmakeCommandLineString(argc, argv, cmdline) ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
{
exit (0);
}
argc -= nargs;
Progname = argv[0] ;
DiagInit(NULL, NULL, NULL) ;
ErrorInit(NULL, NULL, NULL) ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
{
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 3)
{
usage_exit(1);
}
TimerStart(&then) ;
input_file_name = argv[1] ;
output_file_name = argv[2] ;
mri_src = MRIread(input_file_name) ;
if (!mri_src)
ErrorExit(ERROR_NOFILE, "%s: could not read source volume from %s",
Progname, input_file_name) ;
MRIaddCommandLine(mri_src, cmdline) ;
if (mri_src->type != MRI_UCHAR)
{
MRI *mri_tmp ;
printf("changing input type from %d to UCHAR\n", mri_src->type) ;
mri_tmp = MRIchangeType(mri_src, MRI_UCHAR, 0, 1000, 1) ;
MRIfree(&mri_src) ;
mri_src = mri_tmp ;
}
if (thicken > 1)
{
mri_dst = MRIcopy(mri_src, NULL) ;
/* MRIfilterMorphology(mri_dst, mri_dst) ;*/
fprintf(stderr, "removing 1-dimensional structures...\n") ;
MRIremove1dStructures(mri_dst, mri_dst, 10000, 2, NULL) ;
#if 0
MRIcheckRemovals(mri_src, mri_dst, mri_labels, 5) ;
fprintf(stderr, "thickening thin strands....\n") ;
MRIthickenThinWMStrands(mri_src, mri_dst, mri_dst, thickness, nsegments,
wm_hi) ;
#endif
MRIwrite(mri_dst, output_file_name) ;
exit(0) ;
}
mri_labels = MRIclone(mri_src, NULL) ;
if (auto_detect_stats && !wm_low_set) /* widen range to allow
for more variability */
{
wm_low -= 10 ;
}
fprintf(stderr, "doing initial intensity segmentation...\n") ;
mri_tmp = MRIintensitySegmentation(mri_src, NULL, wm_low, wm_hi, gray_hi);
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_tmp, "tmp1.mgz") ;
}
fprintf(stderr, "using local statistics to label ambiguous voxels...\n") ;
MRIhistoSegment(mri_src, mri_tmp, wm_low, wm_hi, gray_hi, wsize, 3.0f) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_tmp, "tmp2.mgz") ;
}
if (auto_detect_stats)
{
fprintf(stderr, "computing class statistics for intensity windows...\n") ;
MRIcomputeClassStatistics(mri_src, mri_tmp, gray_low, WHITE_MATTER_MEAN,
&white_mean, &white_sigma, &gray_mean,
&gray_sigma) ;
if (!finite(white_mean) || !finite(white_sigma) ||
!finite(gray_mean) || !finite(gray_sigma))
ErrorExit
(ERROR_BADPARM,
"%s: class statistics not finite - check input volume!",
Progname);
if (!wm_low_set)
{
if (FZERO(gray_sigma))
{
wm_low = (white_mean+gray_mean) / 2 ;
}
else
{
wm_low = gray_mean + gray_sigma ;
}
}
if (!gray_hi_set)
{
gray_hi = gray_mean + 2*gray_sigma ;
#if 1
if (gray_hi >= white_mean)
{
gray_hi = white_mean-1 ;
}
#endif
}
fprintf(stderr, "setting bottom of white matter range to %2.1f\n",wm_low);
fprintf(stderr, "setting top of gray matter range to %2.1f\n", gray_hi) ;
if (log_stats)
{
FILE *fp ;
fp = fopen("segment.dat", "w") ;
if (fp)
{
fprintf(fp, "WM: %2.1f +- %2.1f\n",white_mean, white_sigma) ;
fprintf(fp, "GM: %2.1f +- %2.1f\n",gray_mean, gray_sigma) ;
fprintf(fp, "setting bottom of white matter range to %2.1f\n",wm_low);
fprintf(fp, "setting top of gray matter range to %2.1f\n", gray_hi) ;
fclose(fp) ;
}
}
fprintf(stderr, "doing initial intensity segmentation...\n") ;
mri_tmp = MRIintensitySegmentation(mri_src, NULL, wm_low, wm_hi, gray_hi);
fprintf(stderr, "using local statistics to label ambiguous voxels...\n") ;
MRIhistoSegment(mri_src, mri_tmp, wm_low, wm_hi, gray_hi, wsize, 3.0f) ;
}
else
{
/* just some not-too-dopey defaults - won't really be used */
white_mean = 110 ;
white_sigma = 5.0 ;
gray_mean = 65 ;
gray_sigma = 12 ;
}
fprintf(stderr,
"using local geometry to label remaining ambiguous voxels...\n") ;
mri_labeled = MRIcpolvMedianCurveSegment(mri_src, mri_tmp, NULL, 5, 3,
gray_hi, wm_low);
fprintf(stderr,
"\nreclassifying voxels using Gaussian border classifier...\n") ;
/*
now use the gray and white matter border voxels to build a Gaussian
classifier at each point in space and reclassify all voxels in the
range [wm_low-5,gray_hi].
