int
main(int argc, char *argv[])
{
char **av, *in_vol, *out_vol;
int ac, nargs;
MRI *mri_in, *mri_out, *mri_tmp ;
LTA *lta = 0;
MATRIX *i_to_r_src = 0; /* src geometry of the input LTA */
MATRIX *V_to_V = 0; /* Final voxel-to-voxel transform */
MATRIX *r_to_i_dst = 0; /* dst geometry of the input LTA */
MATRIX *m_tmp = 0;
MATRIX *i_to_r_reg = 0; /* i_to_r of the volume after registration */
MATRIX *r_to_i_out = 0; /* r_to_i of the final output volume */
VOL_GEOM vgm_in;
int x, y, z;
double maxV, minV, value;
// MATRIX *i_to_r, *r_to_i;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_transform_to_COR.c,v 1.8 2011/03/02 00:04:55 nicks Exp $", "$Name: stable5 $");
if (nargs && argc - nargs == 1)
usage_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)
usage_exit(0) ;
in_vol = argv[1] ;
out_vol = argv[2] ;
printf("reading volume from %s...\n", in_vol) ;
mri_in = MRIread(in_vol) ;
if (!mri_in)
ErrorExit(ERROR_NOFILE, "%s: could not read MRI volume %s", Progname,
in_vol) ;
/* Convert mri_in to float type */
/* double would be more accurate */
if (mri_in->type != MRI_FLOAT)
{
printf("Input volume type is %d\n", mri_in->type);
printf("Change input volume to float type for convenience and accuracy");
mri_tmp = MRIchangeType(mri_in, MRI_FLOAT, 0, 1.0, 1);
MRIfree(&mri_in);
mri_in = mri_tmp; //swap
}
/* Get input volume geometry, which is needed to compute i_to_r
* and r_to_i of input volume. Note that i_to_r and r_to_i assumed
* a certain prespecified c_r, c_a, c_s
*/
getVolGeom(mri_in, &vgm_in);
maxV = -10000.0;
minV = 10000.0;
for (z=0; z < mri_in->depth; z++)
for (y=0; y< mri_in->height; y++)
for (x=0; x < mri_in->width; x++)
{
if (MRIFvox(mri_in, x, y, z) > maxV )
maxV = MRIFvox(mri_in, x, y,z) ;
if (MRIFvox(mri_in, x, y, z) < minV )
minV = MRIFvox(mri_in, x, y,z) ;
}
printf("Input volume has max = %g, min =%g\n", maxV, minV);
printf("Scale input volume by %g \n", scale);
maxV = -10000.0;
minV = 10000.0;
for (z=0; z < mri_in->depth; z++)
for (y=0; y< mri_in->height; y++)
for (x=0; x < mri_in->width; x++)
{
MRIFvox(mri_in, x, y, z) *= scale;
if (MRIFvox(mri_in, x, y, z) > maxV )
maxV = MRIFvox(mri_in, x, y,z) ;
if (MRIFvox(mri_in, x, y, z) < minV )
minV = MRIFvox(mri_in, x, y,z) ;
}
printf("Input volume after scaling has max = %g, min =%g\n", maxV, minV);
/* Try to compute the Voxel_to_Voxel transform from the input volume
* and the registration target/reference volume!
* If no registration is involved, vox_to_vox is simply identity
*/
/* Things become more complicated when allowing inverse transform */
if (transform_flag)
{
int transform_type;
printf("INFO: Applying transformation from file %s...\n",
transform_fname);
transform_type = TransformFileNameType(transform_fname);
/* Read in LTA transform file name */
if (transform_type == MNI_TRANSFORM_TYPE ||
transform_type == TRANSFORM_ARRAY_TYPE ||
transform_type == REGISTER_DAT ||
transform_type == FSLREG_TYPE
)
{
printf("Reading transform ...\n");
lta = LTAreadEx(transform_fname) ;
if (!lta)
ErrorExit(ERROR_NOFILE, "%s: could not read transform file %s",
Progname, transform_fname) ;
if (transform_type == FSLREG_TYPE)
{
if (lta_src == 0 || lta_dst == 0)
{
fprintf(stderr, "ERROR: fslmat does not have information on the src and dst volumes\n");
fprintf(stderr, "ERROR: you must give options '-src' and '-dst' to specify the src and dst volume infos for the registration\n");
}
LTAmodifySrcDstGeom(lta, lta_src, lta_dst); // add src and dst information
//The following is necessary to interpret FSLMAT correctly!!!
