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 */
}
int
main(int argc, char *argv[]) {
char **av, *avg_surf_name, *canon_surf_name, fname[STRLEN],
*mdir, ico_fname[STRLEN], *hemi, *out_sname ;
int ac, nargs, i, vno, n ;
VERTEX *v ;
MRI_SURFACE *mris_ico ;
MRI_SP *mrisp_total ;
LTA *lta ;
VOL_GEOM vg;
float average_surface_area = 0.0 ;
MATRIX *XFM=NULL;
GCA_MORPH *gcam=NULL;
memset((void *) &vg, 0, sizeof (VOL_GEOM));
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mris_make_average_surface.c,v 1.29 2011/03/02 00:04:33 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
mdir = getenv("FREESURFER_HOME") ;
if (!mdir)
ErrorExit(ERROR_BADPARM,
"%s: no FREESURFER_HOME in environment.\n",Progname);
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (sdir == NULL) {
sdir = getenv("SUBJECTS_DIR");
if (!sdir)
ErrorExit(ERROR_BADPARM,
"%s: no SUBJECTS_DIR in environment.\n",Progname);
}
if (sdirout == NULL) sdirout = sdir;
if (argc < 6) usage_exit() ;
hemi = argv[1] ;
avg_surf_name = argv[2] ;
canon_surf_name = argv[3] ;
out_sname = argv[4] ;
printf("---------------------------------------------------\n");
printf("hemi = %s\n",hemi);
printf("avg_surf_name = %s\n",avg_surf_name);
printf("canon_surf_name = %s\n",canon_surf_name);
printf("out_sname = %s\n",out_sname);
printf("xform = %s\n",xform_name);
printf("---------------------------------------------------\n");
printf("\n\n");
fflush(stdout);
#define SCALE 1
mrisp_total = MRISPalloc(SCALE, 3) ;
for (n = 0, i = 5 ; i < argc ; i++) {
MRI *mri;
MRI_SURFACE *mris;
MRI_SP *mrisp;
printf("\n---------------------------------------------------\n");
printf("#@# processing subject %d/%d %s...\n", i-4,argc-5,argv[i]) ;
fflush(stdout);
// read sphere.reg
sprintf(fname, "%s/%s/surf/%s.%s", sdir, argv[i], hemi, canon_surf_name) ;
printf(" Reading %s\n",fname);
fflush(stdout);
mris = MRISread(fname) ;
if (!mris) {
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, fname) ;
exit(1);
}
// get "pial" surface vertex into ->origx, origy, origz
if (MRISreadOriginalProperties(mris, orig_name) != NO_ERROR)
ErrorExit(ERROR_BADFILE,"%s: could not read orig file for %s.\n",
Progname, argv[1]);
// read transform
if (0) {
sprintf(fname, "%s/%s/mri/transforms/%s", sdir, argv[i], xform_name) ;
lta = LTAreadEx(fname) ;
if (!lta)
ErrorExit(ERROR_BADPARM,
"%s: could not read transform from %s", Progname, fname) ;
}
// read T1 volume
sprintf(fname, "%s/%s/mri/T1.mgz", sdir, argv[i]) ;
if (fio_FileExistsReadable(fname)) mri = MRIreadHeader(fname,MRI_MGH_FILE);
else {
sprintf(fname, "%s/%s/mri/T1", sdir, argv[i]) ;
mri = MRIreadHeader(fname, MRI_UCHAR); // MRI_CORONAL_SLICE_DIRECTORY) ;
}
printf(" Read %s\n",fname);
fflush(stdout);
if (!mri)
ErrorExit(ERROR_BADPARM,
"%s: could not read reference MRI volume from %s",
Progname, fname) ;
// save current vertex position into ->cx
MRISsaveVertexPositions(mris, CANONICAL_VERTICES) ;
// get the vertex position from ->origx, ...
// (get the "pial" vertex position)
MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
MRIScomputeMetricProperties(mris) ;
printf(" Surface area: %2.1f cm^2\n", mris->total_area/100) ;
fflush(stdout);
average_surface_area += mris->total_area ;
// this means that we transform "pial" surface
if (xform_name)
{
if (!strcmp(xform_name,"talairach.xfm")) {
printf(" Applying linear transform\n");
fflush(stdout);
XFM = DevolveXFMWithSubjectsDir(argv[i], NULL, "talairach.xfm", sdir);
if (XFM == NULL) exit(1);
MRISmatrixMultiply(mris, XFM);
MatrixFree(&XFM);
} else if (!strcmp(xform_name,"talairach.m3z")) {
printf(" Applying GCA Morph\n");
fflush(stdout);
sprintf(fname, "%s/%s/mri/transforms/talairach.m3z", sdir, argv[i]) ;
gcam = GCAMreadAndInvert(fname);
if (gcam == NULL) exit(1);
GCAMmorphSurf(mris, gcam);
GCAMfree(&gcam);
} else {
printf("ERROR: don't know what to do with %s\n",xform_name);
exit(1);
}
}
// save transformed position in ->orig
// (store "pial" vertices position in orig)
MRIScomputeMetricProperties(mris) ;
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
// get the vertex position from ->cx
// (note that this is not transformed) sphere.reg vertices
MRISrestoreVertexPositions(mris, CANONICAL_VERTICES) ;
// mris contains sphere.reg in vertex and pial vertices in orig
