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 */
}
int
main(int argc, char *argv[])
{
char **av, *in_fname, *out_fname ;
int ac, nargs, i, label ;
MRI *mri_in, *mri_out, *mri_kernel, *mri_smoothed ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mri_extract_label.c,v 1.13 2011/03/02 00:04:15 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 < 4)
usage_exit() ;
in_fname = argv[1] ;
out_fname = argv[argc-1] ;
printf("reading volume from %s...\n", in_fname) ;
mri_in = MRIread(in_fname) ;
if (!mri_in)
ErrorExit(ERROR_NOFILE, "%s: could not read MRI volume %s", Progname,
in_fname) ;
if (out_like_fname)
{
MRI *mri_tmp = MRIread(out_like_fname) ;
if (!mri_tmp)
ErrorExit
(ERROR_NOFILE,
"%s: could not read template volume from %s",
out_like_fname) ;
mri_out = MRIalloc(mri_tmp->width,
mri_tmp->height,
mri_tmp->depth,
mri_tmp->type) ;
/* MRIcopyHeader(mri_tmp, mri_out) ;*/
MRIfree(&mri_tmp) ;
}
else
mri_out = MRIclone(mri_in, NULL) ;
for (i = 2 ; i < argc-1 ; i++)
{
label = atoi(argv[i]) ;
printf("extracting label %d (%s)\n", label, cma_label_to_name(label)) ;
extract_labeled_image(mri_in, transform, label, mri_out) ;
}
if (!FZERO(sigma))
{
printf("smoothing extracted volume...\n") ;
mri_kernel = MRIgaussian1d(sigma, 10*sigma) ;
mri_smoothed = MRIconvolveGaussian(mri_out, NULL, mri_kernel) ;
MRIfree(&mri_out) ;
mri_out = mri_smoothed ;
}
/* removed for gcc3.3
* vsprintf(out_fname, out_fname, (va_list) &label) ;
*/
if (dilate > 0)
{
int i ;
printf("dilating output volume %d times...\n", dilate) ;
for (i = 0 ; i < dilate ; i++)
MRIdilate(mri_out, mri_out) ;
}
if (erode > 0)
{
int i ;
printf("eroding output volume %d times...\n", erode) ;
for (i = 0 ; i < erode ; i++)
MRIerode(mri_out, mri_out) ;
}
printf("writing output to %s.\n", out_fname) ;
MRIwrite(mri_out, out_fname) ;
if (exit_none_found && (nvoxels == 0))
{
printf("No voxels with specified label were found!\n");
exit(1);
}
exit(0) ;
return(0) ; /* for ansi */
}
static MRI *
MRIcomputeSurfaceDistanceProbabilities(MRI_SURFACE *mris, MRI *mri_ribbon, MRI *mri, MRI *mri_aseg)
{
MRI *mri_features, *mri_binary, *mri_white_dist, *mri_pial_dist, *mri_mask ;
int nwhite_bins, npial_bins, x, y, z, label, i ;
HISTOGRAM2D *hw, *hp ;
float pdist, wdist, val ;
double wval, pval ;
mri_features = MRIallocSequence(mri->width, mri->height, mri->depth, MRI_FLOAT, 2) ;
MRIcopyHeader(mri, mri_features) ;
mri_binary = MRIcopy(mri_ribbon, NULL) ;
mri_binary = MRIbinarize(mri_ribbon, NULL, 1, 0, 1) ;
mri_pial_dist = MRIdistanceTransform(mri_binary, NULL, 1, max_pial_dist+1, DTRANS_MODE_SIGNED,NULL);
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
MRIwrite(mri_pial_dist, "pd.mgz") ;
MRIclear(mri_binary) ;
MRIcopyLabel(mri_ribbon, mri_binary, Left_Cerebral_White_Matter) ;
MRIcopyLabel(mri_ribbon, mri_binary, Right_Cerebral_White_Matter) ;
MRIbinarize(mri_binary, mri_binary, 1, 0, 1) ;
mri_white_dist = MRIdistanceTransform(mri_binary, NULL, 1, max_white_dist+1, DTRANS_MODE_SIGNED,NULL);
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
MRIwrite(mri_white_dist, "wd.mgz") ;
nwhite_bins = ceil((max_white_dist - min_white_dist) / white_bin_size)+1 ;
npial_bins = ceil((max_pial_dist - min_pial_dist) / pial_bin_size)+1 ;
hw = HISTO2Dalloc(NBINS, nwhite_bins) ;
hp = HISTO2Dalloc(NBINS, npial_bins) ;
