int
main(int argc, char *argv[]) {
char **av ;
int ac, nargs, nsize ;
MRI_SURFACE *mris ;
MRI *mri ;
nargs = handle_version_option (argc, argv, "$Id: mris_nudge.c,v 1.2 2011/03/02 00:04:31 nicks Exp $", "$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Gx = Gy = Gz = -1 ;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 7)
usage_exit(1) ;
mris = MRISread(argv[1]) ;
if (mris == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read surface from %s", Progname, argv[1]) ;
MRIScomputeMetricProperties(mris) ;
MRISstoreMetricProperties(mris) ;
mri = MRIread(argv[2]) ;
if (mri == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read volume from %s", Progname, argv[2]) ;
target_vnos[nvertices] = atoi(argv[3]) ;
target_vals[nvertices] = atof(argv[4]) ;
nsize = atoi(argv[5]) ;
printf("nudging %d vertex region around vertex %d to target val %2.1f\n",
nsize, target_vnos[nvertices], target_vals[nvertices]) ;
nvertices++ ;
MRISerodeRipped(mris, nsize) ;
MRISrepositionSurface(mris, mri, target_vnos, target_vals, nvertices, nsize, sigma) ;
MRISunrip(mris) ;
printf("writing repositioned surface to %s\n", argv[6]) ;
MRISwrite(mris, argv[6]) ;
return(0) ;
}
int
main(int argc, char *argv[])
{
char **av, *in_fname,fname[STRLEN],hemi[10], path[STRLEN],
name[STRLEN],*cp ;
int ac, nargs, nhandles ;
MRI_SURFACE *mris ;
double ici, fi, var ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$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, surf_fname[STRLEN], *template_fname, *hemi, *sphere_name,
*cp, *subject, fname[STRLEN] ;
int ac, nargs, ino, sno, nbad = 0, failed, n,nfields;
VERTEX *v;
VALS_VP *vp;
MRI_SURFACE *mris ;
MRI_SP *mrisp, /* *mrisp_aligned,*/ *mrisp_template ;
INTEGRATION_PARMS parms ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mris_make_template.c,v 1.27 2011/03/02 00:04:33 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
memset(&parms, 0, sizeof(parms)) ;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
/* setting default values for vectorial registration */
setParms(&parms);
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
{
nargs = get_option(argc, argv,&parms) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 5) usage_exit() ;
/* multiframe registration */
if (multiframes) parms.flags |= IP_USE_MULTIFRAMES;
if (!strlen(subjects_dir)) /* not specified on command line*/
{
cp = getenv("SUBJECTS_DIR") ;
if (!cp)
ErrorExit(ERROR_BADPARM,
"%s: SUBJECTS_DIR not defined in environment.\n",
Progname) ;
strcpy(subjects_dir, cp) ;
}
hemi = argv[1] ;
sphere_name = argv[2] ;
template_fname = argv[argc-1] ;
if (1 || !FileExists(template_fname)) /* first time - create it */
{
fprintf(stderr, "creating new parameterization...\n") ;
if (multiframes)
{
mrisp_template = MRISPalloc(scale, atlas_size * IMAGES_PER_SURFACE );
/* if (no_rot) /\* don't do rigid alignment *\/ */
/* mrisp_aligned = NULL ; */
/* else */
/* mrisp_aligned = MRISPalloc(scale, PARAM_FRAMES); */
}
else
{
mrisp_template = MRISPalloc(scale, PARAM_IMAGES);
/* if (no_rot) /\* don't do rigid alignment *\/ */
/* mrisp_aligned = NULL ; */
/* else */
/* mrisp_aligned = MRISPalloc(scale, PARAM_IMAGES); */
}
}
else
{
fprintf(stderr, "reading template parameterization from %s...\n",
template_fname) ;
/* mrisp_aligned = NULL ; */
mrisp_template = MRISPread(template_fname) ;
if (!mrisp_template)
ErrorExit(ERROR_NOFILE, "%s: could not open template file %s",
Progname, template_fname) ;