// map to a theta-phi space and accumulate values
mrisp = MRIScoordsToParameterization(mris, NULL, SCALE, ORIGINAL_VERTICES) ;
MRISPaccumulate(mrisp, mrisp_total, 0) ;
MRISPaccumulate(mrisp, mrisp_total, 1) ;
MRISPaccumulate(mrisp, mrisp_total, 2) ;
MRISPfree(&mrisp) ;
MRISfree(&mris) ;
MRIfree(&mri) ;
//LTAfree(<a) ;
fflush(stdout);
n++ ;
}
printf("Finished loading all data\n");
average_surface_area /= (float)n ;
printf("Avg surf area = %g cm\n",average_surface_area/100.0);
fflush(stdout);
// mrisp_total lost info on the modified surface
sprintf(ico_fname, "%s/lib/bem/ic%d.tri", mdir, ico_no) ;
printf("Reading icosahedron from %s...\n", ico_fname) ;
mris_ico = ICOread(ico_fname) ;
if (!mris_ico)
ErrorExit(ERROR_NOFILE, "%s: could not read icosahedron file %s\n",
Progname,ico_fname) ;
MRISscaleBrain(mris_ico, mris_ico,
DEFAULT_RADIUS/MRISaverageRadius(mris_ico)) ;
// save current ico position to ->cx, cy, cz
MRISsaveVertexPositions(mris_ico, CANONICAL_VERTICES) ;
// using mrisp_total to calculate position into ->origx, origy, origz
// (orig is the "pial" vertices)
MRIScoordsFromParameterization(mrisp_total, mris_ico, ORIGINAL_VERTICES) ;
// copy geometry info
memcpy((void *) &mris_ico->vg, (void *) &vg, sizeof (VOL_GEOM));
if (Gdiag_no >= 0 && Gdiag_no < mris_ico->nvertices) {
int n ;
VERTEX *vn ;
v = &mris_ico->vertices[Gdiag_no] ;
printf( "v %d: x = (%2.2f, %2.2f, %2.2f)\n",
Gdiag_no, v->origx, v->origy, v->origz) ;
for (n = 0 ; n < v->vnum ; n++) {
vn = &mris_ico->vertices[v->v[n]] ;
printf( "v %d: x = (%2.2f, %2.2f, %2.2f)\n",
v->v[n], vn->origx, vn->origy, vn->origz) ;
}
}
// write *h.sphere.reg
sprintf(fname, "%s/%s/surf/%s.%s",
sdirout, out_sname, hemi, canon_surf_name) ;
if (Gdiag & DIAG_SHOW)
printf("writing average canonical surface to %s\n", fname);
MRISwrite(mris_ico, fname) ;
// get "pial vertices" from orig
MRISrestoreVertexPositions(mris_ico, ORIG_VERTICES);
for (vno = 0 ; vno < mris_ico->nvertices ; vno++) {
v = &mris_ico->vertices[vno] ;
// n = number of subjects
v->x /= (float)n ;
v->y /= (float)n ;
v->z /= (float)n ;
}
if (normalize_area) {
MRIScomputeMetricProperties(mris_ico) ;
printf("setting group surface area to be %2.1f cm^2 (scale=%2.2f)\n",
average_surface_area/100.0,
sqrt(average_surface_area/mris_ico->total_area)) ;
#if 0
MRISscaleBrain(mris_ico, mris_ico,
sqrt(average_surface_area/mris_ico->total_area)) ;
#else
mris_ico->group_avg_surface_area = average_surface_area ;
#endif
MRIScomputeMetricProperties(mris_ico) ;
}
sprintf(fname, "%s/%s/surf/%s.%s", sdirout,out_sname, hemi, avg_surf_name) ;
printf("writing average %s surface to %s\n", avg_surf_name, fname);
MRISwrite(mris_ico, fname) ;
if (0) {
char path[STRLEN] ;
LTA *lta ;
FileNamePath(fname, path) ;
lta = LTAalloc(1, NULL) ;
// write to a different location
sprintf(fname, "%s/../mri/transforms/%s", path,xform_name) ;
LTAwriteEx(lta, fname) ;
LTAfree(<a) ;
}
MRISfree(&mris_ico) ;
MRISPfree(&mrisp_total) ;
printf("mris_make_average_surface done\n");
exit(0) ;
return(0) ; /* for ansi */
}
int
main(int argc, char *argv[]) {
char **av, *cp ;
int ac, nargs, i, dof, no_transform, which, sno = 0, nsubjects = 0 ;
MRI *mri=0, *mri_mean = NULL, *mri_std=0, *mri_T1=0,*mri_binary=0,*mri_dof=NULL,
*mri_priors = NULL ;
char *subject_name, *out_fname, fname[STRLEN] ;
/* LTA *lta;*/
MRI *mri_tmp=0 ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_make_template.c,v 1.26 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 (!strlen(subjects_dir)) {
cp = getenv("SUBJECTS_DIR") ;
if (!cp)
ErrorExit(ERROR_BADPARM,"%s: SUBJECTS_DIR not defined in environment.\n",
Progname) ;
strcpy(subjects_dir, cp) ;
}
if (argc < 3) usage_exit(1) ;
out_fname = argv[argc-1] ;
no_transform = first_transform ;
if (binary_name) /* generate binarized volume with priors and */
{ /* separate means and variances */
for (which = BUILD_PRIORS ; which <= OFF_STATS ; which++) {
/* for each subject specified on cmd line */
for (dof = 0, i = 1 ; i < argc-1 ; i++) {
if (*argv[i] == '-') /* don't do transform for next subject */
{ no_transform = 1 ;
continue ;
}
dof++ ;
subject_name = argv[i] ;
if (which != BUILD_PRIORS) {
sprintf(fname, "%s/%s/mri/%s", subjects_dir, subject_name, T1_name);
fprintf(stderr, "%d of %d: reading %s...\n", i, argc-2, fname) ;
