int
main(int argc, char *argv[]) {
char **av ;
int ac, nargs ;
MRI *mri_src, *mri_ref, *mri_tmp ;
double accuracy ;
MRI_REGION box ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_label_accuracy.c,v 1.2 2011/03/02 00:04:22 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 < 3)
usage_exit(1) ;
mri_src = MRIread(argv[1]) ;
if (mri_src == NULL)
ErrorExit(ERROR_BADPARM, "%s: could not read input volume %s\n", Progname,argv[1]);
MRIboundingBox(mri_src, 0, &box) ;
mri_tmp = MRIextractRegionAndPad(mri_src, NULL, &box, PAD) ;
MRIfree(&mri_src) ; mri_src = mri_tmp ;
if (mri_src->type == MRI_SHORT)
{
mri_tmp = MRIchangeType(mri_src, MRI_FLOAT, 0, 0, 0) ;
MRIfree(&mri_src) ; mri_src = mri_tmp ;
}
mri_ref = MRIread(argv[2]) ;
if (mri_ref == NULL)
ErrorExit(ERROR_BADPARM, "%s: could not read reference volume %s\n", Progname,argv[1]);
MRIboundingBox(mri_ref, 0, &box) ;
mri_tmp = MRIextractRegionAndPad(mri_ref, NULL, &box, PAD) ;
MRIfree(&mri_ref) ; mri_ref = mri_tmp ;
accuracy = MRIcomputeLabelAccuracy(mri_src, mri_ref, MRI_MEAN_MIN_DISTANCE, stdout) ;
if (Gdiag_fp)
fclose(Gdiag_fp) ;
exit(0) ;
return(0) ;
}
static int
init_scaling(MRI *mri_in, MRI *mri_ref, MATRIX *m_L) {
MATRIX *m_scaling ;
float sx, sy, sz, dx, dy, dz ;
MRI_REGION in_bbox, ref_bbox ;
m_scaling = MatrixIdentity(4, NULL) ;
MRIboundingBox(mri_in, 60, &in_bbox) ;
MRIboundingBox(mri_ref, 60, &ref_bbox) ;
sx = (float)ref_bbox.dx / (float)in_bbox.dx ;
sy = (float)ref_bbox.dy / (float)in_bbox.dy ;
sz = (float)ref_bbox.dz / (float)in_bbox.dz ;
dx = (ref_bbox.x+ref_bbox.dx-1)/2 - (in_bbox.x+in_bbox.dx-1)/2 ;
dy = (ref_bbox.y+ref_bbox.dy-1)/2 - (in_bbox.y+in_bbox.dy-1)/2 ;
dz = (ref_bbox.z+ref_bbox.dz-1)/2 - (in_bbox.z+in_bbox.dz-1)/2 ;
if (sx > MAX_DX)
sx = MAX_DX ;
if (sx < MIN_DX)
sx = MIN_DX ;
if (sy > MAX_DY)
sy = MAX_DY ;
if (sy < MIN_DY)
sy = MIN_DY ;
if (sz > MAX_DZ)
sz = MAX_DZ ;
if (sz < MIN_DZ)
sz = MIN_DZ ;
if (Gdiag & DIAG_SHOW)
fprintf(stderr, "initial scaling: (%2.2f, %2.2f, %2.2f) <-- "
"(%d/%d,%d/%d,%d/%d)\n",
sx,sy,sz, ref_bbox.dx, in_bbox.dx, ref_bbox.dy, in_bbox.dy,
ref_bbox.dz, in_bbox.dz) ;
*MATRIX_RELT(m_scaling, 1, 1) = sx ;
*MATRIX_RELT(m_scaling, 2, 2) = sy ;
*MATRIX_RELT(m_scaling, 3, 3) = sz ;
#if 0
*MATRIX_RELT(m_L, 1, 4) = dx ;
*MATRIX_RELT(m_L, 2, 4) = dy ;
*MATRIX_RELT(m_L, 3, 4) = dz ;
#endif
MatrixMultiply(m_scaling, m_L, m_L) ;
return(NO_ERROR) ;
}
int
main(int argc, char *argv[])
{
char **av, *source_fname, *target_fname, *out_fname, fname[STRLEN] ;
int ac, nargs, new_transform = 0, pad ;
MRI *mri_target, *mri_source, *mri_orig_source ;
MRI_REGION box ;
struct timeb start ;
int msec, minutes, seconds ;
GCA_MORPH *gcam ;
MATRIX *m_L/*, *m_I*/ ;
LTA *lta ;
/* initialize the morph params */
memset(&mp, 0, sizeof(GCA_MORPH_PARMS));
/* for nonlinear morph */
mp.l_jacobian = 1 ;
mp.min_sigma = 0.4 ;
mp.l_distance = 0 ;
mp.l_log_likelihood = .025 ;
mp.dt = 0.005 ;
mp.noneg = True ;
mp.exp_k = 20 ;
mp.diag_write_snapshots = 1 ;
