int
main(int argc, char *argv[])
{
char **av, *in_fname,fname[STRLEN],hemi[10], path[STRLEN],
name[STRLEN],*cp ;
int ac, nargs, nhandles ;
MRI_SURFACE *mris ;
double ici, fi, var ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 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 (argc < 2)
{
usage_exit() ;
}
in_fname = argv[1] ;
FileNamePath(in_fname, path) ;
FileNameOnly(in_fname, name) ;
cp = strchr(name, '.') ;
if (!cp)
ErrorExit(ERROR_BADPARM, "%s: could not scan hemisphere from '%s'",
Progname, fname) ;
strncpy(hemi, cp-2, 2) ;
hemi[2] = 0 ;
if (patch_flag) /* read the orig surface, then the patch file */
{
sprintf(fname, "%s/%s.orig", path, hemi) ;
mris = MRISfastRead(fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, in_fname) ;
if (Gdiag & DIAG_SHOW)
{
fprintf(stderr, "reading patch file %s...\n", in_fname) ;
}
if (MRISreadPatch(mris, in_fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read patch file %s",
Progname, in_fname) ;
}
else /* just read the surface normally */
{
mris = MRISread(in_fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, in_fname) ;
}
MRISsetNeighborhoodSize(mris, nbrs) ;
if (nbhd_size > 0)
{
MRISsampleAtEachDistance(mris, nbhd_size, nbrs_per_distance) ;
}
if (max_mm > 0)
{
float ratio ;
MRISstoreMetricProperties(mris) ;
if (MRISreadCanonicalCoordinates(mris, "sphere") != NO_ERROR)
{
ErrorExit(ERROR_NOFILE,
"%s: could not read canonical coordinates from ?h.sphere",
Progname);
}
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
MRISrestoreVertexPositions(mris, CANONICAL_VERTICES) ;
MRIScomputeMetricProperties(mris) ;
ratio = mris->orig_area / M_PI * mris->radius * mris->radius * 4.0 ;
ratio = mris->orig_area / mris->total_area ;
MRISscaleBrain(mris, mris, sqrt(ratio)) ;
MRISsaveVertexPositions(mris, CANONICAL_VERTICES) ;
MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
MRIScomputeMetricProperties(mris) ;
MRIScomputeNeighbors(mris, max_mm) ;
}
if (param_file)
{
MRI_SP *mrisp ;
mrisp = MRISPread(param_file) ;
if (normalize_param)
{
MRISnormalizeFromParameterization(mrisp, mris, param_no) ;
}
else
{
MRISfromParameterization(mrisp, mris, param_no) ;
}
MRISPfree(&mrisp) ;
if (normalize)
{
MRISnormalizeCurvature(mris,which_norm) ;
}
sprintf(fname, "%s/%s%s.param", path,name,suffix) ;
fprintf(stderr, "writing parameterized curvature to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "done.\n") ;
}
else
{
MRIScomputeSecondFundamentalFormThresholded(mris, cthresh) ;
nhandles = nint(1.0 - mris->Ktotal / (4.0*M_PI)) ;
fprintf(stderr, "total integrated curvature = %2.3f*4pi (%2.3f) --> "
"%d handles\n", (float)(mris->Ktotal/(4.0f*M_PI)),
(float)mris->Ktotal, nhandles) ;
#if 0
fprintf(stderr, "0: k1 = %2.3f, k2 = %2.3f, H = %2.3f, K = %2.3f\n",
mris->vertices[0].k1, mris->vertices[0].k2,
mris->vertices[0].H, mris->vertices[0].K) ;
fprintf(stderr, "0: vnum = %d, v2num = %d, total=%d, area=%2.3f\n",
mris->vertices[0].vnum, mris->vertices[0].v2num,
mris->vertices[0].vtotal,mris->vertices[0].area) ;
#endif
MRIScomputeCurvatureIndices(mris, &ici, &fi);
var = MRIStotalVariation(mris) ;
fprintf(stderr,"ICI = %2.1f, FI = %2.1f, variation=%2.3f\n", ici, fi, var);
if (diff_flag)
{
MRISuseCurvatureDifference(mris) ;
MRISaverageCurvatures(mris, navgs) ;
sprintf(fname, "%s/%s%s.diff", path,name,suffix) ;
fprintf(stderr, "writing curvature difference to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "done.\n") ;
}
if (ratio_flag)
{
MRISuseCurvatureRatio(mris) ;
MRISaverageCurvatures(mris, navgs) ;
if (normalize)
{
MRISnormalizeCurvature(mris,which_norm) ;
}
sprintf(fname, "%s/%s%s.ratio", path,name,suffix) ;
fprintf(stderr, "writing curvature ratio to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "done.\n") ;
}
if (contrast_flag)
{
MRISuseCurvatureContrast(mris) ;
MRISaverageCurvatures(mris, navgs) ;
if (normalize)
{
MRISnormalizeCurvature(mris,which_norm) ;
}
sprintf(fname, "%s/%s%s.contrast", path,name,suffix) ;
fprintf(stderr, "writing curvature contrast to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "done.\n") ;
}
if (neg_flag)
{
int neg ;
if (mris->patch)
{
mris->status = MRIS_PLANE ;
}
MRIScomputeMetricProperties(mris) ;
neg = MRIScountNegativeTriangles(mris) ;
MRISuseNegCurvature(mris) ;
MRISaverageCurvatures(mris, navgs) ;
sprintf(fname, "%s/%s%s.neg", path,name,suffix) ;
fprintf(stderr, "writing negative vertex curvature to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "%d negative triangles\n", neg) ;
fprintf(stderr, "done.\n") ;
{
int vno, fno ;
VERTEX *v ;
FACE *f ;
for (vno = 0 ; vno < mris->nvertices ; vno++)
{
v = &mris->vertices[vno] ;
if (v->ripflag)
{
continue ;
}
neg = 0 ;
for (fno = 0 ; fno < v->num ; fno++)
{
f = &mris->faces[v->f[fno]] ;
if (f->area < 0.0f)
{
neg = 1 ;
}
}
if (neg)
{
fprintf(stdout, "%d\n", vno) ;
}
}
}
}
if (max_flag)
{
MRISuseCurvatureMax(mris) ;
MRISaverageCurvatures(mris, navgs) ;
if (normalize)
{
MRISnormalizeCurvature(mris,which_norm) ;
}
sprintf(fname, "%s/%s%s.max", path,name,suffix) ;
fprintf(stderr, "writing curvature maxima to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "done.\n") ;
}
if (min_flag)
{
MRISuseCurvatureMin(mris) ;
MRISaverageCurvatures(mris, navgs) ;
if (normalize)
{
MRISnormalizeCurvature(mris,which_norm) ;
}
sprintf(fname, "%s/%s%s.min", path,name,suffix) ;
fprintf(stderr, "writing curvature minima to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "done.\n") ;
}
if (stretch_flag)
{
MRISreadOriginalProperties(mris, NULL) ;
MRISuseCurvatureStretch(mris) ;
MRISaverageCurvatures(mris, navgs) ;
if (normalize)
{
MRISnormalizeCurvature(mris,which_norm) ;
}
sprintf(fname, "%s/%s%s.stretch", path,name,suffix) ;
fprintf(stderr, "writing curvature stretch to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "done.\n") ;
}
if (write_flag)
{
MRISuseGaussianCurvature(mris) ;
if (cthresh > 0)
{
MRIShistoThresholdCurvature(mris, cthresh) ;
}
MRISaverageCurvatures(mris, navgs) ;
sprintf(fname, "%s/%s%s.K", path,name, suffix) ;
fprintf(stderr, "writing Gaussian curvature to %s...", fname) ;
if (normalize)
{
MRISnormalizeCurvature(mris,which_norm) ;
}
MRISwriteCurvature(mris, fname) ;
MRISuseMeanCurvature(mris) ;
if (cthresh > 0)
{
MRIShistoThresholdCurvature(mris, cthresh) ;
}
MRISaverageCurvatures(mris, navgs) ;
if (normalize)
{
MRISnormalizeCurvature(mris,which_norm) ;
}
sprintf(fname, "%s/%s%s.H", path,name, suffix) ;
fprintf(stderr, "done.\nwriting mean curvature to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "done.\n") ;
}
}
exit(0) ;
return(0) ; /* for ansi */
}
int
main(int argc, char *argv[]) {
char **av, *avg_surf_name, *canon_surf_name, fname[STRLEN],
*mdir, ico_fname[STRLEN], *hemi, *out_sname ;
int ac, nargs, i, vno, n ;
VERTEX *v ;
MRI_SURFACE *mris_ico ;
MRI_SP *mrisp_total ;
LTA *lta ;
VOL_GEOM vg;
float average_surface_area = 0.0 ;
MATRIX *XFM=NULL;
GCA_MORPH *gcam=NULL;
memset((void *) &vg, 0, sizeof (VOL_GEOM));
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mris_make_average_surface.c,v 1.29 2011/03/02 00:04:33 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
mdir = getenv("FREESURFER_HOME") ;
if (!mdir)
ErrorExit(ERROR_BADPARM,
"%s: no FREESURFER_HOME in environment.\n",Progname);
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (sdir == NULL) {
sdir = getenv("SUBJECTS_DIR");
if (!sdir)
ErrorExit(ERROR_BADPARM,
"%s: no SUBJECTS_DIR in environment.\n",Progname);
}
if (sdirout == NULL) sdirout = sdir;
if (argc < 6) usage_exit() ;
hemi = argv[1] ;
avg_surf_name = argv[2] ;
canon_surf_name = argv[3] ;
out_sname = argv[4] ;
printf("---------------------------------------------------\n");
printf("hemi = %s\n",hemi);
printf("avg_surf_name = %s\n",avg_surf_name);
printf("canon_surf_name = %s\n",canon_surf_name);
printf("out_sname = %s\n",out_sname);
printf("xform = %s\n",xform_name);
printf("---------------------------------------------------\n");
printf("\n\n");
fflush(stdout);
#define SCALE 1
mrisp_total = MRISPalloc(SCALE, 3) ;
for (n = 0, i = 5 ; i < argc ; i++) {
MRI *mri;
MRI_SURFACE *mris;
MRI_SP *mrisp;
printf("\n---------------------------------------------------\n");
printf("#@# processing subject %d/%d %s...\n", i-4,argc-5,argv[i]) ;
fflush(stdout);
// read sphere.reg
sprintf(fname, "%s/%s/surf/%s.%s", sdir, argv[i], hemi, canon_surf_name) ;
printf(" Reading %s\n",fname);
fflush(stdout);
mris = MRISread(fname) ;
if (!mris) {
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, fname) ;
exit(1);
}
// get "pial" surface vertex into ->origx, origy, origz
if (MRISreadOriginalProperties(mris, orig_name) != NO_ERROR)
ErrorExit(ERROR_BADFILE,"%s: could not read orig file for %s.\n",
Progname, argv[1]);
// read transform
if (0) {
sprintf(fname, "%s/%s/mri/transforms/%s", sdir, argv[i], xform_name) ;
lta = LTAreadEx(fname) ;
if (!lta)
ErrorExit(ERROR_BADPARM,
"%s: could not read transform from %s", Progname, fname) ;
}
// read T1 volume
sprintf(fname, "%s/%s/mri/T1.mgz", sdir, argv[i]) ;
if (fio_FileExistsReadable(fname)) mri = MRIreadHeader(fname,MRI_MGH_FILE);
else {
sprintf(fname, "%s/%s/mri/T1", sdir, argv[i]) ;
mri = MRIreadHeader(fname, MRI_UCHAR); // MRI_CORONAL_SLICE_DIRECTORY) ;
}
printf(" Read %s\n",fname);
fflush(stdout);
if (!mri)
ErrorExit(ERROR_BADPARM,
"%s: could not read reference MRI volume from %s",
Progname, fname) ;
// save current vertex position into ->cx
MRISsaveVertexPositions(mris, CANONICAL_VERTICES) ;
// get the vertex position from ->origx, ...