mri_T1 = MRIread(fname) ;
if (!mri_T1)
ErrorExit(ERROR_NOFILE,"%s: could not open volume %s",
Progname,fname);
}
sprintf(fname, "%s/%s/mri/%s",subjects_dir,subject_name,binary_name);
fprintf(stderr, "%d of %d: reading %s...\n", i, argc-2, fname) ;
mri_binary = MRIread(fname) ;
if (!mri_binary)
ErrorExit(ERROR_NOFILE,"%s: could not open volume %s",
Progname,fname);
/* only count voxels which are mostly labeled */
MRIbinarize(mri_binary, mri_binary, WM_MIN_VAL, 0, 100) ;
if (transform_fname && no_transform-- <= 0) {
sprintf(fname, "%s/%s/mri/transforms/%s",
subjects_dir, subject_name, transform_fname) ;
fprintf(stderr, "reading transform %s...\n", fname) ;
////////////////////////////////////////////////////////
#if 1
{
TRANSFORM *transform ;
transform = TransformRead(fname) ;
if (transform == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not open transform file %s\n",Progname, fname) ;
mri_tmp = TransformApply(transform, mri_T1, NULL) ;
TransformFree(&transform) ;
}
#else
lta = LTAreadEx(fname);
if (lta == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not open transform file %s\n",
Progname, fname) ;
/* LTAtransform() runs either MRIapplyRASlinearTransform()
for RAS2RAS or MRIlinearTransform() for Vox2Vox. */
/* MRIlinearTransform() calls MRIlinearTransformInterp() */
mri_tmp = LTAtransform(mri_T1, NULL, lta);
MRIfree(&mri_T1) ;
mri_T1 = mri_tmp ;
LTAfree(<a);
lta = NULL;
#endif
if (DIAG_VERBOSE_ON)
fprintf(stderr, "transform application complete.\n") ;
}
if (which == BUILD_PRIORS) {
mri_priors =
MRIupdatePriors(mri_binary, mri_priors) ;
} else {
if (!mri_mean) {
mri_dof = MRIalloc(mri_T1->width, mri_T1->height, mri_T1->depth,
MRI_UCHAR) ;
mri_mean =
MRIalloc(mri_T1->width, mri_T1->height,mri_T1->depth,MRI_FLOAT);
mri_std =
MRIalloc(mri_T1->width,mri_T1->height,mri_T1->depth,MRI_FLOAT);
if (!mri_mean || !mri_std)
ErrorExit(ERROR_NOMEMORY, "%s: could not allocate templates.\n",
Progname) ;
}
if (DIAG_VERBOSE_ON)
fprintf(stderr, "updating mean and variance estimates...\n") ;
if (which == ON_STATS) {
MRIaccumulateMaskedMeansAndVariances(mri_T1, mri_binary, mri_dof,
90, 100, mri_mean, mri_std) ;
fprintf(stderr, "T1 = %d, binary = %d, mean = %2.1f\n",
(int)MRIgetVoxVal(mri_T1, 141,100,127,0),
MRIvox(mri_binary, 141,100,127),
MRIFvox(mri_mean, 141,100,127)) ;
} else /* computing means and vars for off */
MRIaccumulateMaskedMeansAndVariances(mri_T1, mri_binary, mri_dof,
0, WM_MIN_VAL-1,
mri_mean, mri_std) ;
MRIfree(&mri_T1) ;
}
MRIfree(&mri_binary) ;
}
if (which == BUILD_PRIORS) {
mri = MRIcomputePriors(mri_priors, dof, NULL) ;
MRIfree(&mri_priors) ;
fprintf(stderr, "writing priors to %s...\n", out_fname) ;
} else {
MRIcomputeMaskedMeansAndStds(mri_mean, mri_std, mri_dof) ;
mri_mean->dof = dof ;
fprintf(stderr, "writing T1 means with %d dof to %s...\n", mri_mean->dof,
out_fname) ;
if (!which)
MRIwrite(mri_mean, out_fname) ;
else
MRIappend(mri_mean, out_fname) ;
MRIfree(&mri_mean) ;
fprintf(stderr, "writing T1 variances to %s...\n", out_fname);
if (dof <= 1)
MRIreplaceValues(mri_std, mri_std, 0, 1) ;
mri = mri_std ;
}
if (!which)
MRIwrite(mri, out_fname) ;
else
MRIappend(mri, out_fname) ;
MRIfree(&mri) ;
}
}
else {
/* for each subject specified on cmd line */
if (xform_mean_fname) {
m_xform_mean = MatrixAlloc(4,4,MATRIX_REAL) ;
/* m_xform_covariance = MatrixAlloc(12,12,MATRIX_REAL) ;*/
}
dof = 0;
for (i = 1 ; i < argc-1 ; i++) {
if (*argv[i] == '-') {
/* don't do transform for next subject */
no_transform = 1 ;
continue ;
}
dof++ ;
subject_name = argv[i] ;
sprintf(fname, "%s/%s/mri/%s", subjects_dir, subject_name, T1_name);
fprintf(stderr, "%d of %d: reading %s...\n", i, argc-2, fname) ;
mri_T1 = MRIread(fname) ;
if (!mri_T1)
ErrorExit(ERROR_NOFILE,"%s: could not open volume %s",Progname,fname);
check_mri(mri_T1) ;
if (binarize)
MRIbinarize(mri_T1, mri_T1, binarize, 0, 1) ;
if (erode) {
int i ;
printf("eroding input %d times\n", erode) ;
for (i = 0 ; i < erode ; i++)
MRIerode(mri_T1, mri_T1) ;
}
if (open) {
int i ;
printf("opening input %d times\n", open) ;
for (i = 0 ; i < open ; i++)
MRIerode(mri_T1, mri_T1) ;
for (i = 0 ; i < open ; i++)
MRIdilate(mri_T1, mri_T1) ;
}
check_mri(mri_T1) ;
if (transform_fname) {
sprintf(fname, "%s/%s/mri/transforms/%s",