HISTO2Dinit(hw, NBINS, nwhite_bins, 0, NBINS-1, min_white_dist, max_white_dist) ;
HISTO2Dinit(hp, NBINS, npial_bins, 0, NBINS-1, min_pial_dist, max_pial_dist) ;
for (x = 0 ; x < mri->width ; x++)
for (y = 0 ; y < mri->height ; y++)
for (z = 0 ; z < mri->depth ; z++)
{
label = MRIgetVoxVal(mri_aseg, x, y, z, 0) ;
if (IS_CEREBELLUM(label) || IS_VENTRICLE(label) || label == Brain_Stem || IS_CC(label))
continue ;
pdist = MRIgetVoxVal(mri_pial_dist, x, y, z, 0) ;
wdist = MRIgetVoxVal(mri_pial_dist, x, y, z, 0) ;
val = MRIgetVoxVal(mri, x, y, z, 0) ;
if (pdist >= min_pial_dist && pdist <= max_pial_dist)
HISTO2DaddSample(hp, val, pdist, 0, 0, 0, 0) ;
if (wdist >= min_white_dist && wdist <= max_white_dist)
HISTO2DaddSample(hw, val, wdist, 0, 0, 0, 0) ;
}
HISTO2DmakePDF(hp, hp) ;
HISTO2DmakePDF(hw, hw) ;
for (x = 0 ; x < mri->width ; x++)
for (y = 0 ; y < mri->height ; y++)
for (z = 0 ; z < mri->depth ; z++)
{
label = MRIgetVoxVal(mri_aseg, x, y, z, 0) ;
if (IS_CEREBELLUM(label) || IS_VENTRICLE(label) || label == Brain_Stem || IS_CC(label))
continue ;
pdist = MRIgetVoxVal(mri_pial_dist, x, y, z, 0) ;
wdist = MRIgetVoxVal(mri_pial_dist, x, y, z, 0) ;
val = MRIgetVoxVal(mri, x, y, z, 0) ;
wval = HISTO2DgetCount(hw, val, wdist);
if (DZERO(wval) == 0)
MRIsetVoxVal(mri_features, x, y, z, 1, -log10(wval)) ;
pval = HISTO2DgetCount(hp, val, pdist);
if (DZERO(pval) == 0)
MRIsetVoxVal(mri_features, x, y, z, 0, -log10(pval)) ;
}
MRIclear(mri_binary) ;
MRIbinarize(mri_ribbon, mri_binary, 1, 0, 1) ;
mri_mask = MRIcopy(mri_binary, NULL) ;
for (i = 0 ; i < close_order ; i++)
{
MRIdilate(mri_binary, mri_mask) ;
MRIcopy(mri_mask, mri_binary) ;
}
for (i = 0 ; i < close_order ; i++)
{
MRIerode(mri_binary, mri_mask) ;
MRIcopy(mri_mask, mri_binary) ;
}
MRIwrite(mri_mask, "m.mgz") ;
MRImask(mri_features, mri_mask, mri_features, 0, 0) ;
HISTO2Dfree(&hw) ;
HISTO2Dfree(&hp) ;
MRIfree(&mri_white_dist) ; MRIfree(&mri_pial_dist) ; MRIfree(&mri_binary) ;
return(mri_features) ;
}
static int
initialize_surface_position(MRI_SURFACE *mris, MRI *mri_masked, int outside, INTEGRATION_PARMS *parms) {
MRI *mri_dilated ;
int x, y, z, vno ;
double x0, y0, z0, radius = 0, dist, num ;
Real xs, ys, zs ;
VERTEX *v ;
if (outside) {
mri_dilated = MRIdilate(mri_masked, NULL) ;
MRIsubtract(mri_dilated, mri_masked, mri_dilated) ;
MRIwrite(mri_dilated, "outside.mgz") ;
num = x0 = y0 = z0 = 0 ;
for (x = 0 ; x < mri_dilated->width ; x++) {
for (y = 0 ; y < mri_dilated->height ; y++) {
for (z = 0 ; z < mri_dilated->depth ; z++) {
if (MRIgetVoxVal(mri_dilated, x, y, z,0) > 0) {
MRIvoxelToSurfaceRAS(mri_dilated, x, y, z, &xs, &ys, &zs) ;
x0 += xs ;
y0 += ys ;
z0 += zs ;
num++ ;
}
}
}
}
x0 /= num ;
y0 /= num ;
z0 /= num ;
printf("centroid at (%2.1f, %2.1f, %2.1f)\n", x0, y0, z0) ;
num = radius = 0 ;
for (x = 0 ; x < mri_dilated->width ; x++) {
for (y = 0 ; y < mri_dilated->height ; y++) {
for (z = 0 ; z < mri_dilated->depth ; z++) {
if (MRIgetVoxVal(mri_dilated, x, y, z,0) > 0) {
MRIvoxelToSurfaceRAS(mri_dilated, x, y, z, &xs, &ys, &zs) ;
dist = sqrt(SQR(xs-x0)+SQR(ys-y0)+SQR(zs-z0)) ;
radius += dist ;
num++ ;
}
}
}
}
radius /= num ;
printf("average radius = %2.3f\n", radius) ;
MRIfree(&mri_dilated) ;
MRISprojectOntoSphere(mris, mris, radius*1.25) ;
for (vno = 0 ; vno < mris->nvertices ; vno++) {
v = &mris->vertices[vno] ;
v->x += x0 ;
