int
main(int argc, char **argv)
{
/* NIFTI stuff */
nifti_image *nii_ptr;
nifti_image nii_rec;
int nii_dimids[MAX_NII_DIMS];
int nii_dir[MAX_NII_DIMS];
int nii_map[MAX_NII_DIMS];
unsigned long nii_lens[MAX_NII_DIMS];
int nii_ndims;
static int nifti_filetype;
static int nifti_datatype;
static int nifti_signed = 1;
/* MINC stuff */
int mnc_fd; /* MINC file descriptor */
nc_type mnc_type; /* MINC data type as read */
int mnc_ndims; /* MINC image dimension count */
int mnc_dimids[MAX_VAR_DIMS]; /* MINC image dimension identifiers */
long mnc_dlen; /* MINC dimension length value */
double mnc_dstep; /* MINC dimension step value */
int mnc_icv; /* MINC image conversion variable */
int mnc_vid; /* MINC Image variable ID */
long mnc_start[MAX_VAR_DIMS]; /* MINC data starts */
long mnc_count[MAX_VAR_DIMS]; /* MINC data counts */
int mnc_signed; /* MINC if output voxels are signed */
double real_range[2]; /* MINC real range (min, max) */
double input_valid_range[2]; /* MINC valid range (min, max) */
double output_valid_range[2]; /* Valid range of output data. */
double nifti_slope; /* Slope to be applied to output voxels. */
double nifti_inter; /* Intercept to be applied to output voxels. */
double total_valid_range; /* Overall valid range (max - min). */
double total_real_range; /* Overall real range (max - min). */
/* Other stuff */
char out_str[1024]; /* Big string for filename */
char att_str[1024]; /* Big string for attribute values */
int i; /* Generic loop counter the first */
int j; /* Generic loop counter the second */
char *str_ptr; /* Generic ASCIZ string pointer */
int r; /* Result code. */
static int vflag = 0; /* Verbose flag (default is quiet) */
static ArgvInfo argTable[] = {
{NULL, ARGV_HELP, NULL, NULL,
"Output voxel data type specification"},
{"-byte", ARGV_CONSTANT, (char *)DT_INT8, (char *)&nifti_datatype,
"Write voxel data in 8-bit signed integer format."},
{"-short", ARGV_CONSTANT, (char *)DT_INT16, (char *)&nifti_datatype,
"Write voxel data in 16-bit signed integer format."},
{"-int", ARGV_CONSTANT, (char *)DT_INT32, (char *)&nifti_datatype,
"Write voxel data in 32-bit signed integer format."},
{"-float", ARGV_CONSTANT, (char *)DT_FLOAT32, (char *)&nifti_datatype,
"Write voxel data in 32-bit floating point format."},
{"-double", ARGV_CONSTANT, (char *)DT_FLOAT64, (char *)&nifti_datatype,
"Write voxel data in 64-bit floating point format."},
{"-signed", ARGV_CONSTANT, (char *)1, (char *)&nifti_signed,
"Write integer voxel data in signed format."},
{"-unsigned", ARGV_CONSTANT, (char *)0, (char *)&nifti_signed,
"Write integer voxel data in unsigned format."},
{NULL, ARGV_HELP, NULL, NULL,
"Output file format specification"},
{"-dual", ARGV_CONSTANT, (char *)FT_NIFTI_DUAL,
(char *)&nifti_filetype,
"Write NIfTI-1 two-file format (.img and .hdr)"},
{"-ASCII", ARGV_CONSTANT, (char *)FT_NIFTI_ASCII,
(char *)&nifti_filetype,
"Write NIfTI-1 ASCII header format (.nia)"},
{"-nii", ARGV_CONSTANT, (char *)FT_NIFTI_SINGLE,
(char *)&nifti_filetype,
"Write NIfTI-1 one-file format (.nii)"},
{"-analyze", ARGV_CONSTANT, (char *)FT_ANALYZE,
(char *)&nifti_filetype,
"Write an Analyze two-file format file (.img and .hdr)"},
{NULL, ARGV_HELP, NULL, NULL,
"Other options"},
{"-quiet", ARGV_CONSTANT, (char *)0,
(char *)&vflag,
"Quiet operation"},
{"-verbose", ARGV_CONSTANT, (char *)1,
(char *)&vflag,
"Quiet operation"},
{NULL, ARGV_END, NULL, NULL, NULL}
};
ncopts = 0; /* Clear global netCDF error reporting flag */
/* Default NIfTI file type is "NII", single binary file
*/
nifti_filetype = FT_UNSPECIFIED;
nifti_datatype = DT_UNKNOWN;
if (ParseArgv(&argc, argv, argTable, 0) || (argc < 2)) {
fprintf(stderr, "Too few arguments\n");
return usage();
}
if (!nifti_signed) {
switch (nifti_datatype) {
case DT_INT8:
nifti_datatype = DT_UINT8;
break;
case DT_INT16:
nifti_datatype = DT_UINT16;
break;
case DT_INT32:
nifti_datatype = DT_UINT32;
break;
}
}
switch (nifti_datatype){
case DT_INT8:
case DT_UINT8:
mnc_type = NC_BYTE;
break;
case DT_INT16:
case DT_UINT16:
mnc_type = NC_SHORT;
break;
case DT_INT32:
case DT_UINT32:
mnc_type = NC_INT;
break;
case DT_FLOAT32:
mnc_type = NC_FLOAT;
break;
case DT_FLOAT64:
mnc_type = NC_DOUBLE;
break;
}
if (argc == 2) {
strcpy(out_str, argv[1]);
str_ptr = strrchr(out_str, '.');
if (str_ptr != NULL && !strcmp(str_ptr, ".mnc")) {
*str_ptr = '\0';
}
}
else if (argc == 3) {
strcpy(out_str, argv[2]);
str_ptr = strrchr(out_str, '.');
if (str_ptr != NULL) {
/* See if a recognized file extension was specified. If so,
* we trim it off and set the output file type if none was
* specified. If the extension is not recognized, assume
* that we will form the filename by just adding the right
* extension for the selected output format.
