int
main(int argc, char *argv[])
{
char **av, fname[STRLEN], *cp ;
int ac, nargs ;
char *subject, *out_fname, *hemi, *ohemi ;
int msec, minutes, seconds ;
struct timeb start ;
MRI *mri, *mri_features, *mri_ribbon, *mri_aseg, *mri_aparc ;
MRI_SURFACE *mris, *mris_contra ;
LABEL *cortex ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_extract_fcd_features.c,v 1.1 2016/06/15 17:51:09 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 < 4)
usage_exit(1) ;
subject = argv[1] ;
hemi = argv[2] ;
if (strcmp(hemi, "lh") == 0)
ohemi = "rh" ;
else
ohemi = "lh" ;
out_fname = argv[3] ;
printf("reading data for subject %s and writing output to %s\n", subject, out_fname) ;
if (!strlen(sdir))
{
cp = getenv("SUBJECTS_DIR") ;
if (!cp)
ErrorExit(ERROR_BADPARM,
"%s: SUBJECTS_DIR not defined in environment.\n", Progname) ;
strcpy(sdir, cp) ;
}
sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject, hemi, white_name) ;
printf("reading %s\n", fname) ;
mris = MRISread(fname) ;
if (mris == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read surface from %s\n", Progname, fname) ;
MRISsaveVertexPositions(mris, WHITE_VERTICES) ;
sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject, ohemi, white_name) ;
printf("reading %s\n", fname) ;
mris_contra = MRISread(fname) ;
if (mris_contra == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read surface from %s\n", Progname, fname) ;
MRISsaveVertexPositions(mris_contra, WHITE_VERTICES) ;
sprintf(fname, "%s/%s/mri/%s", sdir, subject, ribbon_name) ;
printf("reading %s\n", fname) ;
mri_ribbon = MRIread(fname) ;
if (mri_ribbon == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read ribbon from %s\n", Progname, fname) ;
sprintf(fname, "%s/%s/mri/%s", sdir, subject, aparc_name) ;
printf("reading %s\n", fname) ;
mri_aparc = MRIread(fname) ;
if (mri_aparc == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read ribbon from %s\n", Progname, fname) ;
sprintf(fname, "%s/%s/mri/%s", sdir, subject, aseg_name) ;
printf("reading %s\n", fname) ;
mri_aseg = MRIread(fname) ;
if (mri_aseg == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read aseg from %s\n", Progname, fname) ;
sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject, hemi, pial_name) ;
if (MRISreadPialCoordinates(mris, fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read pial coordinates from %s\n", Progname, fname) ;
sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject, hemi, sphere_name) ;
if (MRISreadCanonicalCoordinates(mris, fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read left/right spherical coordinates from %s\n", Progname, fname) ;
sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject, ohemi, pial_name) ;
if (MRISreadPialCoordinates(mris_contra, fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read pial coordinates from %s\n", Progname, fname) ;
sprintf(fname, "%s/%s/label/%s.%s", sdir, subject, hemi, cortex_label) ;
cortex = LabelRead(NULL, fname) ;
if (cortex == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read cortical label from %s\n", Progname, fname) ;
LabelRipRestOfSurface(cortex, mris) ;
LabelFree(&cortex) ;
sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject, ohemi, sphere_name) ;