v->y += y0 ;
v->z += z0 ;
}
MRIScomputeMetricProperties(mris) ;
}
parms->target_radius = radius ;
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
return(NO_ERROR) ;
}
static RANDOM_FOREST *
train_rforest(MRI *mri_inputs[MAX_SUBJECTS][MAX_TIMEPOINTS], MRI *mri_segs[MAX_SUBJECTS][MAX_TIMEPOINTS], TRANSFORM *transforms[MAX_SUBJECTS][MAX_TIMEPOINTS],
int nsubjects, GCA *gca, RFA_PARMS *parms, float wm_thresh,
int wmsa_whalf, int ntp)
{
RANDOM_FOREST *rf ;
int nfeatures, x, y, z, ntraining, n, tvoxel_size, width, height, depth, xt, yt, zt ;
double xatlas, yatlas, zatlas ;
MRI *mri_in, *mri_seg, *mri_training_voxels, *mri_wmsa_possible ;
TRANSFORM *transform ;
double **training_data ;
int *training_classes, i, label, tlabel, nwmsa, nfuture, nnot, correct, label_time1, label_time2;
nwmsa = nnot = nfuture = 0 ;
/*
features are:
t1 intensity (3 vols)
3 priors
# of unknown voxels in the nbhd
# of neighboring wmsa voxels at t1
*/
nfeatures = parms->wsize*parms->wsize*parms->wsize*parms->nvols + 5 ;
rf = RFalloc(parms->ntrees, nfeatures, NCLASSES, parms->max_depth, single_classifier_names, max_steps) ;
if (rf == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not allocate random forest", Progname) ;
rf->min_step_size = 1 ;
tvoxel_size=1 ;
width = (int)ceil((float)mri_segs[0][0]->width/tvoxel_size) ;
height = (int)ceil((float)mri_segs[0][0]->height/tvoxel_size) ;
depth = (int)ceil((float)mri_segs[0][0]->depth/tvoxel_size) ;
mri_wmsa_possible = MRIalloc(width, height, depth, MRI_UCHAR) ;
GCAcopyDCToMRI(gca, mri_wmsa_possible) ;
mri_in = mri_inputs[0][0] ;
mri_training_voxels = MRIallocSequence(mri_in->width,mri_in->height, mri_in->depth,MRI_UCHAR,nsubjects) ;
#if 1
// update time 1 segmentation based on labels at time1 and time2
for (n = 0 ; n < nsubjects ; n++)
{
mri_seg = mri_segs[n][0] ;
for (x = 0 ; x < mri_in->width ; x++)
for (y = 0 ; y < mri_in->height ; y++)
for (z = 0 ; z < mri_in->depth ; z++)
{
label_time1 = MRIgetVoxVal(mri_segs[n][0], x, y, z, 0) ;
label_time2 = MRIgetVoxVal(mri_segs[n][1], x, y, z, 0) ;
if (IS_WMSA(label_time1))
MRIsetVoxVal(mri_segs[n][0], x, y, z, 0, label_time1) ;
else if (IS_WMSA(label_time2))
MRIsetVoxVal(mri_segs[n][0], x, y, z, 0, future_WMSA) ;
}
}
#endif
// build map of spatial locations that WMSAs can possibly occur in
for (n = 0 ; n < nsubjects ; n++)
{
mri_in = mri_inputs[n][1] ; transform = transforms[n][1] ;
for (x = 0 ; x < mri_in->width ; x++)
for (y = 0 ; y < mri_in->height ; y++)
for (z = 0 ; z < mri_in->depth ; z++)
if (is_possible_wmsa(gca, mri_in, transform, x, y, z, 0))
{
TransformSourceVoxelToAtlas(transform, mri_in, x, y, z, &xatlas, &yatlas, &zatlas) ;
xt = nint(xatlas/tvoxel_size) ;
yt = nint(yatlas/tvoxel_size) ;
zt = nint(zatlas/tvoxel_size) ;
if (xt == Gx && yt == Gy && zt == Gz)
DiagBreak() ;
MRIsetVoxVal(mri_wmsa_possible, xt, yt, zt, 0, 1) ;
}
}
for ( ; wmsa_whalf > 0 ; wmsa_whalf--)
MRIdilate(mri_wmsa_possible, mri_wmsa_possible) ;
// now build map of all voxels in training set
for (nnot = nwmsa = nfuture = ntraining = n = 0 ; n < nsubjects ; n++)
{
mri_in = mri_inputs[n][0] ; mri_seg = mri_segs[n][0] ; transform = transforms[n][0] ;
for (x = 0 ; x < mri_in->width ; x++)
for (y = 0 ; y < mri_in->height; y++)
for (z = 0 ; z < mri_in->depth; z++)
{
label = MRIgetVoxVal(mri_seg, x, y, z, 0) ;