// (get the "pial" vertex position)
MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
MRIScomputeMetricProperties(mris) ;
printf(" Surface area: %2.1f cm^2\n", mris->total_area/100) ;
fflush(stdout);
average_surface_area += mris->total_area ;
// this means that we transform "pial" surface
if (xform_name)
{
if (!strcmp(xform_name,"talairach.xfm")) {
printf(" Applying linear transform\n");
fflush(stdout);
XFM = DevolveXFMWithSubjectsDir(argv[i], NULL, "talairach.xfm", sdir);
if (XFM == NULL) exit(1);
MRISmatrixMultiply(mris, XFM);
MatrixFree(&XFM);
} else if (!strcmp(xform_name,"talairach.m3z")) {
printf(" Applying GCA Morph\n");
fflush(stdout);
sprintf(fname, "%s/%s/mri/transforms/talairach.m3z", sdir, argv[i]) ;
gcam = GCAMreadAndInvert(fname);
if (gcam == NULL) exit(1);
GCAMmorphSurf(mris, gcam);
GCAMfree(&gcam);
} else {
printf("ERROR: don't know what to do with %s\n",xform_name);
exit(1);
}
}
// save transformed position in ->orig
// (store "pial" vertices position in orig)
MRIScomputeMetricProperties(mris) ;
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
// get the vertex position from ->cx
// (note that this is not transformed) sphere.reg vertices
MRISrestoreVertexPositions(mris, CANONICAL_VERTICES) ;
// mris contains sphere.reg in vertex and pial vertices in orig
// map to a theta-phi space and accumulate values
mrisp = MRIScoordsToParameterization(mris, NULL, SCALE, ORIGINAL_VERTICES) ;
MRISPaccumulate(mrisp, mrisp_total, 0) ;
MRISPaccumulate(mrisp, mrisp_total, 1) ;
MRISPaccumulate(mrisp, mrisp_total, 2) ;
MRISPfree(&mrisp) ;
MRISfree(&mris) ;
MRIfree(&mri) ;
//LTAfree(<a) ;
fflush(stdout);
n++ ;
}
printf("Finished loading all data\n");
average_surface_area /= (float)n ;
printf("Avg surf area = %g cm\n",average_surface_area/100.0);
fflush(stdout);
// mrisp_total lost info on the modified surface
sprintf(ico_fname, "%s/lib/bem/ic%d.tri", mdir, ico_no) ;
printf("Reading icosahedron from %s...\n", ico_fname) ;
mris_ico = ICOread(ico_fname) ;
if (!mris_ico)
ErrorExit(ERROR_NOFILE, "%s: could not read icosahedron file %s\n",
Progname,ico_fname) ;
MRISscaleBrain(mris_ico, mris_ico,
DEFAULT_RADIUS/MRISaverageRadius(mris_ico)) ;
// save current ico position to ->cx, cy, cz
MRISsaveVertexPositions(mris_ico, CANONICAL_VERTICES) ;
// using mrisp_total to calculate position into ->origx, origy, origz
// (orig is the "pial" vertices)
MRIScoordsFromParameterization(mrisp_total, mris_ico, ORIGINAL_VERTICES) ;
// copy geometry info
memcpy((void *) &mris_ico->vg, (void *) &vg, sizeof (VOL_GEOM));
if (Gdiag_no >= 0 && Gdiag_no < mris_ico->nvertices) {
int n ;
VERTEX *vn ;
v = &mris_ico->vertices[Gdiag_no] ;
printf( "v %d: x = (%2.2f, %2.2f, %2.2f)\n",
Gdiag_no, v->origx, v->origy, v->origz) ;
for (n = 0 ; n < v->vnum ; n++) {
vn = &mris_ico->vertices[v->v[n]] ;
printf( "v %d: x = (%2.2f, %2.2f, %2.2f)\n",
v->v[n], vn->origx, vn->origy, vn->origz) ;
}
}
// write *h.sphere.reg
sprintf(fname, "%s/%s/surf/%s.%s",
sdirout, out_sname, hemi, canon_surf_name) ;
if (Gdiag & DIAG_SHOW)
printf("writing average canonical surface to %s\n", fname);
MRISwrite(mris_ico, fname) ;
// get "pial vertices" from orig
MRISrestoreVertexPositions(mris_ico, ORIG_VERTICES);
for (vno = 0 ; vno < mris_ico->nvertices ; vno++) {
v = &mris_ico->vertices[vno] ;
// n = number of subjects
v->x /= (float)n ;
v->y /= (float)n ;
v->z /= (float)n ;
}
if (normalize_area) {
MRIScomputeMetricProperties(mris_ico) ;
printf("setting group surface area to be %2.1f cm^2 (scale=%2.2f)\n",
average_surface_area/100.0,
sqrt(average_surface_area/mris_ico->total_area)) ;
#if 0
MRISscaleBrain(mris_ico, mris_ico,
sqrt(average_surface_area/mris_ico->total_area)) ;
#else
mris_ico->group_avg_surface_area = average_surface_area ;
#endif
MRIScomputeMetricProperties(mris_ico) ;
}
sprintf(fname, "%s/%s/surf/%s.%s", sdirout,out_sname, hemi, avg_surf_name) ;
printf("writing average %s surface to %s\n", avg_surf_name, fname);
MRISwrite(mris_ico, fname) ;
if (0) {
char path[STRLEN] ;
LTA *lta ;
FileNamePath(fname, path) ;
lta = LTAalloc(1, NULL) ;
// write to a different location
sprintf(fname, "%s/../mri/transforms/%s", path,xform_name) ;
LTAwriteEx(lta, fname) ;
LTAfree(<a) ;
}
MRISfree(&mris_ico) ;
MRISPfree(&mrisp_total) ;
printf("mris_make_average_surface done\n");
exit(0) ;
return(0) ; /* for ansi */
}
int
main(int argc, char *argv[])
{
char **av, *in_surf_fname, *out_fname, fname[STRLEN], *cp ;
int ac, nargs, msec, err ;
MRI_SURFACE *mris ;
struct timeb then ;
float max_dim ;
char cmdline[CMD_LINE_LEN] ;
make_cmd_version_string
(argc, argv,
"$Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $",
"$Name: stable5 $", cmdline);
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
{
exit (0);
}
argc -= nargs;
#ifdef FS_CUDA
/* print GPU device info */
MRISCdeviceInfo();
#endif // FS_CUDA
TimerStart(&then) ;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
memset(&parms, 0, sizeof(parms)) ;
parms.dt = .05 ;
parms.projection = PROJECT_ELLIPSOID ;
parms.tol = .5 /*1e-1*/ ;
parms.n_averages = 1024 ;
parms.min_averages = 0 ;
parms.l_angle = 0.0 /* L_ANGLE */ ;
parms.l_area = 0.0 /* L_AREA */ ;
parms.l_neg = 0.0 ;
parms.l_dist = 1.0 ;
parms.l_spring = 0.0 ;
parms.l_area = 1.0 ;
parms.l_boundary = 0.0 ;
parms.l_curv = 0.0 ;
parms.niterations = 25 ;
parms.write_iterations = 1000 ;
parms.a = parms.b = parms.c = 0.0f ; /* ellipsoid parameters */
parms.dt_increase = 1.01 /* DT_INCREASE */;
parms.dt_decrease = 0.99 /* DT_DECREASE*/ ;
parms.error_ratio = 1.03 /*ERROR_RATIO */;
parms.integration_type = INTEGRATE_LINE_MINIMIZE ;
parms.momentum = 0.9 ;
parms.desired_rms_height = -1.0 ;
parms.base_name[0] = 0 ;
parms.Hdesired = 0.0 ; /* a flat surface */
parms.nbhd_size = 7 ;
parms.max_nbrs = 8 ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
{
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
parms.scale = scale ;
if (argc != 3) // catches args beyond the expected two
{
usage_exit() ;
}
parms.base_dt = base_dt_scale * parms.dt ;
in_surf_fname = argv[1] ;
out_fname = argv[2] ;
printf("%s\n",vcid);
printf(" %s\n",MRISurfSrcVersion());
fflush(stdout);
if (parms.base_name[0] == 0)
{
FileNameOnly(out_fname, fname) ;
cp = strchr(fname, '.') ;
if (cp)
{
strcpy(parms.base_name, cp+1) ;
}
else
{
strcpy(parms.base_name, "sphere") ;
}
}
mris = MRISread(in_surf_fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, in_surf_fname) ;
MRISaddCommandLine(mris, cmdline) ;
fprintf(stderr, "reading original vertex positions...\n") ;
if (!FZERO(disturb))
{
mrisDisturbVertices(mris, disturb) ;
}
if (quick == 0)
{
// don't need original properties unless preserving metric
err = MRISreadOriginalProperties(mris, orig_name) ;
if(err)
{
exit(1);
}
}
if (smooth_avgs > 0)
{
MRISsaveVertexPositions(mris, TMP_VERTICES) ;
MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
MRISaverageVertexPositions(mris, smooth_avgs) ;
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
MRISrestoreVertexPositions(mris, TMP_VERTICES) ;
}
if (!FZERO(ralpha) || !FZERO(rbeta) || !FZERO(rgamma))
{
MRISrotate(mris,mris,RADIANS(ralpha),RADIANS(rbeta),RADIANS(rgamma)) ;
// if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
MRISwrite(mris, "rot") ;
}
fprintf(stderr, "unfolding cortex into spherical form...\n");
if (talairach)
{
MRIStalairachTransform(mris, mris) ;
MRISwrite(mris, "tal") ;
}
if (xform_fname)
{
LTA *lta ;
MRI *mri ;
TRANSFORM transform ;
lta = LTAread(xform_fname) ;
if (lta == NULL)
{
ErrorExit(ERROR_NOFILE, "%s: could not load %s", xform_fname) ;
}
mri = MRIread(vol_fname) ;
if (mri == NULL)
{
ErrorExit(ERROR_NOFILE, "%s: could not load %s", vol_fname) ;
}
transform.type = lta->type ;
transform.xform = (void *)lta ;
MRIStransform(mris, mri, &transform, mri) ;
MRIfree(&mri) ;
LTAfree(<a) ;
MRISwrite(mris, "xfm") ;
}
#if 0
max_dim = MAX(abs(mris->xlo), abs(mris->xhi)) ;
max_dim = MAX(abs(max_dim), abs(mris->ylo)) ;
max_dim = MAX(abs(max_dim), abs(mris->yhi)) ;
max_dim = MAX(abs(max_dim), abs(mris->zlo)) ;
max_dim = MAX(abs(max_dim), abs(mris->zhi)) ;
#else
max_dim = MAX(abs(mris->xhi-mris->xlo), abs(mris->yhi-mris->ylo)) ;
max_dim = MAX(max_dim,abs(mris->zhi-mris->zlo)) ;
#endif
if (max_dim > .75*DEFAULT_RADIUS)
{
float ratio = .75*DEFAULT_RADIUS / (max_dim) ;
printf("scaling brain by %2.3f...\n", ratio) ;
MRISscaleBrain(mris, mris, ratio) ;
}
if (target_radius < 0)
{
target_radius = sqrt(mris->total_area / (4*M_PI)) ;
printf("setting target radius to be %2.3f to match surface areas\n",
target_radius) ;
}
// MRISsampleAtEachDistance(mris, parms.nbhd_size, parms.max_nbrs) ;
if (!load && inflate)
{
INTEGRATION_PARMS inflation_parms ;
MRIScenter(mris, mris) ;
memset(&inflation_parms, 0, sizeof(INTEGRATION_PARMS)) ;
strcpy(inflation_parms.base_name, parms.base_name) ;
inflation_parms.write_iterations = parms.write_iterations ;
inflation_parms.niterations = inflate_iterations ;
inflation_parms.l_spring_norm = l_spring_norm ;
inflation_parms.l_spring = inflate_spring ;
inflation_parms.l_nlarea = inflate_nlarea ;
inflation_parms.l_area = inflate_area ;
inflation_parms.n_averages = inflate_avgs ;
inflation_parms.l_expand = l_expand ;
inflation_parms.l_tspring = inflate_tspring ;
inflation_parms.l_sphere = l_sphere ;
inflation_parms.l_convex = l_convex ;
#define SCALE_UP 2
inflation_parms.a = SCALE_UP*DEFAULT_RADIUS ;
inflation_parms.tol = inflate_tol ;
inflation_parms.integration_type = INTEGRATE_MOMENTUM ;
inflation_parms.momentum = 0.9 ;
inflation_parms.dt = inflate_dt ;
/* store the inflated positions in the v->c? field so that they can
be used in the repulsive term.