LTAchangeType(lta, LINEAR_VOX_TO_VOX);
}
if (lta->xforms[0].src.valid == 0)
{
if (lta_src == 0)
{
fprintf(stderr, "The transform does not have the valid src volume info.\n");
fprintf(stderr, "Either you give src volume info by option -src or\n");
fprintf(stderr, "make the transform to have the valid src info.\n");
ErrorExit(ERROR_BAD_PARM, "Bailing out...\n");
}
else
{
LTAmodifySrcDstGeom(lta, lta_src, NULL); // add src information
}
}
if (lta->xforms[0].dst.valid == 0)
{
if (lta_dst == 0)
{
fprintf(stderr, "The transform does not have the valid dst volume info.\n");
fprintf(stderr, "Either you give src volume info by option -dst or\n");
fprintf(stderr, "make the transform to have the valid dst info.\n");
fprintf(stderr, "If the dst was average_305, then you can set\n");
fprintf(stderr, "environmental variable USE_AVERAGE305 true\n");
fprintf(stderr, "instead.\n");
ErrorExit(ERROR_BAD_PARM, "Bailing out...\n");
}
else
{
LTAmodifySrcDstGeom(lta, NULL, lta_dst); // add dst information
}
}
// The following procedure aims to apply an LTA computed from COR format to a volume in non-COR format, or vice versa, as long as they share the same RAS
// first change to LINEAR RAS_TO_RAS using old info
if (lta->type != LINEAR_RAS_TO_RAS)
{
LTAchangeType(lta, LINEAR_RAS_TO_RAS);
}
// now possiblly reset the src and dst
if (lta_src != NULL)
{
//always trust the user
LTAmodifySrcDstGeom(lta, lta_src, NULL);
}
if (lta_dst != NULL)
{
//always trust the user
LTAmodifySrcDstGeom(lta, NULL, lta_dst);
}
if (lta->type == LINEAR_RAS_TO_RAS)
{
/* Convert it to VOX_TO_VOX */
/* VOXELsrc_to_VOXELdst = R2Vdst*R2Rlta*V2Rsrc */
/* Note whether the input should be identical to src or dst here depends
* on whether the LTA here is the direct or inverse transform
*/
i_to_r_src = vg_i_to_r(<a->xforms[0].src);
r_to_i_dst = vg_r_to_i(<a->xforms[0].dst);
if (!r_to_i_dst || !i_to_r_src)
ErrorExit(ERROR_BADFILE, "%s: failed to extract volume geometries from input LTA file",Progname);
m_tmp = MatrixMultiply(lta->xforms[0].m_L, i_to_r_src, NULL);
V_to_V = MatrixMultiply(r_to_i_dst, m_tmp, NULL);
MatrixFree(&m_tmp);
MatrixFree(&i_to_r_src);
MatrixFree(&r_to_i_dst);
}
}
else
{
fprintf(stderr, "unknown transform type in file %s\n",
transform_fname);
exit(1);
}
if (invert_flag)
{
/* Geometry of input volume should match that of the dst of the LTA */
if (MYvg_isEqual(<a->xforms[0].dst, &vgm_in) == 0)
{
ErrorExit(ERROR_BADFILE, "%s: dst volume of lta doesn't match that of input volume",Progname);
}
i_to_r_reg = vg_i_to_r(<a->xforms[0].src);
if (!i_to_r_reg)
ErrorExit(ERROR_BADFILE, "%s: failed to extract i_to_r of registered volume from LTA",Progname);
m_tmp = MatrixInverse(V_to_V, NULL);
if (!m_tmp)
ErrorExit(ERROR_BADPARM, "%s: transform is singular!", Progname);
MatrixFree(&V_to_V);
V_to_V = m_tmp;
}
else
{
/* Geometry of input volume should match that of the src of the LTA */
if (MYvg_isEqual(<a->xforms[0].src, &vgm_in) == 0)
{
ErrorExit(ERROR_BADFILE, "%s: src volume of lta doesn't match that of input volume",Progname);
}
i_to_r_reg = vg_i_to_r(<a->xforms[0].dst);
if (!i_to_r_reg)
ErrorExit(ERROR_BADFILE, "%s: failed to extract i_to_r of registered volume from LTA",Progname);
}
}
else
{
/* No registration transform need be applied */
V_to_V = MatrixIdentity(4, NULL);
i_to_r_reg = extract_i_to_r(mri_in);
if (!i_to_r_reg)
ErrorExit(ERROR_BADFILE, "%s: failed to extract i_to_r from input volume",Progname);
}
/* Now need to find the vox-to-vox transformation between registered volume
* (or input volume itself if no registration involved) and the output
* volume, either in COR format or as the out-like volume
*/
/* Given a volume with a certain i_to_r, we need to compute the necessary
* vox-to-voxel transform to change its i_to_r to like another volume.