mp.momentum = 0.9 ;
if (FZERO(mp.l_smoothness))
mp.l_smoothness = 2 ;
mp.sigma = 8 ;
mp.relabel_avgs = -1 ;
mp.navgs = 256 ;
mp.levels = 6 ;
mp.integration_type = GCAM_INTEGRATE_BOTH ;
mp.nsmall = 1 ;
mp.reset_avgs = -1 ;
mp.npasses = 3 ;
mp.regrid = regrid? True : False ;
mp.tol = 0.1 ;
mp.niterations = 1000 ;
TimerStart(&start) ;
setRandomSeed(-1L) ;
DiagInit(NULL, NULL, NULL) ;
ErrorInit(NULL, NULL, NULL) ;
Progname = argv[0] ;
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) ;
source_fname = argv[1] ;
target_fname = argv[2] ;
out_fname = argv[3] ;
FileNameOnly(out_fname, fname) ;
FileNameRemoveExtension(fname, fname) ;
strcpy(mp.base_name, fname) ;
mri_source = MRIread(source_fname) ;
if (!mri_source)
ErrorExit(ERROR_NOFILE, "%s: could not read source label volume %s",
Progname, source_fname) ;
if (mri_source->type == MRI_INT)
{
MRI *mri_tmp = MRIchangeType(mri_source, MRI_FLOAT, 0, 1, 1) ;
MRIfree(&mri_source); mri_source = mri_tmp ;
}
mri_target = MRIread(target_fname) ;
if (!mri_target)
ErrorExit(ERROR_NOFILE, "%s: could not read target label volume %s",
Progname, target_fname) ;
if (mri_target->type == MRI_INT)
{
MRI *mri_tmp = MRIchangeType(mri_target, MRI_FLOAT, 0, 1, 1) ;
MRIfree(&mri_target); mri_target = mri_tmp ;
}
if (erosions > 0)
{
int n ;
for (n = 0 ; n < erosions ; n++)
{
MRIerodeZero(mri_target, mri_target) ;
MRIerodeZero(mri_source, mri_source) ;
}
}
if (scale_values > 0)
{
MRIscalarMul(mri_source, mri_source, scale_values) ;
MRIscalarMul(mri_target, mri_target, scale_values) ;
}
if (transform && transform->type == MORPH_3D_TYPE)
TransformRas2Vox(transform, mri_source,NULL) ;
if (use_aseg == 0)
{
if (match_peak_intensity_ratio)
MRImatchIntensityRatio(mri_source, mri_target, mri_source, .8, 1.2,
100, 125) ;
else if (match_mean_intensity)
MRImatchMeanIntensity(mri_source, mri_target, mri_source) ;
MRIboundingBox(mri_source, 0, &box) ;
pad = (int)ceil(PADVOX *
MAX(mri_target->xsize,MAX(mri_target->ysize,mri_target->zsize)) /
MIN(mri_source->xsize,MIN(mri_source->ysize,mri_source->zsize)));
#if 0
{ MRI *mri_tmp ;
if (pad < 1)
pad = 1 ;
printf("padding source with %d voxels...\n", pad) ;
mri_tmp = MRIextractRegionAndPad(mri_source, NULL, &box, pad) ;
if ((Gdiag & DIAG_WRITE) && DIAG_VERBOSE_ON)
MRIwrite(mri_tmp, "t.mgz") ;
MRIfree(&mri_source) ;
mri_source = mri_tmp ;
}
#endif
}
mri_orig_source = MRIcopy(mri_source, NULL) ;
mp.max_grad = 0.3*mri_source->xsize ;
if (transform == NULL)
transform = TransformAlloc(LINEAR_VOXEL_TO_VOXEL, NULL) ;
if (transform->type != MORPH_3D_TYPE) // initializing m3d from a linear transform
{
new_transform = 1 ;
lta = ((LTA *)(transform->xform)) ;
if (lta->type != LINEAR_VOX_TO_VOX)
{
printf("converting ras xform to voxel xform\n") ;
m_L = MRIrasXformToVoxelXform(mri_source, mri_target, lta->xforms[0].m_L, NULL) ;
MatrixFree(<a->xforms[0].m_L) ;
lta->type = LINEAR_VOX_TO_VOX ;
}
else
{
printf("using voxel xform\n") ;
m_L = lta->xforms[0].m_L ;