}
argv += 3 ;
argc -= 3 ;
for (ino = 0 ; ino < argc-1 ; ino++)
{
failed = 0 ;
subject = argv[ino] ;
fprintf(stderr, "\nprocessing subject %s (%d of %d)\n", subject,
ino+1, argc-1) ;
sprintf(surf_fname, "%s/%s/surf/%s.%s",
subjects_dir, subject, hemi, sphere_name) ;
fprintf(stderr, "reading spherical surface %s...\n", surf_fname) ;
mris = MRISread(surf_fname) ;
if (!mris)
{
nbad++ ;
ErrorPrintf(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, surf_fname) ;
exit(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, CANONICAL_VERTICES) ;
MRIScomputeMetricProperties(mris) ;
MRISstoreMetricProperties(mris) ;
if (Gdiag & DIAG_WRITE)
{
char *cp1 ;
FileNameOnly(template_fname, fname) ;
cp = strchr(fname, '.') ;
if (cp)
{
cp1 = strrchr(fname, '.') ;
if (cp1 && cp1 != cp)
strncpy(parms.base_name, cp+1, cp1-cp-1) ;
else
strcpy(parms.base_name, cp+1) ;
}
else
strcpy(parms.base_name, "template") ;
sprintf(fname, "%s.%s.out", hemi, parms.base_name);
parms.fp = fopen(fname, "w") ;
printf("writing output to '%s'\n", fname) ;
}
/* multiframe registration */
if (multiframes)
{
nfields=parms.nfields;
for ( n = 0; n < mris->nvertices ; n++) /* allocate the VALS_VP
structure */
{
v=&mris->vertices[n];
vp=calloc(1,sizeof(VALS_VP));
vp->nvals=nfields;
vp->orig_vals=(float*)malloc(nfields*sizeof(float)); /* before
blurring */
vp->vals=(float*)malloc(nfields*sizeof(float)); /* values used by
MRISintegrate */
v->vp=(void*)vp;
}
/* load the different fields */
for (n = 0 ; n < parms.nfields ; n++)
{
if (parms.fields[n].name != NULL)
{
sprintf(surf_fname, "%s/%s/%s/%s.%s", subjects_dir,
subject, overlay_dir, hemi, parms.fields[n].name) ;
printf("reading overlay file %s...\n", surf_fname) ;
if (MRISreadValues(mris, surf_fname) != NO_ERROR)
ErrorExit(ERROR_BADPARM, "%s: could not read overlay file %s",
Progname, surf_fname) ;
MRIScopyValuesToCurvature(mris) ;
}
else if (ReturnFieldName(parms.fields[n].field))
{
/* read in precomputed curvature file */
sprintf(surf_fname, "%s/%s/surf/%s.%s", subjects_dir,
subject, hemi, ReturnFieldName(parms.fields[n].field)) ;
// fprintf(stderr,"\nreading field %d from %s(type=%d,frame=%d)\n",parms.fields[n].field,surf_fname,parms.fields[n].type,parms.fields[n].frame);
if (MRISreadCurvatureFile(mris, surf_fname) != NO_ERROR)
{
fprintf(stderr,"\n\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n");
fprintf(stderr, "%s: could not read curvature file '%s'\n",
Progname, surf_fname) ;
failed = 1;
break;
}
}
else
{ /* compute curvature of surface */
sprintf(surf_fname, "%s/%s/surf/%s.%s", subjects_dir,
subject, hemi, surface_names[parms.fields[n].field]) ;
/*if(parms.fields[n].field==0)
sprintf(fname, "inflated") ;
else
sprintf(fname, "smoothwm") ;*/
//fprintf(stderr,"\ngenerating field %d(type=%d,frame=%d) (from %s)\n",parms.fields[n].field,parms.fields[n].type,parms.fields[n].frame,surf_fname);
// MRISsaveVertexPositions(mris, TMP_VERTICES) ;
if (MRISreadVertexPositions(mris, surf_fname) != NO_ERROR)
{
fprintf(stderr,"\n\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n");
ErrorPrintf(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, surf_fname) ;
fprintf(stderr,"setting up correlation coefficient to zero\n");
parms.fields[n].l_corr=parms.fields[n].l_pcorr=0.0;
failed=1;
break;
}
if (nbrs > 1) MRISsetNeighborhoodSize(mris, nbrs) ;
MRIScomputeMetricProperties(mris) ;
MRIScomputeSecondFundamentalForm(mris) ;
MRISuseMeanCurvature(mris) ;