* The vox-to-vox is equal to R2V(r_to_i)_likevol*i_to_r_current_vol.
*/
if (out_like_fname)
{
mri_tmp = MRIread(out_like_fname) ;
if (!mri_tmp)
ErrorExit(ERROR_NOFILE, "%s: could not read template volume from %s",out_like_fname) ;
/* out_type = mri_tmp->type; */
/* specify the out-type to float initially so as not to lose accuracy
* during reslicing, will change type to correct type later.
*/
mri_out = MRIalloc(mri_tmp->width, mri_tmp->height, mri_tmp->depth, MRI_FLOAT) ;
MRIcopyHeader(mri_tmp, mri_out) ;
MRIfree(&mri_tmp);
}
else /* assume output is in COR format */
{
mri_out = MRIalloc(256, 256, 256, MRI_FLOAT) ;
/* out_type = MRI_UCHAR; */
/* Who says MRIlinearTransformInterp will change the header??
* I don't think so!
*/
//E/ set xyzc_ras to coronal ones.. - these'll get zorched
//by MRIlinearTransformInterp() - copy again later - is there
//any use in having them here now? yes, so we can pass mri_out
//to the ras2vox fns.
mri_out->imnr0 = 1; /* what's this? */
mri_out->imnr1 = 256; /* what's this? */
mri_out->thick = 1.0;
mri_out->ps = 1.0; /* what's this? */
mri_out->xsize = mri_out->ysize = mri_out->zsize = 1.0;
mri_out->xstart = mri_out->ystart = mri_out->zstart = -128.0;
mri_out->xend = mri_out->yend = mri_out->zend = 128.0;
mri_out->x_r =-1;
mri_out->y_r = 0;
mri_out->z_r = 0;
mri_out->x_a = 0;
mri_out->y_a = 0;
mri_out->z_a = 1;
mri_out->x_s = 0;
mri_out->y_s =-1;
mri_out->z_s = 0;
/* In this case, the RAS itself is not fully determined, i.e., c_ras.
* It's quite arbitrary, different values just change the final
* sitting of the volume inside the RAS system.
*/
/* NO! The C_RAS has to be set correctly, depending which target
* volume the previous Vox_to_Vox transformation assumes!
* When a registration is involved, the target volume is either
* the src of LTA (direct) or the dst (inverse transform). When
* just change format, the target volume is the input itself!!