*/
/* inflation_parms.l_repulse_ratio = .1 ;*/
MRISsaveVertexPositions(mris, CANONICAL_VERTICES) ;
if (l_expand > 0)
{
MRISexpandSurface(mris, target_radius/2, &inflation_parms, 0, 1) ;
l_expand = parms.l_expand = 0 ;
}
MRIScenter(mris, mris) ;
mris->x0 = mris->xctr ;
mris->y0 = mris->yctr ;
mris->z0 = mris->zctr ;
MRISinflateToSphere(mris, &inflation_parms) ;
if (inflation_parms.l_expand > 0)
{
inflation_parms.l_expand = 0 ;
inflation_parms.niterations += (inflate_iterations*.1) ;
MRISinflateToSphere(mris, &inflation_parms) ;
}
MRISscaleBrain(mris, mris, target_radius/(DEFAULT_RADIUS*SCALE_UP)) ;
parms.start_t = inflation_parms.start_t ;
MRISresetNeighborhoodSize(mris, nbrs) ;
}
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRISwrite(mris, "before") ;
}
MRISprojectOntoSphere(mris, mris, target_radius) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRISwrite(mris, "after") ;
}
fprintf(stderr,"surface projected - minimizing metric distortion...\n");
MRISsetNeighborhoodSize(mris, nbrs) ;
if (quick)
{
if (!load)
{
#if 0
parms.n_averages = 32 ;
parms.tol = .1 ;
parms.l_parea = parms.l_dist = 0.0 ;
parms.l_nlarea = 1 ;
#endif
MRISprintTessellationStats(mris, stderr) ;
MRISquickSphere(mris, &parms, max_passes) ;
}
}
else
{
MRISunfold(mris, &parms, max_passes) ;
}
if (remove_negative)
{
parms.niterations = 1000 ;
MRISremoveOverlapWithSmoothing(mris,&parms) ;
}
if (!load)
{
fprintf(stderr, "writing spherical brain to %s\n", out_fname) ;
MRISwrite(mris, out_fname) ;
}
msec = TimerStop(&then) ;
fprintf(stderr, "spherical transformation took %2.2f hours\n",
(float)msec/(1000.0f*60.0f*60.0f));
exit(0) ;
return(0) ; /* for ansi */
}
int
main(int argc, char *argv[]) {
int nargs, msec, order, i, number, vno, nnum, m, k, b1, b2, cno, flag=0, fno;
struct timeb then ;
MRIS *mris_in, *mris_out, *mris_high;
MRI_SP *mrisp ;
VERTEX *vm_out, *vm_high, *v;
float s_jkm, area;
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 < 4)
ErrorExit(ERROR_BADPARM,
"usage: %s <input surface> <orig surface> <finest order> <output surface>", Progname);
TimerStart(&then) ;
order = atoi (argv[3]);
fprintf(stdout, "Set %s as the finest scale level\n", argv[3]);
if (order > 7)
ErrorExit(ERROR_BADPARM, "the highest order is 7\n");
/*Spherical Wavelet Analysis*/
if (ANALYSIS&&!CURV) {
mris_in = MRISread(argv[1]) ;
if (!mris_in)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, argv[1]) ;
fprintf(stdout, "Reading input spherical surface from %s\n", argv[1]);
MRISreadOriginalProperties(mris_in, argv[2]) ;
fprintf(stdout, "Reading original surface from %s orig area is %f\n", argv[2],mris_in->orig_area);
mris_out = ReadIcoByOrder(order, 100);
for (m = 0; m<mris_out->nvertices; m++)
mris_out->vertices[m].nsize=1;
mrisp = MRISPalloc(1, 3);
#if 1
MRIScoordsToParameterization(mris_in, mrisp, 1, ORIGINAL_VERTICES) ;
MRISPblur(mrisp, mrisp, 1, 0);
MRISPblur(mrisp, mrisp, 1, 1);
MRISPblur(mrisp, mrisp, 1, 2);
MRIScoordsFromParameterization(mrisp, mris_out) ;
#else
MRISreadOriginalProperties(mris_out, argv[2]) ;
#endif
#if 1 /*just to test if the parameterization is correct */
MRISsaveVertexPositions(mris_out, TMP_VERTICES) ;
MRISrestoreVertexPositions(mris_out, ORIGINAL_VERTICES) ;
MRISupdateSurface(mris_out);
fprintf(stderr, "original area becomes %f\n", mris_out->total_area);
center_brain(mris_out, mris_out);
MRISscaleBrain(mris_out, mris_out, sqrt(100000.0f/mris_out->total_area)) ;
MRISupdateSurface(mris_out);
for (fno=0; fno<mris_out->nfaces; fno++)
area += mris_out->faces[fno].area;
fprintf(stderr, "original area becomes %f\n", area);
//MRISwrite(mris_out, "/space/xrt/1/users/btquinn/buckner_paper/010223_61223/surf/lh.sampled") ;
MRISsaveVertexPositions(mris_out, ORIGINAL_VERTICES) ;
MRISrestoreVertexPositions(mris_out, TMP_VERTICES) ;
#endif
/* Initialize Ij,k*/
for (vno = 0 ; vno<mris_out->nvertices; vno++) {
vm_out = &mris_out->vertices[vno];
vm_out->val = 1;
}
/*Iteratively compute Ij,k*/
for (i=order;i>0;i--) {
mris_high = ReadIcoByOrder(i, 100); //higher order surface
for (m = 0; m<mris_high->nvertices; m++)
mris_high->vertices[m].nsize=1;
MRISsetNeighborhoodSize(mris_high, 3) ;
number = IcoNVtxsFromOrder(i-1); //the start of m vertices
for (m = number; m<mris_high->nvertices; m++) {
vm_out = &mris_out->vertices[m];
vm_high = &mris_high->vertices[m];
flag=0;
for (nnum=0; nnum<vm_high->vnum; nnum++)
if ( vm_high->v[nnum]<number ) //A(j,m)
{
k = vm_high->v[nnum];
v = &mris_out->vertices[k];
v->val += 0.5*vm_out->val ;
}
for (; nnum<vm_high->v2num; nnum++)
if ( vm_high->v[nnum]<number ) //B(j,m)
{
k = vm_high->v[nnum];
if (flag==0) b1=k;
else b2=k;
flag++;
v = &mris_out->vertices[k];
v->val += 0.125*vm_out->val ;
}
for (; nnum<vm_high->v3num; nnum++)
if ( vm_high->v[nnum]<number ) //C(j,m)
{
k = vm_high->v[nnum];
flag=0; //C has to be a second-order neighbor of B
for (cno=mris_high->vertices[b1].vnum; cno<mris_high->vertices[b1].v2num;cno++)
if (mris_high->vertices[b1].v[cno]==k) flag=1;
for (cno=mris_high->vertices[b2].vnum; cno<mris_high->vertices[b2].v2num;cno++)
if (mris_high->vertices[b2].v[cno]==k) flag=1;
if (flag) {
v = &mris_out->vertices[k];
v->val -= 0.0625*vm_out->val ;
}
}
}
}
/*Analysis Stage I:*/
for (i=order;i>0;i--) {
mris_high = ReadIcoByOrder(i, 100); //higher order surface
for (m = 0; m<mris_high->nvertices; m++)
mris_high->vertices[m].nsize=1;
MRISsetNeighborhoodSize(mris_high, 3) ;
number = IcoNVtxsFromOrder(i-1); //the start of m vertices
/* compute Yj,m for each m vertices */
for (m = number; m<mris_high->nvertices; m++) {
vm_out = &mris_out->vertices[m];
vm_high = &mris_high->vertices[m];
flag=0;
for (nnum=0; nnum<vm_high->vnum; nnum++) //first order neighborhood
if ( vm_high->v[nnum]<number ) //neighbor A(j,m)
{
k = vm_high->v[nnum] ;
v = &mris_out->vertices[k];
vm_out->origx -= 0.5*v->origx;
vm_out->origy -= 0.5*v->origy;
vm_out->origz -= 0.5*v->origz;
}
for (; nnum<vm_high->v2num; nnum++) //second order neighborhood
if ( vm_high->v[nnum]<number ) //neighbor B(j,m)
{
k = vm_high->v[nnum] ;
if (flag==0) b1=k;
else b2=k;
flag++;
v = &mris_out->vertices[k];
vm_out->origx -= 0.125*v->origx;
vm_out->origy -= 0.125*v->origy;
vm_out->origz -= 0.125*v->origz;
}
for (; nnum<vm_high->v3num; nnum++)
if ( vm_high->v[nnum]<number ) //neighbor C(j,m)
{
k = vm_high->v[nnum] ;
flag=0; //C has to be a second-order neighbor of B
for (cno=mris_high->vertices[b1].vnum; cno<mris_high->vertices[b1].v2num;cno++)
if (mris_high->vertices[b1].v[cno]==k) flag=1;
for (cno=mris_high->vertices[b2].vnum; cno<mris_high->vertices[b2].v2num;cno++)
if (mris_high->vertices[b2].v[cno]==k) flag=1;
if (flag) {
v = &mris_out->vertices[k];
vm_out->origx += 0.0625*v->origx;
vm_out->origy += 0.0625*v->origy;
vm_out->origz += 0.0625*v->origz;
}
}
}
/*Analysis Stage II: */
/*Compute Lamda(j,k) using the Yita(j,m)*/
for (m = number; m<mris_high->nvertices; m++) {
vm_out = &mris_out->vertices[m];
vm_high = &mris_high->vertices[m];
for (nnum=0; nnum<vm_high->vnum; nnum++)
if ( vm_high->v[nnum]<number ) //A(j,m)
{
k = vm_high->v[nnum];
v = &mris_out->vertices[k];
s_jkm = vm_out->val/2/v->val;
v->origx += s_jkm*vm_out->origx;
v->origy += s_jkm*vm_out->origy;
v->origz += s_jkm*vm_out->origz;
}
}
}
MRISsaveVertexPositions(mris_out, TMP_VERTICES) ;
MRISrestoreVertexPositions(mris_out, ORIGINAL_VERTICES) ;
#if 0
for (m=0;m<mris_out->nvertices;m++)
if (mris_out->vertices[m].z>6)
fprintf(stdout, "%d %f %f %f\n", m,mris_out->vertices[m].x, mris_out->vertices[m].y, mris_out->vertices[m].z);
//mris_high = ReadIcoByOrder(0, 100);
//for (m=0;m<mris_high->nvertices;m++)