*/
if (!strcmp(str_ptr, ".nii")) {
if (nifti_filetype == FT_UNSPECIFIED) {
nifti_filetype = FT_NIFTI_SINGLE;
}
*str_ptr = '\0';
}
else if (!strcmp(str_ptr, ".img") ||
!strcmp(str_ptr, ".hdr")) {
if (nifti_filetype == FT_UNSPECIFIED) {
nifti_filetype = FT_NIFTI_DUAL;
}
*str_ptr = '\0';
}
else if (!strcmp(str_ptr, ".nia")) {
if (nifti_filetype == FT_UNSPECIFIED) {
nifti_filetype = FT_NIFTI_ASCII;
}
*str_ptr = '\0';
}
}
}
else {
fprintf(stderr, "Filename argument required\n");
return usage();
}
/* Open the MINC file. It needs to exist.
*/
mnc_fd = miopen(argv[1], NC_NOWRITE);
if (mnc_fd < 0) {
fprintf(stderr, "Can't find input file '%s'\n", argv[1]);
return (-1);
}
/* Find the MINC image variable. If we can't find it, there is no
* further processing possible...
*/
mnc_vid = ncvarid(mnc_fd, MIimage);
if (mnc_vid < 0) {
fprintf(stderr, "Can't locate the image variable (mnc_vid=%d)\n", mnc_vid);
return (-1);
}
/* Find out about the MINC image variable - specifically, how many
* dimensions, and which dimensions.
*/
r = ncvarinq(mnc_fd, mnc_vid, NULL, NULL, &mnc_ndims, mnc_dimids, NULL);
if (r < 0) {
fprintf(stderr, "Can't read information from image variable\n");
return (-1);
}
if (mnc_ndims > MAX_NII_DIMS) {
fprintf(stderr, "NIfTI-1 files may contain at most %d dimensions\n",
MAX_NII_DIMS);
return (-1);
}
/* Initialize the NIfTI structure
*/
nii_ptr = &nii_rec;
init_nifti_header(nii_ptr);
/* For now we just use the mnc2nii command line as the description
* field. Probably we should use something better, perhaps a
* combination of some other standard MINC fields that might
* provide more information.
*/
str_ptr = nii_ptr->descrip;
for (i = 0; i < argc; i++) {
char *arg_ptr = argv[i];
if ((str_ptr - nii_ptr->descrip) >= MAX_NII_DESCRIP) {
break;
}
if (i != 0) {
*str_ptr++ = ' ';
}
while (*arg_ptr != '\0' &&
(str_ptr - nii_ptr->descrip) < MAX_NII_DESCRIP) {
*str_ptr++ = *arg_ptr++;
}
*str_ptr = '\0';
}
nii_ptr->fname = malloc(strlen(out_str) + 4 + 1);
nii_ptr->iname = malloc(strlen(out_str) + 4 + 1);
strcpy(nii_ptr->fname, out_str);
strcpy(nii_ptr->iname, out_str);
switch (nifti_filetype) {
case FT_ANALYZE:
strcat(nii_ptr->fname, ".hdr");
strcat(nii_ptr->iname, ".img");
break;
case FT_NIFTI_SINGLE:
strcat(nii_ptr->fname, ".nii");
strcat(nii_ptr->iname, ".nii");
break;
case FT_NIFTI_DUAL:
strcat(nii_ptr->fname, ".hdr");
strcat(nii_ptr->iname, ".img");
break;
case FT_NIFTI_ASCII:
strcat(nii_ptr->fname, ".nia");
strcat(nii_ptr->iname, ".nia");
break;
default:
fprintf(stderr, "Unknown output file type %d\n", nifti_filetype);
return (-1);
}
/* Get real voxel range for the input file.
*/
miget_image_range(mnc_fd, real_range);
/* Get the actual valid voxel value range.
*/
miget_valid_range(mnc_fd, mnc_vid, input_valid_range);
/* Find the default range for the output type. Our output file
* will use the full legal range of the output type if it is
* an integer.
*/
if (nifti_datatype == DT_UNKNOWN) {
nii_ptr->datatype = DT_FLOAT32; /* Default */
mnc_type = NC_FLOAT;
mnc_signed = 1;
}
else {
nii_ptr->datatype = nifti_datatype;
mnc_signed = nifti_signed;
}
if (vflag) {
fprintf(stderr, "MINC type %d signed %d\n", mnc_type, mnc_signed);
}
miget_default_range(mnc_type, mnc_signed, output_valid_range);
total_valid_range = input_valid_range[1] - input_valid_range[0];
total_real_range = real_range[1] - real_range[0];
if ((output_valid_range[1] - output_valid_range[0]) > total_valid_range) {
/* Empirically, forcing the valid range to be the nearest power
* of two greater than the existing valid range seems to improve
* the behavior of the conversion. This is at least in part because
* of the limited precision of the NIfTI-1 voxel scaling fields.
