int
main(int argc, char *argv[]) {
char **av, surf_fname[100], *template_fname, *out_fname, *surf_dir,
*hemi, *sphere_name ;
int ac, nargs ;
MRI_SURFACE *mris ;
MRI_SP *mrisp, *mrisp_template ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mris_add_template.c,v 1.8 2011/03/02 00:04:26 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 < 5)
usage_exit() ;
surf_dir = argv[1] ;
hemi = argv[2] ;
sphere_name = argv[3] ;
out_fname = template_fname = argv[4] ;
if (argc > 5)
out_fname = argv[5] ;
sprintf(surf_fname, "%s/%s.%s", surf_dir, hemi, sphere_name) ;
fprintf(stderr, "reading new surface %s...\n", surf_fname) ;
mris = MRISread(surf_fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, surf_fname) ;
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
if (!FileExists(template_fname)) /* first time - create it */
{
fprintf(stderr, "creating new parameterization...\n") ;
mrisp_template = MRISPalloc(scale, PARAM_IMAGES);
} 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) ;
}
/*
first read in inflated surface and use it to build the first template
set.
*/
sprintf(surf_fname, "%s/%s.%s", surf_dir, hemi, INFLATED_NAME) ;
if (MRISreadVertexPositions(mris, surf_fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, surf_fname) ;
MRISsetNeighborhoodSize(mris, nbrs) ;
MRIScomputeMetricProperties(mris) ;
MRIScomputeSecondFundamentalForm(mris) ;
MRISuseMeanCurvature(mris) ;
MRISaverageCurvatures(mris, navgs) ;
MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
MRISnormalizeCurvature(mris, which_norm) ;
fprintf(stderr, "computing parameterization for surface %s...\n",surf_fname);
mrisp = MRIStoParameterization(mris, NULL, scale, 0) ;
MRISPcombine(mrisp, mrisp_template, 0) ;
MRISPfree(&mrisp) ;
/*
now do the same thing with the smoothwm curvatures.
*/
sprintf(surf_fname, "%s/%s.%s", surf_dir, hemi, SMOOTH_NAME) ;
if (MRISreadVertexPositions(mris, surf_fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, surf_fname) ;
MRIScomputeMetricProperties(mris) ;
if (curvature_fname[0])
MRISreadCurvatureFile(mris, curvature_fname) ;
else {
MRIScomputeSecondFundamentalForm(mris) ;
MRISuseMeanCurvature(mris) ;
}
MRISaverageCurvatures(mris, navgs) ;
MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
if (curvature_fname[0])
fprintf(stderr, "computing parameterization for surface %s (%s)...\n",
surf_fname, curvature_fname);
else
fprintf(stderr, "computing parameterization for surface %s...\n",
surf_fname);
MRISnormalizeCurvature(mris, which_norm) ;
mrisp = MRIStoParameterization(mris, NULL, scale, 0) ;
MRISPcombine(mrisp, mrisp_template, 3) ;
fprintf(stderr, "writing updated template to %s...\n", out_fname) ;
MRISPwrite(mrisp_template, out_fname) ;
MRISPfree(&mrisp) ;
MRISPfree(&mrisp_template) ;
MRISfree(&mris) ;
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 */
}