subjects_dir, subject_name, transform_fname) ;
fprintf(stderr, "reading transform %s...\n", fname) ;
////////////////////////////////////////////////////////
#if 1
{
TRANSFORM *transform ;
transform = TransformRead(fname) ;
if (transform == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not open transform file %s\n",Progname, fname) ;
mri_tmp = TransformApply(transform, mri_T1, NULL) ;
if (DIAG_VERBOSE_ON)
MRIwrite(mri_tmp, "t1.mgz") ;
TransformFree(&transform) ;
}
#else
lta = LTAreadEx(fname);
if (lta == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not open transform file %s\n",
Progname, fname) ;
printf("transform matrix -----------------------\n");
MatrixPrint(stdout,lta->xforms[0].m_L);
/* LTAtransform() runs either MRIapplyRASlinearTransform()
for RAS2RAS or MRIlinearTransform() for Vox2Vox. */
/* MRIlinearTransform() calls MRIlinearTransformInterp() */
mri_tmp = LTAtransform(mri_T1, NULL, lta);
printf("----- -----------------------\n");
LTAfree(<a);
#endif
MRIfree(&mri_T1);
mri_T1 = mri_tmp ; // reassign pointers
if (DIAG_VERBOSE_ON)
fprintf(stderr, "transform application complete.\n") ;
}
if (!mri_mean) {
mri_mean =
MRIalloc(mri_T1->width, mri_T1->height, mri_T1->depth, MRI_FLOAT) ;
mri_std =
MRIalloc(mri_T1->width, mri_T1->height, mri_T1->depth, MRI_FLOAT) ;
if (!mri_mean || !mri_std)
ErrorExit(ERROR_NOMEMORY, "%s: could not allocate templates.\n",
Progname) ;
// if(transform_fname == NULL){
if (DIAG_VERBOSE_ON)
printf("Copying geometry\n");
MRIcopyHeader(mri_T1,mri_mean);
MRIcopyHeader(mri_T1,mri_std);
// }
}
check_mri(mri_mean) ;
if (!stats_only) {
if (DIAG_VERBOSE_ON)
fprintf(stderr, "updating mean and variance estimates...\n") ;
MRIaccumulateMeansAndVariances(mri_T1, mri_mean, mri_std) ;
}
check_mri(mri_mean) ;
if (DIAG_VERBOSE_ON)
MRIwrite(mri_mean, "t2.mgz") ;
MRIfree(&mri_T1) ;
no_transform = 0;
} /* end loop over subjects */
if (xform_mean_fname) {
FILE *fp ;
VECTOR *v = NULL, *vT = NULL ;
MATRIX *m_vvT = NULL ;
int rows, cols ;
nsubjects = sno ;
fp = fopen(xform_covariance_fname, "w") ;
if (!fp)
ErrorExit(ERROR_NOFILE, "%s: could not open covariance file %s",
Progname, xform_covariance_fname) ;
fprintf(fp, "nsubjects=%d\n", nsubjects) ;
MatrixScalarMul(m_xform_mean, 1.0/(double)nsubjects, m_xform_mean) ;
printf("means:\n") ;
MatrixPrint(stdout, m_xform_mean) ;
MatrixAsciiWrite(xform_mean_fname, m_xform_mean) ;
/* subtract the mean from each transform */
rows = m_xform_mean->rows ;
cols = m_xform_mean->cols ;
for (sno = 0 ; sno < nsubjects ; sno++) {
MatrixSubtract(m_xforms[sno], m_xform_mean, m_xforms[sno]) ;
v = MatrixReshape(m_xforms[sno], v, rows*cols, 1) ;
vT = MatrixTranspose(v, vT) ;
m_vvT = MatrixMultiply(v, vT, m_vvT) ;
if (!m_xform_covariance)
m_xform_covariance =
MatrixAlloc(m_vvT->rows, m_vvT->cols,MATRIX_REAL) ;
MatrixAdd(m_vvT, m_xform_covariance, m_xform_covariance) ;
MatrixAsciiWriteInto(fp, m_xforms[sno]) ;
}
MatrixScalarMul(m_xform_covariance, 1.0/(double)nsubjects,
m_xform_covariance) ;
printf("covariance:\n") ;
MatrixPrint(stdout, m_xform_covariance) ;
MatrixAsciiWriteInto(fp, m_xform_covariance) ;
fclose(fp) ;
if (stats_only)
exit(0) ;
}
MRIcomputeMeansAndStds(mri_mean, mri_std, dof) ;
check_mri(mri_mean) ;
check_mri(mri_std) ;
mri_mean->dof = dof ;
if (smooth) {
MRI *mri_kernel, *mri_smooth ;
printf("applying smoothing kernel\n") ;
mri_kernel = MRIgaussian1d(smooth, 100) ;
mri_smooth = MRIconvolveGaussian(mri_mean, NULL, mri_kernel) ;
MRIfree(&mri_kernel) ;
MRIfree(&mri_mean) ;
mri_mean = mri_smooth ;
}
fprintf(stderr, "\nwriting T1 means with %d dof to %s...\n", mri_mean->dof,
out_fname) ;
MRIwrite(mri_mean, out_fname) ;
MRIfree(&mri_mean) ;
if (dof <= 1) /* can't calculate variances - set them to reasonable val */
{
// src dst
MRIreplaceValues(mri_std, mri_std, 0, 1) ;
}
if (!novar) {
// mri_std contains the variance here (does it?? I don't think so -- BRF)
if (!var_fname) {
fprintf(stderr, "\nwriting T1 standard deviations to %s...\n", out_fname);
MRIappend(mri_std, out_fname) ;
} else {
fprintf(stderr, "\nwriting T1 standard deviations to %s...\n", var_fname);
MRIwrite(mri_std, var_fname) ;
}
}
MRIfree(&mri_std) ;
if (mri)
MRIfree(&mri);
} /* end if binarize */
return(0) ;
}
int main(int argc, char *argv[]) {
char **av;
MRI *mri_T1, *mri_tmp, *mri_ctrl, *mri_in, *mri_out;