//{mris_high->vertices[m].x=mris_out->vertices[m].x;
//mris_high->vertices[m].y=mris_out->vertices[m].y;
//mris_high->vertices[m].z=mris_out->vertices[m].z;
//}
//MRISwrite(mris_high, "/space/xrt/1/users/btquinn/buckner_paper/010223_61223/surf/lh.sampled") ;
#endif
fprintf(stdout, "Writing wavelets coefficient of original surface to %s\n", argv[4]);
MRISwrite(mris_out,argv[4] ) ;
MRISrestoreVertexPositions(mris_out, TMP_VERTICES) ;
MRISPfree(&mrisp) ;
MRISfree(&mris_in) ;
/*End of Analysis*/
} else if (ANALYSIS&&CURV) {
mris_in = MRISread(argv[1]) ;
if (!mris_in)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, argv[1]) ;
fprintf(stdout, "Reading input spherical surface from %s\n", argv[1]);
MRISreadCurvatureFile(mris_in, argv[2]) ;
fprintf(stdout, "Reading input from %s\n", argv[2]);
mris_out = ReadIcoByOrder(order, 100);
for (m = 0; m<mris_out->nvertices; m++)
mris_out->vertices[m].nsize=1;
//mrisp = MRISPalloc(1, 3);
mrisp = MRIStoParameterization(mris_in, NULL, 1, 0) ;
//MRISPblur(mrisp, mrisp, 1, 0);
MRISfromParameterization(mrisp, mris_out, 0) ;
//MRISwriteCurvature(mris_out,"/space/xrt/1/users/btquinn/buckner_paper/010223_61223/surf/lh.thickness.sampled");
/* Initialize Ij,k*/
for (vno = 0 ; vno<mris_out->nvertices; vno++) {
vm_out = &mris_out->vertices[vno];
vm_out->val = 1;
}
/*Iteratively compute Ij,k*/
for (i=order;i>0;i--) {
mris_high = ReadIcoByOrder(i, 100); //higher order surface
for (m = 0; m<mris_high->nvertices; m++)
mris_high->vertices[m].nsize=1;
MRISsetNeighborhoodSize(mris_high, 3) ;
number = IcoNVtxsFromOrder(i-1); //the start of m vertices
for (m = number; m<mris_high->nvertices; m++) {
vm_out = &mris_out->vertices[m];
vm_high = &mris_high->vertices[m];
flag=0;
for (nnum=0; nnum<vm_high->vnum; nnum++)
if ( vm_high->v[nnum]<number ) //A(j,m)
{
k = vm_high->v[nnum];
v = &mris_out->vertices[k];
v->val += 0.5*vm_out->val ;
}
for (; nnum<vm_high->v2num; nnum++)
if ( vm_high->v[nnum]<number ) //B(j,m)
{
k = vm_high->v[nnum];
if (flag==0) b1=k;
else b2=k;
flag++;
v = &mris_out->vertices[k];
v->val += 0.125*vm_out->val ;
}
for (; nnum<vm_high->v3num; nnum++)
if ( vm_high->v[nnum]<number ) //C(j,m)
{
k = vm_high->v[nnum];
flag=0; //C has to be a second-order neighbor of B
for (cno=mris_high->vertices[b1].vnum; cno<mris_high->vertices[b1].v2num;cno++)
if (mris_high->vertices[b1].v[cno]==k) flag=1;
for (cno=mris_high->vertices[b2].vnum; cno<mris_high->vertices[b2].v2num;cno++)
if (mris_high->vertices[b2].v[cno]==k) flag=1;
if (flag) {
v = &mris_out->vertices[k];
v->val -= 0.0625*vm_out->val ;
}
}
}
}
/*Analysis Stage I:*/
for (i=order;i>0;i--) {
mris_high = ReadIcoByOrder(i, 100); //higher order surface
for (m = 0; m<mris_high->nvertices; m++)
mris_high->vertices[m].nsize=1;
MRISsetNeighborhoodSize(mris_high, 3) ;
number = IcoNVtxsFromOrder(i-1); //the start of m vertices
/* compute Yj,m for each m vertices */
for (m = number; m<mris_high->nvertices; m++) {
vm_out = &mris_out->vertices[m];
vm_high = &mris_high->vertices[m];
flag=0;
for (nnum=0; nnum<vm_high->vnum; nnum++) //first order neighborhood
if ( vm_high->v[nnum]<number ) //neighbor A(j,m)
{
k = vm_high->v[nnum] ;
v = &mris_out->vertices[k];
vm_out->curv -= 0.5*v->curv;
}
for (; nnum<vm_high->v2num; nnum++) //second order neighborhood
if ( vm_high->v[nnum]<number ) //neighbor B(j,m)
{
k = vm_high->v[nnum] ;
if (flag==0) b1=k;
else b2=k;
flag++;
v = &mris_out->vertices[k];
vm_out->curv -= 0.125*v->curv;
}
for (; nnum<vm_high->v3num; nnum++)
if ( vm_high->v[nnum]<number ) //neighbor C(j,m)
{
k = vm_high->v[nnum] ;
flag=0; //C has to be a second-order neighbor of B
for (cno=mris_high->vertices[b1].vnum; cno<mris_high->vertices[b1].v2num;cno++)
if (mris_high->vertices[b1].v[cno]==k) flag=1;
for (cno=mris_high->vertices[b2].vnum; cno<mris_high->vertices[b2].v2num;cno++)
if (mris_high->vertices[b2].v[cno]==k) flag=1;
if (flag) {
v = &mris_out->vertices[k];
vm_out->curv += 0.0625*v->curv;
}
}
}
/*Analysis Stage II: */
/*Compute Lamda(j,k) using the Yita(j,m)*/
for (m = number; m<mris_high->nvertices; m++) {
vm_out = &mris_out->vertices[m];
vm_high = &mris_high->vertices[m];
for (nnum=0; nnum<vm_high->vnum; nnum++)
if ( vm_high->v[nnum]<number ) //A(j,m)
{
k = vm_high->v[nnum];
v = &mris_out->vertices[k];
s_jkm = vm_out->val/2/v->val;
v->curv += s_jkm*vm_out->curv;
}
}
}
fprintf(stdout, "Writing wavelets coefficient of original surface to %s\n", argv[4]);
MRISwriteCurvature(mris_out,argv[4] ) ;
MRISPfree(&mrisp) ;
MRISfree(&mris_in) ;
/*End of Analysis*/
} else if (SYNTHESIS) /*Spherical Wavelet Synthesis*/
{
mris_out = ReadIcoByOrder(order, 100); //higher order surface
fprintf(stdout, "Creating a %d order spherical surface\n", order);
MRISreadOriginalProperties(mris_out, argv[1]) ;
fprintf(stdout, "Reading wavelet coefficients from %s\n", argv[1]);
for (m = 0; m<mris_out->nvertices; m++)
mris_out->vertices[m].nsize=1;
MRISsetNeighborhoodSize(mris_out, 3) ;
if (COMPARE) {
mris_in = MRISread(fname);
for (i=1; i<IcoNVtxsFromOrder(order-1); i++) {
if (mris_out->vertices[i].origx==0)
area = fabs(mris_out->vertices[i].origx-mris_in->vertices[i].x);
else area = fabs((mris_out->vertices[i].origx-mris_in->vertices[i].x)/mris_out->vertices[i].origx);
if ( area>5 ) {
mris_out->vertices[i].origx = mris_in->vertices[i].x ;
fprintf(stdout, "%d %f\n", i, area);
}
if (mris_out->vertices[i].origy==0)
area = fabs(mris_out->vertices[i].origy-mris_in->vertices[i].y);
else area = fabs((mris_out->vertices[i].origy-mris_in->vertices[i].y)/mris_out->vertices[i].origy);
if ( area>5 ) {
mris_out->vertices[i].origy = mris_in->vertices[i].y ;
fprintf(stdout, "%d %f\n", i, area);
}
if (mris_out->vertices[i].origz==0)
area = fabs(mris_out->vertices[i].origz-mris_in->vertices[i].z);
else area = fabs((mris_out->vertices[i].origz-mris_in->vertices[i].z)/mris_out->vertices[i].origz);
if ( area>5 ) {
mris_out->vertices[i].origz = mris_in->vertices[i].z ;
fprintf(stdout, "%d %f\n", i, area);
}
}
MRISfree(&mris_in);
}
fprintf(stdout, "Recover the surface using %s order coefficients\n",argv[2]);
number = IcoNVtxsFromOrder(atoi(argv[2]));
for (m = number; m<mris_out->nvertices; m++) {
mris_out->vertices[m].origx = 0;
mris_out->vertices[m].origy = 0;
mris_out->vertices[m].origz = 0;
}
/*Initialize Ij,k*/
for (vno = 0; vno<mris_out->nvertices; vno++) {
vm_out = &mris_out->vertices[vno];
vm_out->val = 1;
}
/*Iteratively compute Ij,k*/
for (i=order;i>0;i--) {
mris_high = ReadIcoByOrder(i, 100); //higher order surface
for (m = 0; m<mris_high->nvertices; m++)
mris_high->vertices[m].nsize=1;
MRISsetNeighborhoodSize(mris_high, 3) ;
number = IcoNVtxsFromOrder(i-1); //the start of m vertices
for (m = number; m<mris_high->nvertices; m++) {
vm_out = &mris_out->vertices[m];
vm_high = &mris_high->vertices[m];
flag=0;
for (nnum=0; nnum<vm_high->vnum; nnum++)
if ( vm_high->v[nnum]<number ) //A(j,m)
{
k = vm_high->v[nnum];
v = &mris_out->vertices[k];
v->val += 0.5*vm_out->val ;
}
for (; nnum<vm_high->v2num; nnum++)
if ( vm_high->v[nnum]<number ) //B(j,m)
{
k = vm_high->v[nnum];
if (flag==0) b1=k;
else b2=k;
flag++;
v = &mris_out->vertices[k];
v->val += 0.125*vm_out->val ;
}
for (; nnum<vm_high->v3num; nnum++)
if ( vm_high->v[nnum]<number ) //C(j,m)
{
k = vm_high->v[nnum];
flag=0; //C has to be a second-order neighbor of B
for (cno=mris_high->vertices[b1].vnum; cno<mris_high->vertices[b1].v2num;cno++)
if (mris_high->vertices[b1].v[cno]==k) flag=1;
for (cno=mris_high->vertices[b2].vnum; cno<mris_high->vertices[b2].v2num;cno++)
if (mris_high->vertices[b2].v[cno]==k) flag=1;
if (flag) {
v = &mris_out->vertices[k];
v->val -= 0.0625*vm_out->val ;
}
}
}