*/
for (i = 0 ; i < niter ; i++)
{
MRIreclassify(mri_src, mri_labeled, mri_labeled, wm_low-5,gray_hi,wsize);
}
MRIfree(&mri_tmp) ;
mri_dst = MRImaskLabels(mri_src, mri_labeled, NULL) ;
MRIfree(&mri_labeled) ;
MRIrecoverBrightWhite(mri_src, mri_dst,mri_dst,wm_low,wm_hi,white_sigma,.33);
fprintf(stderr,
"\nremoving voxels with positive offset direction...\n") ;
#if 0
MRIremoveWrongDirection(mri_dst, mri_dst, 3, wm_low-5, gray_hi, mri_labels) ;
#else
MRIremoveWrongDirection(mri_dst, mri_dst, 3, wm_low-5, gray_hi, NULL) ;
#endif
if (thicken)
{
/* MRIfilterMorphology(mri_dst, mri_dst) ;*/
fprintf(stderr, "removing 1-dimensional structures...\n") ;
MRIremove1dStructures(mri_dst, mri_dst, 10000, 2, mri_labels) ;
#if 0
MRIcheckRemovals(mri_src, mri_dst, mri_labels, 5) ;
#endif
fprintf(stderr, "thickening thin strands....\n") ;
MRIthickenThinWMStrands(mri_src, mri_dst, mri_dst, thickness, nsegments,
wm_hi) ;
}
mri_tmp = MRIfindBrightNonWM(mri_src, mri_dst) ;
MRIbinarize(mri_tmp, mri_tmp, WM_MIN_VAL, 255, 0) ;
MRImaskLabels(mri_dst, mri_tmp, mri_dst) ;
MRIfilterMorphology(mri_dst, mri_dst) ;
if (fill_bg)
{
fprintf(stderr, "filling basal ganglia....\n") ;
MRIfillBasalGanglia(mri_src, mri_dst) ;
}
if (fill_ventricles)
{
fprintf(stderr, "filling ventricles....\n") ;
MRIfillVentricles(mri_dst, mri_dst) ;
}
MRIfree(&mri_src) ;
msec = TimerStop(&then) ;
fprintf(stderr, "white matter segmentation took %2.1f minutes\n",
(float)msec/(1000.0f*60.0f));
fprintf(stderr, "writing output to %s...\n", output_file_name) ;
if (keep_edits)
{
MRI *mri_old ;
mri_old = MRIread(output_file_name) ;
if (!mri_old)
{
ErrorPrintf
(ERROR_NOFILE, "%s: could not read file %s to preserve edits",
Progname, output_file_name) ;
exit(1);
}
else
{
MRIcopyLabel(mri_old, mri_dst, WM_EDITED_ON_VAL) ;
MRIcopyLabel(mri_old, mri_dst, WM_EDITED_OFF_VAL) ;
MRIfree(&mri_old) ;
}
}
MRIwrite(mri_dst, output_file_name) ;
MRIfree(&mri_dst) ;
exit(0) ;
return(0) ;
}
int
main(int argc, char *argv[])
{
char **av, fname[STRLEN], *out_fname, *subject_name, *cp, *tp1_name, *tp2_name ;
char s1_name[STRLEN], s2_name[STRLEN], *sname ;
int ac, nargs, i, n, options, max_index ;
int msec, minutes, seconds, nsubjects, input ;
struct timeb start ;
MRI *mri_seg, *mri_tmp, *mri_in ;
TRANSFORM *transform ;
// int counts ;
int t;
RANDOM_FOREST *rf = NULL ;
GCA *gca = NULL ;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
TimerStart(&start) ;
parms.width = parms.height = parms.depth = DEFAULT_VOLUME_SIZE ;
parms.ntrees = 10 ;
parms.max_depth = 10 ;
parms.wsize = 1 ;
parms.training_size = 100 ;
parms.training_fraction = .5 ;
parms.feature_fraction = 1 ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mri_rf_long_train.c,v 1.5 2012/06/15 12:22:28 fischl Exp $",
"$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
// parse command line args
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
{
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (!strlen(subjects_dir)) /* hasn't been set on command line */
{
cp = getenv("SUBJECTS_DIR") ;
if (!cp)
