static int
initialize_cluster_centers(MRI_SURFACE *mris, MRI *mri_profiles, CLUSTER *ct, int k) {
int i, j, done, vno, nsamples, vnos[MAX_CLUSTERS], iter ;
double dist, min_dist ;
VERTEX *v, *vn ;
nsamples = mri_profiles->nframes ;
min_dist = sqrt(mris->total_area/k) / 2 ;
for (i = 0 ; i < k ; i++) {
iter = 0 ;
do {
do {
vno = (int)randomNumber(0, mris->nvertices-1) ;
v = &mris->vertices[vno] ;
} while (v->ripflag) ;
// see if any of the other centers are too close to this one
done = 1 ;
for (j = 0 ; done && j < i ; j++) {
if (j == i)
continue ;
vn = &mris->vertices[vnos[j]] ;
dist = sqrt(SQR(vn->x-v->x)+SQR(vn->y-v->y)+SQR(vn->z-v->z)) ;
if (dist < min_dist) {
done = 0 ;
break ;
}
}
if (iter++ > mris->nvertices)
done = 1 ;
} while (!done) ;
vnos[i] = vno ;
for (j = 0 ; j < nsamples ; j++)
VECTOR_ELT(ct[i].v_mean, j+1) = MRIgetVoxVal(mri_profiles, vno, 0, 0, j) ;
}
mris->ct = CTABalloc(k) ;
for (i = 0 ; i < k ; i++) {
mris->vertices[vnos[i]].curv = i ;
ct[i].npoints++ ;
ct[i].vno = vnos[i] ;
CTABannotationAtIndex(mris->ct, i, &mris->vertices[vnos[i]].annotation) ;
}
return(NO_ERROR) ;
}
/* ------------------------------------------------------------
int sclustAnnot(MRIS *surf, int NClusters)
Convert clusters into annotation
------------------------------------------------------------*/
int sclustAnnot(MRIS *surf, int NClusters)
{
COLOR_TABLE *ct ;
int vtxno, vtx_clusterno, annot, n;
ct = CTABalloc(NClusters+1);
surf->ct = ct;
for(n=1; n < NClusters; n++) // no cluster 0
sprintf(surf->ct->entries[n]->name, "%s-%03d","cluster",n);
for(vtxno = 0; vtxno < surf->nvertices; vtxno++) {
vtx_clusterno = surf->vertices[vtxno].undefval;
if(vtx_clusterno == 0 || vtx_clusterno > NClusters){
surf->vertices[vtxno].annotation = 0;
continue;
}
CTABannotationAtIndex(surf->ct, vtx_clusterno, &annot);
surf->vertices[vtxno].annotation = annot;
}
return(0);
}
static int
initialize_cluster_centers_with_ico(MRI_SURFACE *mris, MRI *mri_profiles, CLUSTER *ct, MRI_SURFACE *mris_ico) {
int i, j, vno, nsamples, vnos[MAX_CLUSTERS], k ;
double r1, r2, res ;
float fmin ;
MRIS_HASH_TABLE *mht ;
VERTEX *vico ;
k = mris_ico->nvertices ;
MRISstoreRipFlags(mris) ;
MRISunrip(mris) ;
r1 = MRISaverageRadius(mris) ;
r2 = MRISaverageRadius(mris_ico) ;
MRISscaleBrain(mris_ico,mris_ico, r1/r2);
res = sqrt(mris->total_area/mris->nvertices) ;
mht = MHTfillVertexTableRes(mris, NULL, CURRENT_VERTICES, 2*res) ;
nsamples = mri_profiles->nframes ;
for (i = 0 ; i < mris_ico->nvertices ; i++) {
vico = &mris_ico->vertices[i] ;
vno = MRISfindClosestVertex(mris, vico->x, vico->y, vico->z, &fmin) ;
if (vno < 0)
continue ;
vnos[i] = vno ;