if (MRISreadCanonicalCoordinates(mris_contra, fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read left/right spherical coordinates from %s\n", Progname, fname) ;
sprintf(fname, "%s/%s/mri/%s", sdir, subject, vol_name) ;
printf("reading %s\n", fname) ;
mri = MRIread(fname) ;
if (mri == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read volume from %s\n", Progname, fname) ;
if (0)
mri_features = MRIcomputeSurfaceDistanceProbabilities(mris, mri_ribbon, mri, mri_aseg) ;
else
{
MRI *mri_ohemi_features, *mri_ohemi_mapped_to_hemi_features ;
mri_features = MRIcomputeSurfaceDistanceIntensities(mris, mri_ribbon, mri_aparc, mri, mri_aseg, whalf) ;
mri_ohemi_features = MRIcomputeSurfaceDistanceIntensities(mris_contra, mri_ribbon, mri_aparc, mri, mri_aseg, whalf) ;
mri_ohemi_mapped_to_hemi_features = MRISmapToSurface(mris_contra, mris, mri_ohemi_features, NULL) ; // map contra feature to this surface
// MRIwrite(mri_ohemi_mapped_to_hemi_features, "test.mgz") ;
MRIsubtract(mri_features, mri_ohemi_mapped_to_hemi_features, mri_features) ;
}
if (navgs > 0)
{
MRI *mri_tmp ;
mri_tmp = MRISsmoothMRI(mris, mri_features, navgs, NULL, NULL);
MRIfree(&mri_features) ;
mri_features = mri_tmp ;
}
printf("writing output to %s\n", out_fname) ;
if (Gdiag_no >= 0)
printf("feature(%d) = %f\n", Gdiag_no, MRIgetVoxVal(mri_features, Gdiag_no, 0, 0, 0)) ;
MRIwrite(mri_features, out_fname) ;
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
fprintf(stderr, "feature extraction took %d minutes and %d seconds.\n", minutes, seconds) ;
exit(0) ;
return(0) ;
}
int
main(int argc, char *argv[]) {
int ac, nargs ;
char **av, *cp, surf_name[100], *hemi, *subject_name, *label_name,
*out_fname ;
MRI_SURFACE *mris ;
LABEL *label ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: label2patch.c,v 1.3 2011/03/02 00:04:11 nicks Exp $", "$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
/* read in command-line options */
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 4)
print_usage() ;
subject_name = argv[1] ;
hemi = argv[2] ;
label_name = argv[3] ;
out_fname = argv[4] ;
if (strlen(subjects_dir) == 0)
{
cp = getenv("SUBJECTS_DIR") ;
if (!cp)
ErrorExit(ERROR_BADPARM, "no subjects directory in environment.\n") ;
strcpy(subjects_dir, cp) ;
}
sprintf(surf_name,"%s/%s/surf/%s.inflated",subjects_dir,subject_name,hemi);
fprintf(stderr, "reading %s...\n", surf_name) ;
mris = MRISread(surf_name) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s\n",
surf_name) ;
MRIScomputeMetricProperties(mris) ;
label = LabelRead(subject_name, label_name) ;
if (ndilate)
LabelDilate(label, mris, ndilate) ;
if (nerode)
LabelErode(label, mris, nerode) ;
if (nclose)
{
LabelDilate(label, mris, nclose) ;
LabelErode(label, mris, nclose) ;
}
LabelRipRestOfSurface(label, mris) ;
MRISripFaces(mris) ;
MRISwritePatch(mris, out_fname) ;
if (verbose)
fprintf(stderr, "done.\n") ;
exit(0) ;
return(0) ; /* ansi */
}
int
main(int argc, char *argv[]) {
char **av, *cp, fname[STRLEN], *subject, *out_fname ;
int ac, nargs, msec, minutes, n, seconds, nsubjects, i, sno, nfeatures, correct ;
struct timeb start ;
LABEL *cortex_label, *training_label ;
RANDOM_FOREST *rf ;
double **training_data ;