}
for (i=1;i<=order;i++) {
mris_high = ReadIcoByOrder(i, 100); //higher order surface
for (m = 0; m<mris_high->nvertices; m++)
mris_high->vertices[m].nsize=1;
MRISsetNeighborhoodSize(mris_high, 3) ;
number = IcoNVtxsFromOrder(i-1); //the start of m vertices
/* Synthesis Stage I */
/* Compute Lamda(j+1,k) using the Yita(j,m) */
for (m = number; m<mris_high->nvertices; m++) {
vm_out = &mris_out->vertices[m];
vm_high = &mris_high->vertices[m];
for (nnum=0; nnum<vm_high->vnum; nnum++)
if ( vm_high->v[nnum]<number ) //A(j,m)
{
k = vm_high->v[nnum];
v = &mris_out->vertices[k];
s_jkm = vm_out->val/2/v->val;
v->origx -= s_jkm*vm_out->origx;
v->origy -= s_jkm*vm_out->origy;
v->origz -= s_jkm*vm_out->origz;
}
}
/* compute Lamda(j+1,m) for each m vertices */
for (m = number; m<mris_high->nvertices; m++) {
vm_out = &mris_out->vertices[m];
vm_high = &mris_high->vertices[m];
flag=0;
for (nnum=0; nnum<vm_high->vnum; nnum++) //first order neighborhood
if ( vm_high->v[nnum]<number ) //neighbor A(j,m)
{
k = vm_high->v[nnum] ;
v = &mris_out->vertices[k];
vm_out->origx += 0.5*v->origx;
vm_out->origy += 0.5*v->origy;
vm_out->origz += 0.5*v->origz;
}
for (; nnum<vm_high->v2num; nnum++) //second order neighborhood
if ( vm_high->v[nnum]<number ) //neighbor B(j,m)
{
k = vm_high->v[nnum] ;
if (flag==0) b1=k;
else b2=k;
flag++;
v = &mris_out->vertices[k];
vm_out->origx += 0.125*v->origx;
vm_out->origy += 0.125*v->origy;
vm_out->origz += 0.125*v->origz;
}
for (; nnum<vm_high->v3num; nnum++) //third order neighborhood
if ( vm_high->v[nnum]<number ) //neighbor C(j,m)
{
k = vm_high->v[nnum] ;
flag=0; //C has to be a second-order neighbor of B
for (cno=mris_high->vertices[b1].vnum; cno<mris_high->vertices[b1].v2num;cno++)
if (mris_high->vertices[b1].v[cno]==k) flag=1;
for (cno=mris_high->vertices[b2].vnum; cno<mris_high->vertices[b2].v2num;cno++)
if (mris_high->vertices[b2].v[cno]==k) flag=1;
if (flag) {
v = &mris_out->vertices[k];
vm_out->origx -= 0.0625*v->origx;
vm_out->origy -= 0.0625*v->origy;
vm_out->origz -= 0.0625*v->origz;
}
}
}
}
MRISsaveVertexPositions(mris_out, TMP_VERTICES) ;
MRISrestoreVertexPositions(mris_out, ORIGINAL_VERTICES) ;
fprintf(stdout, "Writing recovered surface to %s\n", argv[4]);
MRISwrite(mris_out, argv[4]) ;
#if 0
mris_high = ReadIcoByOrder(4, 100);
for (m=0;m<mris_high->nvertices;m++) {
mris_high->vertices[m].x=mris_out->vertices[m].x;
mris_high->vertices[m].y=mris_out->vertices[m].y;
mris_high->vertices[m].z=mris_out->vertices[m].z;
}
MRISwrite(mris_high, "/space/xrt/1/users/btquinn/buckner_paper/010223_61223/surf/lh.wavelet.recon") ;
#endif
MRISrestoreVertexPositions(mris_out, TMP_VERTICES) ;
/*End of Synthesis*/
}
MRISfree(&mris_out);
MRISfree(&mris_high) ;
msec = TimerStop(&then) ;
fprintf(stdout, "spherical wavelet took %2.1f minutes\n", (float)msec/(1000.0f*60.0f));
exit(0) ;
return(0) ;
}
int
main(int argc, char *argv[])
{
char **av, *surf_fname, *template_fname, *out_fname, fname[STRLEN],*cp;
int ac, nargs,err, msec ;
MRI_SURFACE *mris ;
MRI_SP *mrisp_template ;
char cmdline[CMD_LINE_LEN] ;
struct timeb start ;
make_cmd_version_string
(argc, argv,
"$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $",
"$Name: stable5 $",
cmdline);
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
{
exit (0);
}
argc -= nargs;
TimerStart(&start) ;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
memset(&parms, 0, sizeof(parms)) ;
parms.projection = PROJECT_SPHERE ;
parms.flags |= IP_USE_CURVATURE ;
parms.tol = 0.5 ; // was 1e-0*2.5
parms.min_averages = 0 ;
parms.l_area = 0.0 ;
parms.l_parea = 0.1f ; // used to be 0.2
parms.l_dist = 5.0 ; // used to be 0.5, and before that 0.1
parms.l_corr = 1.0f ;
parms.l_nlarea = 1 ;
parms.l_pcorr = 0.0f ;
parms.niterations = 25 ;
parms.n_averages = 1024 ; // used to be 256
parms.write_iterations = 100 ;
parms.dt_increase = 1.01 /* DT_INCREASE */;
parms.dt_decrease = 0.99 /* DT_DECREASE*/ ;
parms.error_ratio = 1.03 /*ERROR_RATIO */;
parms.dt_increase = 1.0 ;
parms.dt_decrease = 1.0 ;
parms.l_external = 10000 ; /* in case manual label is specified */
parms.error_ratio = 1.1 /*ERROR_RATIO */;
parms.integration_type = INTEGRATE_ADAPTIVE ;
parms.integration_type = INTEGRATE_MOMENTUM /*INTEGRATE_LINE_MINIMIZE*/ ;
parms.integration_type = INTEGRATE_LINE_MINIMIZE ;
parms.dt = 0.9 ;
parms.momentum = 0.95 ;
parms.desired_rms_height = -1.0 ;
parms.nbhd_size = -10 ;
parms.max_nbrs = 10 ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
{
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (nsigmas > 0)
{
MRISsetRegistrationSigmas(sigmas, nsigmas) ;
}
parms.which_norm = which_norm ;
if (argc < 4)
{
usage_exit() ;
}
printf("%s\n", vcid) ;
printf(" %s\n",MRISurfSrcVersion());
fflush(stdout);
surf_fname = argv[1] ;
template_fname = argv[2] ;
out_fname = argv[3] ;
if (parms.base_name[0] == 0)
{
FileNameOnly(out_fname, fname) ;
cp = strchr(fname, '.') ;
if (cp)
{
strcpy(parms.base_name, cp+1) ;
}
else
{
strcpy(parms.base_name, "sphere") ;
}
}
fprintf(stderr, "reading surface from %s...\n", surf_fname) ;
mris = MRISread(surf_fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, surf_fname) ;
if (parms.var_smoothness)
{
parms.vsmoothness = (float *)calloc(mris->nvertices, sizeof(float)) ;
if (parms.vsmoothness == NULL)
{
ErrorExit(ERROR_NOMEMORY, "%s: could not allocate vsmoothness array",
Progname) ;
}
parms.dist_error = (float *)calloc(mris->nvertices, sizeof(float)) ;
if (parms.dist_error == NULL)
{
ErrorExit(ERROR_NOMEMORY, "%s: could not allocate dist_error array",
Progname) ;
}
parms.area_error = (float *)calloc(mris->nvertices, sizeof(float)) ;
if (parms.area_error == NULL)
{
ErrorExit(ERROR_NOMEMORY, "%s: could not allocate area_error array",
Progname) ;
}
parms.geometry_error = (float *)calloc(mris->nvertices, sizeof(float)) ;
if (parms.geometry_error == NULL)
{
ErrorExit(ERROR_NOMEMORY, "%s: could not allocate geometry_error array",
Progname) ;
}
}
MRISresetNeighborhoodSize(mris, 1) ;
if (annot_name)
{
if (MRISreadAnnotation(mris, annot_name) != NO_ERROR)
ErrorExit(ERROR_BADPARM,
"%s: could not read annot file %s",
Progname, annot_name) ;
MRISripMedialWall(mris) ;
}
MRISsaveVertexPositions(mris, TMP2_VERTICES) ;
MRISaddCommandLine(mris, cmdline) ;
if (!FZERO(dalpha) || !FZERO(dbeta) || !FZERO(dgamma))
MRISrotate(mris, mris, RADIANS(dalpha), RADIANS(dbeta),
RADIANS(dgamma)) ;
if (curvature_fname[0])
{
fprintf(stderr, "reading source curvature from %s\n",curvature_fname) ;
MRISreadCurvatureFile(mris, curvature_fname) ;
}
if (single_surf)
{
char fname[STRLEN], *cp, surf_dir[STRLEN], hemi[10] ;
MRI_SURFACE *mris_template ;
int sno, tnbrs=3 ;
FileNamePath(template_fname, surf_dir) ;
cp = strrchr(template_fname, '/') ;
if (cp == NULL) // no path - start from beginning of file name
{
cp = template_fname ;
}
cp = strchr(cp, '.') ;
if (cp == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could no scan hemi from %s",
Progname, template_fname) ;
strncpy(hemi, cp-2, 2) ;
hemi[2] = 0 ;
fprintf(stderr, "reading spherical surface %s...\n", template_fname) ;
mris_template = MRISread(template_fname) ;
if (mris_template == NULL)
{
ErrorExit(ERROR_NOFILE, "") ;
}
#if 0
if (reverse_flag)
{
MRISreverse(mris_template, REVERSE_X, 1) ;
}
#endif
MRISsaveVertexPositions(mris_template, CANONICAL_VERTICES) ;
MRIScomputeMetricProperties(mris_template) ;
MRISstoreMetricProperties(mris_template) ;
if (noverlays > 0)
{
mrisp_template = MRISPalloc(scale, IMAGES_PER_SURFACE*noverlays);
for (sno = 0; sno < noverlays ; sno++)
{
sprintf(fname, "%s/../label/%s.%s", surf_dir, hemi, overlays[sno]) ;