*/
double new_range = nearest_power_of_two(total_valid_range);
if (new_range - 1.0 >= total_valid_range) {
new_range -= 1.0;
}
if (output_valid_range[1] > total_valid_range) {
output_valid_range[0] = 0;
output_valid_range[1] = new_range;
}
else {
output_valid_range[1] = output_valid_range[0] + new_range;
}
}
else {
/* The new range can't fully represent the input range. Use the
* full available range, and warn the user that they may have a
* problem.
*/
printf("WARNING: Range of input exceeds range of output format.\n");
}
if (vflag) {
printf("Real range: %f %f Input valid range: %f %f Output valid range: %f %f\n",
real_range[0], real_range[1],
input_valid_range[0], input_valid_range[1],
output_valid_range[0], output_valid_range[1]);
}
/* If the output type is not floating point, we may need to scale the
* voxel values.
*/
if (mnc_type != NC_FLOAT && mnc_type != NC_DOUBLE) {
/* Figure out how to map pixel values into the range of the
* output datatype.
*/
nifti_slope = ((real_range[1] - real_range[0]) /
(output_valid_range[1] - output_valid_range[0]));
if (nifti_slope == 0.0) {
nifti_slope = 1.0;
}
nifti_inter = real_range[0] - (output_valid_range[0] * nifti_slope);
/* One problem with NIfTI-1 is the limited precision of the
* scl_slope and scl_inter fields (they are just 32-bits). So
* we look for possible issues and warn about that here.
*/
if (nifti_inter != (float) nifti_inter ||
nifti_slope != (float) nifti_slope) {
double epsilon_i = nifti_inter - (float) nifti_inter;
double epsilon_s = nifti_slope - (float) nifti_slope;
/* If the loss in precision is more than one part per thousand
* of the real range, flag this as a problem!
*/
if ((epsilon_i > total_real_range / 1.0e3) ||
(epsilon_s > total_real_range / 1.0e3)) {
fprintf(stderr, "ERROR: Slope and intercept cannot be represented in the NIfTI-1 header.\n");
fprintf(stderr, " slope %f (%f), intercept %f (%f)\n",
nifti_slope, (float) nifti_slope,
nifti_inter, (float) nifti_inter);
return (-1);
}
}
}
else {
nifti_slope = 0.0;
}
nii_ptr->scl_slope = nifti_slope;
nii_ptr->scl_inter = nifti_inter;
nii_ptr->nvox = 1; /* Initial value for voxel count */
/* Find all of the dimensions of the MINC file, in the order they
* will be listed in the NIfTI-1/Analyze file. We use this to build
* a map for restructuring the data according to the normal rules
* of NIfTI-1.
*/
nii_ndims = 0;
for (i = 0; i < MAX_NII_DIMS; i++) {
if (dimnames[i] == NULL) {
nii_dimids[nii_ndims] = -1;
continue;
}
nii_dimids[nii_ndims] = ncdimid(mnc_fd, dimnames[i]);
if (nii_dimids[nii_ndims] == -1) {
continue;
}
/* Make sure the dimension is actually used to define the image.
*/
for (j = 0; j < mnc_ndims; j++) {
if (nii_dimids[nii_ndims] == mnc_dimids[j]) {
nii_map[nii_ndims] = j;
break;
}
}
if (j < mnc_ndims) {
mnc_dlen = 1;
mnc_dstep = 0;
ncdiminq(mnc_fd, nii_dimids[nii_ndims], NULL, &mnc_dlen);
ncattget(mnc_fd, ncvarid(mnc_fd, dimnames[i]), MIstep, &mnc_dstep);
if (mnc_dstep < 0) {
nii_dir[nii_ndims] = -1;
mnc_dstep = -mnc_dstep;
}
else {
nii_dir[nii_ndims] = 1;
}
nii_lens[nii_ndims] = mnc_dlen;
nii_ndims++;
}
nii_ptr->dim[dimmap[i]] = (int) mnc_dlen;
nii_ptr->nvox *= mnc_dlen;
nii_ptr->pixdim[dimmap[i]] = (float) mnc_dstep;
}
/* Here we do some "post-processing" of the results. Make certain that
* the nt value is never zero, and make certain that ndim is set to
* 4 if there is a time dimension and 5 if there is a vector dimension
*/
if (nii_ptr->dim[3] > 1 && nii_ndims < 4) {
nii_ndims = 4;
}
if (nii_ptr->dim[4] > 1) {
nii_ptr->intent_code = NIFTI_INTENT_VECTOR;
nii_ndims = 5;
}
nii_ptr->ndim = nii_ndims; /* Total number of dimensions in file */
nii_ptr->nx = nii_ptr->dim[0];
nii_ptr->ny = nii_ptr->dim[1];
nii_ptr->nz = nii_ptr->dim[2];
nii_ptr->nt = nii_ptr->dim[3];
nii_ptr->nu = nii_ptr->dim[4];
nii_ptr->dx = nii_ptr->pixdim[0];
nii_ptr->dy = nii_ptr->pixdim[1];
nii_ptr->dz = nii_ptr->pixdim[2];
nii_ptr->dt = nii_ptr->pixdim[3];
nii_ptr->du = 1; /* MINC files don't define a sample size for a vector_dimension */
nii_ptr->nifti_type = nifti_filetype;
/* Load the direction_cosines and start values into the NIfTI-1
* sform structure.