int *training_classes, ntraining ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mris_rf_train.c,v 1.1 2012/06/07 12:09:47 fischl Exp $", "$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ; setRandomSeed(0L);
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) ;
if (strlen(sdir) == 0) {
cp = getenv("SUBJECTS_DIR") ;
if (!cp)
ErrorExit(ERROR_BADPARM, "%s: SUBJECTS_DIR not defined in env or cmd line",Progname) ;
strcpy(sdir, cp) ;
}
nsubjects = argc-(ARGC_OFFSET+1) ;
printf("training random forest classifier using %d subjects\n", nsubjects) ;
for (n = ARGC_OFFSET ; n < argc-1 ; n++)
{
subject = argv[n] ;
sno = n-ARGC_OFFSET ;
printf("processing subject %s: %d of %d\n", subject, sno+1, nsubjects) ;
sprintf(fname, "%s/%s/label/lh.%s.label", sdir, subject, label_name) ;
if (FileExists(fname) == 0)
{
sprintf(fname, "%s/%s/label/rh.%s.label", sdir, subject, label_name) ;
if (FileExists(fname) == 0)
ErrorExit(ERROR_NOFILE, "%s: subject %s has no training label for either hemisphere", Progname, subject) ;
hemi = "rh" ;
}
else
hemi = "lh" ;
training_label = LabelRead(NULL, fname) ;
if (training_label == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read training label %s\n", Progname, fname) ;
sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject, hemi, surf_name) ;
mris[sno] = MRISread(fname) ;
if (!mris[sno])
ErrorExit(ERROR_NOFILE, "%s: could not read surface from %s",Progname, fname) ;
MRIScomputeMetricProperties(mris[sno]) ;
if (nbhd_size > mris[sno]->nsize)
MRISsetNeighborhoodSize(mris[sno], nbhd_size) ;
sprintf(fname, "%s/%s/label/%s.%s", sdir, subject, hemi, cortex_label_name) ;
cortex_label = LabelRead(NULL, fname) ;
if (cortex_label == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read cortex label %s\n", Progname, fname) ;
LabelRipRestOfSurface(cortex_label, mris[sno]) ;
MRISclearMarks(mris[sno]) ;
LabelFillUnassignedVertices(mris[sno], training_label, CURRENT_VERTICES);
LabelDilate(training_label, mris[sno], ndilates) ;
LabelMark(training_label, mris[sno]) ;
LabelFree(&training_label) ;
for (i = 0 ; i < noverlays ; i++)
{
sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject, hemi, overlay_names[i]) ;
mri_overlays[sno][i] = MRIread(fname) ;
if (mri_overlays[sno][i] == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read overlay %s (%d)\n", Progname, fname, i) ;
}
LabelFree(&cortex_label) ;
}
nfeatures = noverlays*(nbhd_size+1) ;
rf = RFalloc(ntrees, nfeatures, 2, max_depth, class_names, 100) ;
rf->feature_names = (char **)calloc(nfeatures, sizeof(char *)) ;
for (i = 0 ; i < noverlays ; i++)
{
rf->feature_names[i] = (char *)calloc(strlen(overlay_names[i])+1, sizeof(char)) ;
strcpy(rf->feature_names[i], overlay_names[i]) ;
}
assemble_training_data_and_free_mris(mris, mri_overlays, nsubjects, noverlays, &training_classes, &training_data, &ntraining) ;
RFtrain(rf, 1.0, training_fraction, training_classes, training_data, ntraining);
correct = RFcomputeOutOfBagCorrect(rf, training_classes, training_data, ntraining);
printf("out of bag accuracy = %2.1f (%d of %d)\n", (float)correct*100.0f/ntraining, correct, ntraining) ;
RFevaluateFeatures(rf, stdout) ;
out_fname = argv[argc-1] ;
printf("writing output to %s\n", out_fname) ;
RFwrite(rf, out_fname) ;