if (MRISreadValues(mris_template, fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE,
"%s: could not read overlay from %s",
Progname, fname) ;
MRIScopyValuesToCurvature(mris_template) ;
MRISaverageCurvatures(mris_template, navgs) ;
MRISnormalizeCurvature(mris_template, which_norm) ;
fprintf(stderr,
"computing parameterization for overlay %s...\n",
fname);
MRIStoParameterization(mris_template, mrisp_template, scale, sno*3) ;
MRISPsetFrameVal(mrisp_template, sno*3+1, 1.0) ;
}
}
else
{
mrisp_template = MRISPalloc(scale, PARAM_IMAGES);
for (sno = 0; sno < SURFACES ; sno++)
{
if (curvature_names[sno]) /* read in precomputed curvature file */
{
sprintf(fname, "%s/%s.%s", surf_dir, hemi, curvature_names[sno]) ;
if (MRISreadCurvatureFile(mris_template, fname) != NO_ERROR)
ErrorExit(Gerror,
"%s: could not read curvature file '%s'\n",
Progname, fname) ;
/* the two next lines were not in the original code */
MRISaverageCurvatures(mris_template, navgs) ;
MRISnormalizeCurvature(mris_template, which_norm) ;
}
else /* compute curvature of surface */
{
sprintf(fname, "%s/%s.%s", surf_dir, hemi, surface_names[sno]) ;
if (MRISreadVertexPositions(mris_template, fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE,
"%s: could not read surface file %s",
Progname, fname) ;
if (tnbrs > 1)
{
MRISresetNeighborhoodSize(mris_template, tnbrs) ;
}
MRIScomputeMetricProperties(mris_template) ;
MRIScomputeSecondFundamentalForm(mris_template) ;
MRISuseMeanCurvature(mris_template) ;
MRISaverageCurvatures(mris_template, navgs) ;
MRISrestoreVertexPositions(mris_template, CANONICAL_VERTICES) ;
MRISnormalizeCurvature(mris_template, which_norm) ;
}
fprintf(stderr,
"computing parameterization for surface %s...\n",
fname);
MRIStoParameterization(mris_template, mrisp_template, scale, sno*3) ;
MRISPsetFrameVal(mrisp_template, sno*3+1, 1.0) ;
}
}
}
else
{
fprintf(stderr, "reading template parameterization from %s...\n",
template_fname) ;
mrisp_template = MRISPread(template_fname) ;
if (!mrisp_template)
ErrorExit(ERROR_NOFILE, "%s: could not open template file %s",
Progname, template_fname) ;
if (noverlays > 0)
{
if (mrisp_template->Ip->num_frame != IMAGES_PER_SURFACE*noverlays)
ErrorExit(ERROR_BADPARM,
"template frames (%d) doesn't match input (%d x %d) = %d\n",
mrisp_template->Ip->num_frame, IMAGES_PER_SURFACE,noverlays,
IMAGES_PER_SURFACE*noverlays) ;
}
}
if (use_defaults)
{
if (*IMAGEFseq_pix(mrisp_template->Ip, 0, 0, 2) <= 1.0) /* 1st time */
{
parms.l_dist = 5.0 ;
parms.l_corr = 1.0 ;
parms.l_parea = 0.2 ;
}
else /* subsequent alignments */
{
parms.l_dist = 5.0 ;
parms.l_corr = 1.0 ;
parms.l_parea = 0.2 ;
}
}
if (nbrs > 1)
{
MRISresetNeighborhoodSize(mris, nbrs) ;
}
MRISprojectOntoSphere(mris, mris, DEFAULT_RADIUS) ;
mris->status = MRIS_PARAMETERIZED_SPHERE ;
MRIScomputeMetricProperties(mris) ;
if (!FZERO(parms.l_dist))
{
MRISscaleDistances(mris, scale) ;
}
#if 0
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
MRISzeroNegativeAreas(mris) ;
MRISstoreMetricProperties(mris) ;
#endif
MRISstoreMeanCurvature(mris) ; /* use curvature from file */
MRISsetOriginalFileName(orig_name) ;
if (inflated_name)
{
MRISsetInflatedFileName(inflated_name) ;
}
err = MRISreadOriginalProperties(mris, orig_name) ;
if (err != 0)
{
printf("ERROR %d from MRISreadOriginalProperties().\n",err);
exit(1);
}
if (MRISreadCanonicalCoordinates(mris, canon_name) != NO_ERROR)
ErrorExit(ERROR_BADFILE, "%s: could not read canon surface %s",
Progname, canon_name) ;
if (reverse_flag)
{
MRISreverse(mris, REVERSE_X, 1) ;
MRISsaveVertexPositions(mris, TMP_VERTICES) ;
MRISrestoreVertexPositions(mris, CANONICAL_VERTICES) ;
MRISreverse(mris, REVERSE_X, 0) ;
MRISsaveVertexPositions(mris, CANONICAL_VERTICES) ;
MRISrestoreVertexPositions(mris, TMP_VERTICES) ;
MRIScomputeMetricProperties(mris) ;
}
#if 0
MRISsaveVertexPositions
(mris, CANONICAL_VERTICES) ; // uniform spherical positions
#endif
if (starting_reg_fname)
if (MRISreadVertexPositions(mris, starting_reg_fname) != NO_ERROR)
{
exit(Gerror) ;
}
if (multiframes)
{
if (use_initial_registration)
MRISvectorRegister(mris, mrisp_template, &parms, max_passes,
min_degrees, max_degrees, nangles) ;
parms.l_corr=parms.l_pcorr=0.0f;
#if 0
parms.l_dist = 0.0 ;
parms.l_corr = 0.0 ;
parms.l_parea = 0.0 ;
parms.l_area = 0.0 ;
parms.l_parea = 0.0f ;
parms.l_dist = 0.0 ;
parms.l_corr = 0.0f ;
parms.l_nlarea = 0.0f ;
parms.l_pcorr = 0.0f ;
#endif
MRISvectorRegister(mris,
mrisp_template,
&parms,
max_passes,
min_degrees,
max_degrees,
nangles) ;
}
else
{
double l_dist = parms.l_dist ;
if (multi_scale > 0)
{
int i ;
parms.l_dist = l_dist * pow(5.0, (multi_scale-1.0)) ;
parms.flags |= IPFLAG_NOSCALE_TOL ;
parms.flags &= ~IP_USE_CURVATURE ;
for (i = 0 ; i < multi_scale ; i++)
{
printf("*************** round %d, l_dist = %2.3f **************\n", i,
parms.l_dist) ;
MRISregister(mris, mrisp_template,
&parms, max_passes,
min_degrees, max_degrees, nangles) ;
parms.flags |= IP_NO_RIGID_ALIGN ;
parms.flags &= ~IP_USE_INFLATED ;
parms.l_dist /= 5 ;
}
if (parms.nbhd_size < 0)
{
parms.nbhd_size *= -1 ;
printf("**** starting 2nd epoch, with long-range distances *****\n");
parms.l_dist = l_dist * pow(5.0, (multi_scale-2.0)) ;
for (i = 1 ; i < multi_scale ; i++)
{
printf("*********** round %d, l_dist = %2.3f *************\n", i,
parms.l_dist) ;
MRISregister(mris, mrisp_template,
&parms, max_passes,
min_degrees, max_degrees, nangles) ;
parms.l_dist /= 5 ;
}
}
printf("****** final curvature registration ***************\n") ;
if (parms.nbhd_size > 0)
{
parms.nbhd_size *= -1 ; // disable long-range stuff
}
parms.l_dist *= 5 ;
parms.flags |= (IP_USE_CURVATURE | IP_NO_SULC);
MRISregister(mris, mrisp_template,
&parms, max_passes,
min_degrees, max_degrees, nangles) ;
}
else
MRISregister(mris, mrisp_template,
&parms, max_passes,
min_degrees, max_degrees, nangles) ;
}
if (remove_negative)
{
parms.niterations = 1000 ;
MRISremoveOverlapWithSmoothing(mris,&parms) ;
}
fprintf(stderr, "writing registered surface to %s...\n", out_fname) ;
MRISwrite(mris, out_fname) ;
if (jacobian_fname)
{
MRIScomputeMetricProperties(mris) ;
compute_area_ratios(mris) ; /* will put results in v->curv */
#if 0
MRISwriteArea(mris, jacobian_fname) ;
#else
MRISwriteCurvature(mris, jacobian_fname) ;
#endif
}
msec = TimerStop(&start) ;
if (Gdiag & DIAG_SHOW)
printf("registration took %2.2f hours\n",
(float)msec/(1000.0f*60.0f*60.0f));
MRISPfree(&mrisp_template) ;
MRISfree(&mris) ;
exit(0) ;
return(0) ; /* for ansi */
}
int
main(int argc, char *argv[]) {
char **av, fname[STRLEN] ;
int ac, nargs, i, j, nbins ;
char *avg_subject, *cp, *hemi, *subject, *output_prefix ;
int msec, minutes, seconds, nsubjects, vno ;
struct timeb start ;
MRI_SURFACE *mris, *mris_avg ;
float ***histograms ;
FILE *fp ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mris_surface_to_vol_distances.c,v 1.4 2011/03/02 00:04:34 nicks Exp $", "$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
if (strlen(subjects_dir) == 0) {
cp = getenv("SUBJECTS_DIR") ;
if (!cp)
ErrorExit(ERROR_BADPARM, "%s: SUBJECTS_DIR must be specified on the command line (-sdir) or the env", Progname) ;
strcpy(subjects_dir, cp) ;
}
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) ;
avg_subject = argv[1] ;
hemi = argv[2] ;
nsubjects = argc-4 ;
output_prefix = argv[argc-1] ;
sprintf(fname, "%s/%s/surf/%s.sphere", subjects_dir, avg_subject, hemi) ;
mris_avg = MRISread(fname) ;
if (mris_avg == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read spherical surface from %s", Progname, fname) ;
nbins = nint(max_distance - min_distance) ;
histograms = (float ***)calloc(mris_avg->nvertices, sizeof(float **)) ;