for (j = 0 ; j < nsamples ; j++)
VECTOR_ELT(ct[i].v_mean, j+1) = MRIgetVoxVal(mri_profiles, vno, 0, 0, j) ;
}
mris->ct = CTABalloc(k) ;
for (i = 0 ; i < k ; i++) {
mris->vertices[vnos[i]].curv = i ;
ct[i].npoints++ ;
ct[i].vno = vnos[i] ;
CTABannotationAtIndex(mris->ct, i, &mris->vertices[vnos[i]].annotation) ;
}
MRISrestoreRipFlags(mris) ;
return(NO_ERROR) ;
}
int
main(int argc, char *argv[])
{
char **av, fname[STRLEN] ;
int ac, nargs, i ;
char *subject, *cp, mdir[STRLEN], *out_fname, *name ;
int r, g, b, nedits = 0 ;
MRI *mri=NULL, *mri_edits=NULL, *mri_aseg_auto=NULL;
// default output file name:
out_fname = strcpyalloc("edits.mgz");
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mri_compile_edits.c,v 1.6 2011/03/02 00:04:14 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(1) ;
if (strlen(sdir) == 0)
{
cp = getenv("SUBJECTS_DIR") ;
if (cp == NULL)
ErrorExit
(ERROR_BADPARM,
"%s: SUBJECTS_DIR must be defined in the env or on cmdline "
"with -sdir", Progname) ;
strcpy(sdir, cp) ;
}
subject = argv[1] ;
if (argv[2]) out_fname = argv[2] ;
printf("Compiling volume edits for subject %s...\n", subject) ;
fflush(stdout);
sprintf(mdir, "%s/%s/mri", sdir, subject) ;
/*
* brain.mgz
*/
sprintf(fname, "%s/brain.mgz", mdir) ;
mri = MRIread(fname) ;
if (mri)
{
if(NULL == mri_edits) mri_edits = MRIclone(mri, NULL) ;
int edits = MRIsetVoxelsWithValue(mri,
mri_edits,
WM_EDITED_OFF_VAL,
EDIT_BRAIN_OFF) ;
edits += MRIsetVoxelsWithValue(mri,
mri_edits,
WM_EDITED_ON_VAL,
EDIT_BRAIN_ON) ;
nedits += edits;
MRIfree(&mri) ;
if (edits) printf("Found %d edits in brain.mgz\n",edits);
fflush(stdout);
}
/*
* wm.mgz
*/
sprintf(fname, "%s/wm.mgz", mdir) ;
mri = MRIread(fname) ;
if (mri)
{
if(NULL == mri_edits) mri_edits = MRIclone(mri, NULL) ;
int edits = MRIsetVoxelsWithValue(mri,
mri_edits,
WM_EDITED_OFF_VAL,
EDIT_WM_OFF) ;
edits += MRIsetVoxelsWithValue(mri, mri_edits,
WM_EDITED_ON_VAL,
EDIT_WM_ON) ;
nedits += edits;
MRIfree(&mri) ;
if (edits) printf("Found %d edits in wm.mgz\n",edits);
fflush(stdout);
}
/*
* brainmask.mgz
*/
sprintf(fname, "%s/brainmask.mgz", mdir) ;
mri = MRIread(fname) ;
if (mri)
{
if(NULL == mri_edits) mri_edits = MRIclone(mri, NULL) ;
int edits = MRIsetVoxelsWithValue(mri,
mri_edits,
WM_EDITED_OFF_VAL,
EDIT_BRAINMASK_OFF) ;
edits += MRIsetVoxelsWithValue(mri, mri_edits,
WM_EDITED_ON_VAL,
EDIT_BRAINMASK_ON) ;
nedits += edits;
MRIfree(&mri) ;
if (edits) printf("Found %d edits in brainmask.mgz\n",edits);
fflush(stdout);
}
/*
* brain.finalsurfs.mgz
*/
sprintf(fname, "%s/brain.finalsurfs.mgz", mdir) ;
mri = MRIread(fname) ;
if (mri)
{
if(NULL == mri_edits) mri_edits = MRIclone(mri, NULL) ;