*/
if (transform_flag)
{
if (invert_flag)
{
mri_out->c_r = lta->xforms[0].src.c_r;
mri_out->c_a = lta->xforms[0].src.c_a;
mri_out->c_s = lta->xforms[0].src.c_s;
}
else
{
mri_out->c_r = lta->xforms[0].dst.c_r;
mri_out->c_a = lta->xforms[0].dst.c_a;
mri_out->c_s = lta->xforms[0].dst.c_s;
}
}
else
{
mri_out->c_r = mri_in->c_r;
mri_out->c_a = mri_in->c_a;
mri_out->c_s = mri_in->c_s;
}
mri_out->ras_good_flag=1; /* What does this flag mean ? */
/* since output is just transformed input */
MRIcopyPulseParameters(mri_in, mri_out) ;
}
/* Compute the final input-to-output VOX_to_VOX transformation matrix */
r_to_i_out = extract_r_to_i(mri_out);
m_tmp = MatrixMultiply(r_to_i_out, i_to_r_reg, NULL);
V_to_V = MatrixMultiply(m_tmp, V_to_V, V_to_V);
MatrixFree(&m_tmp);
printf("InterpMethod = %d\n", InterpMethod);
/* Modify the MyMRIlinearTr... if I want to implement my cubic-B-spline
* interpolation method. Otherwise, unnecessary
*/
/* mri_out = MyMRIlinearTransformInterp(mri_in, mri_out, V_to_V, InterpMethod); */
if (InterpMethod == SAMPLE_BSPLINE)
mri_out = MRIlinearTransformInterpBSpline(mri_in, mri_out, V_to_V,
SplineDegree);
else
mri_out = MRIlinearTransformInterp(mri_in, mri_out, V_to_V, InterpMethod);
maxV = -10000.0;
minV = 10000.0;
for (z=0; z < mri_out->depth; z++)
for (y=0; y< mri_out->height; y++)
for (x=0; x < mri_out->width; x++)
{
if (MRIFvox(mri_out, x, y, z) > maxV )
maxV = MRIFvox(mri_out, x, y,z) ;
if (MRIFvox(mri_out, x, y, z) < minV )
minV = MRIFvox(mri_out, x, y,z) ;
}
if (autoscale)
{
noscale = 1;
/* compute histogram of output volume */
HISTOGRAM *h, *hsmooth ;
float fmin, fmax, val, peak, smooth_peak;
int i, nbins, bin;
fmin = minV;
fmax = maxV;
if (fmin < 0) fmin = 0;
nbins = 256 ;
h = HISTOalloc(nbins) ;
hsmooth = HISTOcopy(h, NULL) ;
HISTOclear(h, h) ;
h->bin_size = (fmax-fmin)/255.0 ;
for (i = 0 ; i < nbins ; i++)
h->bins[i] = (i+1)*h->bin_size ;
for (z=0; z < mri_out->depth; z++)
for (y=0; y< mri_out->height; y++)
for (x=0; x < mri_out->width; x++)
{
val = MRIFvox(mri_out, x, y, z);
if (val <= 0) continue;
bin = nint((val - fmin)/h->bin_size);
if (bin >= h->nbins)
bin = h->nbins-1;
else if (bin < 0)
bin = 0;
h->counts[bin] += 1.0;
}
HISTOfillHoles(h) ;
HISTOsmooth(h, hsmooth, 5) ;
peak =
hsmooth->bins[HISTOfindHighestPeakInRegion(h, 1, h->nbins)] ;
// smooth_peak =
// hsmooth->bins[HISTOfindHighestPeakInRegion(hsmooth, 1, hsmooth->nbins)] ;
smooth_peak =
hsmooth->bins[HISTOfindLastPeak(hsmooth, 5, 0.8)] ;
/*
bin = nint((smooth_peak - fmin)/hsmooth->bin_size) ;
printf("Highest peak has count = %d\n", (int)hsmooth->counts[bin]);
bin = nint((420 - fmin)/hsmooth->bin_size) ;
printf("bin at 420 has count = %d\n", (int)hsmooth->counts[bin]);
*/
scale = 110.0/smooth_peak;
printf("peak of output volume is %g, smooth-peak is %g, multiply by %g to scale it to 110\n", peak, smooth_peak, scale);
for (z=0; z < mri_out->depth; z++)
for (y=0; y< mri_out->height; y++)
for (x=0; x < mri_out->width; x++)
{
val = MRIFvox(mri_out, x, y, z);
MRIFvox(mri_out, x, y, z) = val*scale;
}
}
printf("Output volume (before type-conversion) has max = %g, min =%g\n", maxV, minV);
/* Finally change type to desired */
if (mri_out->type != out_type)
{
printf("Change output volume to type %d\n", out_type);
/* I need to modify the MIRchangeType function to make sure
* it does roundoff instead of simple truncation!