MRI *mri_snr, *mri_bias;
MRI *mri_mask1 = NULL;
MRI *mri_mask2 = NULL;
int ac, nargs;
int width, height, depth, x, y, z;
int mask1_set = 0;
int mask2_set = 0;
int i, j, k, cx, cy, cz, count;
LTA *lta = 0;
int transform_type;
double mean, std, value, src, bias, norm;
// HISTOGRAM *h;
// float bin_size;
// int nbins, bin_no;
double mean1, std1, mean2, std2, count1, count2, slope, offset;
VOL_GEOM vgtmp;
LT *lt = NULL;
MATRIX *m_tmp = NULL;
Progname = argv[0];
nargs = handle_version_option
(argc, argv,
"$Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs ;
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 (tp1_ctrl_fname == NULL || tp1_T1_fname == NULL) {
printf("Use options to specify ctrl volume and T1 volume for tp1\n");
usage(1);
}
mri_in = MRIread(argv[1]) ;
if (!mri_in)
ErrorExit(ERROR_BADPARM, "%s: could not read input volume %s",
Progname, argv[1]) ;
mri_T1 = MRIread(tp1_T1_fname) ;
if (!mri_T1)
ErrorExit(ERROR_BADPARM, "%s: could not read T1 volume for tp1 %s",
Progname, tp1_T1_fname) ;
mri_ctrl = MRIread(tp1_ctrl_fname) ;
if (!mri_ctrl)
ErrorExit(ERROR_BADPARM,
"%s: could not read control points volume for tp1 %s",
Progname, tp1_ctrl_fname) ;
if ((mri_in->width != mri_T1->width) ||
(mri_in->height != mri_T1->height) ||
(mri_in->depth != mri_T1->depth) ||
(mri_in->width != mri_ctrl->width) ||
(mri_in->height != mri_ctrl->height) ||
(mri_in->depth != mri_ctrl->depth)
) ErrorExit
(ERROR_BADPARM,
"%s: three input volumes have different sizes \n", Progname);
if (mask1_fname) {
mri_mask1 = MRIread(mask1_fname) ;
if (!mri_mask1)
ErrorExit(ERROR_BADPARM,
"%s, could not read mask volume for tp1 %s",
Progname, mask1_fname);
mask1_set = 1;
if ((mri_mask1->width != mri_in->width) ||
(mri_mask1->height != mri_in->height) ||
(mri_mask1->depth != mri_in->depth))
ErrorExit
(ERROR_BADPARM,
"%s: mask volumes have different sizes than other volumes \n",
Progname);
}
if (mask2_fname) {
mri_mask2 = MRIread(mask2_fname) ;
if (!mri_mask2)
ErrorExit
(ERROR_BADPARM,
"%s, could not read mask volume for tp2 %s",
Progname, mask2_fname);
mask2_set = 1;
if ((mri_mask2->width != mri_T1->width) ||
(mri_mask2->height != mri_T1->height) ||
(mri_mask2->depth != mri_T1->depth)
)
ErrorExit
(ERROR_BADPARM,
"%s: mask volumes have different sizes than other volumes \n",
Progname);
}
width = mri_in->width ;
height = mri_in->height ;
depth = mri_in->depth ;
//nbins = 200;
//h = HISTOalloc(nbins);
mri_out = MRIclone(mri_in, NULL) ;
/* Read LTA transform and apply it to mri_ctrl */
if (xform_fname != NULL) {
// read transform
transform_type = TransformFileNameType(xform_fname);
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(xform_fname) ;
if (!lta)
ErrorExit(ERROR_NOFILE, "%s: could not read transform file %s",
Progname, xform_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 '-lta_src' and "
"'-lta_dst' to specify the src and dst volume infos\n");
}
LTAmodifySrcDstGeom
(lta, lta_src, lta_dst); // add src and dst information
LTAchangeType(lta, LINEAR_VOX_TO_VOX); //this is necessary
}
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 -lta_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
// getVolGeom(lta_src, <->src);
}
}
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 -lta_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,
"without giving the dst volume for RAS-to-RAS transform.\n");
ErrorExit(ERROR_BAD_PARM, "Bailing out...\n");
} else {
LTAmodifySrcDstGeom(lta, NULL, lta_dst); // add dst information
}
}
} else {
ErrorExit
(ERROR_BADPARM,
"transform is not of MNI, nor Register.dat, nor FSLMAT type");
}
if (invert) {
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) {
fprintf
(stderr,
"WARNING:***********************************************\n");
fprintf
(stderr,
"WARNING: dst volume infor is invalid. "
"Most likely produce wrong inverse.\n");
fprintf
(stderr,
"WARNING:***********************************************\n");
}
copyVolGeom(<->dst, &vgtmp);
copyVolGeom(<->src, <->dst);
copyVolGeom(&vgtmp, <->src);
}
// LTAchangeType(lta, LINEAR_VOX_TO_VOX);
/* apply lta to the ctrl volume */
mri_tmp = MRIalloc(mri_ctrl->width,
mri_ctrl->height,
mri_ctrl->depth,
mri_ctrl->type) ;
MRIcopyHeader(mri_in, mri_tmp) ;
// this function doesn't do NEAREST at all!!