TransformSourceVoxelToAtlas(transform, mri_in, x, y, z, &xatlas, &yatlas, &zatlas) ;
xt = nint(xatlas/tvoxel_size) ;
yt = nint(yatlas/tvoxel_size) ;
zt = nint(zatlas/tvoxel_size) ;
if (xt == Gx && yt == Gy && zt == Gz)
DiagBreak() ;
if ((IS_WMSA(label) == 0) &&
MRIgetVoxVal(mri_wmsa_possible,xt,yt, zt,0) == 0)
continue ;
if (NOT_TRAINING_LABEL(label))
continue ;
ntraining++ ;
if (IS_FUTURE_WMSA(label))
{
label = FUTURE_WMSA;
nfuture++ ;
}
else if (IS_WMSA(label))
{
label = WMSA ;
nwmsa++ ;
}
else
{
label = NOT_WMSA ;
nnot++ ;
}
// set label to one more than it will be for training so that 0 means this is not a training voxel
MRIsetVoxVal(mri_training_voxels, x, y, z, n, label+1) ;
}
}
correct = MRIcountNonzero(mri_training_voxels) ;
if (correct != ntraining)
DiagBreak() ;
printf("total training set size = %2.1fM\n", (float)ntraining/(1024.0f*1024.0f)) ;
printf("initial training set found with %dK FUTURE WMSA labels, %dK WMSA labels, and %dK non (ratio=%2.1f:%2.1f)\n",
nfuture/1000, nwmsa/1000, nnot/1000, (float)nnot/(float)nfuture, (float)nnot/(float)nwmsa) ;
MRIfree(&mri_wmsa_possible) ;
if (max_wm_wmsa_ratio*(nfuture+nwmsa) < nnot) // too many wm labels w.r.t. # of wmsas - remove some wm
{
int removed, total_to_remove = nnot - (max_wm_wmsa_ratio*(nfuture+nwmsa)) ;
double premove ;
premove = (double)total_to_remove / (double)nnot ;
printf("removing %dK WM indices to reduce training set imbalance (p < %f)\n", total_to_remove/1000, premove) ;
for (removed = n = 0 ; n < nsubjects ; n++)
for (x = 0 ; x < mri_in->width ; x++)
for (y = 0 ; y < mri_in->height; y++)
for (z = 0 ; z < mri_in->depth; z++)
{
label = MRIgetVoxVal(mri_training_voxels, x, y, z, n) ;
if (label == 1) // a WM voxel
{
if (randomNumber(0,1) < premove)
{
removed++ ;
MRIsetVoxVal(mri_training_voxels, x, y, z, n, 0) ; // remove it from training set
}
}
}
ntraining -= removed ;
printf("%d WM voxels removed, new training set size = %dM (ratio = %2.1f)\n",
removed, ntraining/(1024*1024), (double)(nnot-removed)/(double)(nwmsa+nfuture)) ;
}
correct = MRIcountNonzero(mri_training_voxels) ;
if (correct != ntraining)
DiagBreak() ;
// if (Gx >= 0)
{
int whalf = (parms->wsize-1)/2 ;
char buf[STRLEN] ;
rf->feature_names = (char **)calloc(rf->nfeatures, sizeof(char *)) ;
for (i = 0, x = -whalf ; x <= whalf ; x++)
for (y = -whalf ; y <= whalf ; y++)
for (z = -whalf ; z <= whalf ; z++)
for (n = 0 ; n < mri_in->nframes ; n++, i++)
{
switch (n)
{
default:
case 0: sprintf(buf, "T1(%d, %d, %d)", x, y, z) ; break ;
case 1: sprintf(buf, "T2(%d, %d, %d)", x, y, z) ;
break ;
case 2: sprintf(buf, "FLAIR(%d, %d, %d)", x, y, z) ;
if (x == 0 && y == 0 && z == 0)
Gdiag_no = i ;
break ;
}
rf->feature_names[i] = (char *)calloc(strlen(buf)+1, sizeof(char)) ;
strcpy(rf->feature_names[i], buf) ;
}
printf("FLAIR(0,0,0) = %dth feature\n", Gdiag_no) ;
sprintf(buf, "CSF voxels in nbhd") ;
rf->feature_names[i] = (char *)calloc(strlen(buf)+1, sizeof(char)) ;
strcpy(rf->feature_names[i], buf) ;
i++ ; sprintf(buf, "gm prior") ;
rf->feature_names[i] = (char *)calloc(strlen(buf)+1, sizeof(char)) ;
strcpy(rf->feature_names[i], buf) ;
i++ ; sprintf(buf, "wm prior") ;
rf->feature_names[i] = (char *)calloc(strlen(buf)+1, sizeof(char)) ;
strcpy(rf->feature_names[i], buf) ;
i++ ; sprintf(buf, "csf prior") ;
rf->feature_names[i] = (char *)calloc(strlen(buf)+1, sizeof(char)) ;