*
*/
for (i = 0; i < MAX_SPACE_DIMS; i++) {
int id = ncvarid(mnc_fd, mnc_spatial_names[i]);
double start;
double step;
double dircos[MAX_SPACE_DIMS];
int tmp;
if (id < 0) {
continue;
}
/* Set default values */
start = 0.0;
step = 1.0;
dircos[DIM_X] = dircos[DIM_Y] = dircos[DIM_Z] = 0.0;
dircos[i] = 1.0;
miattget(mnc_fd, id, MIstart, NC_DOUBLE, 1, &start, &tmp);
miattget(mnc_fd, id, MIstep, NC_DOUBLE, 1, &step, &tmp);
miattget(mnc_fd, id, MIdirection_cosines, NC_DOUBLE, MAX_SPACE_DIMS,
dircos, &tmp);
ncdiminq(mnc_fd, ncdimid(mnc_fd, mnc_spatial_names[i]), NULL,
&mnc_dlen);
if (step < 0) {
step = -step;
start = start - step * (mnc_dlen - 1);
}
nii_ptr->sto_xyz.m[0][i] = step * dircos[0];
nii_ptr->sto_xyz.m[1][i] = step * dircos[1];
nii_ptr->sto_xyz.m[2][i] = step * dircos[2];
nii_ptr->sto_xyz.m[0][3] += start * dircos[0];
nii_ptr->sto_xyz.m[1][3] += start * dircos[1];
nii_ptr->sto_xyz.m[2][3] += start * dircos[2];
miattgetstr(mnc_fd, id, MIspacetype, sizeof(att_str), att_str);
/* Try to set the S-transform code correctly.
*/
if (!strcmp(att_str, MI_TALAIRACH)) {
nii_ptr->sform_code = NIFTI_XFORM_TALAIRACH;
}
else if (!strcmp(att_str, MI_CALLOSAL)) {
/* TODO: Not clear what do do here... */
nii_ptr->sform_code = NIFTI_XFORM_SCANNER_ANAT;
}
else { /* MI_NATIVE or unknown */
nii_ptr->sform_code = NIFTI_XFORM_SCANNER_ANAT;
}
}
/* So the last row is right... */
nii_ptr->sto_xyz.m[3][0] = 0.0;
nii_ptr->sto_xyz.m[3][1] = 0.0;
nii_ptr->sto_xyz.m[3][2] = 0.0;
nii_ptr->sto_xyz.m[3][3] = 1.0;
nii_ptr->sto_ijk = nifti_mat44_inverse(nii_ptr->sto_xyz);
nifti_datatype_sizes(nii_ptr->datatype,
&nii_ptr->nbyper, &nii_ptr->swapsize);
if (vflag) {
nifti_image_infodump(nii_ptr);
}
/* Now load the actual MINC data. */
nii_ptr->data = malloc(nii_ptr->nbyper * nii_ptr->nvox);
if (nii_ptr->data == NULL) {
fprintf(stderr, "Out of memory.\n");
return (-1);
}
mnc_icv = miicv_create();
miicv_setint(mnc_icv, MI_ICV_TYPE, mnc_type);
miicv_setstr(mnc_icv, MI_ICV_SIGN, (mnc_signed) ? MI_SIGNED : MI_UNSIGNED);
miicv_setdbl(mnc_icv, MI_ICV_VALID_MAX, output_valid_range[1]);
miicv_setdbl(mnc_icv, MI_ICV_VALID_MIN, output_valid_range[0]);
miicv_setdbl(mnc_icv, MI_ICV_IMAGE_MAX, real_range[1]);
miicv_setdbl(mnc_icv, MI_ICV_IMAGE_MIN, real_range[0]);
miicv_setdbl(mnc_icv, MI_ICV_DO_NORM, TRUE);
miicv_setdbl(mnc_icv, MI_ICV_USER_NORM, TRUE);
miicv_attach(mnc_icv, mnc_fd, mnc_vid);
/* Read in the entire hyperslab from the file.
*/
for (i = 0; i < mnc_ndims; i++) {
ncdiminq(mnc_fd, mnc_dimids[i], NULL, &mnc_count[i]);
mnc_start[i] = 0;
}
r = miicv_get(mnc_icv, mnc_start, mnc_count, nii_ptr->data);
if (r < 0) {
fprintf(stderr, "Read error\n");
return (-1);
}
/* Shut down the MINC stuff now that it has done its work.
*/
miicv_detach(mnc_icv);
miicv_free(mnc_icv);
miclose(mnc_fd);
if (vflag) {
/* Debugging stuff - just to check the contents of these arrays.
*/
for (i = 0; i < nii_ndims; i++) {
printf("%d: %ld %d %d\n",
i, nii_lens[i], nii_map[i], nii_dir[i]);
}
printf("bytes per voxel %d\n", nii_ptr->nbyper);
printf("# of voxels %ld\n", nii_ptr->nvox);
}
/* Rearrange the data to correspond to the NIfTI dimension ordering.
*/
restructure_array(nii_ndims,
nii_ptr->data,
nii_lens,
nii_ptr->nbyper,
nii_map,
nii_dir);
if (vflag) {
/* More debugging stuff - check coordinate transform.