}
#if 0
if (Gsx >= 0) // update debugging coords
{
VECTOR *v1, *v2 ;
v1 = VectorAlloc(4, MATRIX_REAL) ;
Gsx -= (box.x-pad) ;
Gsy -= (box.y-pad) ;
Gsz -= (box.z-pad) ;
V3_X(v1) = Gsx ; V3_Y(v1) = Gsy ; V3_Z(v1) = Gsz ;
VECTOR_ELT(v1,4) = 1.0 ;
v2 = MatrixMultiply(m_L, v1, NULL) ;
Gsx = nint(V3_X(v2)) ; Gsy = nint(V3_Y(v2)) ; Gsz = nint(V3_Z(v2)) ;
MatrixFree(&v2) ; MatrixFree(&v1) ;
printf("mapping by transform (%d, %d, %d) --> (%d, %d, %d) for rgb writing\n",
Gx, Gy, Gz, Gsx, Gsy, Gsz) ;
}
#endif
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
write_snapshot(mri_target, mri_source, m_L, &mp, 0, 1, "linear_init");
lta->xforms[0].m_L = m_L ;
printf("initializing GCAM with vox->vox matrix:\n") ;
MatrixPrint(stdout, m_L) ;
gcam = GCAMcreateFromIntensityImage(mri_source, mri_target, transform) ;
#if 0
gcam->gca = gcaAllocMax(1, 1, 1,
mri_target->width, mri_target->height,
mri_target->depth,
0, 0) ;
#endif
GCAMinitVolGeom(gcam, mri_source, mri_target) ;
if (use_aseg)
{
if (ribbon_name)
{
char fname[STRLEN], path[STRLEN], *str, *hemi ;
int h, s, label ;
MRI_SURFACE *mris_white, *mris_pial ;
MRI *mri ;
for (s = 0 ; s <= 1 ; s++) // source and target
{
if (s == 0)
{
str = source_surf ;
mri = mri_source ;
FileNamePath(mri->fname, path) ;
strcat(path, "/../surf") ;
}
else
{
mri = mri_target ;
FileNamePath(mri->fname, path) ;
strcat(path, "/../elastic") ;
str = target_surf ;
}
// sorry - these values come from FreeSurferColorLUT.txt
MRIreplaceValueRange(mri, mri, 1000, 1034, Left_Cerebral_Cortex) ;
MRIreplaceValueRange(mri, mri, 1100, 1180, Left_Cerebral_Cortex) ;
MRIreplaceValueRange(mri, mri, 2000, 2034, Right_Cerebral_Cortex) ;
MRIreplaceValueRange(mri, mri, 2100, 2180, Right_Cerebral_Cortex) ;
for (h = LEFT_HEMISPHERE ; h <= RIGHT_HEMISPHERE ; h++)
{
if (h == LEFT_HEMISPHERE)
{
hemi = "lh" ;
label = Left_Cerebral_Cortex ;
}
else
{
label = Right_Cerebral_Cortex ;
hemi = "rh" ;
}
sprintf(fname, "%s/%s%s.white", path, hemi, str) ;
mris_white = MRISread(fname) ;
if (mris_white == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read surface %s", Progname, fname) ;
MRISsaveVertexPositions(mris_white, WHITE_VERTICES) ;
sprintf(fname, "%s/%s%s.pial", path, hemi, str) ;
mris_pial = MRISread(fname) ;
if (mris_pial == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read surface %s", Progname, fname) ;
MRISsaveVertexPositions(mris_pial, PIAL_VERTICES) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
sprintf(fname, "sb.mgz") ;
MRIwrite(mri_source, fname) ;
sprintf(fname, "tb.mgz") ;
MRIwrite(mri_target, fname) ;
}
insert_ribbon_into_aseg(mri, mri, mris_white, mris_pial, h) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
sprintf(fname, "sa.mgz") ;
MRIwrite(mri_source, fname) ;
sprintf(fname, "ta.mgz") ;
MRIwrite(mri_target, fname) ;
}
MRISfree(&mris_white) ; MRISfree(&mris_pial) ;
}
}
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
sprintf(fname, "s.mgz") ;
MRIwrite(mri_source, fname) ;