ErrorExit(ERROR_BADPARM, "%s: SUBJECTS_DIR not defined in environment",
Progname);
strcpy(subjects_dir, cp) ;
}
if (argc < 3)
usage_exit(1) ;
// options parsed. subjects, tp1 and tp2 and rf name remaining
out_fname = argv[argc-1] ;
nsubjects = (argc-2)/3 ;
for (options = i = 0 ; i < nsubjects ; i++)
{
if (argv[i+1][0] == '-')
{
nsubjects-- ;
options++ ;
}
}
printf("training on %d subject and writing results to %s\n",
nsubjects, out_fname) ;
// rf_inputs can be T1, PD, ...per subject
if (parms.nvols == 0)
parms.nvols = ninputs ;
/* gca reads same # of inputs as we read
from command line - not the case if we are mapping to flash */
n = 0 ;
//////////////////////////////////////////////////////////////////
// set up gca direction cosines, width, height, depth defaults
gca = GCAread(gca_name) ;
if (gca == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read GCA from %s", Progname, gca_name) ;
/////////////////////////////////////////////////////////////////////////
// weird way options and subject name are mixed here
/////////////////////////////////////////////////////////
// first calculate mean
////////////////////////////////////////////////////////
// going through the subject one at a time
max_index = nsubjects+options ;
nargs = 0 ;
mri_in = NULL ;
#ifdef HAVE_OPENMP
subject_name = NULL ; sname = NULL ; t = 0 ;
// counts = 0 ; would be private
input = 0 ;
transform = NULL ;
tp1_name = tp2_name = NULL ;
mri_tmp = mri_seg = NULL ;
#pragma omp parallel for firstprivate(tp1_name, tp2_name, mri_in,mri_tmp, input, xform_name, transform, subjects_dir, force_inputs, conform, Progname, mri_seg, subject_name, s1_name, s2_name, sname, t, fname) shared(mri_inputs, transforms, mri_segs,argv) schedule(static,1)
#endif
for (i = 0 ; i < max_index ; i++)
{
subject_name = argv[3*i+1] ;
tp1_name = argv[3*i+2] ;
tp2_name = argv[3*i+3] ;
sprintf(s1_name, "%s_%s.long.%s_base", subject_name, tp1_name, subject_name) ;
sprintf(s2_name, "%s_%s.long.%s_base", subject_name, tp2_name, subject_name) ;
//////////////////////////////////////////////////////////////
printf("***************************************"
"************************************\n");
printf("processing subject %s, %d of %d (%s and %s)...\n", subject_name,i+1-nargs,
nsubjects, s1_name,s2_name);
for (t = 0 ; t < 2 ; t++)
{
sname = t == 0 ? s1_name : s2_name;
// reading this subject segmentation
sprintf(fname, "%s/%s/mri/%s", subjects_dir, sname, seg_dir) ;
if (Gdiag & DIAG_SHOW && DIAG_VERBOSE_ON)
fprintf(stderr, "Reading segmentation from %s...\n", fname) ;
mri_seg = MRIread(fname) ;
if (!mri_seg)
ErrorExit(ERROR_NOFILE, "%s: could not read segmentation file %s",
Progname, fname) ;
if ((mri_seg->type != MRI_UCHAR) && (make_uchar != 0))
{
MRI *mri_tmp ;
mri_tmp = MRIchangeType(mri_seg, MRI_UCHAR, 0, 1,1);
MRIfree(&mri_seg) ;
mri_seg = mri_tmp ;
}
if (wmsa_fname)
{
MRI *mri_wmsa ;
sprintf(fname, "%s/%s/mri/%s", subjects_dir, sname, wmsa_fname) ;
printf("reading WMSA labels from %s...\n", fname) ;
mri_wmsa = MRIread(fname) ;
if (mri_wmsa == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read WMSA file %s", fname) ;