MRISaverageCurvatures(mris, navgs) ;
MRISrestoreVertexPositions(mris, CANONICAL_VERTICES) ;
}
/* if(parms.fields[n].field!=SULC_CORR_FRAME)*/
MRISnormalizeField(mris,parms.fields[n].type,
parms.fields[n].which_norm); /* normalize values */
MRISsetCurvaturesToOrigValues(mris,n);
MRISsetCurvaturesToValues(mris,n);
}
if (failed)
{
fprintf(stderr,"\n\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n");
fprintf(stderr,"Subject %s Failed",subject);
fprintf(stderr,"XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n\n");
/* free cal structure*/
for ( n = 0; n < mris->nvertices ; n++)
{
v=&mris->vertices[n];
vp=(VALS_VP*)v->vp;
free(vp->orig_vals);
free(vp->vals);
free(vp);
v->vp=NULL;
}
/* free surface */
MRISfree(&mris);
/* go onto the next subject */
continue;
}
}
if (multiframes && (!no_rot))
{ /* rigid body alignment */
parms.frame_no = 3 ; /* don't use single field correlation functions */
parms.l_corr = parms.l_pcorr = 0.0f ;
parms.mrisp = MRIStoParameterization(mris, NULL, scale, 0) ;
parms.mrisp_template = mrisp_template ;
MRISrigidBodyAlignVectorGlobal(mris, &parms, 1.0, 64.0, 8) ;
if (Gdiag & DIAG_WRITE) MRISwrite(mris, "sphere.rot.global") ;
MRISrigidBodyAlignVectorLocal(mris, &parms) ;
if (Gdiag & DIAG_WRITE) MRISwrite(mris, "sphere.rot.local") ;
MRISPfree(&parms.mrisp) ;
MRISsaveVertexPositions(mris, CANONICAL_VERTICES) ;
};
if ((!multiframes) && (!no_rot) && ino > 0)
{ /* rigid body alignment */
sprintf(surf_fname, "%s/%s/surf/%s.%s",
subjects_dir, subject, hemi, "sulc") ;
if (MRISreadCurvatureFile(mris, surf_fname) != NO_ERROR)
{
ErrorPrintf(Gerror, "%s: could not read curvature file '%s'\n",
Progname, surf_fname) ;
nbad++ ;
MRISfree(&mris) ;
continue ;
}
parms.frame_no = 3 ; /* use sulc for rigid registration */
parms.mrisp = MRIStoParameterization(mris, NULL, scale, 0) ;
parms.mrisp_template = mrisp_template ;
parms.l_corr = 1.0f ;
MRISrigidBodyAlignGlobal(mris, &parms, 1.0, 64.0, 8) ;
if (Gdiag & DIAG_WRITE)
MRISwrite(mris, "sphere.rot.global") ;
MRISrigidBodyAlignLocal(mris, &parms) ;
if (Gdiag & DIAG_WRITE)
MRISwrite(mris, "sphere.rot.local") ;
MRISPfree(&parms.mrisp) ;
MRISsaveVertexPositions(mris, CANONICAL_VERTICES) ;
}
if (multiframes)
{
for (n = 0; n < parms.nfields ; n++)
{
MRISsetOrigValuesToCurvatures(mris,n);
MRISaverageCurvatures(mris, parms.fields[n].navgs) ;
mrisp = MRIStoParameterization(mris, NULL, scale, 0) ;
MRISPcombine(mrisp,
mrisp_template,
parms.fields[n].frame * IMAGES_PER_SURFACE) ;
MRISPfree(&mrisp) ;
}
/* free the VALS_VP structure */
for ( n = 0; n < mris->nvertices ; n++)
{
v=&mris->vertices[n];
vp=(VALS_VP*)v->vp;
free(vp->orig_vals);
free(vp->vals);
free(vp);
v->vp=NULL;
}
MRISfree(&mris) ;
}
else
{
for (sno = 0; sno < SURFACES ; sno++)
{
if (curvature_names[sno]) /* read in precomputed curvature file */
{
sprintf(surf_fname, "%s/%s/surf/%s.%s",
subjects_dir, subject, hemi, curvature_names[sno]) ;
if (MRISreadCurvatureFile(mris, surf_fname) != NO_ERROR)
{
nbad++ ;
ErrorPrintf(Gerror, "%s: could not read curvature file '%s'\n",
Progname, surf_fname) ;
failed = 1 ;
break ;
}
/* the two next lines were not in the original code */
MRISaverageCurvatures(mris, navgs) ;
MRISnormalizeCurvature(mris, which_norm) ;
} else /* compute curvature of surface */
{
sprintf(surf_fname, "%s/%s/surf/%s.%s",
subjects_dir, subject, hemi, surface_names[sno]) ;
if (MRISreadVertexPositions(mris, surf_fname) != NO_ERROR)
{