*/
test_xform(nii_ptr->sto_xyz, 0, 0, 0);
test_xform(nii_ptr->sto_xyz, 10, 0, 0);
test_xform(nii_ptr->sto_xyz, 0, 10, 0);
test_xform(nii_ptr->sto_xyz, 0, 0, 10);
test_xform(nii_ptr->sto_xyz, 10, 10, 10);
}
if (vflag) {
fprintf(stdout, "Writing NIfTI-1 file...");
}
nifti_image_write(nii_ptr);
if (vflag) {
fprintf(stdout, "done.\n");
}
return (0);
}
/* *************************************************************** */
nifti_image *reg_io_nrdd2nifti(Nrrd *nrrdImage)
{
// Check if the file can be converted
if(nrrdImage->dim>7){
fprintf(stderr, "[NiftyReg ERROR] reg_io_nrdd2nifti - The Nifti format only support 7 dimensions\n");
exit(1);
}
// Need first to extract the input image dimension
int dim[8]={1,1,1,1,1,1,1,1};
dim[0]=nrrdImage->dim;
int vectorIncrement=0;
if(nrrdImage->axis[0].kind==nrrdKindVector)
vectorIncrement=1;
for(int i=0;i<(dim[0]<7?dim[0]:7);++i)
dim[i+1]=(int)nrrdImage->axis[i+vectorIncrement].size;
if(vectorIncrement==1){
dim[0]=5;
dim[4]=1;
dim[5]=nrrdImage->axis[0].size;
}
// The nifti_image pointer is created
nifti_image *niiImage=NULL;
// The nifti image is generated based on the nrrd image datatype
switch(nrrdImage->type){
case nrrdTypeUChar:
niiImage=nifti_make_new_nim(dim,NIFTI_TYPE_UINT8,true);
break;
case nrrdTypeChar:
niiImage=nifti_make_new_nim(dim,NIFTI_TYPE_INT8,true);
break;
case nrrdTypeUShort:
niiImage=nifti_make_new_nim(dim,NIFTI_TYPE_UINT16,true);
break;
case nrrdTypeShort:
niiImage=nifti_make_new_nim(dim,NIFTI_TYPE_INT16,true);
break;
case nrrdTypeUInt:
niiImage=nifti_make_new_nim(dim,NIFTI_TYPE_UINT32,true);
break;
case nrrdTypeInt:
niiImage=nifti_make_new_nim(dim,NIFTI_TYPE_INT32,true);
break;
case nrrdTypeFloat:
niiImage=nifti_make_new_nim(dim,NIFTI_TYPE_FLOAT32,true);
break;
case nrrdTypeDouble:
niiImage=nifti_make_new_nim(dim,NIFTI_TYPE_FLOAT64,true);
break;
default:
fprintf(stderr, "[NiftyReg ERROR] reg_io_nrdd2nifti - The data type is not supported\n");
exit(1);
}
// The data are copied over from the nrrd to the nifti structure
memcpy(niiImage->data, nrrdImage->data, niiImage->nvox*niiImage->nbyper);
// We set the spacing information for every axis
double spaceDir[NRRD_SPACE_DIM_MAX], spacing;
for(int i=0;i<7;++i){
nrrdSpacingCalculate(nrrdImage,i+vectorIncrement,&spacing,spaceDir);
if(spacing==spacing)
niiImage->pixdim[i+1]=(float)spacing;
else niiImage->pixdim[i+1]=1.0f;
}
niiImage->dx=niiImage->pixdim[1];
niiImage->dy=niiImage->pixdim[2];
niiImage->dz=niiImage->pixdim[3];
niiImage->dt=niiImage->pixdim[4];
niiImage->du=niiImage->pixdim[5];
niiImage->dv=niiImage->pixdim[6];
niiImage->dw=niiImage->pixdim[7];
// Set the slope and intersection
niiImage->scl_inter=0;
niiImage->scl_slope=1;
// Set the min and max intensities
niiImage->cal_min=reg_tools_getMinValue(niiImage);
niiImage->cal_max=reg_tools_getMaxValue(niiImage);
// The space orientation is extracted and converted into a matrix
mat44 qform_orientation_matrix;
reg_mat44_eye(&qform_orientation_matrix);
if(nrrdImage->space==nrrdSpaceRightAnteriorSuperior ||
nrrdImage->space==nrrdSpaceRightAnteriorSuperiorTime ||
nrrdImage->space==nrrdSpace3DRightHanded ||
nrrdImage->space==nrrdSpace3DRightHandedTime ){
qform_orientation_matrix.m[0][0]=1.f; // NIFTI_L2R
qform_orientation_matrix.m[1][1]=1.f; // NIFTI_P2A
qform_orientation_matrix.m[2][2]=1.f; // NIFTI_I2S
niiImage->qform_code=1;
}
else if(nrrdImage->space==nrrdSpaceLeftAnteriorSuperior ||
nrrdImage->space==nrrdSpaceLeftAnteriorSuperiorTime ||