strcpy(rf->feature_names[i], buf) ;
i++ ; sprintf(buf, "WMSA in nbhd") ;
rf->feature_names[i] = (char *)calloc(strlen(buf)+1, sizeof(char)) ;
strcpy(rf->feature_names[i], buf) ;
if (Gdiag & DIAG_WRITE)
{
printf("writing training voxels to tv.mgz\n") ;
MRIwrite(mri_training_voxels, "tv.mgz") ;
}
}
// now build training features and classes
training_classes = (int *)calloc(ntraining, sizeof(training_classes[0])) ;
if (training_classes == NULL)
ErrorExit(ERROR_NOFILE, "train_rforest: could not allocate %d-length training buffers",ntraining);
training_data = (double **)calloc(ntraining, sizeof(training_data[0])) ;
if (training_classes == NULL)
ErrorExit(ERROR_NOFILE, "train_rforest: could not allocate %d-length training buffers",ntraining);
for (i = n = 0 ; n < nsubjects ; n++)
{
mri_in = mri_inputs[n][0] ; mri_seg = mri_segs[n][0] ; transform = transforms[n][0] ;
for (x = 0 ; x < mri_in->width ; x++)
for (y = 0 ; y < mri_in->height; y++)
for (z = 0 ; z < mri_in->depth; z++)
{
if ((int)MRIgetVoxVal(mri_training_voxels, x, y, z, n) == 0)
continue ;
label = MRIgetVoxVal(mri_seg, x, y, z, 0) ;
TransformSourceVoxelToAtlas(transform, mri_in, x, y, z, &xatlas, &yatlas, &zatlas) ;
xt = nint(xatlas/tvoxel_size) ; yt = nint(yatlas/tvoxel_size) ; zt = nint(zatlas/tvoxel_size) ;
if (IS_FUTURE_WMSA(label))
tlabel = FUTURE_WMSA ;
else if (IS_WMSA(label))
tlabel = WMSA ;
else
tlabel= NOT_WMSA ;
training_classes[i] = tlabel ;
training_data[i] = (double *)calloc(nfeatures, sizeof(double)) ;
if (training_data[i] == NULL)
ErrorExit(ERROR_NOMEMORY, "train_rforest: could not allocate %d-len feature vector #%d",
nfeatures, i) ;
training_classes[i] = training_classes[i] ;
// extract_feature(mri_in, parms->wsize, x, y, z, training_data[i], xatlas, yatlas, zatlas) ;
extract_long_features(mri_in, mri_seg, transform, gca, parms->wsize, x, y, z, training_data[i]) ;
if (training_data[i][Gdiag_no] < 80 && training_classes[i] == 1)
DiagBreak() ;
i++ ;
}
MRIfree(&mri_in) ; MRIfree(&mri_seg) ; TransformFree(&transform) ;
}
if (i < ntraining)
{
printf("warning!!!! i (%d) < ntraining (%d)! Setting ntraining=i\n", i, ntraining) ;
ntraining = i ;
}
printf("training random forest with %dK FUTURE WMSA labels, %dK WMSA labels, and %dK non (ratio=%2.1f:%2.1f)\n",
nfuture/1000, nwmsa/1000, nnot/1000, (float)nnot/(float)nfuture, (float)nnot/(float)nwmsa) ;
RFtrain(rf, parms->feature_fraction, parms->training_fraction, training_classes, training_data, ntraining);
correct = RFcomputeOutOfBagCorrect(rf, training_classes, training_data,ntraining);
printf("out of bag accuracy: %d of %d = %2.2f%%\n", correct, ntraining,
100.0*correct/ntraining) ;
if (log_file_name)
{
struct flock fl;
int fd;
char line[MAX_LINE_LEN] ;
printf("writing results to train.log file %s\n", log_file_name) ;
fd = open(log_file_name, O_WRONLY|O_APPEND|O_CREAT, S_IRWXU|S_IRWXG);
if (fd < 0)
ErrorExit(ERROR_NOFILE, "%s: could not open test log file %s",
Progname, log_file_name);
fcntl(fd, F_SETLKW, &fl); /* F_GETLK, F_SETLK, F_SETLKW */
sprintf(line, "%f %d %d %f\n",
rf->training_fraction,
rf->max_depth,
rf->ntrees,
100.0*correct/ntraining) ;
write(fd, line, (strlen(line))*sizeof(char)) ;
fl.l_type = F_UNLCK; /* tell it to unlock the region */
fcntl(fd, F_SETLK, &fl); /* set the region to unlocked */
close(fd) ;