*/
/* Note if the last flag is set to 1, then it won't do scaling
and small float numbers will become zero after convert to
BYTE
*/
if (out_type == 0 && noscale == 1)
{
//convert data to UCHAR
mri_tmp = MRIalloc(mri_out->width, mri_out->height, mri_out->depth, out_type) ;
MRIcopyHeader(mri_out, mri_tmp);
for (z=0; z < mri_out->depth; z++)
for (y=0; y< mri_out->height; y++)
for (x=0; x < mri_out->width; x++)
{
value = floor(MRIgetVoxVal(mri_out, x, y, z, 0) + 0.5);
if (value < 0 ) value = 0;
if (value > 255) value = 255;
MRIvox(mri_tmp,x,y,z) = (unsigned char)value;
}
}
else
mri_tmp = MRIchangeType(mri_out, out_type, thred_low, thred_high, noscale);
MRIfree(&mri_out);
mri_out = mri_tmp; //swap
}
MRIwrite(mri_out, out_vol) ;
MRIfree(&mri_in);
MRIfree(&mri_out);
if (lta_src)
MRIfree(<a_src);
if (lta_dst)
MRIfree(<a_dst);
MatrixFree(&V_to_V);
if (!r_to_i_out)
MatrixFree(&r_to_i_out);
if (!i_to_r_reg)
MatrixFree(&i_to_r_reg);
return(0) ; /* for ansi */
}
static MRI *
MRIremoveWMOutliers(MRI *mri_src, MRI *mri_src_ctrl, MRI *mri_dst_ctrl,
int intensity_below)
{
MRI *mri_bin, *mri_outliers = NULL ;
float max, thresh, val;
HISTOGRAM *histo, *hsmooth ;
int wm_peak, x, y, z, nremoved = 0, whalf = 5, total ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_src_ctrl, "sc.mgz") ;
}
if (mri_dst_ctrl == NULL)
{
mri_dst_ctrl = MRIcopy(mri_src_ctrl, NULL) ;
}
mri_bin = MRIbinarize(mri_src_ctrl, NULL, 1, 0, CONTROL_MARKED) ;
histo = MRIhistogramLabel(mri_src, mri_bin, 1, 256) ;
hsmooth = HISTOcopy(histo, NULL) ;
HISTOsmooth(histo, hsmooth, 2) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
HISTOplot(histo, "h.plt") ;
HISTOplot(hsmooth, "hs.plt") ;
}
wm_peak = HISTOfindHighestPeakInRegion(hsmooth, 1, hsmooth->nbins-1) ;
wm_peak = hsmooth->bins[wm_peak] ;
thresh = wm_peak-intensity_below ;
HISTOfree(&histo) ;
HISTOfree(&hsmooth) ;
if (Gdiag & DIAG_WRITE)
{
mri_outliers = MRIclone(mri_dst_ctrl, NULL) ;
}
for (total = x = 0 ; x < mri_src->width ; x++)
{
for (y = 0 ; y < mri_src->height ; y++)
{
for (z = 0 ; z < mri_src->depth ; z++)
{
if (x == Gx && y == Gy && z == Gz)
{
DiagBreak() ;
}
if (nint(MRIgetVoxVal(mri_dst_ctrl, x, y, z, 0)) == 0)
{
continue ;
}
max = MRImaxInLabelInRegion(mri_src, mri_bin, 1, x, y, z, whalf);
val = MRIgetVoxVal(mri_src, x, y, z, 0) ;
total++ ;
if (val+intensity_below < max && val < thresh)
{
MRIsetVoxVal(mri_dst_ctrl, x, y, z, 0, 0) ;
if (mri_outliers)
{
MRIsetVoxVal(mri_outliers, x, y, z, 0, 128) ;
}
nremoved++ ;
}
}
}
}
printf( "%d control points removed (%2.1f%%)\n",
nremoved, 100.0*(double)nremoved/(double)total) ;
if (mri_outliers)
{
printf( "writing out.mgz outlier volume\n") ;
MRIwrite(mri_outliers, "out.mgz") ;
MRIfree(&mri_outliers) ;
}
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_dst_ctrl, "dc.mgz") ;
}
MRIfree(&mri_bin) ;
