static int
normalize_timepoints_with_samples(MRI *mri, GCA_SAMPLE *gcas, int nsamples, int nsoap)
{
int frame, i, x, y, z ;
double target, val ;
MRI *mri_ctrl, *mri_bias, *mri_target, *mri_frame ;
mri_ctrl = MRIcloneDifferentType(mri, MRI_UCHAR) ;
mri_bias = MRIcloneDifferentType(mri, MRI_FLOAT) ;
mri_target = MRIcloneDifferentType(mri, MRI_FLOAT) ;
for (i = 0 ; i < nsamples ; i++)
{
if (i == Gdiag_no)
DiagBreak() ;
x = nint(gcas[i].x) ; y = nint(gcas[i].y) ; z = nint(gcas[i].z) ;
MRIsetVoxVal(mri_ctrl, x, y, z, 0, CONTROL_MARKED) ;
for (target = 0.0, frame = 0 ; frame < mri->nframes ; frame++)
target += MRIgetVoxVal(mri, x, y, z, frame) ;
target /= mri->nframes ;
MRIsetVoxVal(mri_target, x, y, z, 0, target) ;
}
// build a bias correction for each time point (which each has its own frame)
for (frame = 0 ; frame < mri->nframes ; frame++)
{
MRIclear(mri_bias) ;
for (i = 0 ; i < nsamples ; i++)
{
if (i == Gdiag_no)
DiagBreak() ;
x = nint(gcas[i].x) ; y = nint(gcas[i].y) ; z = nint(gcas[i].z) ;
target = MRIgetVoxVal(mri_target, x, y, z, 0) ;
val = MRIgetVoxVal(mri, x, y, z, frame) ;
if (FZERO(val))
val = 1.0 ;
MRIsetVoxVal(mri_bias, x, y, z, 0, target/val) ;
}
MRIbuildVoronoiDiagram(mri_bias, mri_ctrl, mri_bias) ;
MRIsoapBubble(mri_bias, mri_ctrl, mri_bias, nsoap) ;
mri_frame = MRIcopyFrame(mri, NULL, frame, 0) ;
MRImultiply(mri_frame, mri_bias, mri_frame) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
char fname[STRLEN] ;
sprintf(fname, "frame%d.mgz", frame) ;
MRIwrite(mri_frame, fname) ;
sprintf(fname, "bias%d.mgz", frame) ;
MRIwrite(mri_bias, fname) ;
sprintf(fname, "target%d.mgz", frame) ;
MRIwrite(mri_target, fname) ;
}
MRIcopyFrame(mri_frame, mri, 0, frame) ;
}
MRIfree(&mri_bias) ; MRIfree(&mri_target) ; MRIfree(&mri_ctrl) ;
return(NO_ERROR) ;
}
static int
normalize_timepoints(MRI *mri, double thresh, double cross_time_sigma)
{
int frame, x, y, z, skip, nvox ;
double target, val ;
MRI *mri_ctrl, *mri_bias, *mri_target, *mri_frame, *mri_kernel ;
mri_ctrl = MRIcloneDifferentType(mri, MRI_UCHAR) ;
mri_bias = MRIcloneDifferentType(mri, MRI_FLOAT) ;
mri_target = MRIcloneDifferentType(mri, MRI_FLOAT) ;
mri_kernel = MRIgaussian1d(cross_time_sigma, -1) ;
for (nvox = x = 0 ; x < mri->width ; x++)
for (y = 0 ; y < mri->height ; y++)
for (z = 0 ; z < mri->depth ; z++)
{
if (x == Gx && y == Gy && z == Gz)
DiagBreak() ;
for (target = 0.0, frame = 0 ; frame < mri->nframes ; frame++)
target += MRIgetVoxVal(mri, x, y, z, frame) ;
target /= mri->nframes ;
if (FZERO(target))
continue ; // both vals 0
skip = 0 ;
for (frame = 0 ; frame < mri->nframes ; frame++)
{
val = MRIgetVoxVal(mri, x, y, z, frame) ;
if (fabs(val-target) > thresh)
{
skip = 1 ;
break ;
}
}
if (skip)
continue ;
nvox++ ;
MRIsetVoxVal(mri_ctrl, x, y, z, 0, CONTROL_MARKED) ;
MRIsetVoxVal(mri_target, x, y, z, 0, target) ;
}
printf("%d voxels found to base intensity correction on\n", nvox) ;
// build a bias correction for each time point (which each has its own frame)
for (frame = 0 ; frame < mri->nframes ; frame++)
{
MRIclear(mri_bias) ;
for (x = 0 ; x < mri->width ; x++)
for (y = 0 ; y < mri->height ; y++)
for (z = 0 ; z < mri->depth ; z++)
{
target = MRIgetVoxVal(mri_target, x, y, z, 0) ;
val = MRIgetVoxVal(mri, x, y, z, frame) ;
if (FZERO(val))
val = 1.0 ;
MRIsetVoxVal(mri_bias, x, y, z, 0, target/val) ;
}
MRIbuildVoronoiDiagram(mri_bias, mri_ctrl, mri_bias) ;
MRIconvolveGaussian(mri_bias, mri_bias, mri_kernel) ;
// MRIsoapBubble(mri_bias, mri_ctrl, mri_bias, nsoap) ;
mri_frame = MRIcopyFrame(mri, NULL, frame, 0) ;
MRImultiply(mri_frame, mri_bias, mri_frame) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
char fname[STRLEN] ;
sprintf(fname, "frame%d.mgz", frame) ;
MRIwrite(mri_frame, fname) ;
sprintf(fname, "bias%d.mgz", frame) ;
MRIwrite(mri_bias, fname) ;
sprintf(fname, "target%d.mgz", frame) ;
MRIwrite(mri_target, fname) ;
}
MRIcopyFrame(mri_frame, mri, 0, frame) ;
}
MRIfree(&mri_bias) ; MRIfree(&mri_kernel) ; MRIfree(&mri_target) ; MRIfree(&mri_ctrl) ;