}
for (i = 0 ; i < ntraining ; i++) // allow for augmenting with other wmsa examples
free(training_data[i]) ;
free(training_data) ;
free(training_classes) ;
MRIfree(&mri_training_voxels) ;
return(rf) ;
}
int
main(int argc, char *argv[]) {
char **av, *cp ;
int ac, nargs, i, dof, no_transform, which, sno = 0, nsubjects = 0 ;
MRI *mri=0, *mri_mean = NULL, *mri_std=0, *mri_T1=0,*mri_binary=0,*mri_dof=NULL,
*mri_priors = NULL ;
char *subject_name, *out_fname, fname[STRLEN] ;
/* LTA *lta;*/
MRI *mri_tmp=0 ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_make_template.c,v 1.26 2011/03/02 00:04:22 nicks Exp $", "$Name: stable5 $");
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 (!strlen(subjects_dir)) {
cp = getenv("SUBJECTS_DIR") ;
if (!cp)
ErrorExit(ERROR_BADPARM,"%s: SUBJECTS_DIR not defined in environment.\n",
Progname) ;
strcpy(subjects_dir, cp) ;
}
if (argc < 3) usage_exit(1) ;
out_fname = argv[argc-1] ;
no_transform = first_transform ;
if (binary_name) /* generate binarized volume with priors and */
{ /* separate means and variances */
for (which = BUILD_PRIORS ; which <= OFF_STATS ; which++) {
/* for each subject specified on cmd line */
for (dof = 0, i = 1 ; i < argc-1 ; i++) {
if (*argv[i] == '-') /* don't do transform for next subject */
{ no_transform = 1 ;
continue ;
}
dof++ ;
subject_name = argv[i] ;
if (which != BUILD_PRIORS) {
sprintf(fname, "%s/%s/mri/%s", subjects_dir, subject_name, T1_name);
fprintf(stderr, "%d of %d: reading %s...\n", i, argc-2, fname) ;
mri_T1 = MRIread(fname) ;
if (!mri_T1)
ErrorExit(ERROR_NOFILE,"%s: could not open volume %s",
Progname,fname);
}
sprintf(fname, "%s/%s/mri/%s",subjects_dir,subject_name,binary_name);
fprintf(stderr, "%d of %d: reading %s...\n", i, argc-2, fname) ;
mri_binary = MRIread(fname) ;
if (!mri_binary)
ErrorExit(ERROR_NOFILE,"%s: could not open volume %s",
Progname,fname);
/* only count voxels which are mostly labeled */
MRIbinarize(mri_binary, mri_binary, WM_MIN_VAL, 0, 100) ;
if (transform_fname && no_transform-- <= 0) {
sprintf(fname, "%s/%s/mri/transforms/%s",
subjects_dir, subject_name, transform_fname) ;
fprintf(stderr, "reading transform %s...\n", fname) ;
////////////////////////////////////////////////////////
#if 1
{
TRANSFORM *transform ;
transform = TransformRead(fname) ;
if (transform == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not open transform file %s\n",Progname, fname) ;
mri_tmp = TransformApply(transform, mri_T1, NULL) ;
TransformFree(&transform) ;
}
#else
lta = LTAreadEx(fname);
if (lta == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not open transform file %s\n",
Progname, fname) ;
/* LTAtransform() runs either MRIapplyRASlinearTransform()
for RAS2RAS or MRIlinearTransform() for Vox2Vox. */
/* MRIlinearTransform() calls MRIlinearTransformInterp() */
mri_tmp = LTAtransform(mri_T1, NULL, lta);
MRIfree(&mri_T1) ;
mri_T1 = mri_tmp ;
LTAfree(<a);
lta = NULL;
#endif
if (DIAG_VERBOSE_ON)
fprintf(stderr, "transform application complete.\n") ;
}
if (which == BUILD_PRIORS) {
mri_priors =
MRIupdatePriors(mri_binary, mri_priors) ;
} else {
if (!mri_mean) {
mri_dof = MRIalloc(mri_T1->width, mri_T1->height, mri_T1->depth,
MRI_UCHAR) ;
mri_mean =
MRIalloc(mri_T1->width, mri_T1->height,mri_T1->depth,MRI_FLOAT);
mri_std =
MRIalloc(mri_T1->width,mri_T1->height,mri_T1->depth,MRI_FLOAT);