MRIbinarize(mri_wmsa, mri_wmsa, 1, 0, WM_hypointensities) ;
MRIcopyLabel(mri_wmsa, mri_seg, WM_hypointensities) ;
lateralize_hypointensities(mri_seg) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON )
{
char s[STRLEN] ;
sprintf(s, "%s/%s/mri/seg_%s",
subjects_dir, subject_name, wmsa_fname) ;
MRIwrite(mri_seg, s) ;
}
}
if (binarize)
{
int j ;
for (j = 0 ; j < 256 ; j++)
{
if (j == binarize_in)
MRIreplaceValues(mri_seg, mri_seg, j, binarize_out) ;
else
MRIreplaceValues(mri_seg, mri_seg, j, 0) ;
}
}
if (insert_fname)
{
MRI *mri_insert ;
sprintf(fname, "%s/%s/mri/%s",
subjects_dir, subject_name, insert_fname) ;
mri_insert = MRIread(fname) ;
if (mri_insert == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not read volume from %s for insertion",
Progname, insert_fname) ;
MRIbinarize(mri_insert, mri_insert, 1, 0, insert_label) ;
MRIcopyLabel(mri_insert, mri_seg, insert_label) ;
MRIfree(&mri_insert) ;
}
replaceLabels(mri_seg) ;
MRIeraseBorderPlanes(mri_seg, 1) ;
////////////////////////////////////////////////////////////
if (DIAG_VERBOSE_ON)
fprintf(stderr,
"Gather all input volumes for the subject %s.\n",
subject_name);
// inputs must be coregistered
// note that inputs are T1, PD, ... per subject (same TE, TR, FA)
for (input = 0 ; input < ninputs ; input++)
{
//////////// set the gca type //////////////////////////////
// is this T1/PD training?
// how can we allow flash data training ???????
// currently checks the TE, TR, FA to be the same for all inputs
// thus we cannot allow flash data training.
////////////////////////////////////////////////////////////
sprintf(fname, "%s/%s/mri/%s", subjects_dir, sname,input_names[input]);
if (DIAG_VERBOSE_ON)
printf("reading co-registered input from %s...\n", fname) ;
fprintf(stderr, " reading input %d: %s\n", input, fname);
mri_tmp = MRIread(fname) ;
if (!mri_tmp)
ErrorExit
(ERROR_NOFILE,
"%s: could not read image from file %s", Progname, fname) ;
// input check 1
if (getSliceDirection(mri_tmp) != MRI_CORONAL)
{
ErrorExit
(ERROR_BADPARM,
"%s: must be in coronal direction, but it is not\n",
fname);
}
// input check 2
if (conform &&
(mri_tmp->xsize != 1 || mri_tmp->ysize != 1 || mri_tmp->zsize != 1))
{
ErrorExit
(ERROR_BADPARM,
"%s: must have 1mm voxel size, but have (%f, %f, %f)\n",
fname, mri_tmp->xsize, mri_tmp->ysize, mri_tmp->ysize);
}
// input check 3 is removed. now we can handle c_(ras) != 0 case
// input check 4
if (i == 0)
{
TRs[input] = mri_tmp->tr ;
FAs[input] = mri_tmp->flip_angle ;
TEs[input] = mri_tmp->te ;
}
else if ((force_inputs == 0) &&
(!FEQUAL(TRs[input],mri_tmp->tr) ||
!FEQUAL(FAs[input],mri_tmp->flip_angle) ||
!FEQUAL(TEs[input], mri_tmp->te)))
ErrorExit
(ERROR_BADPARM,
"%s: subject %s input volume %s: sequence parameters "
"(%2.1f, %2.1f, %2.1f)"
"don't match other inputs (%2.1f, %2.1f, %2.1f)",
Progname, subject_name, fname,
mri_tmp->tr, DEGREES(mri_tmp->flip_angle), mri_tmp->te,
TRs[input], DEGREES(FAs[input]), TEs[input]) ;
// first time do the following
if (input == 0)
{
int nframes = ninputs ;