return(NO_ERROR) ;
}
int
main(int argc, char *argv[])
{
char **av ;
int ac, nargs, n ;
MRI *mri_src, *mri_dst = NULL, *mri_bias, *mri_orig, *mri_aseg = NULL ;
char *in_fname, *out_fname ;
int msec, minutes, seconds ;
struct timeb start ;
char cmdline[CMD_LINE_LEN] ;
make_cmd_version_string
(argc, argv,
"$Id: mri_normalize.c,v 1.80 2012/10/16 21:38:35 nicks Exp $",
"$Name: $",
cmdline);
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mri_normalize.c,v 1.80 2012/10/16 21:38:35 nicks Exp $",
"$Name: $");
if (nargs && argc - nargs == 1)
{
exit (0);
}
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
mni.max_gradient = MAX_GRADIENT ;
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) ;
}
if (argc < 1)
{
ErrorExit(ERROR_BADPARM, "%s: no input name specified", Progname) ;
}
in_fname = argv[1] ;
if (argc < 2)
{
ErrorExit(ERROR_BADPARM, "%s: no output name specified", Progname) ;
}
out_fname = argv[2] ;
if(verbose)
{
printf( "reading from %s...\n", in_fname) ;
}
mri_src = MRIread(in_fname) ;
if (!mri_src)
ErrorExit(ERROR_NO_FILE, "%s: could not open source file %s",
Progname, in_fname) ;
MRIaddCommandLine(mri_src, cmdline) ;
if(nsurfs > 0)
{
MRI_SURFACE *mris ;
MRI *mri_dist=NULL, *mri_dist_sup=NULL, *mri_ctrl, *mri_dist_one ;
LTA *lta= NULL ;
int i ;
TRANSFORM *surface_xform ;
if (control_point_fname) // do one pass with only file control points first
{
MRI3dUseFileControlPoints(mri_src, control_point_fname) ;
mri_dst =
MRI3dGentleNormalize(mri_src,
NULL,
DEFAULT_DESIRED_WHITE_MATTER_VALUE,
NULL,
intensity_above,
intensity_below/2,1,
bias_sigma, mri_not_control);
}
else
{
mri_dst = MRIcopy(mri_src, NULL) ;
}
for (i = 0 ; i < nsurfs ; i++)
{
mris = MRISread(surface_fnames[i]) ;
if (mris == NULL)
ErrorExit(ERROR_NOFILE,"%s: could not surface %s",
Progname,surface_fnames[i]);
surface_xform = surface_xforms[i] ;
TransformInvert(surface_xform, NULL) ;
if (surface_xform->type == MNI_TRANSFORM_TYPE ||
surface_xform->type == TRANSFORM_ARRAY_TYPE ||
surface_xform->type == REGISTER_DAT)
{
lta = (LTA *)(surface_xform->xform) ;
#if 0
if (invert)
{
VOL_GEOM vgtmp;
LT *lt;
MATRIX *m_tmp = lta->xforms[0].m_L ;
lta->xforms[0].m_L = MatrixInverse(lta->xforms[0].m_L, NULL) ;
MatrixFree(&m_tmp) ;
lt = <a->xforms[0];
if (lt->dst.valid == 0 || lt->src.valid == 0)
{
printf( "WARNING:***************************************************************\n");
printf( "WARNING:dst volume infor is invalid. Most likely produce wrong inverse.\n");
printf( "WARNING:***************************************************************\n");
}
copyVolGeom(<->dst, &vgtmp);
copyVolGeom(<->src, <->dst);
copyVolGeom(&vgtmp, <->src);
}
#endif
}
if (stricmp(surface_xform_fnames[i], "identity.nofile") != 0)
{
MRIStransform(mris, NULL, surface_xform, NULL) ;
}
mri_dist_one = MRIcloneDifferentType(mri_dst, MRI_FLOAT) ;
printf("computing distance transform\n") ;
MRIScomputeDistanceToSurface(mris, mri_dist_one, mri_dist_one->xsize) ;
if (i == 0)
{
mri_dist = MRIcopy(mri_dist_one, NULL) ;
}
else
{
MRIcombineDistanceTransforms(mri_dist_one, mri_dist, mri_dist) ;
}
// MRIminAbs(mri_dist_one, mri_dist, mri_dist) ;
MRIfree(&mri_dist_one) ;
}
MRIscalarMul(mri_dist, mri_dist, -1) ;
if (nonmax_suppress)
{
printf("computing nonmaximum suppression\n") ;
mri_dist_sup = MRInonMaxSuppress(mri_dist, NULL, 0, 1) ;
mri_ctrl = MRIcloneDifferentType(mri_dist_sup, MRI_UCHAR) ;
MRIbinarize(mri_dist_sup, mri_ctrl, min_dist, CONTROL_NONE, CONTROL_MARKED) ;
}
else if (erode)
{
int i ;
mri_ctrl = MRIcloneDifferentType(mri_dist, MRI_UCHAR) ;
MRIbinarize(mri_dist, mri_ctrl, min_dist, CONTROL_NONE, CONTROL_MARKED) ;
for (i = 0 ; i < erode ; i++)
{
MRIerode(mri_ctrl, mri_ctrl) ;
}
}
else
{
mri_ctrl = MRIcloneDifferentType(mri_dist, MRI_UCHAR) ;
MRIbinarize(mri_dist, mri_ctrl, min_dist, CONTROL_NONE, CONTROL_MARKED) ;
}
if (control_point_fname)
{
MRInormAddFileControlPoints(mri_ctrl, CONTROL_MARKED) ;
}
if (mask_sigma > 0)
{