ErrorPrintf(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, surf_fname) ;
nbad++ ;
failed = 1 ;
break ;
}
if (nbrs > 1)
MRISsetNeighborhoodSize(mris, nbrs) ;
MRIScomputeMetricProperties(mris) ;
MRIScomputeSecondFundamentalForm(mris) ;
MRISuseMeanCurvature(mris) ;
MRISaverageCurvatures(mris, navgs) ;
MRISrestoreVertexPositions(mris, CANONICAL_VERTICES) ;
MRISnormalizeCurvature(mris, which_norm) ;
}
fprintf(stderr, "computing parameterization for surface %s...\n",
surf_fname);
if (failed)
{
continue ;
MRISfree(&mris) ;
}
mrisp = MRIStoParameterization(mris, NULL, scale, 0) ;
MRISPcombine(mrisp, mrisp_template, sno*3) ;
MRISPfree(&mrisp) ;
}
MRISfree(&mris) ;
}
}
#if 0
if (mrisp_aligned) /* new parameterization - use rigid alignment */
{
MRI_SP *mrisp_tmp ;
if (Gdiag & DIAG_WRITE)
{
char *cp1 ;
FileNameOnly(template_fname, fname) ;
cp = strchr(fname, '.') ;
if (cp)
{
cp1 = strrchr(fname, '.') ;
if (cp1 && cp1 != cp)
strncpy(parms.base_name, cp+1, cp1-cp-1) ;
else
strcpy(parms.base_name, cp+1) ;
}
else
strcpy(parms.base_name, "template") ;
sprintf(fname, "%s.%s.out", hemi, parms.base_name);
parms.fp = fopen(fname, "w") ;
printf("writing output to '%s'\n", fname) ;
}
for (ino = 0 ; ino < argc-1 ; ino++)
{
subject = argv[ino] ;
if (Gdiag & DIAG_WRITE)
fprintf(parms.fp, "processing subject %s\n", subject) ;
fprintf(stderr, "processing subject %s\n", subject) ;
sprintf(surf_fname, "%s/%s/surf/%s.%s",
subjects_dir, subject, hemi, sphere_name) ;
fprintf(stderr, "reading spherical surface %s...\n", surf_fname) ;
mris = MRISread(surf_fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, surf_fname) ;
MRIScomputeMetricProperties(mris) ;
MRISstoreMetricProperties(mris) ;
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
sprintf(surf_fname, "%s/%s/surf/%s.%s",
subjects_dir, subject, hemi, "sulc") ;
if (MRISreadCurvatureFile(mris, surf_fname) != NO_ERROR)
ErrorExit(Gerror, "%s: could not read curvature file '%s'\n",
Progname, surf_fname) ;
parms.frame_no = 3 ;
parms.mrisp = MRIStoParameterization(mris, NULL, scale, 0) ;
parms.mrisp_template = mrisp_template ;
parms.l_corr = 1.0f ;
MRISrigidBodyAlignGlobal(mris, &parms, 1.0, 32.0, 8) ;
if (Gdiag & DIAG_WRITE)
MRISwrite(mris, "sphere.rot.global") ;
MRISrigidBodyAlignLocal(mris, &parms) ;
if (Gdiag & DIAG_WRITE)
MRISwrite(mris, "sphere.rot.local") ;
MRISPfree(&parms.mrisp) ;
#if 0
/* write out rotated surface */
sprintf(surf_fname, "%s.rot", mris->fname) ;
fprintf(stderr, "writing out rigidly aligned surface to '%s'\n",
surf_fname) ;
MRISwrite(mris, surf_fname) ;
#endif
/* now generate new parameterization using the optimal alignment */
for (sno = 0; sno < SURFACES ; sno++)
{
if (curvature_names[sno]) /* read in precomputed curvature file */
{
sprintf(surf_fname, "%s/%s/surf/%s.%s",
subjects_dir, subject, hemi, curvature_names[sno]) ;
if (MRISreadCurvatureFile(mris, surf_fname) != NO_ERROR)
ErrorExit(Gerror, "%s: could not read curvature file '%s'\n",
Progname, surf_fname) ;
} else /* compute curvature of surface */
{
sprintf(surf_fname, "%s/%s/surf/%s.%s",
subjects_dir, subject, hemi, surface_names[sno]) ;
if (MRISreadVertexPositions(mris, surf_fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, surf_fname) ;
if (nbrs > 1)
MRISsetNeighborhoodSize(mris, nbrs) ;
MRIScomputeMetricProperties(mris) ;
MRIScomputeSecondFundamentalForm(mris) ;
MRISuseMeanCurvature(mris) ;
MRISaverageCurvatures(mris, navgs) ;
MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
MRISnormalizeCurvature(mris) ;
}
fprintf(stderr, "computing parameterization for surface %s...\n",
surf_fname);
mrisp = MRIStoParameterization(mris, NULL, scale, 0) ;
MRISPcombine(mrisp, mrisp_aligned, sno*3) ;
MRISPfree(&mrisp) ;
}
MRISfree(&mris) ;
}
if (Gdiag & DIAG_WRITE)
fclose(parms.fp) ;
mrisp_tmp = mrisp_aligned ;
mrisp_aligned = mrisp_template ;
mrisp_template = mrisp_tmp ;
MRISPfree(&mrisp_aligned) ;
}
#endif
fprintf(stderr,
"writing updated template with %d subjects to %s...\n",
argc-1-nbad, template_fname) ;
MRISPwrite(mrisp_template, template_fname) ;
MRISPfree(&mrisp_template) ;
exit(0) ;
return(0) ; /* for ansi */
}
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, 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 **av, *in_fname, *out_fname, fname[STRLEN], path[STRLEN] ;
int ac, nargs, start_t, pass ;
MRI_SURFACE *mris ;
char cmdline[CMD_LINE_LEN] ;
make_cmd_version_string
(argc, argv,
"$Id: mris_smooth.c,v 1.28 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_smooth.c,v 1.28 2011/03/02 00:04:34 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 < 3)
{
print_help() ;
}
in_fname = argv[1] ;
out_fname = argv[2] ;
FileNamePath(out_fname, path) ;
mris = MRISfastRead(in_fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, in_fname) ;
MRISaddCommandLine(mris, cmdline) ;
MRISremoveTriangleLinks(mris) ;
fprintf(stderr, "smoothing surface tessellation for %d iterations...\n",
niterations);
MRIScomputeMetricProperties(mris) ;
MRISstoreMetricProperties(mris) ;
MRISsetNeighborhoodSize(mris, nbrs) ;
#define DT 0.5
if (gaussian_norm > 0)
{
int i, done, start_avgs = gaussian_avgs, j ;
done = 0;
start_t = 0 ;
pass = 0 ;
do
{
for (i = start_t ; i < niterations+start_t ; i++)
{
MRIScomputeMetricProperties(mris) ;
MRISsaveVertexPositions(mris, TMP_VERTICES) ;
for (j = 0 ; j < 5 ; j++)
{
MRISaverageVertexPositions(mris, 2) ; // turn flat spikes into tubular ones
MRIScomputeMetricProperties(mris) ;
MRIScomputeSecondFundamentalForm(mris) ;
MRIShistoThresholdGaussianCurvatureToMarked(mris, (float)(mris->nvertices-20)/mris->nvertices) ;
}
MRISrestoreVertexPositions(mris, TMP_VERTICES) ;
MRIScomputeMetricProperties(mris) ;
MRISsmoothSurfaceNormals(mris, gaussian_avgs) ;
MRISclearMarks(mris) ;
MRISthresholdGaussianCurvatureToMarked(mris, 10, 50);
MRIScomputeSecondFundamentalForm(mris) ;
MRIShistoThresholdGaussianCurvatureToMarked(mris, (float)(mris->nvertices-20)/mris->nvertices) ;
MRISthresholdGaussianCurvatureToMarked(mris, 10, 50);
if ((write_iterations > 0) && ((i % write_iterations) == 0))
{
char fname[STRLEN] ;
sprintf(fname, "%s%04d", out_fname, i) ;
printf("writing snapshot to %s...\n", fname) ;
MRISwrite(mris, fname) ;
if (Gdiag & DIAG_WRITE)
{
MRISuseGaussianCurvature(mris) ;
sprintf(fname, "%s_K%04d", out_fname, i) ;
printf("writing curvature to %s...\n", fname) ;
MRISwriteCurvature(mris, fname) ;
sprintf(fname, "%s_marked%04d", out_fname, i) ;
printf("writing marks to %s...\n", fname) ;
MRISwriteMarked(mris, fname) ;
}
}
for (j = 0 ; j <= 5*nint(1/DT) ; j++)
{
MRISmarkedSpringTerm(mris, l_spring) ;
MRISaverageGradients(mris, gaussian_avgs) ;
MRISmomentumTimeStep(mris, momentum, DT, 1, gaussian_avgs) ;
MRISclearGradient(mris) ;
MRIScomputeMetricProperties(mris) ;
MRISsmoothSurfaceNormals(mris, gaussian_avgs) ;
{
int vno ;
VERTEX *v ;
for (vno = 0 ; vno < mris->nvertices ; vno++)
{