nrrdImage->space==nrrdSpace3DLeftHanded ||
nrrdImage->space==nrrdSpace3DLeftHandedTime ){
qform_orientation_matrix.m[0][0]=-1.f; //NIFTI_R2L
qform_orientation_matrix.m[1][1]=1.f; // NIFTI_P2A
qform_orientation_matrix.m[2][2]=1.f; // NIFTI_I2S
niiImage->qform_code=1;
}
else if(nrrdImage->space!=nrrdSpaceScannerXYZ &&
nrrdImage->space!=nrrdSpaceScannerXYZTime ){
niiImage->qform_code=0;
fprintf(stderr, "[NiftyReg WARNING] reg_io_nrdd2nifti - nrrd space value unrecognised: the Nifti qform is set to identity\n");
}
if(niiImage->qform_code>0){
// The origin is set
// Note that x and y origin are negated to fit with ITK conversion
if(niiImage->ndim>=1)
qform_orientation_matrix.m[0][3]=niiImage->qoffset_x=-nrrdImage->spaceOrigin[0];
if(niiImage->ndim>=2)
qform_orientation_matrix.m[1][3]=niiImage->qoffset_y=-nrrdImage->spaceOrigin[1];
if(niiImage->ndim>=3)
qform_orientation_matrix.m[2][3]=niiImage->qoffset_z=nrrdImage->spaceOrigin[2];
// Flipp the orientation to fit ITK's filters
qform_orientation_matrix.m[0][0] *= -1.0f;
qform_orientation_matrix.m[1][1] *= -1.0f;
// Extract the quaternions and qfac values
nifti_mat44_to_quatern(qform_orientation_matrix,
&niiImage->quatern_b,
&niiImage->quatern_c,
&niiImage->quatern_d,
&niiImage->qoffset_x,
&niiImage->qoffset_y,
&niiImage->qoffset_z,
&niiImage->dx,
&niiImage->dy,
&niiImage->dz,
&niiImage->qfac);
// Set the qform matrices
niiImage->qto_xyz=nifti_quatern_to_mat44(niiImage->quatern_b,
niiImage->quatern_c,
niiImage->quatern_d,
niiImage->qoffset_x,
niiImage->qoffset_y,
niiImage->qoffset_z,
niiImage->dx,
niiImage->dy,
niiImage->dz,
niiImage->qfac);
}
else{
// diagonal matrix is assumed
niiImage->qto_xyz=qform_orientation_matrix;
niiImage->qto_xyz.m[0][0]=niiImage->dx;
niiImage->qto_xyz.m[1][1]=niiImage->dy;
if(niiImage->ndim>2)
niiImage->qto_xyz.m[2][2]=niiImage->dz;
}
niiImage->qto_ijk=nifti_mat44_inverse(niiImage->qto_xyz);
// The sform has to be set if required
// Check if the spaceDirection array is set
// The check is performed in the dim in case you are dealing with a vector
if(nrrdImage->axis[1].spaceDirection[0]!=std::numeric_limits<double>::quiet_NaN()){
niiImage->sform_code=1;
reg_mat44_eye(&niiImage->sto_xyz);
for(int i=0;i<(niiImage->ndim<3?niiImage->ndim:3);++i){
for(int j=0;j<(niiImage->ndim<3?niiImage->ndim:3);++j){
niiImage->sto_xyz.m[i][j]=(float)nrrdImage->axis[i+vectorIncrement].spaceDirection[j];
}
niiImage->sto_xyz.m[i][3]=(float)nrrdImage->spaceOrigin[i];
}
// The matrix is flipped to go from nrrd to nifti
// and follow the ITK style
for(unsigned int i=0;i<2;++i)
for(unsigned int j=0;j<4;++j)
niiImage->sto_xyz.m[i][j]*=-1.0f;
niiImage->sto_ijk=nifti_mat44_inverse(niiImage->sto_xyz);
}
// Set the space unit if it is defined
if(nrrdImage->spaceUnits[1]!=NULL){
if(strcmp(nrrdImage->spaceUnits[1],"m")==0)
niiImage->xyz_units=NIFTI_UNITS_METER;
else if(strcmp(nrrdImage->spaceUnits[1],"mm")==0)
niiImage->xyz_units=NIFTI_UNITS_MM;
else if(strcmp(nrrdImage->spaceUnits[1],"um")==0)
niiImage->xyz_units=NIFTI_UNITS_MICRON;
}
// Set the time unit if it is defined
if(nrrdImage->axis[3].size>1){
if(nrrdImage->spaceUnits[4]!=NULL){
if(strcmp(nrrdImage->spaceUnits[4],"sec"))
niiImage->time_units=NIFTI_UNITS_SEC;
else if(strcmp(nrrdImage->spaceUnits[4],"msec"))
niiImage->time_units=NIFTI_UNITS_MSEC;
}
}
// Check if the nrrd image was a NiftyReg velocity field parametrisation
if(vectorIncrement == 1){