MRI *mri_smooth, *mri_mag, *mri_grad ;
mri_smooth = MRIgaussianSmooth(mri_dst, mask_sigma, 1, NULL) ;
mri_mag = MRIcloneDifferentType(mri_dst, MRI_FLOAT) ;
mri_grad = MRIsobel(mri_smooth, NULL, mri_mag) ;
MRIbinarize(mri_mag, mri_mag, mask_thresh, 1, 0) ;
MRImask(mri_ctrl, mri_mag, mri_ctrl, 0, CONTROL_NONE) ;
MRIfree(&mri_grad) ;
MRIfree(&mri_mag) ;
MRIfree(&mri_smooth) ;
}
if (mask_orig_fname)
{
MRI *mri_orig ;
mri_orig = MRIread(mask_orig_fname) ;
MRIbinarize(mri_orig, mri_orig, mask_orig_thresh, 0, 1) ;
MRImask(mri_ctrl, mri_orig, mri_ctrl, 0, CONTROL_NONE) ;
MRIfree(&mri_orig) ;
}
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_dist, "d.mgz");
MRIwrite(mri_dist_sup, "dm.mgz");
MRIwrite(mri_ctrl, "c.mgz");
}
MRIeraseBorderPlanes(mri_ctrl, 4) ;
if (aseg_fname)
{
mri_aseg = MRIread(aseg_fname) ;
if (mri_aseg == NULL)
{
ErrorExit(ERROR_NOFILE,
"%s: could not load aseg from %s", Progname, aseg_fname) ;
}
remove_nonwm_voxels(mri_ctrl, mri_aseg, mri_ctrl) ;
MRIfree(&mri_aseg) ;
}
else
{
remove_surface_outliers(mri_ctrl, mri_dist, mri_dst, mri_ctrl) ;
}
mri_bias = MRIbuildBiasImage(mri_dst, mri_ctrl, NULL, 0.0) ;
if (mri_dist)
{
MRIfree(&mri_dist) ;
}
if (mri_dist_sup)
{
MRIfree(&mri_dist_sup) ;
}
if (bias_sigma> 0)
{
MRI *mri_kernel = MRIgaussian1d(bias_sigma, -1) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_bias, "b.mgz") ;
}
printf("smoothing bias field\n") ;
MRIconvolveGaussian(mri_bias, mri_bias, mri_kernel) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_bias, "bs.mgz") ;
}
MRIfree(&mri_kernel);
}
MRIfree(&mri_ctrl) ;
mri_dst = MRIapplyBiasCorrectionSameGeometry
(mri_dst, mri_bias, mri_dst,
DEFAULT_DESIRED_WHITE_MATTER_VALUE) ;
printf("writing normalized volume to %s\n", out_fname) ;
MRIwrite(mri_dst, out_fname) ;
exit(0) ;
} // end if(surface_fname)
if (!mriConformed(mri_src) && conform > 0)
{
printf("unconformed source detected - conforming...\n") ;
mri_src = MRIconform(mri_src) ;
}
if (mask_fname)
{
MRI *mri_mask ;
mri_mask = MRIread(mask_fname) ;
if (!mri_mask)
ErrorExit(ERROR_NOFILE, "%s: could not open mask volume %s.\n",
Progname, mask_fname) ;
MRImask(mri_src, mri_mask, mri_src, 0, 0) ;
MRIfree(&mri_mask) ;
}
if (read_flag)
{
MRI *mri_ctrl ;
double scale ;
mri_bias = MRIread(bias_volume_fname) ;
if (!mri_bias)
ErrorExit
(ERROR_BADPARM,
"%s: could not read bias volume %s", Progname, bias_volume_fname) ;
mri_ctrl = MRIread(control_volume_fname) ;
if (!mri_ctrl)
ErrorExit
(ERROR_BADPARM,
"%s: could not read control volume %s",
Progname, control_volume_fname) ;
MRIbinarize(mri_ctrl, mri_ctrl, 1, 0, 128) ;
mri_dst = MRImultiply(mri_bias, mri_src, NULL) ;
scale = MRImeanInLabel(mri_dst, mri_ctrl, 128) ;
printf("mean in wm is %2.0f, scaling by %2.2f\n", scale, 110/scale) ;
scale = 110/scale ;
MRIscalarMul(mri_dst, mri_dst, scale) ;
MRIwrite(mri_dst, out_fname) ;
exit(0) ;
}
if(long_flag)
{
MRI *mri_ctrl ;
double scale ;
mri_bias = MRIread(long_bias_volume_fname) ;
if (!mri_bias)
ErrorExit
(ERROR_BADPARM,
"%s: could not read bias volume %s", Progname, long_bias_volume_fname) ;
mri_ctrl = MRIread(long_control_volume_fname) ;
if (!mri_ctrl)
ErrorExit
(ERROR_BADPARM,
"%s: could not read control volume %s",
Progname, long_control_volume_fname) ;
MRIbinarize(mri_ctrl, mri_ctrl, 1, 0, CONTROL_MARKED) ;
if (mri_ctrl->type != MRI_UCHAR)
{
MRI *mri_tmp ;
mri_tmp = MRIchangeType(mri_ctrl, MRI_UCHAR, 0, 1,1);
MRIfree(&mri_ctrl) ;
mri_ctrl = mri_tmp ;
}
scale = MRImeanInLabel(mri_src, mri_ctrl, CONTROL_MARKED) ;
printf("mean in wm is %2.0f, scaling by %2.2f\n", scale, 110/scale) ;
scale = DEFAULT_DESIRED_WHITE_MATTER_VALUE/scale ;
mri_dst = MRIscalarMul(mri_src, NULL, scale) ;
MRIremoveWMOutliers(mri_dst, mri_ctrl, mri_ctrl, intensity_below/2) ;
mri_bias = MRIbuildBiasImage(mri_dst, mri_ctrl, NULL, 0.0) ;
MRIsoapBubble(mri_bias, mri_ctrl, mri_bias, 50, 1) ;
MRIapplyBiasCorrectionSameGeometry(mri_dst, mri_bias, mri_dst,
DEFAULT_DESIRED_WHITE_MATTER_VALUE);
// MRIwrite(mri_dst, out_fname) ;