if (histograms == NULL)
ErrorExit(ERROR_NOMEMORY, "%s: could not allocate %d histogram pointers", Progname, mris_avg->nvertices) ;
for (vno = 0 ; vno < mris_avg->nvertices ; vno++) {
histograms[vno] = (float **)calloc(nbins+1, sizeof(float *)) ;
if (histograms[vno] == NULL)
ErrorExit(ERROR_NOMEMORY, "%s: could not allocate histogram bins %d", Progname, vno) ;
for (i = 0 ; i < nbins ; i++) {
histograms[vno][i] = (float *)calloc(MAX_SURFACE_SCALE*nbins+1, sizeof(float)) ;
if (histograms[vno][i] == NULL)
ErrorExit(ERROR_NOMEMORY, "%s: could not allocate histogram bins %d", Progname, vno) ;
}
}
printf("processing %d subjects and writing results to %s*\n", nsubjects, output_prefix) ;
for (i = 0 ; i < nsubjects ; i++) {
subject = argv[i+3] ;
printf("processing subject %s: %d of %d...\n", subject, i+1, nsubjects) ;
sprintf(fname, "%s/%s/surf/%s.sphere.reg", subjects_dir, subject, hemi) ;
mris = MRISread(fname) ;
if (mris == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read spherical surface from %s", Progname, fname) ;
sprintf(fname, "%s/%s/surf/%s.sphere", subjects_dir, subject, hemi) ;
if (MRISreadCanonicalCoordinates(mris, fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read spherical surface from %s", Progname, fname) ;
sprintf(fname, "%s/%s/surf/%s.white", subjects_dir, subject, hemi) ;
if (MRISreadOriginalProperties(mris, fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read white surface from %s", Progname, fname) ;
if (MRISreadCurvatureFile(mris, "thickness") != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read thickness file", Progname) ;
mrisFindMiddleOfGray(mris) ;
update_histograms(mris, mris_avg, histograms, nbins) ;
MRISfree(&mris) ;
}
printf("writing log files with prefix %s...\n", output_prefix) ;
for (vno = 0 ; vno < mris_avg->nvertices ; vno++) {
sprintf(fname, "%s%7.7d.histo", output_prefix, vno) ;
fp = fopen(fname, "w") ;
for (i = 0 ; i < nbins ; i++) {
for (j = 0 ; j < nbins*MAX_SURFACE_SCALE ; j++) {
fprintf(fp, "%f ", histograms[vno][i][j]) ;
}
fprintf(fp, "\n") ;
}
fclose(fp) ;
}
/* compute average, store it in vertex 0 histgram, and write it out */
for (vno = 1 ; vno < mris_avg->nvertices ; vno++) {
for (i = 0 ; i < nbins ; i++)
for (j = 0 ; j < nbins*MAX_SURFACE_SCALE ; j++)
histograms[0][i][j] += histograms[vno][i][j] ;
}
sprintf(fname, "%s.average.histo", output_prefix) ;
fp = fopen(fname, "w") ;
for (i = 0 ; i < nbins ; i++) {
for (j = 0 ; j < nbins*MAX_SURFACE_SCALE ; j++) {
fprintf(fp, "%f ", histograms[0][i][j]) ;
}
fprintf(fp, "\n") ;
}
fclose(fp) ;
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
printf("distance histogram compilation took %d minutes"
" and %d seconds.\n", minutes, seconds) ;
exit(0) ;
return(0) ;
}
int
main(int argc, char *argv[])
{
char **av, in_surf_fname[STRLEN], *in_patch_fname, *out_patch_fname,
fname[STRLEN], path[STRLEN], *cp, hemi[10] ;
int ac, nargs ;
MRI_SURFACE *mris ;
MRI *mri_vertices ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mris_flatten.c,v 1.42 2016/12/10 22:57:46 fischl Exp $",
"$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Gdiag |= DIAG_SHOW ;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
Gdiag |= (DIAG_SHOW | DIAG_WRITE) ;
memset(&parms, 0, sizeof(parms)) ;
parms.dt = .1 ;
parms.projection = PROJECT_PLANE ;
parms.tol = 0.2 ;
parms.n_averages = 1024 ;
parms.l_dist = 1.0 ;
parms.l_nlarea = 1.0 ;
parms.niterations = 40 ;
parms.area_coef_scale = 1.0 ;
parms.dt_increase = 1.01 /* DT_INCREASE */;
parms.dt_decrease = 0.98 /* DT_DECREASE*/ ;
parms.error_ratio = 1.03 /*ERROR_RATIO */;
parms.integration_type = INTEGRATE_LINE_MINIMIZE ;
parms.momentum = 0.9 ;
parms.desired_rms_height = -1.0 ;
parms.base_name[0] = 0 ;
parms.nbhd_size = 7 ; /* out to 7-connected neighbors */
parms.max_nbrs = 12 ; /* 12 at each distance */
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
{
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 3)
print_help() ;
parms.base_dt = base_dt_scale * parms.dt ;
in_patch_fname = argv[1] ;
out_patch_fname = argv[2] ;
FileNamePath(in_patch_fname, path) ;
cp = strrchr(in_patch_fname, '/') ;
if (!cp)
cp = in_patch_fname ;
cp = strchr(cp, '.') ;
if (cp)
{
strncpy(hemi, cp-2, 2) ;
hemi[2] = 0 ;
}
else
strcpy(hemi, "lh") ;
if (one_surf_flag)
sprintf(in_surf_fname, "%s", in_patch_fname) ;
else
sprintf(in_surf_fname, "%s/%s.%s", path, hemi, original_surf_name) ;
if (parms.base_name[0] == 0)
{
FileNameOnly(out_patch_fname, fname) ;
cp = strchr(fname, '.') ;
if (cp)
strcpy(parms.base_name, cp+1) ;
else
strcpy(parms.base_name, "flattened") ;
}
mris = MRISread(in_surf_fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, in_surf_fname) ;
if (sphere_flag)
{
MRIScenter(mris, mris) ;
mris->radius = MRISaverageRadius(mris) ;
MRISstoreMetricProperties(mris) ;
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
}
if (Gdiag_no >= 0)
{
int n ;
printf("vertex %d has %d nbrs before patch:\n",
Gdiag_no, mris->vertices[Gdiag_no].vnum) ;
for (n = 0 ; n < mris->vertices[Gdiag_no].vnum ; n++)
printf("\t%d\n", mris->vertices[Gdiag_no].v[n]) ;
}
if (one_surf_flag) /* only have the 1 surface - no patch file */
{
mris->patch = 1 ;
mris->status = MRIS_PATCH ;
if (!FEQUAL(rescale,1))
{
MRISscaleBrain(mris, mris, rescale) ;
MRIScomputeMetricProperties(mris) ;
}
MRISstoreMetricProperties(mris) ;
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
}
else
{
MRISresetNeighborhoodSize(mris, mris->vertices[0].nsize) ; // set back to max
if (label_fname) // read in a label instead of a patch
{
LABEL *area ;
area = LabelRead(NULL, label_fname) ;
if (area == NULL)
ErrorExit(ERROR_BADPARM, "%s: could not read label file %s",
Progname, label_fname) ;
LabelDilate(area, mris, dilate_label, CURRENT_VERTICES) ;
MRISclearMarks(mris) ;
LabelMark(area, mris) ;
MRISripUnmarked(mris) ;
MRISripFaces(mris);
mris->patch = 1 ;
mris->status = MRIS_CUT ;
LabelFree(&area) ;
printf("%d valid vertices (%2.1f %% of total)\n",
MRISvalidVertices(mris),
100.0*MRISvalidVertices(mris)/mris->nvertices) ;
}
else
{
if (MRISreadPatch(mris, in_patch_fname) != NO_ERROR)
ErrorExit(ERROR_BADPARM, "%s: could not read patch file %s",
Progname, in_patch_fname) ;
if (dilate)
{
printf("dilating patch %d times\n", dilate) ;
MRISdilateRipped(mris, dilate) ;
printf("%d valid vertices (%2.1f %% of total)\n",
MRISvalidVertices(mris), 100.0*MRISvalidVertices(mris)/mris->nvertices) ;
}
}
MRISremoveRipped(mris) ;
MRISupdateSurface(mris) ;
#if 0
mris->nsize = 1 ; // before recalculation of 2 and 3-nbrs
{
int vno ;
VERTEX *v ;
for (vno= 0 ; vno < mris->nvertices ; vno++)
{
v = &mris->vertices[vno] ;
v->vtotal = v->vnum ;
v->nsize = 1 ;
}
}
MRISsetNeighborhoodSize(mris, nbrs) ;
#endif
}
if (Gdiag_no >= 0)
printf("vno %d is %sin patch\n", Gdiag_no,
mris->vertices[Gdiag_no].ripflag ? "NOT " : "") ;
if (Gdiag_no >= 0 && mris->vertices[Gdiag_no].ripflag == 0)
{
int n ;
printf("vertex %d has %d nbrs after patch:\n",
Gdiag_no, mris->vertices[Gdiag_no].vnum) ;
for (n = 0 ; n < mris->vertices[Gdiag_no].vnum ; n++)
printf("\t%d\n", mris->vertices[Gdiag_no].v[n]) ;
}
fprintf(stderr, "reading original vertex positions...\n") ;
if (!FZERO(disturb))
mrisDisturbVertices(mris, disturb) ;
if (parms.niterations > 0)
{
MRISresetNeighborhoodSize(mris, nbrs) ;
if (!FZERO(parms.l_unfold) || !FZERO(parms.l_expand))
{
static INTEGRATION_PARMS p2 ;
sprintf(in_surf_fname, "%s/%s.%s", path, hemi, original_surf_name) ;
if (stricmp(original_unfold_surf_name,"none") == 0)
{
printf("using current position of patch as initial position\n") ;
MRISstoreMetricProperties(mris) ; /* use current positions */
}
else if (!sphere_flag && !one_surf_flag)