return(mri_dst_ctrl);
}
static MRI *
MRIremoveWMOutliersAndRetainMedialSurface(MRI *mri_src,
MRI *mri_src_ctrl,
MRI *mri_dst_ctrl,
int intensity_below)
{
MRI *mri_inside, *mri_bin ;
HISTOGRAM *histo, *hsmooth ;
int wm_peak, x, y, z, nremoved ;
float thresh, hi_thresh ;
double val, lmean, max ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_src_ctrl, "sc.mgz") ;
}
if (mri_dst_ctrl != mri_src_ctrl)
{
mri_dst_ctrl = MRIcopy(mri_src_ctrl, mri_dst_ctrl) ;
}
mri_inside = MRIerode(mri_dst_ctrl, NULL) ;
MRIbinarize(mri_inside, mri_inside, 1, 0, 1) ;
histo = MRIhistogramLabel(mri_src, mri_inside, 1, 256) ;
hsmooth = HISTOcopy(histo, NULL) ;
HISTOsmooth(histo, hsmooth, 2) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
HISTOplot(histo, "h.plt") ;
HISTOplot(hsmooth, "hs.plt") ;
}
printf("using wm (%d) threshold %2.1f for removing exterior voxels\n",
wm_peak, thresh) ;
wm_peak = HISTOfindHighestPeakInRegion(hsmooth, 1, hsmooth->nbins-1) ;
wm_peak = hsmooth->bins[wm_peak] ;
thresh = wm_peak-intensity_below ;
hi_thresh = wm_peak-.5*intensity_below ;
printf("using wm (%d) threshold %2.1f for removing exterior voxels\n",
wm_peak, thresh) ;
// now remove stuff that's on the border and is pretty dark
for (nremoved = x = 0 ; x < mri_src->width ; x++)
{
for (y = 0 ; y < mri_src->height ; y++)
{
for (z = 0 ; z < mri_src->depth ; z++)
{
if (x == Gx && y == Gy && z == Gz)
{
DiagBreak() ;
}
/* if it's a control point,
it's not in the interior of the wm,
and it's T1 val is too low */
if (MRIgetVoxVal(mri_dst_ctrl, x, y, z, 0) == 0)
{
continue ; // not a control point
}
/* if it's way far from the wm mode
then remove it even if it's in the interior */
val = MRIgetVoxVal(mri_src, x, y, z, 0) ;
if (val < thresh-5)
{
MRIsetVoxVal(mri_dst_ctrl, x, y, z, 0, 0) ;
nremoved++ ;
}
if (nint(MRIgetVoxVal(mri_inside, x, y, z, 0)) > 0)
// don't process interior voxels further
{
continue ; // in the interior
}
if (val < thresh)
{
MRIsetVoxVal(mri_dst_ctrl, x, y, z, 0, 0) ;
nremoved++ ;
}
else
{
lmean =
MRImeanInLabelInRegion(mri_src, mri_inside, 1, x, y, z, 7);
if (val < lmean-10)
{
MRIsetVoxVal(mri_dst_ctrl, x, y, z, 0, 0) ;
nremoved++ ;
}
}
}
}
}
#if 0
for (x = 0 ; x < mri_src->width ; x++)
{
for (y = 0 ; y < mri_src->height ; y++)
{
for (z = 0 ; z < mri_src->depth ; z++)
{
if (x == Gx && y == Gy && z == Gz)
{
DiagBreak() ;
}
/* if it's a control point,
it's not in the interior of the wm,
and it's T1 val is too low */
if (MRIgetVoxVal(mri_dst_ctrl, x, y, z, 0) == 0)
{
continue ; // not a control point
}
if (MRIcountNonzeroInNbhd(mri_dst_ctrl,3, x, y, z)<=2)
{
MRIsetVoxVal(mri_dst_ctrl, x, y, z, 0, 0) ;
nremoved++ ;
}
}
}
}
#endif
/* now take out voxels that have too big an intensity diff
with surrounding ones */
mri_bin = MRIbinarize(mri_dst_ctrl, NULL, 1, 0, 1) ;
for (x = 0 ; x < mri_src->width ; x++)