// exit(0) ;
} // end if(long_flag)
if (grad_thresh > 0)
{
float thresh ;
MRI *mri_mag, *mri_grad, *mri_smooth ;
MRI *mri_kernel = MRIgaussian1d(.5, -1) ;
mri_not_control = MRIcloneDifferentType(mri_src, MRI_UCHAR) ;
switch (scan_type)
{
case MRI_MGH_MPRAGE:
thresh = 15 ;
break ;
case MRI_WASHU_MPRAGE:
thresh = 20 ;
break ;
case MRI_UNKNOWN:
default:
thresh = 12 ;
break ;
}
mri_smooth = MRIconvolveGaussian(mri_src, NULL, mri_kernel) ;
thresh = grad_thresh ;
mri_mag = MRIcloneDifferentType(mri_src, MRI_FLOAT) ;
mri_grad = MRIsobel(mri_smooth, NULL, mri_mag) ;
MRIwrite(mri_mag, "m.mgz") ;
MRIbinarize(mri_mag, mri_not_control, thresh, 0, 1) ;
MRIwrite(mri_not_control, "nc.mgz") ;
MRIfree(&mri_mag) ;
MRIfree(&mri_grad) ;
MRIfree(&mri_smooth) ;
MRIfree(&mri_kernel) ;
}
#if 0
#if 0
if ((mri_src->type != MRI_UCHAR) ||
(!(mri_src->xsize == 1 && mri_src->ysize == 1 && mri_src->zsize == 1)))
#else
if (conform || (mri_src->type != MRI_UCHAR && conform > 0))
#endif
{
MRI *mri_tmp ;
fprintf
(stderr,
"downsampling to 8 bits and scaling to isotropic voxels...\n") ;
mri_tmp = MRIconform(mri_src) ;
mri_src = mri_tmp ;
}
#endif
if(aseg_fname)
{
printf("Reading aseg %s\n",aseg_fname);
mri_aseg = MRIread(aseg_fname) ;
if (mri_aseg == NULL)
ErrorExit
(ERROR_NOFILE,
"%s: could not read aseg from file %s", Progname, aseg_fname) ;
if (!mriConformed(mri_aseg))
{
ErrorExit(ERROR_UNSUPPORTED, "%s: aseg volume %s must be conformed",
Progname, aseg_fname) ;
}
}
else
{
mri_aseg = NULL ;
}
if(verbose)
{
printf( "normalizing image...\n") ;
}
fflush(stdout);
fflush(stderr);
TimerStart(&start) ;
if (control_point_fname)
{
MRI3dUseFileControlPoints(mri_src, control_point_fname) ;
}
// this just setup writing control-point volume saving
if(control_volume_fname)
{
MRI3dWriteControlPoints(control_volume_fname) ;
}
/* first do a gentle normalization to get
things in the right intensity range */
if(long_flag == 0) // if long, then this will already have been done with base control points
{
if(control_point_fname != NULL) /* do one pass with only
file control points first */
mri_dst =
MRI3dGentleNormalize(mri_src,
NULL,
DEFAULT_DESIRED_WHITE_MATTER_VALUE,
NULL,
intensity_above,
intensity_below/2,1,
bias_sigma, mri_not_control);
else
{
mri_dst = MRIcopy(mri_src, NULL) ;
}
}
fflush(stdout);
fflush(stderr);
if(mri_aseg)
{
MRI *mri_ctrl, *mri_bias ;
int i ;
printf("processing with aseg\n");
mri_ctrl = MRIclone(mri_aseg, NULL) ;
for (i = 0 ; i < NWM_LABELS ; i++)
{
MRIcopyLabel(mri_aseg, mri_ctrl, aseg_wm_labels[i]) ;
}
printf("removing outliers in the aseg WM...\n") ;
MRIremoveWMOutliersAndRetainMedialSurface(mri_dst,
mri_ctrl,
mri_ctrl,
intensity_below) ;
MRIbinarize(mri_ctrl, mri_ctrl, 1, CONTROL_NONE, CONTROL_MARKED) ;
MRInormAddFileControlPoints(mri_ctrl, CONTROL_MARKED) ;
if (interior_fname1)
{
MRIS *mris_interior1, *mris_interior2 ;
mris_interior1 = MRISread(interior_fname1) ;
if (mris_interior1 == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not read white matter surface from %s\n",
Progname, interior_fname1) ;
mris_interior2 = MRISread(interior_fname2) ;
if (mris_interior2 == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not read white matter surface from %s\n",
Progname, interior_fname2) ;
add_interior_points(mri_ctrl,
mri_dst,
intensity_above,
1.25*intensity_below,
mris_interior1,
mris_interior2,
mri_aseg,
mri_ctrl) ;
MRISfree(&mris_interior1) ;
MRISfree(&mris_interior2) ;
}
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_ctrl, "norm_ctrl.mgz") ;
}
printf("Building bias image\n");
fflush(stdout);
fflush(stderr);
mri_bias = MRIbuildBiasImage(mri_dst, mri_ctrl, NULL, 0.0) ;
fflush(stdout);
fflush(stderr);
if (bias_sigma> 0)
{
printf("Smoothing with sigma %g\n",bias_sigma);
MRI *mri_kernel = MRIgaussian1d(bias_sigma, -1) ;
MRIconvolveGaussian(mri_bias, mri_bias, mri_kernel) ;
MRIfree(&mri_kernel);
fflush(stdout);
fflush(stderr);
}
MRIfree(&mri_ctrl) ;
MRIfree(&mri_aseg) ;