v = &mris->vertices[vno] ;
if (v->marked > 0)
{
v->K = 1.0/(v->marked) ;
}
else
{
v->K = 0 ;
}
}
}
}
}
MRISclearGradient(mris) ;
if (gaussian_avgs == 2)
{
if (pass++ > 4)
{
done = 1 ;
}
else
{
int num = count_big_curvatures(mris, 2) ;
printf("------------------------------------------------------\n") ;
printf("------------------------------------------------------\n") ;
printf("------------------ pass %d (num=%d) ------------------\n",
pass, num) ;
printf("------------------------------------------------------\n") ;
printf("------------------------------------------------------\n") ;
gaussian_avgs = start_avgs ;
}
}
else
{
gaussian_avgs /= 2 ;
if (done ==0)
{
printf("----------------- setting avgs to %d -----------------\n", gaussian_avgs) ;
}
}
start_t = i ;
}
while (!done) ;
#if 0
// more smoothing with principal curvatures
gaussian_avgs = start_avgs ;
printf("--------------------------------------------------------------------------\n") ;
printf("--------------------------------------------------------------------------\n") ;
printf("---------------------- starting threshold smoothing ----------------------\n") ;
printf("--------------------------------------------------------------------------\n") ;
printf("--------------------------------------------------------------------------\n") ;
do
{
for (i = start_t ; i < niterations+start_t ; i++)
{
MRIScomputeMetricProperties(mris) ;
MRIScomputeSecondFundamentalForm(mris) ;
MRISsmoothSurfaceNormals(mris, 16) ;
#define KTHRESH 1.5 // everything with kmin less than this will not move
MRISthresholdPrincipalCurvatures(mris, KTHRESH) ;
MRISspringTermWithGaussianCurvature(mris, gaussian_norm, l_spring) ;
MRISaverageGradients(mris, gaussian_avgs) ;
MRISmomentumTimeStep(mris, 0, 0.1, 1, gaussian_avgs) ;
MRISclearGradient(mris) ;
if ((write_iterations > 0) && (((i+1) % write_iterations) == 0))
{
char fname[STRLEN] ;
sprintf(fname, "%s%04d", out_fname, i+1) ;
printf("writing snapshot to %s...\n", fname) ;
MRISwrite(mris, fname) ;
if (Gdiag & DIAG_WRITE/* && DIAG_VERBOSE_ON*/)
{
MRISuseGaussianCurvature(mris) ;
sprintf(fname, "%s_K%04d", out_fname, i+1) ;
printf("writing curvature to %s...\n", fname) ;
MRISwriteCurvature(mris, fname) ;
}
}
}
MRISclearGradient(mris) ;
done = (gaussian_avgs == 2) ;
gaussian_avgs /= 2 ;
if (done ==0)
{
printf("---------------------- setting avgs to %d ----------------------\n", gaussian_avgs) ;
}
start_t = i ;
}
while (!done) ;
#endif
}
else
{
MRISaverageVertexPositions(mris, niterations) ;
}
fprintf(stderr, "smoothing complete - recomputing first and second "
"fundamental forms...\n") ;
MRIScomputeMetricProperties(mris) ;
if (rescale)
{
MRISscaleBrainArea(mris) ;
}
MRIScomputeSecondFundamentalForm(mris) ;
MRISuseMeanCurvature(mris) ;
MRISaverageCurvatures(mris, navgs) ;
if (normalize_flag)
{
MRISnormalizeCurvature(mris, which_norm) ;
}
sprintf(fname, "%s.%s", mris->hemisphere == LEFT_HEMISPHERE?"lh":"rh",
curvature_fname);
if (no_write == 0)
{
fprintf(stderr, "writing smoothed curvature to %s/%s\n", path,fname) ;
MRISwriteCurvature(mris, fname) ;
sprintf(fname, "%s.%s", mris->hemisphere == LEFT_HEMISPHERE?"lh":"rh",
area_fname);
fprintf(stderr, "writing smoothed area to %s/%s\n", path, fname) ;
MRISwriteArea(mris, fname) ;
}
if (Gdiag & DIAG_SHOW)
{
fprintf(stderr, "writing smoothed surface to %s\n", out_fname) ;
}
MRISwrite(mris, out_fname) ;
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 */
}