{
for (y = 0 ; y < mri_src->height ; y++)
{
for (z = 0 ; z < mri_src->depth ; z++)
{
if (x == Gx && y == Gy && z == Gz)
{
DiagBreak() ;
}
/* if it's a control point,
it's not in the interior of the wm,
and it's T1 val is too low */
if (MRIgetVoxVal(mri_dst_ctrl, x, y, z, 0) == 0)
{
continue ; // not a control point
}
val = MRIgetVoxVal(mri_src, x, y, z, 0) ;
max = MRImaxInLabelInRegion(mri_src, mri_bin, 1, x, y, z, 3);
if (val+7 < max && val < hi_thresh)
{
MRIsetVoxVal(mri_dst_ctrl, x, y, z, 0, 0) ;
nremoved++ ;
}
}
}
}
MRIfree(&mri_bin) ;
printf( "%d control points removed\n", nremoved) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_dst_ctrl, "dc.mgz") ;
}
HISTOfree(&histo) ;
HISTOfree(&hsmooth) ;
MRIfree(&mri_inside) ;
return(mri_dst_ctrl) ;
}
static MRI *
MRIremoveWMOutliersAndRetainMedialSurface(MRI *mri_src,
MRI *mri_src_ctrl,
MRI *mri_dst_ctrl,
int intensity_below)
{
MRI *mri_bin, *mri_dist, *mri_dist_sup, *mri_outliers = NULL ;
float max, thresh, val;
HISTOGRAM *histo, *hsmooth ;
int wm_peak, x, y, z, nremoved = 0, whalf = 5 ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_src_ctrl, "sc.mgz") ;
}
mri_bin = MRIbinarize(mri_dst_ctrl, NULL, 1, 0, 1) ;
mri_dist = MRIdistanceTransform(mri_bin, NULL, 1, -1,
DTRANS_MODE_SIGNED, NULL);
MRIscalarMul(mri_dist, mri_dist, -1) ;
mri_dist_sup = MRInonMaxSuppress(mri_dist, NULL, 0, 1) ;
mri_dst_ctrl = MRIbinarize(mri_dist_sup, mri_dst_ctrl, 1, 0, 1) ;
histo = MRIhistogramLabel(mri_src, mri_src_ctrl, 1, 256) ;
hsmooth = HISTOcopy(histo, NULL) ;
HISTOsmooth(histo, hsmooth, 2) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
HISTOplot(histo, "h.plt") ;
HISTOplot(hsmooth, "hs.plt") ;
}
wm_peak = HISTOfindHighestPeakInRegion(hsmooth, 1, hsmooth->nbins-1) ;
wm_peak = hsmooth->bins[wm_peak] ;
thresh = wm_peak-intensity_below ;
HISTOfree(&histo) ;
HISTOfree(&hsmooth) ;
if (Gdiag & DIAG_WRITE)
{
mri_outliers = MRIclone(mri_dst_ctrl, NULL) ;
}
for (x = 0 ; x < mri_src->width ; x++)
{
for (y = 0 ; y < mri_src->height ; y++)
{
for (z = 0 ; z < mri_src->depth ; z++)
{
if (x == Gx && y == Gy && z == Gz)
{
DiagBreak() ;
}
if (nint(MRIgetVoxVal(mri_dst_ctrl, x, y, z, 0)) == 0)
{
continue ;
}
max = MRImaxInLabelInRegion(mri_src, mri_dst_ctrl, 1, x, y, z, whalf);
val = MRIgetVoxVal(mri_src, x, y, z, 0) ;
if (val+intensity_below < max && val < thresh)
{
MRIsetVoxVal(mri_dst_ctrl, x, y, z, 0, 0) ;
if (mri_outliers)
{
MRIsetVoxVal(mri_outliers, x, y, z, 0, 128) ;
}
nremoved++ ;
}
}
}
}
printf( "%d control points removed\n", nremoved) ;
if (mri_outliers)
{
printf( "writing out.mgz outlier volume\n") ;
MRIwrite(mri_outliers, "out.mgz") ;
MRIfree(&mri_outliers) ;
}
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_dst_ctrl, "dc.mgz") ;
}
MRIfree(&mri_bin) ;
MRIfree(&mri_dist);
MRIfree(&mri_dist_sup);
return(mri_dst_ctrl);
}