printf("Applying bias correction\n");
mri_dst = MRIapplyBiasCorrectionSameGeometry
(mri_dst, mri_bias, mri_dst,
DEFAULT_DESIRED_WHITE_MATTER_VALUE) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_dst, "norm_1.mgz") ;
}
fflush(stdout);
fflush(stderr);
} // if(mri_aseg)
else
{
printf("processing without aseg, no1d=%d\n",no1d);
if (!no1d)
{
printf("MRInormInit(): \n");
MRInormInit(mri_src, &mni, 0, 0, 0, 0, 0.0f) ;
printf("MRInormalize(): \n");
mri_dst = MRInormalize(mri_src, NULL, &mni) ;
if (!mri_dst)
{
no1d = 1 ;
printf("1d normalization failed - trying no1d...\n") ;
// ErrorExit(ERROR_BADPARM, "%s: normalization failed", Progname) ;
}
}
if(no1d)
{
if ((file_only && nosnr) ||
((gentle_flag != 0) && (control_point_fname != NULL)))
{
if (mri_dst == NULL)
{
mri_dst = MRIcopy(mri_src, NULL) ;
}
}
else
{
if (nosnr)
{
if (interior_fname1)
{
MRIS *mris_interior1, *mris_interior2 ;
MRI *mri_ctrl ;
printf("computing initial normalization using surface interiors\n");
mri_ctrl = MRIcloneDifferentType(mri_src, MRI_UCHAR) ;
mris_interior1 = MRISread(interior_fname1) ;
if (mris_interior1 == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not read white matter surface from %s\n",
Progname, interior_fname1) ;
mris_interior2 = MRISread(interior_fname2) ;
if (mris_interior2 == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not read white matter surface from %s\n",
Progname, interior_fname2) ;
add_interior_points(mri_ctrl,
mri_dst,
intensity_above,
1.25*intensity_below,
mris_interior1,
mris_interior2,
mri_aseg,
mri_ctrl) ;
MRISfree(&mris_interior1) ;
MRISfree(&mris_interior2) ;
mri_bias = MRIbuildBiasImage(mri_dst, mri_ctrl, NULL, 0.0) ;
if (bias_sigma> 0)
{
MRI *mri_kernel = MRIgaussian1d(bias_sigma, -1) ;
MRIconvolveGaussian(mri_bias, mri_bias, mri_kernel) ;
MRIfree(&mri_kernel);
}
mri_dst = MRIapplyBiasCorrectionSameGeometry
(mri_src,
mri_bias,
mri_dst,
DEFAULT_DESIRED_WHITE_MATTER_VALUE) ;
MRIfree(&mri_ctrl) ;
}
else if (long_flag == 0) // no initial normalization specified
{
mri_dst = MRIcopy(mri_src, NULL) ;
}
}
else
{
printf("computing initial normalization using SNR...\n") ;
mri_dst = MRInormalizeHighSignalLowStd
(mri_src, mri_dst, bias_sigma,
DEFAULT_DESIRED_WHITE_MATTER_VALUE) ;
}
}
if (!mri_dst)
ErrorExit
(ERROR_BADPARM, "%s: could not allocate volume", Progname) ;
}
} // else (not using aseg)
fflush(stdout);
fflush(stderr);
if (file_only == 0)
MRI3dGentleNormalize(mri_dst, NULL, DEFAULT_DESIRED_WHITE_MATTER_VALUE,
mri_dst,
intensity_above, intensity_below/2,
file_only, bias_sigma, mri_not_control);
mri_orig = MRIcopy(mri_dst, NULL) ;
printf("\n");
printf("Iterating %d times\n",num_3d_iter);
for (n = 0 ; n < num_3d_iter ; n++)
{
if(file_only)
{
break ;
}
printf( "---------------------------------\n");
printf( "3d normalization pass %d of %d\n", n+1, num_3d_iter) ;
if (gentle_flag)
MRI3dGentleNormalize(mri_dst, NULL, DEFAULT_DESIRED_WHITE_MATTER_VALUE,
mri_dst,
intensity_above/2, intensity_below/2,
file_only, bias_sigma, mri_not_control);
else
MRI3dNormalize(mri_orig, mri_dst, DEFAULT_DESIRED_WHITE_MATTER_VALUE,
mri_dst,
intensity_above, intensity_below,
file_only, prune, bias_sigma, scan_type, mri_not_control);
}
printf( "Done iterating ---------------------------------\n");
// this just setup writing control-point volume saving
if(control_volume_fname)
{
MRI3dWriteControlPoints(control_volume_fname) ;
}
if(bias_volume_fname)
{
mri_bias = compute_bias(mri_src, mri_dst, NULL) ;
printf("writing bias field to %s....\n", bias_volume_fname) ;
MRIwrite(mri_bias, bias_volume_fname) ;
MRIfree(&mri_bias) ;
}
if (verbose)
{
printf("writing output to %s\n", out_fname) ;
}
MRIwrite(mri_dst, out_fname) ;
msec = TimerStop(&start) ;
MRIfree(&mri_src);
MRIfree(&mri_dst);
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
printf( "3D bias adjustment took %d minutes and %d seconds.\n",
minutes, seconds) ;
exit(0) ;
return(0) ;
}
int
main(int argc, char *argv[]) {
char **av ;
int ac, nargs ;
MRI *mri_orig, *mri_norm, *mri_bias ;