if (!mri_mean || !mri_std)
ErrorExit(ERROR_NOMEMORY, "%s: could not allocate templates.\n",
Progname) ;
}
if (DIAG_VERBOSE_ON)
fprintf(stderr, "updating mean and variance estimates...\n") ;
if (which == ON_STATS) {
MRIaccumulateMaskedMeansAndVariances(mri_T1, mri_binary, mri_dof,
90, 100, mri_mean, mri_std) ;
fprintf(stderr, "T1 = %d, binary = %d, mean = %2.1f\n",
(int)MRIgetVoxVal(mri_T1, 141,100,127,0),
MRIvox(mri_binary, 141,100,127),
MRIFvox(mri_mean, 141,100,127)) ;
} else /* computing means and vars for off */
MRIaccumulateMaskedMeansAndVariances(mri_T1, mri_binary, mri_dof,
0, WM_MIN_VAL-1,
mri_mean, mri_std) ;
MRIfree(&mri_T1) ;
}
MRIfree(&mri_binary) ;
}
if (which == BUILD_PRIORS) {
mri = MRIcomputePriors(mri_priors, dof, NULL) ;
MRIfree(&mri_priors) ;
fprintf(stderr, "writing priors to %s...\n", out_fname) ;
} else {
MRIcomputeMaskedMeansAndStds(mri_mean, mri_std, mri_dof) ;
mri_mean->dof = dof ;
fprintf(stderr, "writing T1 means with %d dof to %s...\n", mri_mean->dof,
out_fname) ;
if (!which)
MRIwrite(mri_mean, out_fname) ;
else
MRIappend(mri_mean, out_fname) ;
MRIfree(&mri_mean) ;
fprintf(stderr, "writing T1 variances to %s...\n", out_fname);
if (dof <= 1)
MRIreplaceValues(mri_std, mri_std, 0, 1) ;
mri = mri_std ;
}
if (!which)
MRIwrite(mri, out_fname) ;
else
MRIappend(mri, out_fname) ;
MRIfree(&mri) ;
}
}
else {
/* for each subject specified on cmd line */
if (xform_mean_fname) {
m_xform_mean = MatrixAlloc(4,4,MATRIX_REAL) ;
/* m_xform_covariance = MatrixAlloc(12,12,MATRIX_REAL) ;*/
}
dof = 0;
for (i = 1 ; i < argc-1 ; i++) {
if (*argv[i] == '-') {
/* don't do transform for next subject */
no_transform = 1 ;
continue ;
}
dof++ ;
subject_name = argv[i] ;
sprintf(fname, "%s/%s/mri/%s", subjects_dir, subject_name, T1_name);
fprintf(stderr, "%d of %d: reading %s...\n", i, argc-2, fname) ;
mri_T1 = MRIread(fname) ;
if (!mri_T1)
ErrorExit(ERROR_NOFILE,"%s: could not open volume %s",Progname,fname);
check_mri(mri_T1) ;
if (binarize)
MRIbinarize(mri_T1, mri_T1, binarize, 0, 1) ;
if (erode) {
int i ;
printf("eroding input %d times\n", erode) ;
for (i = 0 ; i < erode ; i++)
MRIerode(mri_T1, mri_T1) ;
}
if (open) {
int i ;
printf("opening input %d times\n", open) ;
for (i = 0 ; i < open ; i++)
MRIerode(mri_T1, mri_T1) ;
for (i = 0 ; i < open ; i++)
MRIdilate(mri_T1, mri_T1) ;
}
check_mri(mri_T1) ;
if (transform_fname) {
sprintf(fname, "%s/%s/mri/transforms/%s",
subjects_dir, subject_name, transform_fname) ;
fprintf(stderr, "reading transform %s...\n", fname) ;
////////////////////////////////////////////////////////
#if 1
{
TRANSFORM *transform ;
transform = TransformRead(fname) ;
if (transform == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not open transform file %s\n",Progname, fname) ;
mri_tmp = TransformApply(transform, mri_T1, NULL) ;
if (DIAG_VERBOSE_ON)
MRIwrite(mri_tmp, "t1.mgz") ;
TransformFree(&transform) ;
}
#else
lta = LTAreadEx(fname);
if (lta == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not open transform file %s\n",
Progname, fname) ;
printf("transform matrix -----------------------\n");
MatrixPrint(stdout,lta->xforms[0].m_L);
/* LTAtransform() runs either MRIapplyRASlinearTransform()
for RAS2RAS or MRIlinearTransform() for Vox2Vox. */
/* MRIlinearTransform() calls MRIlinearTransformInterp() */