// The intensity array has to be reoriented
switch(niiImage->datatype){
case NIFTI_TYPE_FLOAT32:
reg_convertVectorField_nrrd_to_nifti<float>(nrrdImage,niiImage);
break;
case NIFTI_TYPE_FLOAT64:
reg_convertVectorField_nrrd_to_nifti<double>(nrrdImage,niiImage);
break;
default:
fprintf(stderr, "[NiftyReg ERROR] - reg_convertVectorField_nrrd_to_nifti - unsupported datatype\n");
exit(1);
}
// The orientation flag are re-organised
niiImage->ndim=5;
niiImage->dim[4]=niiImage->nt=1;
niiImage->dim[5]=niiImage->nu=nrrdImage->axis[0].size;
niiImage->intent_code=NIFTI_INTENT_VECTOR;
// Check if the image is a stationary field from NiftyReg
if(nrrdImage->axis[0].label!=NULL){
std::string str=nrrdImage->axis[0].label;
size_t it;
if((it=str.find("NREG_VEL_STEP "))!=std::string::npos){
str=str.substr(it+13);
memset(niiImage->intent_name, 0, 16);
strcpy(niiImage->intent_name,"NREG_VEL_STEP");
niiImage->intent_p1=atof(str.c_str());
}
if(str.find("NREG_CPP_FILE")!=std::string::npos){
memset(niiImage->intent_name, 0, 16);
strcpy(niiImage->intent_name,"NREG_CPP_FILE");
}
}
}
// returns the new nii image
return niiImage;
}
int Matvec_2_WarpData(ATR_float *atr_flo, THD_affine_warp *ww, float *wdv)
{
int ans=0;
mat44 Mfor, Mbac;
int k;
int dbg = 0;
ENTRY("Matvec_2_WarpData") ;
if (!atr_flo) {
fprintf(stderr,"NULL atr_flo!\n");
RETURN(ans);
}
if (atr_flo->nfl != 12) {
fprintf(stderr,"atr_flo->nfl != 12\n");
RETURN(ans);
}
if (!ww) {
fprintf(stderr,"NULL ww\n");
RETURN(ans);
}
ww->type = WARP_AFFINE_TYPE;
ww->resam_type = 0 ; /* not used */
ww->warp.type = MAPPING_LINEAR_TYPE ;
k = 0;
Mfor.m[0][0] = atr_flo->fl[k]; ++k;
Mfor.m[0][1] = atr_flo->fl[k]; ++k;
Mfor.m[0][2] = atr_flo->fl[k]; ++k;
Mfor.m[0][3] = atr_flo->fl[k]; ++k;
Mfor.m[1][0] = atr_flo->fl[k]; ++k;
Mfor.m[1][1] = atr_flo->fl[k]; ++k;
Mfor.m[1][2] = atr_flo->fl[k]; ++k;
Mfor.m[1][3] = atr_flo->fl[k]; ++k;
Mfor.m[2][0] = atr_flo->fl[k]; ++k;
Mfor.m[2][1] = atr_flo->fl[k]; ++k;
Mfor.m[2][2] = atr_flo->fl[k]; ++k;
Mfor.m[2][3] = atr_flo->fl[k]; ++k;
Mfor.m[3][0] = 0.0;
Mfor.m[3][1] = 0.0;
Mfor.m[3][2] = 0.0;
Mfor.m[3][3] = 0.0;
if (dbg) {
DUMP_MAT44("Mfor:\n",Mfor);
}
/* calculate the backward transform */
Mbac = nifti_mat44_inverse(Mfor);
if (dbg) {
DUMP_MAT44("Mbac:\n",Mbac);
}
if (wdv) {
/* Load the forward transform */
/* Now load the 30 values of Wd */
k=0;
wdv[k] = Mfor.m[0][0]; ++k;
wdv[k] = Mfor.m[0][1]; ++k;
wdv[k] = Mfor.m[0][2]; ++k;
wdv[k] = Mfor.m[1][0]; ++k;
wdv[k] = Mfor.m[1][1]; ++k;
wdv[k] = Mfor.m[1][2]; ++k;
wdv[k] = Mfor.m[2][0]; ++k;
wdv[k] = Mfor.m[2][1]; ++k;
wdv[k] = Mfor.m[2][2]; ++k;
wdv[k] = Mbac.m[0][0]; ++k;
wdv[k] = Mbac.m[0][1]; ++k;
wdv[k] = Mbac.m[0][2]; ++k;
wdv[k] = Mbac.m[1][0]; ++k;
wdv[k] = Mbac.m[1][1]; ++k;
wdv[k] = Mbac.m[1][2]; ++k;
wdv[k] = Mbac.m[2][0]; ++k;
wdv[k] = Mbac.m[2][1]; ++k;
wdv[k] = Mbac.m[2][2]; ++k;
wdv[k] = -Mfor.m[0][3]; ++k;
wdv[k] = -Mfor.m[1][3]; ++k;
wdv[k] = -Mfor.m[2][3]; ++k;
wdv[k] = -Mbac.m[0][3]; ++k;
wdv[k] = -Mbac.m[1][3]; ++k;
wdv[k] = -Mbac.m[2][3]; ++k;
/* bot and top are filled as to not cause trouble for Talairach bounding box at a minimum from:
[-80 ; -80 ; -65] to [80 ; 110 ; 85] */
wdv[k] = -80 * 2; ++k; /* x 2 ? be generous, it is free! */
wdv[k] = -80 * 2; ++k;
wdv[k] = -65 * 2; ++k;
wdv[k] = 80 * 2; ++k;
wdv[k] = 110 * 2; ++k;
wdv[k] = 85 * 2; ++k;
}
/* Now load the 30 values into warp */
ww->warp.mfor.mat[0][0] = Mfor.m[0][0];
ww->warp.mfor.mat[0][1] = Mfor.m[0][1];