// I found the bug, in LTAtransformInterp()
mri_tmp = LTAtransformInterp(mri_ctrl, mri_tmp, lta, SAMPLE_NEAREST);
MRIfree(&mri_ctrl);
mri_ctrl = mri_tmp;
if (mask1_fname != NULL && mask2_fname == NULL) {
printf("map mask for tp1 to get mask for tp2 ...\n");
mri_mask2 = MRIalloc(mri_in->width,
mri_in->height,
mri_in->depth,
mri_mask1->type) ;
MRIcopyHeader(mri_in, mri_mask2) ;
mri_mask2 = LTAtransformInterp(mri_mask1,
mri_mask2,
lta,
SAMPLE_NEAREST);
mask2_set = 1;
if (debug_flag)
MRIwrite(mri_mask2, "mri_mask2.mgz");
} else if (mask2_fname != NULL && mask1_fname == NULL) {
printf("map mask for tp2 to get mask for tp1 ...\n");
//need to invert lta first
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];
copyVolGeom(<->dst, &vgtmp);
copyVolGeom(<->src, <->dst);
copyVolGeom(&vgtmp, <->src);
mri_mask1 = MRIalloc(mri_T1->width,
mri_T1->height,
mri_T1->depth,
mri_mask2->type) ;
MRIcopyHeader(mri_T1, mri_mask1) ;
mri_mask1 = LTAtransformInterp(mri_mask2,
mri_mask1,
lta,
SAMPLE_NEAREST);
mask1_set = 1;
if (debug_flag)
MRIwrite(mri_mask1, "mri_mask1.mgz");
}
if (lta_src)
MRIfree(<a_src);
if (lta_dst)
MRIfree(<a_dst);
if (lta)
LTAfree(<a);
} /* if (xform_fname != NULL) */
if (debug_flag) {
// MRIwrite(mri_snr, "snr.mgz");
MRIwrite(mri_ctrl, "ctrl.mgz");
}
if (mask1_set == 0) {
//create mask1
mri_mask1 = MRIalloc(mri_T1->width,
mri_T1->height,
mri_T1->depth,
MRI_UCHAR) ;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_T1, x, y, z, 0) < noise_threshold) {
MRIvox(mri_mask1,x,y,z) = 0;
} else
MRIvox(mri_mask1,x,y,z) = 1;
}
}
if (mask2_set == 0) {
//create mask2
mri_mask2 = MRIalloc(mri_in->width,
mri_in->height,
mri_in->depth,
MRI_UCHAR) ;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_in, x, y, z, 0) < noise_threshold) {
MRIvox(mri_mask2,x,y,z) = 0;
} else
MRIvox(mri_mask2,x,y,z) = 1;
}
}
#if 0
/* compute the mean and std of T1 volume */
/* Using only high SNR points */
mri_snr = MRIalloc(mri_T1->width, mri_T1->height, mri_T1->depth, MRI_FLOAT) ;
MRIcopyHeader(mri_T1, mri_snr) ;
h->bin_size = bin_size = 0.5;
for (bin_no = 0; bin_no < nbins; bin_no++)
h->bins[bin_no] = (bin_no)*bin_size;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_T1, x, y, z, 0) < noise_threshold) {
MRIFvox(mri_snr,x,y,z) = 0;
continue;
}
mean = 0;
std = 0;
count = 0;
for (i=-1; i<=1; i++)
for (j=-1; j<=1; j++)
for (k=-1;k<=1;k++) {
cx = x+i;
cy = y+j, cz = z+k;
if (cx < 0 ||
cx >= width ||
cy < 0 ||
cy >= height ||
cz < 0 ||
cz >= depth) continue;
count++;
value = MRIgetVoxVal(mri_T1, cx, cy, cz, 0);
mean += value;
std += value*value;
}
mean /= (count + 1e-30);
std /= (count + 1e-30);
std = std - mean *mean;
if (std <= 0)
std = 0;
value = mean/sqrt(std);
MRIFvox(mri_snr,x,y,z) = value;
bin_no = nint((float)value/(float)bin_size);
if (bin_no >= nbins) bin_no = nbins - 1;
h->counts[bin_no]++;
}
for (num = 0.0f, b = h->nbins - 1; b >= 1; b --) {
num += h->counts[b];
if (num > 20000) /* this may make me only use WM points,
is it good to use only WM to compute
scale of intensity?? */
break;
}
printf("using SNR threshold %2.3f at bin %d\n", h->bins[b], b);
mean1 = 0;
std1 = 0;
count1 = 0;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_T1, x, y, z, 0) < noise_threshold) {
continue;
}
value = MRIFvox(mri_snr,x,y,z);
if (value < h->bins[b]) continue;
value = MRIgetVoxVal(mri_T1, x, y, z, 0);
count1++;
mean1 += value;
std1 += value*value;
}
MRIfree(&mri_snr);
#else
printf("compute mean and std of tp1 volume within masked area...\n");
mean1 = 0;
std1 = 0;
count1 = 0;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_mask1, x, y, z, 0) <= 1e-30) {
continue;
}
value = MRIgetVoxVal(mri_T1, x, y, z, 0);
count1++;
mean1 += value;
std1 += value*value;
}
#endif
mean1 /= (count1 + 1e-30);
std1 /= (count1 + 1e-30);
std1 = std1 - mean1*mean1;
if (std1 <= 0)
printf("warning: negative std for T1 volume. \n");
else
printf("mean and variance for tp1 volume are %g and %g\n", mean1, std1);
printf("now compute SNR and stats for input volume ... \n");
mri_snr = MRIalloc(mri_in->width, mri_in->height, mri_in->depth, MRI_FLOAT) ;
MRIcopyHeader(mri_in, mri_snr) ;
//HISTOclear(h,h);
