MRI *
correct_largestCC_and_fill_holes(MRI *segmri, MRI *outmri)
{
int i, x, y, z, width, height, depth = 0, val;
width = segmri->width ;
height = segmri->height ;
depth = segmri->depth ;
// char fname[STR_LEN];
if (!outmri)
printf("no outmri volume exists!\n") ;
//outmri = MRIclone(segmri, NULL) ;
//outmri = MRIalloc(width, height, depth, MRI_INT);
int *segidlist;
int nsegids = 0;
segidlist = MRIsegIdListNot0(segmri, &nsegids, 0);
MRI *currlabelvol = MRIalloc(width, height, depth, MRI_INT);
int currlabel = 0;
for (i = 0; i < nsegids; i++)
{
currlabel = segidlist[i];
if (currlabel > 0)
{
// label volume
for (x = 0 ; x < width ; x++)
for (y = 0 ; y < height ; y++)
for (z = 0 ; z < depth ; z++)
if (MRIgetVoxVal(segmri,x,y,z,0) == currlabel)
MRIsetVoxVal(currlabelvol,x,y,z,0,1);
else
MRIsetVoxVal(currlabelvol,x,y,z,0,0);
// choose largest connected components
// sprintf(fname, "/tmp/%d.%s", currlabel, "before-largest-conn-component.mgz") ;
// MRIwrite(currlabelvol, fname) ;
GetLargestCC6(currlabelvol); // Note: how to fill the background???!! -- WM
// sprintf(fname, "/tmp/%d.%s", currlabel, "largest-conn-component.mgz") ;
// MRIwrite(currlabelvol, fname) ;
// remove holes on that component
RemoveHoles(currlabelvol);
// sprintf(fname, "/tmp/%d.%s", currlabel, "holes-removed.mgz") ;
// MRIwrite(currlabelvol, fname) ;
//fill ouput volume with new labels
for (x = 0 ; x < width ; x++)
for (y = 0 ; y < height ; y++)
for (z = 0 ; z < depth ; z++)
{
val = MRIgetVoxVal(currlabelvol,x,y,z,0);
if (val == 1)
MRIsetVoxVal(outmri,x,y,z,0,currlabel);
}
}
}
return(outmri) ;
}
int main(int argc, char *argv[]) {
char **av;
MRI *mri_seg;
int ac, nargs;
int x, y, z;
int target_value = 255;
Progname = argv[0];
nargs = handle_version_option (argc, argv, "$Id: mri_extract_largest_CC.c,v 1.6 2011/03/02 00:04:15 nicks Exp $", "$Name: stable5 $");
argc -= nargs ;
if (1 == argc)
exit (0);
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc != 3)
usage(1);
if (!stricmp(hemi, "lh")) {
target_value = lh_label;
} else {
target_value = rh_label;
}
mri_seg = MRIread(argv[1]) ;
if (!mri_seg)
ErrorExit(ERROR_BADPARM, "%s: could not read label volume %s",
Progname, argv[1]) ;
for (z = 0; z < mri_seg->depth; z++)
for (y = 0; y < mri_seg->height; y++)
for (x = 0; x < mri_seg->width; x++) {
if (MRIgetVoxVal(mri_seg, x, y, z, 0) < threshold)
MRIsetVoxVal(mri_seg, x, y, z, 0, 0);
else
MRIsetVoxVal(mri_seg, x, y, z, 0, 255);
}
GetLargestCC6(mri_seg);
for (z = 0; z < mri_seg->depth; z++)
for (y = 0; y < mri_seg->height; y++)
for (x = 0; x < mri_seg->width; x++) {
if (MRIgetVoxVal(mri_seg, x, y, z, 0) > 0)
MRIsetVoxVal(mri_seg, x, y, z, 0, target_value);
}
MRIwrite(mri_seg, argv[2]);
exit(0);
} /* end main() */
