int main(int argc, char *argv[]) {
char *inner_mris_fname,*outer_mris_fname,*input_mri_pref,*output_mri_pref;
MRI *mri=0,*mri_src=0;
MRI_SURFACE *inner_mris=0,*outer_mris=0;
int nargs;
LABEL *area = NULL ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mri_ribbon.c,v 1.15 2011/03/02 00:04:24 nicks Exp $",
"$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname=argv[0];
if (argc > 1)
while (*argv[1] == '-')
{
int nargs = 0 ;
switch (toupper(argv[1][1]))
{
case 'L':
printf("cropping ribbon to label file %s\n", argv[2]) ;
nargs = 1 ;
area = LabelRead(NULL, argv[2]) ;
if (area == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not read label file %s\n",
argv[2]) ;
break ;
default:
break ;
}
argc -= (nargs+1) ;
if (argc == 1) break;
argv += (nargs+1) ;
}
/* Set command-line parameters */
if (argc!=5) {
printf("Usage: mri_ribbon [-l fname.label] \\ \n"
" inner_surface_fname \\ \n"
" outer_surface_fname \\ \n"
" input_volume_pref \\ \n"
" output_volume_pref\n");
exit(1);
}
inner_mris_fname=argv[1];
outer_mris_fname=argv[2];
input_mri_pref=argv[3];
output_mri_pref=argv[4];
/* Read surface information from inner surface file */
printf("Reading surface file %s.\n",inner_mris_fname);
inner_mris=MRISread(inner_mris_fname);
if (!inner_mris) {
printf("Could not read surface file %s.\n",inner_mris_fname);
exit(1);
}
/* Read surface information from outer surface file */
printf("Reading surface file %s.\n",outer_mris_fname);
outer_mris=MRISread(outer_mris_fname);
if (!outer_mris) {
printf("Could not read surface file %s.\n",outer_mris_fname);
exit(1);
}
/* Read example volume from file */
printf("Reading MRI volume directory %s.\n",input_mri_pref);
mri_src=MRIread(input_mri_pref);
if (!mri_src) {
printf("Could not read MRI volume directory %s.\n",input_mri_pref);
exit(1);
}
/* Extract ribbon */
printf("Extracting ribbon.\n");
mri=MRISribbon(inner_mris,outer_mris,mri_src,NULL);
if (area)
MRIcropVolumeToLabel(mri, mri, area, inner_mris, outer_mris) ;
/* Save MRI volume to directory */
printf("Writing volume file %s.\n",output_mri_pref);
MRIwrite(mri,output_mri_pref);
MRIfree(&mri);
MRIfree(&mri_src);
MRISfree(&inner_mris);
MRISfree(&outer_mris);
return 0;
}
int
insert_ribbon_into_aseg(MRI *mri_src_aseg, MRI *mri_aseg,
MRI_SURFACE *mris_white, MRI_SURFACE *mris_pial,
int hemi)
{
MRI *mri_ribbon, *mri_white ;
int x, y, z, gm_label, wm_label, label, nbr_label, dont_change ;
if (mri_src_aseg != mri_aseg)
mri_aseg = MRIcopy(mri_src_aseg, mri_aseg) ;
gm_label = hemi == LEFT_HEMISPHERE ?
Left_Cerebral_Cortex : Right_Cerebral_Cortex ;
wm_label = hemi == LEFT_HEMISPHERE ?
Left_Cerebral_White_Matter : Right_Cerebral_White_Matter ;
mri_white = MRIclone(mri_aseg, NULL) ;
mri_ribbon = MRISribbon(mris_white, mris_pial, mri_aseg, NULL) ;
MRISfillInterior(mris_white, mri_aseg->xsize, mri_white) ;
for (x = 0 ; x < mri_aseg->width ; x++)
for (y = 0 ; y < mri_aseg->height ; y++)
for (z = 0 ; z < mri_aseg->depth ; z++)
{
if (x == Gx && y == Gy && z == Gz)
DiagBreak() ;
label = nint(MRIgetVoxVal(mri_aseg, x, y, z, 0)) ;
if (nint(MRIgetVoxVal(mri_ribbon, x, y, z, 0)) == 255) // in ribbon, set to GM
{
if (IS_CORTEX(label) || IS_WHITE_CLASS(label))
{
int xi, yi, zi, xk, yk, zk ;
// check to make sure we are really in cortex
for (dont_change = 0, xk = -1 ; xk <= 1 ; xk++)
{
xi = mri_aseg->xi[xk+x] ;
for (yk = -1 ; yk <= 1 ; yk++)
{
yi = mri_aseg->yi[yk+y] ;
for (zk = -1 ; zk <= 1 ; zk++)
{
zi = mri_aseg->zi[zk+z] ;
nbr_label = (int)MRIgetVoxVal(mri_aseg, xi, yi, zi, 0) ;
switch (nbr_label)
{
default:
break ;
case Left_Hippocampus:
case Right_Hippocampus:
case Left_Amygdala:
case Right_Amygdala:
case Left_VentralDC:
case Right_VentralDC:
case Brain_Stem:
case Left_Lateral_Ventricle:
case Right_Lateral_Ventricle:
case Left_Inf_Lat_Vent:
case Right_Inf_Lat_Vent:
case Left_Thalamus_Proper:
case Right_Thalamus_Proper:
case Left_choroid_plexus:
case Right_choroid_plexus:
case CC_Posterior:
case CC_Mid_Posterior:
case CC_Central:
case CC_Mid_Anterior:
case CC_Anterior:
dont_change = 1 ;
break ;
}
}
}
}
if (dont_change == 0)
MRIsetVoxVal(mri_aseg, x, y, z, 0, gm_label) ;
}
}
else // not in ribbon
{
if (MRIgetVoxVal(mri_white, x, y, z, 0) > 0) // inside white surface - disambiguate
{
if (label == gm_label) // gm inside white surface should be wm
MRIsetVoxVal(mri_aseg, x, y, z, 0, wm_label) ;
}
else if (label == gm_label) // gm outside ribbon should be unknown
MRIsetVoxVal(mri_aseg, x, y, z, 0, Unknown) ;
}
}
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_ribbon, "r.mgz") ;
MRIwrite(mri_white, "w.mgz");
}
MRIfree(&mri_ribbon) ; MRIfree(&mri_white) ;
return(NO_ERROR) ;
}