//h->bin_size = bin_size = 0.5;
//for (bin_no = 0; bin_no < nbins; bin_no++)
// h->bins[bin_no] = (bin_no)*bin_size;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_in, x, y, z, 0) < noise_threshold) {
MRIFvox(mri_snr,x,y,z) = 0;
continue;
}
mean = 0;
std = 0;
count = 0;
for (i=-1; i<=1; i++)
for (j=-1; j<=1; j++)
for (k=-1;k<=1;k++) {
cx = x+i;
cy = y+j, cz = z+k;
if (cx < 0 ||
cx >= width ||
cy < 0 ||
cy >= height ||
cz < 0 ||
cz >= depth) continue;
count++;
value = MRIgetVoxVal(mri_in, cx, cy, cz, 0);
mean += value;
std += value*value;
}
mean /= (count + 1e-30);
std /= (count + 1e-30);
std = std - mean *mean;
if (std <= 0)
std = 0;
value = mean/sqrt(std);
MRIFvox(mri_snr,x,y,z) = value;
//bin_no = nint((float)value/(float)bin_size);
//if (bin_no >= nbins) bin_no = nbins - 1;
//h->counts[bin_no]++;
}
#if 0
for (num = 0.0f, b = h->nbins - 1; b >= 1; b --) {
num += h->counts[b];
if (num > 20000) /* this may make me only use WM points, is it good to
use only WM to compute scale of intensity?? */
break;
}
printf("using SNR threshold %2.3f at bin %d\n", h->bins[b], b);
mean2 = 0;
std2 = 0;
count2 = 0;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_in, x, y, z, 0) < noise_threshold) {
continue;
}
value = MRIFvox(mri_snr,x,y,z);
if (value >= h->bins[b]) {
count2++;
mean2 += value;
std2 += value*value;
}
}
#else
printf("compute mean and std of tp2 volume within masked area\n");
/* somehow mri_watershed seems to leave some unzero voxels around
image border, so I will skip image boundaries
no, that's not a problem of most recent mri_watershed;
something wrong previously */
mean2 = 0;
std2 = 0;
count2 = 0;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_mask2, x, y, z, 0) <= 1e-30) {
continue;
}
value = MRIgetVoxVal(mri_in, x, y, z, 0);
count2++;
mean2 += value;
std2 += value*value;
}
#endif
mean2 /= (count2 + 1e-30);
std2 /= (count2 + 1e-30);
std2 = std2 - mean2*mean2;
if (std2 <= 0)
printf("warning: negative std for input volume. \n");
else
printf("mean and variance for input tp2 volume are %g and %g\n",
mean2, std2);
//compute intensity scale
slope = sqrt(std1/std2);
offset = mean1 - slope*mean2;
printf("scale input volume by %g x + %g\n", slope, offset);
// first change mri_in to FLOAT type
mri_tmp = MRIchangeType(mri_in, MRI_FLOAT, 0, 1.0, 1);
MRIfree(&mri_in);
mri_in = mri_tmp;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
value = MRIFvox(mri_in, x, y, z);
MRIFvox(mri_in, x, y, z) = value*slope + offset;
}
// printf("compute SNR map of tp2 volume\n"); //already done above
// mri_snr = MRIalloc(mri_ctrl->width,
// mri_ctrl->height, mri_ctrl->depth, MRI_FLOAT) ;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_in, x, y, z, 0) < noise_threshold) {
// MRIFvox(mri_snr,x,y,z) = 0;
continue;
}
value = MRIFvox(mri_snr,x,y,z);
if (value < 20) MRIvox(mri_ctrl, x, y, z) = 0;
else if (MRIvox(mri_ctrl, x, y, z) > 0) {
MRIvox(mri_ctrl, x, y, z) = 1;
}
}
if (debug_flag) {
MRIwrite(mri_snr, "snr.mgz");
// MRIwrite(mri_ctrl, "ctrl.mgz");
}
// SNR >= 20 seems a good threshold
// Now use ctrl points to normalize tp2
printf("normalize tp2...\n");
mri_bias = MRIbuildBiasImage(mri_in, mri_ctrl, NULL, bias_sigma) ;
for (z = 0 ; z < depth ; z++) {
for (y = 0 ; y < height ; y++) {
for (x = 0 ; x < width ; x++) {
src = MRIgetVoxVal(mri_in, x, y, z, 0) ;
bias = MRIgetVoxVal(mri_bias, x, y, z, 0) ;
if (!bias) /* should never happen */
norm = (float)src ;
else
norm = (float)src * 110.0 / (float)bias ;
if (norm > 255.0f && mri_out->type == MRI_UCHAR)
norm = 255.0f ;
else if (norm < 0.0f && mri_out->type == MRI_UCHAR)
norm = 0.0f ;
MRIsetVoxVal(mri_out, x, y, z, 0, norm) ;
}
}
}
printf("writing normalized volume to %s...\n", argv[2]) ;
MRIwrite(mri_out, argv[2]);
MRIfree(&mri_in);
MRIfree(&mri_bias);
MRIfree(&mri_out);
MRIfree(&mri_T1);
MRIfree(&mri_ctrl);
MRIfree(&mri_snr);
//HISTOfree(&h);
exit(0);
} /* end main() */
int main(int argc, char *argv[])
{
char **av;
MRI *mri_src, *mri_mask, *mri_dst ;
int nargs, ac, nmask;
int x, y, z;
float value;
MRI_REGION *region;
LTA *lta = 0;
int transform_type;
MRI *mri_tmp;
nargs =
handle_version_option