sprintf(fname, "t.mgz") ;
MRIwrite(mri_target, fname) ;
}
}
GCAMinitLabels(gcam, mri_target) ;
GCAMsetVariances(gcam, 1.0) ;
mp.mri_dist_map = create_distance_transforms(mri_source, mri_target, NULL, 40.0, gcam) ;
}
}
else /* use a previously create morph and integrate it some more */
{
printf("using previously create gcam...\n") ;
gcam = (GCA_MORPH *)(transform->xform) ;
GCAMrasToVox(gcam, mri_source) ;
if (use_aseg)
{
GCAMinitLabels(gcam, mri_target) ;
GCAMsetVariances(gcam, 1.0) ;
mp.mri_dist_map = create_distance_transforms(mri_source, mri_target, NULL, 40.0, gcam) ;
}
else
GCAMaddIntensitiesFromImage(gcam, mri_target) ;
}
if (gcam->width != mri_source->width ||
gcam->height != mri_source->height ||
gcam->depth != mri_source->depth)
ErrorExit(ERROR_BADPARM, "%s: warning gcam (%d, %d, %d), doesn't match source vol (%d, %d, %d)",
Progname, gcam->width, gcam->height, gcam->depth,
mri_source->width, mri_source->height, mri_source->depth) ;
mp.mri_diag = mri_source ;
mp.diag_morph_from_atlas = 0 ;
mp.diag_write_snapshots = 1 ;
mp.diag_sample_type = use_aseg ? SAMPLE_NEAREST : SAMPLE_TRILINEAR ;
mp.diag_volume = use_aseg ? GCAM_LABEL : GCAM_MEANS ;
if (renormalize)
GCAMnormalizeIntensities(gcam, mri_target) ;
if (mp.write_iterations != 0)
{
char fname[STRLEN] ;
MRI *mri_gca ;
if (getenv("DONT_COMPRESS"))
sprintf(fname, "%s_target.mgh", mp.base_name) ;
else
sprintf(fname, "%s_target.mgz", mp.base_name) ;
if (mp.diag_morph_from_atlas == 0)
{
printf("writing target volume to %s...\n", fname) ;
MRIwrite(mri_target, fname) ;
sprintf(fname, "%s_target", mp.base_name) ;
MRIwriteImageViews(mri_target, fname, IMAGE_SIZE) ;
}
else
{
if (use_aseg)
mri_gca = GCAMwriteMRI(gcam, NULL, GCAM_LABEL) ;
else
{
mri_gca = MRIclone(mri_source, NULL) ;
GCAMbuildMostLikelyVolume(gcam, mri_gca) ;
}
printf("writing target volume to %s...\n", fname) ;
MRIwrite(mri_gca, fname) ;
sprintf(fname, "%s_target", mp.base_name) ;
MRIwriteImageViews(mri_gca, fname, IMAGE_SIZE) ;
MRIfree(&mri_gca) ;
}
}
if (nozero)
{
printf("disabling zero nodes\n") ;
GCAMignoreZero(gcam, mri_target) ;
}
mp.mri = mri_target ;
if (mp.regrid == True && new_transform == 0)
GCAMregrid(gcam, mri_target, PAD, &mp, &mri_source) ;
mp.write_fname = out_fname ;
GCAMregister(gcam, mri_source, &mp) ; // atlas is target, morph target into register with it
if (apply_transform)
{
MRI *mri_aligned ;
char fname[STRLEN] ;
FileNameRemoveExtension(out_fname, fname) ;
strcat(fname, ".mgz") ;
mri_aligned = GCAMmorphToAtlas(mp.mri, gcam, NULL, -1, mp.diag_sample_type) ;
printf("writing transformed output volume to %s...\n", fname) ;
MRIwrite(mri_aligned, fname) ;
MRIfree(&mri_aligned) ;
}
printf("writing warp vector field to %s\n", out_fname) ;
GCAMvoxToRas(gcam) ;
GCAMwrite(gcam, out_fname) ;
GCAMrasToVox(gcam, mri_source) ;
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
printf("registration took %d minutes and %d seconds.\n",
minutes, seconds) ;
exit(0) ;
return(0) ;
}
int