///////////////////////////////////////////////////////////
mri_in = MRIallocSequence(mri_tmp->width, mri_tmp->height, mri_tmp->depth,
mri_tmp->type, nframes) ;
if (!mri_in)
ErrorExit
(ERROR_NOMEMORY,
"%s: could not allocate input volume %dx%dx%dx%d",
mri_tmp->width, mri_tmp->height, mri_tmp->depth,nframes) ;
MRIcopyHeader(mri_tmp, mri_in) ;
}
// -mask option ////////////////////////////////////////////
if (mask_fname)
{
MRI *mri_mask ;
sprintf(fname, "%s/%s/mri/%s",
subjects_dir, subject_name, mask_fname);
printf("reading volume %s for masking...\n", fname) ;
mri_mask = MRIread(fname) ;
if (!mri_mask)
ErrorExit(ERROR_NOFILE, "%s: could not open mask volume %s.\n",
Progname, fname) ;
MRImask(mri_tmp, mri_mask, mri_tmp, 0, 0) ;
MRIfree(&mri_mask) ;
}
MRIcopyFrame(mri_tmp, mri_in, 0, input) ;
MRIfree(&mri_tmp) ;
}// end of inputs per subject
/////////////////////////////////////////////////////////
// xform_name is given, then we can use the consistent c_(r,a,s) for gca
/////////////////////////////////////////////////////////
if (xform_name)
{
// we read talairach.xfm which is a RAS-to-RAS
sprintf(fname, "%s/%s/mri/transforms/%s", subjects_dir, sname, xform_name) ;
if (Gdiag & DIAG_SHOW && DIAG_VERBOSE_ON)
printf("INFO: reading transform file %s...\n", fname);
if (!FileExists(fname))
{
fprintf(stderr,"ERROR: cannot find transform file %s\n",fname);
exit(1);
}
transform = TransformRead(fname);
if (!transform)
ErrorExit(ERROR_NOFILE, "%s: could not read transform from file %s",
Progname, fname);
// modify_transform(transform, mri_in, gca);
// Here we do 2 things
// 1. modify gca direction cosines to
// that of the transform destination (both linear and non-linear)
// 2. if ras-to-ras transform,
// then change it to vox-to-vox transform (linear case)
// modify transform to store inverse also
TransformInvert(transform, mri_in) ;
}
else
{
// GCAreinit(mri_in, gca);
// just use the input value, since dst = src volume
transform = TransformAlloc(LINEAR_VOXEL_TO_VOXEL, NULL) ;
}
/////////////////////////////////////////////////////////
if (do_sanity_check)
{
// conduct a sanity check of particular labels, most importantly
// hippocampus, that such labels do not exist in talairach coords
// where they are known not to belong (indicating a bad manual edit)
int errs = check(mri_seg, subjects_dir, subject_name);
if (errs)
{
printf(
"ERROR: mri_ca_train: possible bad training data! subject:\n"
"\t%s/%s\n\n", subjects_dir, subject_name);
fflush(stdout) ;
sanity_check_badsubj_count++;
}
}
mri_segs[i][t] = mri_seg ;
mri_inputs[i][t] = mri_in ;
transforms[i][t] = transform ;
}
}
rf = train_rforest(mri_inputs, mri_segs, transforms, nsubjects, gca, &parms, wm_thresh,wmsa_whalf, 2) ;
printf("writing random forest to %s\n", out_fname) ;
if (RFwrite(rf, out_fname) != NO_ERROR)
ErrorExit
(ERROR_BADFILE, "%s: could not write rf to %s", Progname, out_fname) ;
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
printf("classifier array training took %d minutes and %d seconds.\n", minutes, seconds) ;
exit(0) ;
return(0) ;
}
