int main(int argc, char *argv[]) { char **av, *surf_fname, *profile_fname, *seg_fname ; int ac, nargs ; MRI_SURFACE *mris, *mris_ico = NULL ; // LABEL *label = NULL ; MRI *mri_profiles ; CLUSTER *ct ; setRandomSeed(10L) ; /* rkt: check for and handle version tag */ nargs = handle_version_option (argc, argv, "$Id: mris_cluster_profiles.c,v 1.4 2011/03/02 00:04:34 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() ; profile_fname = argv[1] ; surf_fname = argv[2] ; seg_fname = argv[3] ; mris = MRISread(surf_fname) ; if (!mris) ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s", Progname, surf_fname) ; MRISsetNeighborhoodSize(mris, 2) ; if (MRISreadAnnotation(mris, "ad_aparc") != NO_ERROR) { if (MRISreadAnnotation(mris, "aparc") != NO_ERROR) ErrorExit(ERROR_NOFILE, "%s: could not read annotation file ad_aparc", Progname) ; } printf("reading intensity profile volume from %s...\n", profile_fname) ; mri_profiles = MRIread(profile_fname) ; if (!mri_profiles) ErrorExit(ERROR_NOFILE, "%s: could not read intensity volume %s", Progname, profile_fname) ; rip_vertices_out_of_fov(mris, mri_profiles) ; rip_bad_vertices(mris, mri_profiles) ; MRISclearAnnotations(mris) ; #if 0 if (nlabels > 0) { int l ; char label_name[STRLEN] ; LABEL *ltotal = NULL ; for (l = 0 ; l < nlabels ; l++) { sprintf(label_name, "%s/%s/label/%s.%s.label", sdir, sname, hemi,label_names[l]) ; label = LabelRead(NULL, label_name) ; if (!label) ErrorExit(ERROR_NOFILE, "%s: could not read label file %s...\n", Progname, label_name) ; if (num_erode > 0) { printf("eroding label %d times, npoints went from %d ", num_erode,label->n_points) ; LabelErode(label, mris, num_erode) ; printf("to %d ", label->n_points) ; } ltotal = LabelCombine(label, ltotal) ; } if (nlabels == 0) ltotal = LabelInFOV(mris, mri, MIN_BORDER_DIST) ; LabelRipRestOfSurfaceWithThreshold(ltotal, mris, thresh) ; } #endif if (navgs > 0) { printf("smoothing profiles %d times\n", navgs) ; MRISsmoothFrames(mris, mri_profiles, navgs) ; } if (ico_fname) { mris_ico = MRISread(ico_fname) ; if (mris_ico == NULL) ErrorExit(ERROR_BADPARM, "%s: could not read icosahedron from %s...\n", Progname, ico_fname) ; } ct = MRIScluster(mris, mri_profiles, cluster_type, k, start_fname, mris_ico) ; printf("writing cortical intensity clusters to %s...\n", seg_fname) ; MRISwriteAnnotation(mris, seg_fname) ; { int vno ; VERTEX *v ; int c, i ; char fname[STRLEN], ext[STRLEN] ; // write average profiles into mri_profiles and write it out for (vno = 0 ; vno < mris->nvertices ; vno++) { v = &mris->vertices[vno] ; if (v->ripflag) continue ; c = v->curv ; if (c < 0) continue ; for (i = 0 ; i < mri_profiles->nframes ; i++) MRIsetVoxVal(mri_profiles, vno, 0, 0, i, VECTOR_ELT(ct[c].v_mean,i+1)) ; } FileNameExtension(seg_fname, ext) ; FileNameRemoveExtension(seg_fname, fname) ; strcat(fname, "_cluster_avg.mgz") ; printf("writing average cluster profiles to %s...\n", fname) ; MRIwrite(mri_profiles, fname) ; } MRIfree(&mri_profiles) ; exit(0) ; return(0) ; /* for ansi */ }
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[]) { 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 */ }