int msec, minutes, seconds ;
struct timeb start ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mri_apply_bias.c,v 1.5 2011/03/02 00:04:13 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
TimerStart(&start) ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 4)
usage_exit(1) ;
mri_orig = MRIread(argv[1]) ;
if (mri_orig == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read %s",Progname, argv[1]) ;
mri_bias = MRIread(argv[2]) ;
if (mri_bias == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read %s",Progname, argv[2]) ;
if (xform_fname)
{
TRANSFORM *transform ;
MRI *mri ;
transform = TransformRead(xform_fname) ;
if (transform == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not load transform %s", Progname, xform_fname) ;
mri = MRIcloneDifferentType(mri_orig, MRI_FLOAT) ;
TransformApplyInverse(transform, mri_bias, mri) ;
MRIfree(&mri_bias) ; mri_bias = mri ;
}
mri_norm = apply_bias(mri_orig, NULL, mri_bias);
fprintf(stderr, "writing to %s...\n", argv[3]) ;
MRIwrite(mri_norm, argv[3]) ;
MRIfree(&mri_norm) ;
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
fprintf(stderr, "bias correction took %d minutes and %d seconds.\n",
minutes, seconds) ;
exit(0) ;
return(0) ;
}
int
MRIcomputePartialVolumeFractions(MRI *mri_src, MATRIX *m_vox2vox,
MRI *mri_seg, MRI *mri_wm, MRI *mri_subcort_gm, MRI *mri_cortex,
MRI *mri_csf,
int wm_val, int subcort_gm_val, int cortex_val, int csf_val)
{
int x, y, z, xs, ys, zs, label ;
VECTOR *v1, *v2 ;
MRI *mri_counts ;
float val, count ;
MATRIX *m_inv ;
m_inv = MatrixInverse(m_vox2vox, NULL) ;
if (m_inv == NULL)
{
MatrixPrint(stdout, m_vox2vox) ;
ErrorExit(ERROR_BADPARM, "MRIcomputePartialVolumeFractions: non-invertible vox2vox matrix");
}
mri_counts = MRIcloneDifferentType(mri_src, MRI_INT) ;
v1 = VectorAlloc(4, MATRIX_REAL) ;
v2 = VectorAlloc(4, MATRIX_REAL) ;
VECTOR_ELT(v1, 4) = 1.0 ; VECTOR_ELT(v2, 4) = 1.0 ;
for (x = 0 ; x < mri_seg->width ; x++)
{
V3_X(v1) = x ;
for (y = 0 ; y < mri_seg->height ; y++)
{
V3_Y(v1) = y ;
for (z = 0 ; z < mri_seg->depth ; z++)
{
if (x == Gx && y == Gy && z == Gz)
DiagBreak() ;
V3_Z(v1) = z ;
MatrixMultiply(m_vox2vox, v1, v2) ;
xs = nint(V3_X(v2)) ; ys = nint(V3_Y(v2)) ; zs = nint(V3_Z(v2)) ;
if (xs >= 0 && ys >= 0 && zs >= 0 &&
xs < mri_src->width && ys < mri_src->height && zs < mri_src->depth)
{
val = MRIgetVoxVal(mri_counts, xs, ys, zs, 0) ;
MRIsetVoxVal(mri_counts, xs, ys, zs, 0, val+1) ;
label = MRIgetVoxVal(mri_seg, x, y, z, 0) ;
if (label == csf_val)
{
val = MRIgetVoxVal(mri_csf, xs, ys, zs, 0) ;
MRIsetVoxVal(mri_csf, xs, ys, zs, 0, val+1) ;
}
else if (label == wm_val)
{
val = MRIgetVoxVal(mri_wm, xs, ys, zs, 0) ;
MRIsetVoxVal(mri_wm, xs, ys, zs, 0, val+1) ;
}
else if (label == subcort_gm_val)
{
val = MRIgetVoxVal(mri_subcort_gm, xs, ys, zs, 0) ;
MRIsetVoxVal(mri_subcort_gm, xs, ys, zs, 0, val+1) ;
}
else if (label == cortex_val)
{
val = MRIgetVoxVal(mri_cortex, xs, ys, zs, 0) ;
MRIsetVoxVal(mri_cortex, xs, ys, zs, 0, val+1) ;
}
else
DiagBreak() ;
}
}
}
}
for (x = 0 ; x < mri_src->width ; x++)
for (y = 0 ; y < mri_src->height ; y++)
for (z = 0 ; z < mri_src->depth ; z++)
{
count = MRIgetVoxVal(mri_counts, x, y, z, 0) ;
if (count >= 1)
{
if (x == Gx && y == Gy && z == Gz)
DiagBreak() ;
val = MRIgetVoxVal(mri_wm, x, y, z, 0) ;
MRIsetVoxVal(mri_wm, x, y, z, 0, val/count) ;
val = MRIgetVoxVal(mri_subcort_gm, x, y, z, 0) ;
MRIsetVoxVal(mri_subcort_gm, x, y, z, 0, val/count) ;
val = MRIgetVoxVal(mri_cortex, x, y, z, 0) ;
MRIsetVoxVal(mri_cortex, x, y, z, 0, val/count) ;
val = MRIgetVoxVal(mri_csf, x, y, z, 0) ;
MRIsetVoxVal(mri_csf, x, y, z, 0, val/count) ;
}
else // sample in other direction
{
V3_X(v1) = x ; V3_Y(v1) = y ; V3_Z(v1) = z ;
MatrixMultiply(m_inv, v1, v2) ;
MatrixMultiply(m_inv, v1, v2) ;
xs = nint(V3_X(v2)) ; ys = nint(V3_Y(v2)) ; zs = nint(V3_Z(v2)) ;
if (xs >= 0 && ys >= 0 && zs >= 0 &&
xs < mri_seg->width && ys < mri_seg->height && zs < mri_seg->depth)
{