main(int argc, char *argv[]) {
char **av ;
int ac, nargs, width, height, depth, x, y, z, xborder, yborder, zborder,
xrborder, yrborder, zrborder ;
char *in_fname, *out_fname ;
MRI *mri_smooth, *mri_grad, *mri_filter_src, *mri_filter_dst, *mri_dst,
*mri_tmp, *mri_blur, *mri_src, *mri_filtered, *mri_direction,
*mri_offset, *mri_up, *mri_polv, *mri_dir, *mri_clip, *mri_full ;
MRI_REGION region, clip_region ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_nlfilter.c,v 1.14 2011/03/02 00:04:23 nicks Exp $", "$Name: $");
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 < 3)
usage_exit() ;
in_fname = argv[1] ;
out_fname = argv[2] ;
mri_full = mri_src = MRIread(in_fname) ;
if (!mri_src)
ErrorExit(ERROR_NOFILE, "%s: could not read '%s'", Progname, in_fname) ;
if (!FZERO(blur_sigma)) /* allocate a blurring kernel */
{
mri_blur = MRIgaussian1d(blur_sigma, 0) ;
if (!mri_blur)
ErrorExit(ERROR_BADPARM,
"%s: could not allocate blurring kernel with sigma=%2.3f",
Progname, blur_sigma) ;
} else
mri_blur = NULL ;
MRIboundingBox(mri_full, 0, &clip_region) ;
REGIONexpand(&clip_region, &clip_region, (filter_window_size+1)/2) ;
mri_src = MRIextractRegion(mri_full, NULL, &clip_region) ;
width = mri_src->width ;
height = mri_src->height ;
depth = mri_src->depth ;
mri_dst = MRIclone(mri_src, NULL) ;
if (!mri_dst)
ErrorExit(ERROR_NOFILE, "%s: could allocate space for destination image",
Progname) ;
for (z = 0 ; z < depth ; z += region_size) {
for (y = 0 ; y < height ; y += region_size) {
DiagHeartbeat((float)(z*height+y) / (float)(height*(depth-1))) ;
for (x = 0 ; x < width ; x += region_size) {
region.x = x ;
region.y = y ;
region.z = z ;
region.dx = region.dy = region.dz = region_size ;
if (region.x == 142)
DiagBreak() ;
REGIONexpand(®ion, ®ion, (filter_window_size+1)/2) ;
MRIclipRegion(mri_src, ®ion, ®ion) ;
if (region.x == 142)
DiagBreak() ;
/* check for < 0 width regions */
xborder = x-region.x ;
yborder = y-region.y ;
zborder = z-region.z ;
xrborder = MAX(0, (region.dx-xborder) - region_size) ;
yrborder = MAX(0, (region.dy-yborder) - region_size) ;
zrborder = MAX(0, (region.dz-zborder) - region_size) ;
#if 0
if (region.dx < 2*xborder || region.dy<2*yborder||region.dz<2*zborder)
continue ;
#endif
if (DIAG_VERBOSE_ON && (Gdiag & DIAG_SHOW))
fprintf(stderr, "extracting region (%d, %d, %d) --> (%d, %d, %d)...",
region.x,region.y,region.z, region.x+region.dx-1,
region.y+region.dy-1,region.z+region.dz-1) ;
mri_clip = MRIextractRegion(mri_src, NULL, ®ion) ;
if (DIAG_VERBOSE_ON && (Gdiag & DIAG_SHOW))
fprintf(stderr, "done.\nsmoothing region and up-sampling...") ;
if (mri_blur) /* smooth the input image to generate offset field */
mri_smooth = MRIconvolveGaussian(mri_clip, NULL, mri_blur) ;
else
mri_smooth = MRIcopy(mri_clip, NULL) ; /* no smoothing */
if (!mri_smooth)
ErrorExit(ERROR_BADPARM, "%s: image smoothing failed", Progname) ;
/* now up-sample the smoothed image, and compute offset field in
up-sampled domain */