MRISreadOriginalProperties(mris, original_unfold_surf_name) ;
*(&p2) = *(&parms) ;
p2.l_dist = 0 ;
p2.niterations = 100 ;
p2.nbhd_size = p2.max_nbrs = 1 ;
p2.n_averages = 0 ;
p2.write_iterations = parms.write_iterations > 0 ? 25 : 0 ;
p2.tol = -1 ;
p2.dt = 0.5 ;
p2.l_area = 0.0 ;
p2.l_spring = 0.9 ;
p2.l_convex = 0.9 ;
p2.momentum = 0 ;
p2.integration_type = INTEGRATE_MOMENTUM ;
MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
#if 0
p2.flags |= IPFLAG_NO_SELF_INT_TEST ;
printf("expanding surface....\n") ;
MRISexpandSurface(mris, 4.0, &p2) ; // push it away from fissure
#endif
p2.niterations = 100 ;
MRISunfold(mris, &p2, 1) ;
p2.niterations = 300 ;
p2.l_unfold *= 0.25 ;
MRISunfold(mris, &p2, 1) ;
p2.l_unfold *= 0.25 ;
MRISunfold(mris, &p2, 1) ;
#if 0
printf("smoothing unfolded surface..\n");
p2.niterations = 200 ;
p2.l_unfold = 0 ; // just smooth it
MRISunfold(mris, &p2, max_passes) ;
#endif
parms.start_t = p2.start_t ;
parms.l_unfold = parms.l_convex = parms.l_boundary = parms.l_expand=0 ;
MRIfree(&parms.mri_dist) ;
}
sprintf(in_surf_fname, "%s/%s.%s", path, hemi, original_surf_name) ;
if (!sphere_flag && !one_surf_flag)
MRISreadOriginalProperties(mris, original_surf_name) ;
if (randomly_flatten)
MRISflattenPatchRandomly(mris) ;
else
MRISflattenPatch(mris) ;
/* optimize metric properties of flat map */
fprintf(stderr,"minimizing metric distortion induced by projection...\n");
MRISscaleBrain(mris, mris, scale) ;
MRIScomputeMetricProperties(mris) ;
MRISunfold(mris, &parms, max_passes) ;
MRIScenter(mris, mris) ;
fprintf(stderr, "writing flattened patch to %s\n", out_patch_fname) ;
MRISwritePatch(mris, out_patch_fname) ;
}
if (plane_flag || sphere_flag)
{
char fname[STRLEN] ;
FILE *fp ;
#if 0
sprintf(fname, "%s.%s.out",
mris->hemisphere == RIGHT_HEMISPHERE ? "rh" : "lh",
parms.base_name);
#else
sprintf(fname, "flatten.log") ;
#endif
fp = fopen(fname, "a") ;
if (plane_flag)
MRIScomputeAnalyticDistanceError(mris, MRIS_PLANE, fp) ;
else if (sphere_flag)
MRIScomputeAnalyticDistanceError(mris, MRIS_SPHERE, fp) ;
fclose(fp) ;
}
if (mri_overlay)
{
MRI *mri_flattened ;
char fname[STRLEN] ;
// if it is NxNx1x1 reshape it to be Nx1x1xN
if ( mri_overlay->width == mri_overlay->height &&
mri_overlay->depth == 1 &&
mri_overlay->nframes == 1)
{
MRI *mri_tmp ;
printf("reshaping to move 2nd dimension to time\n") ;
mri_tmp = mri_reshape( mri_overlay, mri_overlay->width, 1, 1, mri_overlay->height);
MRIfree( &mri_overlay );
mri_overlay = mri_tmp;
}
// put in some special code that knows about icosahedra
if (mris->nvertices == 163842 || // ic7
mris->nvertices == 40962 || // ic6
mris->nvertices == 10242 || // ic5
mris->nvertices == 2562) // ic4
{
int nvals, start_index, end_index ;
MRI *mri_tmp ;
printf("cross-hemispheric correlation matrix detected, reshaping...\n") ;
nvals = mri_overlay->width * mri_overlay->height * mri_overlay->depth ;
if (nvals == 2*mris->nvertices) // it's a corr matrix for both hemis
{
if (mris->hemisphere == LEFT_HEMISPHERE || mris->hemisphere == RIGHT_HEMISPHERE)
{
if (mris->hemisphere == LEFT_HEMISPHERE)
{
start_index = 0 ;
end_index = mris->nvertices-1 ;
}
else
{
start_index = mris->nvertices ;
end_index = 2*mris->nvertices-1 ;
}
mri_tmp = MRIextract(mri_overlay, NULL, start_index, 0, 0, mris->nvertices, 1, 1) ;
MRIfree(&mri_overlay) ;
mri_overlay = mri_tmp;
}
else // both hemis
{
}
}
}
printf("resampling overlay (%d x %d x %d x %d) into flattened coordinates..\n",
mri_overlay->width, mri_overlay->height, mri_overlay->depth, mri_overlay->nframes) ;
if (synth_name)
{
LABEL *area_lh, *area_rh ;
char fname[STRLEN], path[STRLEN], fname_no_path[STRLEN] ;
int vno, n, vno2, n2 ;
MRIsetValues(mri_overlay, 0) ;
FileNameOnly(synth_name, fname_no_path) ;
FileNamePath(synth_name, path) ;
sprintf(fname, "%s/lh.%s", path, fname_no_path) ;
area_lh = LabelRead(NULL, fname) ;
if (area_lh == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read label from %s",
Progname,fname) ;
sprintf(fname, "%s/rh.%s", path, fname_no_path) ;
area_rh = LabelRead(NULL, fname) ;
if (area_rh == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read label from %s",
Progname,fname) ;
#if 0
for (n = 0 ; n < area_lh->n_points ; n++)
{
vno = area_lh->lv[n].vno ;
MRIsetVoxVal(mri_overlay, vno, 0, 0, vno, 1) ;
printf("synthesizing map with vno %d: (%2.1f, %2.1f)\n", vno, mris->vertices[vno].x, mris->vertices[vno].y) ;
break ;
}
#else
for (n = 0 ; n < area_lh->n_points ; n++)
{
vno = area_lh->lv[n].vno ;
if (vno >= 0)
{
for (n2 = 0 ; n2 < area_lh->n_points ; n2++)
{
vno2 = area_lh->lv[n2].vno ;
if (vno2 >= 0)
MRIsetVoxVal(mri_overlay, vno, 0, 0, vno2, 1) ;
}
for (n2 = 0 ; n2 < area_rh->n_points ; n2++)
{
vno2 = area_rh->lv[n2].vno ;
if (vno2 >= 0)
MRIsetVoxVal(mri_overlay, vno, 0, 0, mris->nvertices+vno2, 1) ;
}
}
}
#endif
}
mri_flattened = MRIflattenOverlay(mris, mri_overlay, NULL, 1.0, label_overlay, &mri_vertices) ;
printf("writing flattened overlay to %s\n", out_patch_fname) ;
MRIwrite(mri_flattened, out_patch_fname) ;
MRIfree(&mri_flattened) ;
FileNameRemoveExtension(out_patch_fname, fname) ;
strcat(fname, ".vnos.mgz") ;
printf("writing flattened vertex #s to %s\n", fname) ;
MRIwrite(mri_vertices, fname) ;
MRIfree(&mri_vertices) ;
}
#if 0
sprintf(fname, "%s.area_error", out_fname) ;
printf("writing area errors to %s\n", fname) ;
MRISwriteAreaError(mris, fname) ;
sprintf(fname, "%s.angle_error", out_fname) ;
printf("writing angle errors to %s\n", fname) ;
MRISwriteAngleError(mris, fname) ;
MRISfree(&mris) ;
#endif
exit(0) ;
return(0) ; /* for ansi */
}
int
main(int argc, char *argv[]) {
char *cp, **av, *in_fname, fname[100], path[100],
name[100], hemi[100] ;
int ac, nargs ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mris_errors.c,v 1.11 2011/03/02 00:04:31 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)
usage_exit() ;
in_fname = argv[1] ;
#if 0
out_fname = argv[2] ;
cp = strrchr(out_fname, '.') ;
#endif
if (patch_flag) /* read in orig surface before reading in patch */
{
FileNamePath(in_fname, path) ;
FileNameOnly(in_fname, name) ;
cp = strchr(name, '.') ;
if (cp) {
strncpy(hemi, cp-2, 2) ;
hemi[2] = 0 ;
} else
strcpy(hemi, "lh") ;
sprintf(fname, "%s/%s.smoothwm", path, hemi) ;
mris = MRISread(fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, fname) ;
FileNameOnly(in_fname, name) ;
MRISstoreMetricProperties(mris) ;
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
if (MRISreadPatch(mris, name) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read patch file %s",
Progname, name) ;
} else {
mris = MRISread(in_fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, in_fname) ;
MRISreadOriginalProperties(mris, "smoothwm") ;
}
MRISsaveVertexPositions(mris, TMP_VERTICES) ;
MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
MRISsampleAtEachDistance(mris, nbhd_size, max_nbrs) ;
MRIScomputeMetricProperties(mris) ;
MRISstoreMetricProperties(mris) ;
MRISrestoreVertexPositions(mris, TMP_VERTICES) ;
MRIScomputeMetricProperties(mris) ;
MRIScomputeDistanceErrors(mris, nbhd_size, max_nbrs) ;
#if 0
if (write_flag) {
MRISareaErrors(mris) ;
MRISangleErrors(mris) ;
}
if (area_flag) {
sprintf(fname, "%s.area_error", in_fname) ;
printf("writing area errors to %s\n", fname) ;
MRISwriteAreaError(mris, fname) ;
sprintf(fname, "%s.angle_error", in_fname) ;
printf("writing angle errors to %s\n", fname) ;
MRISwriteAngleError(mris, fname) ;
}
#else
sprintf(fname, "%s.distance_error", in_fname) ;
fprintf(stderr, "writing errors to %s\n", fname) ;
MRISwriteValues(mris, fname) ;
#endif
MRISfree(&mris) ;
exit(0) ;
return(0) ; /* for ansi */
}