label = MRIgetVoxVal(mri_seg, xs, ys, zs, 0) ;
if (label == csf_val)
MRIsetVoxVal(mri_csf, x, y, z, 0, 1) ;
else if (label == wm_val)
MRIsetVoxVal(mri_wm, x, y, z, 0, 1) ;
else if (label == subcort_gm_val)
MRIsetVoxVal(mri_subcort_gm, x, y, z, 0, 1) ;
else if (cortex_val)
MRIsetVoxVal(mri_cortex, x, y, z, 0, 1) ;
else
DiagBreak() ;
}
}
}
VectorFree(&v1) ; VectorFree(&v2) ; MatrixFree(&m_inv) ;
MRIfree(&mri_counts) ;
return(NO_ERROR) ;
}
static int
relabel_hypointensities(MRI *mri, MRI_SURFACE *mris, int right)
{
int x, y, z, label, changed ;
MRIS_HASH_TABLE *mht ;
VERTEX *v ;
float dx, dy, dz, dot, dist ;
Real xw, yw, zw ;
MRI *mri_dist ;
mri_dist = MRIcloneDifferentType(mri, MRI_FLOAT) ;
MRIScomputeDistanceToSurface(mris, mri_dist, mri_dist->xsize) ;
mht = MHTfillVertexTableRes(mris,NULL, CURRENT_VERTICES, 8.0f) ;
for (changed = x = 0 ; x < mri->width ; x++) {
for (y = 0 ; y < mri->height ; y++) {
for (z = 0 ; z < mri->depth ; z++) {
if (x == Gx && y == Gy && z == Gz) {
DiagBreak() ;
}
label = MRIgetVoxVal(mri, x, y, z, 0) ;
if (label == Left_WM_hypointensities) {
MRIsetVoxVal(mri, x, y, z,0, WM_hypointensities) ;
} else if (label == Right_WM_hypointensities) {
MRIsetVoxVal(mri, x, y, z, 0, WM_hypointensities) ;
}
if ((!right && (label != Left_Cerebral_Cortex)) ||
(right && (label != Right_Cerebral_Cortex))) {
continue ;
}
// MRIvoxelToWorld(mri, x, y, z, &xw, &yw, &zw) ;
MRIvoxelToSurfaceRAS(mri, x, y, z, &xw, &yw, &zw);
v = MHTfindClosestVertexInTable(mht, mris, xw, yw, zw, 0) ;
if (v == NULL) /* no vertices within range -
assume it is hypointensity */
{
dot = -1 ;
dist = MRIgetVoxVal(mri_dist, x, y, z, 0) ;
if (dist > 0) {
dot = 1 ;
}
} else {
dx = xw - v->x ;
dy = yw - v->y ;
dz = zw - v->z ;
dot = v->nx*dx + v->ny*dy + v->nz*dz ;
dist = sqrt(dx*dx+dy*dy+dz*dz) ;
}
if (dot < 0 && dist > 1) {
changed++ ;
MRIsetVoxVal(mri, x, y, z, 0, WM_hypointensities) ;
}
}
}
}
printf("%d voxels changed to hypointensity...\n", changed) ;
MHTfree(&mht) ;
MRIfree(&mri_dist) ;
return(NO_ERROR) ;
}
FCD_DATA *
FCDloadData(char *sdir, char *subject)
{
FCD_DATA *fcd ;
char fname[STRLEN] ;
MRI *mri_interior, *mri_dist, *mri_int_lh, *mri_int_rh, *mri_pvals ;
fcd = (FCD_DATA *)calloc(1, sizeof(FCD_DATA)) ;
sprintf(fname, "%s/%s/surf/lh.white", sdir, subject) ;
fcd->mris_lh = MRISread(fname) ;
if (fcd->mris_lh == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
MRISsaveVertexPositions(fcd->mris_lh, WHITE_VERTICES) ;
if (MRISreadPialCoordinates(fcd->mris_lh, "pial") != NO_ERROR)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load lh pial vertices") ;
}
sprintf(fname, "%s/%s/surf/lh.pial", sdir, subject) ;
fcd->mris_lh_pial = MRISread(fname) ;
if (fcd->mris_lh_pial == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
sprintf(fname, "%s/%s/surf/lh.sphere.d1.left_right", sdir, subject) ;
fcd->mris_lh_sphere_d1 = MRISread(fname) ;
if (fcd->mris_lh_sphere_d1 == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
exec_progress_callback(1, 12, 0, 1) ;
sprintf(fname, "%s/%s/surf/rh.white", sdir, subject) ;
fcd->mris_rh = MRISread(fname) ;
if (fcd->mris_rh == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
MRISsaveVertexPositions(fcd->mris_rh, WHITE_VERTICES) ;
if (MRISreadPialCoordinates(fcd->mris_rh, "pial") != NO_ERROR)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load rh pial vertices") ;
}
sprintf(fname, "%s/%s/surf/rh.pial", sdir, subject) ;
fcd->mris_rh_pial = MRISread(fname) ;
if (fcd->mris_rh_pial == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
sprintf(fname, "%s/%s/surf/rh.sphere.d1.left_right", sdir, subject) ;
fcd->mris_rh_sphere_d1 = MRISread(fname) ;
if (fcd->mris_rh_sphere_d1 == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
exec_progress_callback(2, 12, 0, 1) ;
sprintf(fname, "%s/%s/mri/aseg.mgz", sdir, subject) ;
fcd->mri_aseg = MRIread(fname) ;
if (fcd->mri_aseg == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
exec_progress_callback(3, 12, 0, 1) ;
