int
regio_write_surfacexform_to_register_dat(MATRIX *B, char *fname,
MRI_SURFACE *mris, MRI *mri,
char *subject, int float2int)
{
MATRIX *Ta, *Sa, *invTa, *A, *R, *S, *invS, *T, *m1, *m2 ;
MRI *mri_surf = MRIallocHeader(mris->vg.width, mris->vg.height,
mris->vg.depth, MRI_UCHAR,1) ;
MRIcopyVolGeomToMRI(mri_surf, &mris->vg) ;
T = MRIxfmCRS2XYZtkreg(mri) ;
S = MRIgetVoxelToRasXform(mri) ;
invS = MatrixInverse(S, NULL) ;
Ta = MRIxfmCRS2XYZtkreg(mri_surf);
Sa = MRIgetVoxelToRasXform(mri_surf);
invTa = MatrixInverse(Ta,NULL);
A = MatrixMultiply(Sa,invTa, NULL);
m1 = MatrixMultiply(A, B, NULL) ;
m2 = MatrixMultiply(invS, m1, NULL) ;
R = MatrixMultiply(T, m2, NULL) ;
regio_write_register(fname,subject,mri->xsize, mri->zsize,1,R,float2int);
MatrixFree(&A) ; MatrixFree(&Ta) ; MatrixFree(&Sa) ; MatrixFree(&invTa) ;
MatrixFree(&R) ; MatrixFree(&m1) ; MatrixFree(&m2) ; MatrixFree(&S) ;
MatrixFree(&invS);
MatrixFree(&T) ;
MRIfree(&mri_surf) ;
return(NO_ERROR) ;
}
static int
test(MRI *mri1, MRI *mri2, MRI *mri3, MATRIX *m_vol1_to_vol2_ras) {
VECTOR *v_test, *v_vox ;
float x_ras1, y_ras1, z_ras1, x_ras2, y_ras2, z_ras2, x_vox1, y_vox1,
z_vox1, x_vox2, y_vox2, z_vox2 ;
MATRIX *m_vol2_vox2ras, *m_vol2_ras2vox, *m_vol1_ras2vox, *m_vol1_vox2ras,
*m_vol3_ras2vox, *m_vol3_vox2ras ;
int val ;
v_test = VectorAlloc(4, MATRIX_REAL) ;
m_vol1_vox2ras = MRIgetVoxelToRasXform(mri1) ;
m_vol2_vox2ras = MRIgetVoxelToRasXform(mri2) ;
m_vol1_ras2vox = MRIgetRasToVoxelXform(mri1) ;
m_vol2_ras2vox = MRIgetRasToVoxelXform(mri2) ;
m_vol3_vox2ras = MRIgetVoxelToRasXform(mri3) ;
m_vol3_ras2vox = MRIgetRasToVoxelXform(mri3) ;
x_ras1 = 126.50 ;
y_ras1 = -125.500 ;
z_ras1 = 127.50 ;
V3_X(v_test) = x_ras1 ;
V3_Y(v_test) = y_ras1 ;
V3_Z(v_test) = z_ras1 ;
*MATRIX_RELT(v_test, 4, 1) = 1.0 ;
v_vox = MatrixMultiply(m_vol1_ras2vox, v_test, NULL) ;
x_vox1 = V3_X(v_vox) ;
y_vox1 = V3_Y(v_vox) ;
z_vox1 = V3_Z(v_vox) ;
val = MRISvox(mri1, nint(x_vox1), nint(y_vox1), nint(z_vox1)) ;
printf("VOL1: ras (%1.1f, %1.1f, %1.1f) --> VOX (%1.1f, %1.1f, %1.1f) = %d\n",
x_ras1, y_ras1, z_ras1, x_vox1, y_vox1, z_vox1, val) ;
x_ras2 = 76.5421 ;
y_ras2 = 138.5352 ;
z_ras2 = 96.0910 ;
V3_X(v_test) = x_ras2 ;
V3_Y(v_test) = y_ras2 ;
V3_Z(v_test) = z_ras2 ;
*MATRIX_RELT(v_test, 4, 1) = 1.0 ;
v_vox = MatrixMultiply(m_vol2_ras2vox, v_test, NULL) ;
x_vox2 = V3_X(v_vox) ;
y_vox2 = V3_Y(v_vox) ;
z_vox2 = V3_Z(v_vox) ;
val = MRISvox(mri2, nint(x_vox2), nint(y_vox2), nint(z_vox2)) ;
printf("VOL2: ras (%2.1f, %2.1f, %2.1f) --> VOX (%2.1f, %2.1f, %2.1f) = %d\n",
x_ras2, y_ras2, z_ras2, x_vox2, y_vox2, z_vox2, val) ;
MatrixFree(&v_test) ;
return(NO_ERROR) ;
}
MATRIX *
regio_read_surfacexform_from_register_dat(char *fname, MRI_SURFACE *mris,
MRI *mri, char **subject)
{
MATRIX *Ta, *Sa, *invT, *A, *R, *S, *invSa, *T, *m1, *m2, *B ;
float pres, bres, intensity ;
int float2int ;
MRI *mri_surf = MRIallocHeader(mris->vg.width, mris->vg.height,
mris->vg.depth, MRI_UCHAR,1) ;
if (regio_read_register(fname, subject, &pres, &bres, &intensity,&B,&float2int) != 0)