mri_tmp = LTAtransform(mri_T1, NULL, lta);
printf("----- -----------------------\n");
LTAfree(<a);
#endif
MRIfree(&mri_T1);
mri_T1 = mri_tmp ; // reassign pointers
if (DIAG_VERBOSE_ON)
fprintf(stderr, "transform application complete.\n") ;
}
if (!mri_mean) {
mri_mean =
MRIalloc(mri_T1->width, mri_T1->height, mri_T1->depth, MRI_FLOAT) ;
mri_std =
MRIalloc(mri_T1->width, mri_T1->height, mri_T1->depth, MRI_FLOAT) ;
if (!mri_mean || !mri_std)
ErrorExit(ERROR_NOMEMORY, "%s: could not allocate templates.\n",
Progname) ;
// if(transform_fname == NULL){
if (DIAG_VERBOSE_ON)
printf("Copying geometry\n");
MRIcopyHeader(mri_T1,mri_mean);
MRIcopyHeader(mri_T1,mri_std);
// }
}
check_mri(mri_mean) ;
if (!stats_only) {
if (DIAG_VERBOSE_ON)
fprintf(stderr, "updating mean and variance estimates...\n") ;
MRIaccumulateMeansAndVariances(mri_T1, mri_mean, mri_std) ;
}
check_mri(mri_mean) ;
if (DIAG_VERBOSE_ON)
MRIwrite(mri_mean, "t2.mgz") ;
MRIfree(&mri_T1) ;
no_transform = 0;
} /* end loop over subjects */
if (xform_mean_fname) {
FILE *fp ;
VECTOR *v = NULL, *vT = NULL ;
MATRIX *m_vvT = NULL ;
int rows, cols ;
nsubjects = sno ;
fp = fopen(xform_covariance_fname, "w") ;
if (!fp)
ErrorExit(ERROR_NOFILE, "%s: could not open covariance file %s",
Progname, xform_covariance_fname) ;
fprintf(fp, "nsubjects=%d\n", nsubjects) ;
MatrixScalarMul(m_xform_mean, 1.0/(double)nsubjects, m_xform_mean) ;
printf("means:\n") ;
MatrixPrint(stdout, m_xform_mean) ;
MatrixAsciiWrite(xform_mean_fname, m_xform_mean) ;
/* subtract the mean from each transform */
rows = m_xform_mean->rows ;
cols = m_xform_mean->cols ;
for (sno = 0 ; sno < nsubjects ; sno++) {
MatrixSubtract(m_xforms[sno], m_xform_mean, m_xforms[sno]) ;
v = MatrixReshape(m_xforms[sno], v, rows*cols, 1) ;
vT = MatrixTranspose(v, vT) ;
m_vvT = MatrixMultiply(v, vT, m_vvT) ;
if (!m_xform_covariance)
m_xform_covariance =
MatrixAlloc(m_vvT->rows, m_vvT->cols,MATRIX_REAL) ;
MatrixAdd(m_vvT, m_xform_covariance, m_xform_covariance) ;
MatrixAsciiWriteInto(fp, m_xforms[sno]) ;
}
MatrixScalarMul(m_xform_covariance, 1.0/(double)nsubjects,
m_xform_covariance) ;
printf("covariance:\n") ;
MatrixPrint(stdout, m_xform_covariance) ;
MatrixAsciiWriteInto(fp, m_xform_covariance) ;
fclose(fp) ;
if (stats_only)
exit(0) ;
}
MRIcomputeMeansAndStds(mri_mean, mri_std, dof) ;
check_mri(mri_mean) ;
check_mri(mri_std) ;
mri_mean->dof = dof ;
if (smooth) {
MRI *mri_kernel, *mri_smooth ;
printf("applying smoothing kernel\n") ;
mri_kernel = MRIgaussian1d(smooth, 100) ;
mri_smooth = MRIconvolveGaussian(mri_mean, NULL, mri_kernel) ;
MRIfree(&mri_kernel) ;
MRIfree(&mri_mean) ;
mri_mean = mri_smooth ;
}
fprintf(stderr, "\nwriting T1 means with %d dof to %s...\n", mri_mean->dof,
out_fname) ;
MRIwrite(mri_mean, out_fname) ;
MRIfree(&mri_mean) ;
if (dof <= 1) /* can't calculate variances - set them to reasonable val */
{
// src dst
MRIreplaceValues(mri_std, mri_std, 0, 1) ;
}
if (!novar) {
// mri_std contains the variance here (does it?? I don't think so -- BRF)
if (!var_fname) {
fprintf(stderr, "\nwriting T1 standard deviations to %s...\n", out_fname);
MRIappend(mri_std, out_fname) ;
} else {
fprintf(stderr, "\nwriting T1 standard deviations to %s...\n", var_fname);
MRIwrite(mri_std, var_fname) ;
}
}
MRIfree(&mri_std) ;
if (mri)
MRIfree(&mri);
} /* end if binarize */
return(0) ;
}