mri_up = MRIupsample2(mri_smooth, NULL) ;
if (!mri_up)
ErrorExit(ERROR_BADPARM, "%s: up sampling failed", Progname) ;
MRIfree(&mri_smooth) ;
if (DIAG_VERBOSE_ON && (Gdiag & DIAG_SHOW))
fprintf(stderr, "done.\n") ;
mri_smooth = mri_up ;
mri_grad = MRIsobel(mri_smooth, NULL, NULL) ;
mri_dir = MRIclone(mri_smooth, NULL) ;
MRIfree(&mri_smooth) ;
if (DIAG_VERBOSE_ON && (Gdiag & DIAG_SHOW))
fprintf(stderr, "computing direction map...") ;
mri_direction =
MRIoffsetDirection(mri_grad, offset_window_size, NULL, mri_dir) ;
if (DIAG_VERBOSE_ON && (Gdiag & DIAG_SHOW))
fprintf(stderr, "computing offset magnitudes...") ;
MRIfree(&mri_grad) ;
mri_offset =
MRIoffsetMagnitude(mri_direction, NULL, offset_search_len);
MRIfree(&mri_direction) ;
if (!mri_offset)
ErrorExit(ERROR_NOMEMORY,
"%s: offset calculation failed", Progname) ;
if (DIAG_VERBOSE_ON && (Gdiag & DIAG_SHOW))
fprintf(stderr, "done.\nfiltering image...") ;
mri_filter_src = MRIupsample2(mri_clip, NULL) ;
MRIfree(&mri_clip) ;
switch (filter_type) {
case FILTER_CPOLV_MEDIAN:
mri_polv = MRIplaneOfLeastVarianceNormal(mri_filter_src,NULL,5);
mri_filter_dst =
MRIpolvMedian(mri_filter_src, NULL, mri_polv,filter_window_size);
MRIfree(&mri_polv) ;
break ;
case FILTER_GAUSSIAN:
mri_filter_dst =
MRIconvolveGaussian(mri_filter_src, NULL, mri_gaussian) ;
if (!mri_filter_dst)
ErrorExit(ERROR_NOMEMORY,
"%s: could not allocate temporary buffer space",Progname);
break ;
case FILTER_MEDIAN:
mri_filter_dst = MRImedian(mri_filter_src,NULL,filter_window_size, NULL);
if (!mri_filter_dst)
ErrorExit(ERROR_NOMEMORY,
"%s: could not allocate temporary buffer space",Progname);
break ;
case FILTER_MEAN:
mri_filter_dst = MRImean(mri_filter_src, NULL, filter_window_size) ;
if (!mri_filter_dst)
ErrorExit(ERROR_NOMEMORY,
"%s: could not allocate temporary buffer space",Progname);
break ;
case FILTER_MINMAX:
mri_filter_dst =
MRIminmax(mri_filter_src, NULL, mri_dir, filter_window_size) ;
if (!mri_filter_dst)
ErrorExit(ERROR_NOMEMORY,
"%s: could not allocate space for filtered image",
Progname) ;
break ;
default:
mri_filter_dst = MRIcopy(mri_filter_src, NULL) ; /* no filtering */
break ;
}
MRIfree(&mri_dir) ;
MRIfree(&mri_filter_src) ;
if (no_offset)
{
mri_filtered = MRIcopy(mri_filter_dst, NULL) ;
}
else
{
if (DIAG_VERBOSE_ON && (Gdiag & DIAG_SHOW))
fprintf(stderr, "applying offset field...") ;
if (Gdiag & DIAG_WRITE)
MRIwrite(mri_filter_dst, "minmax.mgz") ;
mri_filtered = MRIapplyOffset(mri_filter_dst, NULL, mri_offset) ;
if (!mri_filtered)
ErrorExit(ERROR_NOMEMORY,
"%s: could not allocate filtered image", Progname) ;
if (DIAG_VERBOSE_ON && (Gdiag & DIAG_SHOW))
fprintf(stderr, "done.\n") ;
if (region.x == 142)
DiagBreak() ;
MRIfree(&mri_offset) ;
}
MRIfree(&mri_filter_dst) ;
if (Gdiag & DIAG_WRITE)
MRIwrite(mri_filtered, "upfilt.mgz") ;
mri_tmp = MRIdownsample2(mri_filtered, NULL) ;
MRIfree(&mri_filtered) ;
if (Gdiag & DIAG_WRITE)
MRIwrite(mri_tmp, "downfilt.mgz") ;
region.x += xborder ;