sprintf(fname, "%s/%s/mri/aparc+aseg.mgz", sdir, subject) ;
fcd->mri_aparc = MRIread(fname) ;
if (fcd->mri_aparc == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
exec_progress_callback(4, 12, 0, 1) ;
fcd->mri_flair = NULL;
sprintf(fname, "%s/%s/mri/flair.reg.norm.mgz", sdir, subject) ;
if ( ! FileExists(fname))
{
sprintf(fname, "%s/%s/mri/FLAIR.mgz", sdir, subject) ;
if ( ! FileExists(fname))
{
sprintf(fname, "%s/%s/mri/FLAIRax.mgz", sdir, subject) ;
if ( ! FileExists(fname))
{
sprintf(fname, "%s/%s/mri/FLAIRcor.mgz", sdir, subject) ;
if ( ! FileExists(fname))
{
sprintf(fname, " ");
}
}
}
}
if (strlen(fname) > 1)
{
fcd->mri_flair = MRIread(fname) ;
if (fcd->mri_flair == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load $s", fname) ;
}
}
fcd->mri_t2 = NULL;
sprintf(fname, "%s/%s/mri/T2.mgz", sdir, subject) ;
if ( ! FileExists(fname))
{
sprintf(fname, "%s/%s/mri/T2ax.mgz", sdir, subject) ;
if ( ! FileExists(fname))
{
sprintf(fname, "%s/%s/mri/T2cor.mgz", sdir, subject) ;
if ( ! FileExists(fname))
{
sprintf(fname, " ");
}
}
}
if (strlen(fname) > 1)
{
fcd->mri_t2 = MRIread(fname) ;
if (fcd->mri_t2 == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load $s", fname) ;
}
}
exec_progress_callback(5, 12, 0, 1) ;
sprintf(fname, "%s/%s/mri/norm.mgz", sdir, subject) ;
fcd->mri_norm = MRIread(fname) ;
if (fcd->mri_norm == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
fcd->mri_thickness_increase =
MRIcloneDifferentType(fcd->mri_aseg, MRI_FLOAT) ;
fcd->mri_thickness_decrease =
MRIcloneDifferentType(fcd->mri_aseg, MRI_FLOAT) ;
fcd->mri_thickness_difference = MRIadd(fcd->mri_thickness_increase, fcd->mri_thickness_decrease, NULL);
exec_progress_callback(6, 12, 0, 1) ;
sprintf(fname, "%s/%s/surf/lh.rh.thickness.smooth0.mgz", sdir, subject) ;
fcd->rh_thickness_on_lh = MRIread(fname) ;
if (fcd->mri_aseg == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
exec_progress_callback(7, 12, 0, 1) ;
sprintf(fname, "%s/%s/surf/rh.thickness.mgz", sdir, subject) ;
fcd->rh_thickness_on_rh = MRIread(fname) ;
if (fcd->rh_thickness_on_rh == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
exec_progress_callback(8, 12, 0, 1) ;
sprintf(fname, "%s/%s/surf/lh.thickness.mgz", sdir, subject) ;
fcd->lh_thickness_on_lh = MRIread(fname) ;
if (fcd->lh_thickness_on_lh == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
exec_progress_callback(9, 12, 0, 1) ;
sprintf(fname, "%s/%s/surf/rh.lh.thickness.smooth0.mgz", sdir, subject) ;
if ( ! FileExists(fname))
{
sprintf(fname, "%s/%s/surf/rh.lh.thickness.mgz", sdir, subject) ;
if (fcd->lh_thickness_on_rh == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
}
fcd->lh_thickness_on_rh = MRIread(fname) ;
exec_progress_callback(10, 12, 0, 1) ;
mri_int_lh = MRIclone(fcd->mri_norm, NULL) ;
mri_int_rh = MRIclone(fcd->mri_norm, NULL) ;
mri_interior = MRIclone(fcd->mri_norm, NULL) ;
mri_dist = MRIcloneDifferentType(mri_interior, MRI_FLOAT) ;
MRISrestoreVertexPositions(fcd->mris_lh, PIAL_VERTICES) ;
MRISrestoreVertexPositions(fcd->mris_rh, PIAL_VERTICES) ;
MRISfillInterior(fcd->mris_lh, mri_interior->xsize, mri_int_lh) ;
MRISfillInterior(fcd->mris_rh, mri_interior->xsize, mri_int_rh) ;
exec_progress_callback(11, 12, 0, 1) ;
MRIor(mri_int_lh, mri_int_rh, mri_interior, 0) ;
MRIfree(&mri_int_lh) ;
MRIfree(&mri_int_rh) ;
MRIbinarize(mri_interior, mri_interior, 1, 0, 1) ;
if (Gdiag & DIAG_WRITE)
{
MRIwrite(mri_interior, "int.mgz") ;
}
MRIdistanceTransform(mri_interior,
mri_dist,
1,
2*MAX_DIST,
DTRANS_MODE_SIGNED,
NULL);
if (Gdiag & DIAG_WRITE)
{
MRIwrite(mri_dist, "dist.mgz") ;
}
mri_pvals = build_distance_by_intensity_histo(fcd->mri_norm,
mri_dist,
fcd->mri_aseg,
DIST_SPACING,
MAX_DIST) ;
exec_progress_callback(12, 12, 0, 1) ;
augment_thicknesses(fcd, mri_pvals, 1.5, 5, 1) ;
MRISrestoreVertexPositions(fcd->mris_lh, WHITE_VERTICES) ;
MRISrestoreVertexPositions(fcd->mris_rh, WHITE_VERTICES) ;
MRIfree(&mri_dist) ;
MRIfree(&mri_interior) ;
MRIfree(&mri_pvals) ;
return(fcd) ;
}