int edits = MRIsetVoxelsWithValue(mri,
mri_edits,
WM_EDITED_OFF_VAL,
EDIT_FINALSURFS_OFF) ;
edits += MRIsetVoxelsWithValue(mri,
mri_edits,
WM_EDITED_ON_VAL,
EDIT_FINALSURFS_ON) ;
nedits += edits;
MRIfree(&mri) ;
if (edits) printf("Found %d edits in brain.finalsurfs.mgz\n",edits);
fflush(stdout);
}
/*
* aseg.mgz
*/
sprintf(fname, "%s/aseg.mgz", mdir) ;
mri = MRIread(fname) ;
if (mri)
{
if(NULL == mri_edits) mri_edits = MRIclone(mri, NULL) ;
sprintf(fname, "%s/aseg.auto.mgz", mdir) ;
mri_aseg_auto = MRIread(fname) ;
if (mri_aseg_auto)
{
int edits = MRIsetDifferentVoxelsWithValue(mri,
mri_aseg_auto,
mri_edits,
EDIT_ASEG_CHANGED);
nedits += edits;
MRIfree(&mri) ;
MRIfree(&mri_aseg_auto) ;
if (edits) printf("Found %d edits in aseg.mgz\n",edits);
fflush(stdout);
}
}
if (mri_edits)
{
mri_edits->ct = CTABalloc(CTAB_ENTRIES) ;
strcpy (mri_edits->fname, "mri_compile_edits");
for (i = 0 ; i < CTAB_ENTRIES ; i++)
{
switch (i)
{
case EDIT_WM_OFF:
name = "wm-OFF" ;
r = 0 ;
g = 0 ;
b = 255 ;
break ;
case EDIT_WM_ON:
name = "wm-ON" ;
r = 255 ;
g = 0 ;
b = 0 ;
break ;
case EDIT_BRAIN_OFF:
name = "brain-OFF" ;
r = 0 ;
g = 255 ;
b = 255 ;
break ;
case EDIT_BRAIN_ON:
name = "brain-ON" ;
r = 255 ;
g = 255 ;
b = 0 ;
break ;
case EDIT_BRAINMASK_OFF:
name = "brainmask-OFF" ;
r = 0 ;
g = 64 ;
b = 255 ;
break ;
case EDIT_BRAINMASK_ON:
name = "brainmask-ON" ;
r = 255 ;
g = 26 ;
b = 0 ;
break ;
case EDIT_FINALSURFS_OFF:
name = "brain.finalsurf-OFF" ;
r = 0 ;
g = 128 ;
b = 255 ;
break ;
case EDIT_FINALSURFS_ON:
name = "brain.finalsurfs-ON" ;
r = 255 ;
g = 128 ;
b = 0 ;
break ;
case EDIT_ASEG_CHANGED:
name = "aseg-CHANGED" ;
r = 255 ;
g = 255 ;
b = 128 ;
break ;
default:
continue ;
}
strcpy(mri_edits->ct->entries[i]->name, name) ;
mri_edits->ct->entries[i]->ri = r ;
mri_edits->ct->entries[i]->gi = g ;
mri_edits->ct->entries[i]->bi = b ;
mri_edits->ct->entries[i]->ai = 255;
/* Now calculate the float versions. */
mri_edits->ct->entries[i]->rf =
(float)mri_edits->ct->entries[i]->ri / 255.0;
mri_edits->ct->entries[i]->gf =
(float)mri_edits->ct->entries[i]->gi / 255.0;
mri_edits->ct->entries[i]->bf =
(float)mri_edits->ct->entries[i]->bi / 255.0;
mri_edits->ct->entries[i]->af =
(float)mri_edits->ct->entries[i]->ai / 255.0;
}
}
// recon-all -show-edits greps on this text, so dont change it
if (nedits && mri_edits)
{
printf("%d mri_compile_edits_found, saving results to %s\n",
nedits, out_fname) ;
MRIwrite(mri_edits, out_fname);
printf("Edits can be viewed with command:\n");
printf("tkmedit %s T1.mgz -segmentation %s\n",subject,out_fname);
}
else
{
printf("0 mri_compile_edits_found\n") ;
}
exit(0) ;
return(0) ;
}