(
argc, argv,
"$Id: mri_mask.c,v 1.18 2012/12/07 22:45:50 greve 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 != 4)
{
printf("Incorrect number of arguments, argc = %d\n", argc);
usage(1);
}
mri_src = MRIread(argv[1]) ;
if (!mri_src)
ErrorExit(ERROR_BADPARM, "%s: could not read source volume %s",
Progname, argv[1]) ;
mri_mask = MRIread(argv[2]) ;
if (!mri_mask)
ErrorExit(ERROR_BADPARM, "%s: could not read mask volume %s",
Progname, argv[2]) ;
if(mri_src->width != mri_mask->width)
{
printf("ERROR: dimension mismatch between source and mask\n");
exit(1);
}
printf("DoAbs = %d\n",DoAbs);
/* Read LTA transform and apply it to mri_mask */
if (xform_fname != NULL)
{
printf("Apply the given LTA xfrom to the mask volume\n");
// read transform
transform_type = TransformFileNameType(xform_fname);
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(xform_fname) ;
if (!lta)
ErrorExit(ERROR_NOFILE, "%s: could not read transform file %s",
Progname, xform_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 '-lta_src' "
"and '-lta_dst' to specify the src and dst volume infos\n");
}
LTAmodifySrcDstGeom(lta, lta_src, lta_dst);
// add src and dst information
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 -lta_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
// getVolGeom(lta_src, <->src);
}
}
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 -lta_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,
"without giving the dst volume for RAS-to-RAS transform.\n");
ErrorExit(ERROR_BAD_PARM, "Bailing out...\n");
}
else
{
LTAmodifySrcDstGeom(lta, NULL, lta_dst); // add dst information
}
}
}
else
{
ErrorExit(ERROR_BADPARM,
"transform is not of MNI, nor Register.dat, nor FSLMAT type");
}
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)
{
fprintf(stderr,
"WARNING:**************************************"
"*************************\n");
fprintf(stderr,
"WARNING:dst volume information is invalid. "
"Most likely produced wrong inverse.\n");
fprintf(stderr,
"WARNING:**************************************"
"*************************\n");
}
copyVolGeom(<->dst, &vgtmp);
copyVolGeom(<->src, <->dst);
copyVolGeom(&vgtmp, <->src);
}
// LTAchangeType(lta, LINEAR_VOX_TO_VOX);
mri_tmp =
MRIalloc(mri_src->width,
mri_src->height,
mri_src->depth,
mri_mask->type) ;
MRIcopyHeader(mri_src, mri_tmp) ;
mri_tmp = LTAtransformInterp(mri_mask, mri_tmp, lta, InterpMethod);
// mri_tmp =
//MRIlinearTransformInterp
// (
// mri_mask, mri_tmp, lta->xforms[0].m_L, InterpMethod
// );
MRIfree(&mri_mask);
mri_mask = mri_tmp;
if (lta_src)
{
MRIfree(<a_src);
}
if (lta_dst)
{
MRIfree(<a_dst);
}
if (lta)
{
LTAfree(<a);
}
} /* if (xform_fname != NULL) */
// Threshold mask
nmask = 0;
for (z = 0 ; z <mri_mask->depth ; z++)
{
for (y = 0 ; y < mri_mask->height ; y++)
{
for (x = 0 ; x < mri_mask->width ; x++)
{
value = MRIgetVoxVal(mri_mask, x, y, z, 0);
if(DoAbs)
{
value = fabs(value);
}
if(value <= threshold)
{
MRIsetVoxVal(mri_mask,x,y,z,0,0);
}
else
{
nmask ++;
}
}
}
}
printf("Found %d voxels in mask (pct=%6.2f)\n",nmask,
100.0*nmask/(mri_mask->width*mri_mask->height*mri_mask->depth));
if(DoBB){
printf("Computing bounding box, npad = %d\n",nPadBB);
region = REGIONgetBoundingBox(mri_mask,nPadBB);
REGIONprint(stdout, region);
mri_tmp = MRIextractRegion(mri_mask, NULL, region);
if(mri_tmp == NULL) exit(1);
MRIfree(&mri_mask);
mri_mask = mri_tmp;
mri_tmp = MRIextractRegion(mri_src, NULL, region);
if(mri_tmp == NULL) exit(1);
MRIfree(&mri_src);
mri_src = mri_tmp;
}
int mask=0;
float out_val=0;
if (do_transfer)
{
mask = (int)transfer_val;
out_val = transfer_val;
}
mri_dst = MRImask(mri_src, mri_mask, NULL, mask, out_val) ;
if (!mri_dst)
{
ErrorExit(Gerror, "%s: stripping failed", Progname) ;
}
if (keep_mask_deletion_edits)
{
mri_dst = MRImask(mri_dst, mri_mask, NULL, 1, 1) ; // keep voxels = 1
if (!mri_dst)
ErrorExit(Gerror, "%s: stripping failed on keep_mask_deletion_edits",
Progname) ;
}
printf("Writing masked volume to %s...", argv[3]) ;
MRIwrite(mri_dst, argv[3]);
printf("done.\n") ;
MRIfree(&mri_src);
MRIfree(&mri_mask);
MRIfree(&mri_dst);
exit(0);
} /* end main() */