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
printf("random forest training took %d minutes and %d seconds.\n", minutes, seconds) ;
exit(0) ;
return(0) ;
}
MRI *
MRIflattenOverlay(MRI_SURFACE *mris, MRI *mri_overlay, MRI *mri_flat, double res, LABEL *label_overlay,
MRI **pmri_vertices)
{
double xmin, ymin, xmax, ymax, fdist, lambda[3], xf, yf, val0, val1, val2, val ;
int width, height, x, y, fno, ret, z ;
MHT *mht ;
FACE *face;
MRI *mri_vertices ;
find_biggest_inscribed_rectangle(mris, &xmin, &ymin, &xmax, &ymax) ;
width = (int)ceil((xmax-xmin)/res) ; width = (int)(floor(width/2.0)*2.0+1) ; xmax=xmin+width;
height = (int)ceil((ymax-ymin)/res) ;height = (int)(floor(height/2.0)*2.0+1) ; ymax=ymin+height;
// 1st frame is correlations and 2nd is vertex #
mri_vertices = MRIalloc(width, height, 1, MRI_FLOAT) ;
MRIsetValues(mri_vertices, -1) ;
mri_flat = MRIalloc(width, height, mri_overlay->nframes, MRI_FLOAT) ;
mri_vertices->xstart = mri_flat->xstart = xmin ; mri_vertices->xend = mri_flat->xend = xmax ;
mri_vertices->ystart = mri_flat->ystart = ymin ; mri_vertices->yend = mri_flat->yend = ymax ;
mri_vertices->zstart = mri_flat->zstart = 0 ;
mri_vertices->zend = mri_flat->zend = mri_overlay->nframes-1 ;
mri_vertices->c_r = mri_flat->c_r = xmin ; mri_vertices->c_a = mri_flat->c_a = ymin ;
mri_vertices->c_s = mri_flat->c_s = 0 ;
MRIsetResolution(mri_flat, res, res, 1) ;
MRIsetResolution(mri_vertices, res, res, 1) ;
if (label_overlay) // constrain processing to only this label
LabelRipRestOfSurface(label_overlay, mris) ;
mht = MHTfillTableAtResolution(mris, NULL, CURRENT_VERTICES, 1.0) ;
for (x = 0 ; x < width; x++)
for (y = 0 ; y < height ; y++)
{
xf = x*res + xmin ; yf = y*res + ymin ; // back to flattened coords
MHTfindClosestFaceGeneric(mht, mris, xf, yf, 0.0, 10*res, 2, 1, &face, &fno, &fdist) ;
if (fno >= 0) // otherwise this point is not in a face
{
ret = face_barycentric_coords(mris, fno, CURRENT_VERTICES, xf, yf, 0, &lambda[0], &lambda[1],&lambda[2]);
if (ret >= 0)
{
if (lambda[0] > lambda[1])
{
if (lambda[0] > lambda[2])
{
if (face->v[0] == Gdiag_no)
DiagBreak() ;
MRIsetVoxVal(mri_vertices, x, y, 0, 0, face->v[0]) ;
}
else
{
if (face->v[2] == Gdiag_no)
DiagBreak() ;
MRIsetVoxVal(mri_vertices, x, y, 0, 0, face->v[2]) ;
}
}
else
{
if (lambda[1] > lambda[2])
{
if (face->v[1] == Gdiag_no)
DiagBreak() ;
MRIsetVoxVal(mri_vertices, x, y, 0, 0, face->v[1]) ;
}
else
{
if (face->v[2] == Gdiag_no)
DiagBreak() ;
MRIsetVoxVal(mri_vertices, x, y, 0, 0, face->v[2]) ;
}
}
for (z = 0 ;z < mri_flat->depth ; z++)
{
val0 = MRIgetVoxVal(mri_overlay, face->v[0], 0, 0, z) ;
val1 = MRIgetVoxVal(mri_overlay, face->v[1], 0, 0, z) ;
val2 = MRIgetVoxVal(mri_overlay, face->v[2], 0, 0, z) ;
val = lambda[0]*val0 + lambda[1]*val1 + lambda[2]*val2 ;
MRIsetVoxVal(mri_flat, x, y, z, 0, val) ;
}
}
else if (fabs(xf) < 10 && fabs(yf) < 10)
{
MHTfindClosestFaceGeneric(mht, mris, xf, yf, 0.0, 1000, -1, 1, &face, &fno, &fdist) ;
printf("(%d, %d) --> %f %f unmapped (goes to face %d, v (%d, %d, %d) if projected\n",
x, y, xf, yf, fno, face->v[0], face->v[1], face->v[2]) ;
DiagBreak() ;
}
}
}
if (pmri_vertices)
*pmri_vertices = mri_vertices ;
MHTfree(&mht) ;
return(mri_flat) ;
}