ErrorReturn(NULL, (ERROR_NOFILE,
"regio_read_surfacexform_from_register_dat(%s) failed",
fname)) ;
MRIcopyVolGeomToMRI(mri_surf, &mris->vg) ;
T = MRIxfmCRS2XYZtkreg(mri) ;
S = MRIgetVoxelToRasXform(mri) ;
Ta = MRIxfmCRS2XYZtkreg(mri_surf);
Sa = MRIgetVoxelToRasXform(mri_surf);
invSa = MatrixInverse(Sa, NULL) ;
invT = MatrixInverse(T,NULL);
A = MatrixMultiply(S,invT, NULL);
m1 = MatrixMultiply(A, B, NULL) ;
m2 = MatrixMultiply(invSa, m1, NULL) ;
R = MatrixMultiply(Ta, m2, NULL) ;
MatrixFree(&A) ; MatrixFree(&Ta) ; MatrixFree(&Sa) ; MatrixFree(&invT) ;
MatrixFree(&B) ; MatrixFree(&m1) ; MatrixFree(&m2) ; MatrixFree(&S) ;
MatrixFree(&invSa);
MatrixFree(&T) ;
MRIfree(&mri_surf) ;
return(R) ;
}
int
main(int argc, char *argv[])
{
char **av, *out_name ;
int ac, nargs ;
int msec, minutes, seconds ;
struct timeb start ;
GCA_MORPH *gcam ;
MRI *mri = NULL ;
MATRIX *m;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_warp_convert.c,v 1.1 2012/02/13 23:05:52 jonp Exp $", "$Name: $");
if (nargs && argc - nargs == 1)
{
exit (0);
}
argc -= nargs;
Progname = basename(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 < 3)
{
usage_exit(1) ;
}
// mri_convert expects a relative warp
fprintf(stdout, "[%s]: reading warp file '%s'\n", Progname, argv[1]);
fprintf(stdout, "assuming RELATIVE warp convention\n");
// TODO: add support for absolute warps as well, add option to specify convention
mri = MRIread(argv[1]) ;
if (mri == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read warp volume %s\n", Progname,argv[1]) ;
m = MRIgetVoxelToRasXform(mri) ;
// NOTE: this assumes a standard siemens image orientation in which
// case a neurological orientation means that the first frame is
// flipped
if ( MatrixDeterminant(m) > 0 )
{
fprintf(stdout, "non-negative Jacobian determinant -- converting to radiological ordering\n");
}
{
// 2012/feb/08: tested with anisotropic voxel sizes
MRI *mri2 = NULL ;
int c=0,r=0,s=0;
float v;
mri2 = MRIcopy(mri,NULL);
for(c=0; c < mri->width; c++)
{
for(r=0; r < mri->height; r++)
{
for(s=0; s < mri->depth; s++)
{
// only flip first frame (by negating relative shifts)
v = MRIgetVoxVal(mri, c,r,s,0) / mri->xsize;
if ( MatrixDeterminant(m) > 0 )
MRIsetVoxVal( mri2,c,r,s,0,-v);
else
MRIsetVoxVal( mri2,c,r,s,0, v);
v = MRIgetVoxVal(mri, c,r,s,1) / mri->ysize;
MRIsetVoxVal( mri2,c,r,s,1, v);
v = MRIgetVoxVal(mri, c,r,s,2) / mri->zsize;
MRIsetVoxVal( mri2,c,r,s,2, v);
}
}
}
MRIfree(&mri);
mri = mri2;
}
MatrixFree(&m) ;
// this does all the work! (gcamorph.c)
gcam = GCAMalloc(mri->width, mri->height, mri->depth) ;
GCAMinitVolGeom(gcam, mri, mri) ;
// not sure if removing singularities is ever a bad thing
#if 1
GCAMremoveSingularitiesAndReadWarpFromMRI(gcam, mri) ;
#else
GCAMreadWarpFromMRI(gcam, mri) ;
#endif
fprintf(stdout, "[%s]: writing warp file '%s'\n", Progname, argv[2]);
out_name = argv[2] ;
GCAMwrite(gcam, out_name) ;
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
fprintf(stderr, "conversion took %d minutes and %d seconds.\n", minutes, seconds) ;
exit(0) ;
return(0) ;
}