region.y += yborder ;
region.z += zborder ;
#if 0
region.dx -=2*xborder;
region.dy-= 2*yborder;
region.dz -= 2 * zborder;
#else
region.dx -= xrborder + xborder;
region.dy -= yrborder + yborder;
region.dz -= zrborder + zborder;
#endif
if (region.dx <= 0 || region.dy <= 0 || region.dz <= 0) {
fprintf(stderr, "invalid region: (%d,%d,%d) --> (%d,%d,%d)\n",
region.x,region.y,region.z,region.dx,region.dy,region.dz);
} else
MRIextractIntoRegion(mri_tmp,mri_dst,xborder,yborder,zborder,®ion);
MRIfree(&mri_tmp);
}
}
}
MRIextractIntoRegion(mri_dst,mri_full, 0, 0, 0, &clip_region);
MRIfree(&mri_dst) ;
if (DIAG_VERBOSE_ON && (Gdiag & DIAG_SHOW))
fprintf(stderr, "writing output image %s...", out_fname) ;
MRIwrite(mri_full, out_fname) ;
MRIfree(&mri_full) ;
if (DIAG_VERBOSE_ON && (Gdiag & DIAG_SHOW))
fprintf(stderr, "done.\n") ;
exit(0) ;
return(0) ; /* for ansi */
}
int
main(int argc, char *argv[]) {
char **av ;
int ac, nargs, x0, y0, z0, dx, dy, dz ;
MRI *mri_src, *mri_dst = NULL ;
char *in_dir, *out_dir ;
MRI_REGION box ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_extract.c,v 1.8 2016/06/08 13:42:17 fischl Exp $", "$Name: $");
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++) {
if (isdigit(*(argv[1]+1)))
break ; // not an option - a negative number
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
/*
command line:
mri_extract <src_dir> x0 y0 z0 dx dy dz <dst_dir>
*/
if (argc < 8)
ErrorExit(ERROR_BADPARM,
"usage: %s <src volume> x0 y0 z0 dx dy dz <dst volume>", Progname) ;
in_dir = argv[1] ;
if (sscanf(argv[2], "%d", &x0) != 1)
ErrorExit(ERROR_BADPARM,
"%s: could not scan x0 from '%s'", Progname, argv[2]) ;
if (sscanf(argv[3], "%d", &y0) != 1)
ErrorExit(ERROR_BADPARM,
"%s: could not scan y0 from '%s'", Progname, argv[3]) ;
if (sscanf(argv[4], "%d", &z0) != 1)
ErrorExit(ERROR_BADPARM,
"%s: could not scan z0 from '%s'", Progname, argv[4]) ;
if (sscanf(argv[5], "%d", &dx) != 1)
ErrorExit(ERROR_BADPARM,
"%s: could not scan dx from '%s'", Progname, argv[5]) ;
if (sscanf(argv[6], "%d", &dy) != 1)
ErrorExit(ERROR_BADPARM,
"%s: could not scan dy from '%s'", Progname, argv[6]) ;
if (sscanf(argv[7], "%d", &dz) != 1)
ErrorExit(ERROR_BADPARM,
"%s: could not scan dz from '%s'", Progname, argv[7]) ;
out_dir = argv[8] ;
if (verbose)
fprintf(stderr, "reading from %s...", in_dir) ;
mri_src = MRIread(in_dir) ;
if (verbose)
fprintf(stderr, "done\n") ;
if (!mri_src)
exit(1) ;
MRIboundingBox(mri_src, thresh, &box) ;
if (x0 < 0)
x0 = box.x-pad ;
if (y0 < 0)
y0 = box.y-pad ;
if (z0 < 0)
z0 = box.z-pad ;
if (dx < 0)
dx = box.dx+2*pad ;
if (dy < 0)
dy = box.dy+2*pad ;
if (dz < 0)
dz = box.dz+2*pad ;
printf("using bounding box (%d, %d, %d) -> (%d, %d, %d)\n", x0, y0,z0, x0+dx-1, y0+dy-1,z0+dz-1) ;
mri_dst = MRIextract(mri_src, NULL, x0, y0, z0, dx, dy, dz) ;
if (!mri_dst)
exit(1) ;
if (verbose)
fprintf(stderr, "\nwriting to %s", out_dir) ;
MRIwrite(mri_dst, out_dir) ;
if (verbose)
fprintf(stderr, "\n") ;
exit(0) ;
return(0) ;
}