ww->warp.mfor.mat[0][2] = Mfor.m[0][2];
ww->warp.mfor.mat[1][0] = Mfor.m[1][0];
ww->warp.mfor.mat[1][1] = Mfor.m[1][1];
ww->warp.mfor.mat[1][2] = Mfor.m[1][2];
ww->warp.mfor.mat[2][0] = Mfor.m[2][0];
ww->warp.mfor.mat[2][1] = Mfor.m[2][1];
ww->warp.mfor.mat[2][2] = Mfor.m[2][2];
ww->warp.mbac.mat[0][0] = Mbac.m[0][0];
ww->warp.mbac.mat[0][1] = Mbac.m[0][1];
ww->warp.mbac.mat[0][2] = Mbac.m[0][2];
ww->warp.mbac.mat[1][0] = Mbac.m[1][0];
ww->warp.mbac.mat[1][1] = Mbac.m[1][1];
ww->warp.mbac.mat[1][2] = Mbac.m[1][2];
ww->warp.mbac.mat[2][0] = Mbac.m[2][0];
ww->warp.mbac.mat[2][1] = Mbac.m[2][1];
ww->warp.mbac.mat[2][2] = Mbac.m[2][2];
ww->warp.bvec.xyz[0] = -Mfor.m[0][3];
ww->warp.bvec.xyz[1] = -Mfor.m[1][3];
ww->warp.bvec.xyz[2] = -Mfor.m[2][3];
ww->warp.svec.xyz[0] = -Mbac.m[0][3];
ww->warp.svec.xyz[1] = -Mbac.m[1][3];
ww->warp.svec.xyz[2] = -Mbac.m[2][3];
/* bot and top are filled as to not cause trouble for Talairach bounding box at a minimum from:
[-80 ; -80 ; -65] to [80 ; 110 ; 85] */
ww->warp.bot.xyz[0] = -80 * 2; /* x 2 ? be generous, it is free! */
ww->warp.bot.xyz[1] = -80 * 2;
ww->warp.bot.xyz[2] = -65 * 2;
ww->warp.top.xyz[0] = 80 * 2;
ww->warp.top.xyz[1] = 110 * 2;
ww->warp.top.xyz[2] = 85 * 2;
RETURN(1);
}
int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"ConvertSurface"};
int kar, volexists, i, j, Doinv, randseed, Domergesurfs=0, pciref;
float DoR2S, fv[3], *pcxyzref;
double xcen[3], sc[3];
double xform[4][4];
char *if_name = NULL, *of_name = NULL, *if_name2 = NULL,
*of_name2 = NULL, *sv_name = NULL, *vp_name = NULL,
*OF_name = NULL, *OF_name2 = NULL, *tlrc_name = NULL,
*acpc_name=NULL, *xmat_name = NULL, *ifpar_name = NULL,
*ifpar_name2 = NULL;
SUMA_SO_File_Type iType = SUMA_FT_NOT_SPECIFIED,
iparType = SUMA_FT_NOT_SPECIFIED,
oType = SUMA_FT_NOT_SPECIFIED;
SUMA_SO_File_Format iForm = SUMA_FF_NOT_SPECIFIED,
iparForm = SUMA_FF_NOT_SPECIFIED,
oFormat = SUMA_FF_NOT_SPECIFIED;
SUMA_SurfaceObject *SO = NULL, *SOpar = NULL, *SOsurf = NULL;
SUMA_PARSED_NAME *of_name_strip = NULL, *of_name2_strip = NULL;
SUMA_SFname *SF_name = NULL;
void *SO_name = NULL;
char orsurf[6], orcode[6], *PCprojpref=NULL, *NodeDepthpref=NULL;
THD_warp *warp=NULL ;
THD_3dim_dataset *aset=NULL;
SUMA_Boolean brk, Do_tlrc, Do_mni_RAI, Do_mni_LPI, Do_acpc, Docen, Do_flip;
SUMA_Boolean Doxmat, Do_wind, Do_p2s, onemore, Do_native, Do_PolDec;
int Do_PCproj, Do_PCrot, Do_NodeDepth;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_Boolean exists;
SUMA_Boolean LocalHead = NOPE;
SUMA_STANDALONE_INIT;
SUMA_mainENTRY;
/* Allocate space for DO structure */
SUMAg_DOv = SUMA_Alloc_DisplayObject_Struct (SUMA_MAX_DISPLAYABLE_OBJECTS);
ps = SUMA_Parse_IO_Args(argc, argv, "-o;-i;-sv;-ipar;");
kar = 1;
xmat_name = NULL;
xcen[0] = 0.0; xcen[1] = 0.0; xcen[2] = 0.0;
brk = NOPE;
orcode[0] = '\0';
randseed = 1234;
sprintf(orsurf,"RAI");
Docen = NOPE;
Doxmat = NOPE;
Do_tlrc = NOPE;
Do_mni_RAI = NOPE;
Do_mni_LPI = NOPE;
Do_acpc = NOPE;
Do_wind = NOPE;
Do_flip = NOPE;
Do_p2s = NOPE;
Do_native = NOPE;
DoR2S = 0.0;
Do_PolDec = NOPE;
Do_PCproj = NO_PRJ;
Do_PCrot = NO_ROT;
pciref = -1;
pcxyzref = NULL;
PCprojpref = NULL;
NodeDepthpref = NULL;
Do_NodeDepth = 0;
Doinv = 0;
Domergesurfs = 0;
onemore = NOPE;
while (kar < argc) { /* loop accross command ine options */
/*fprintf(stdout, "%s verbose: Parsing command line...\n", FuncName);*/
if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0) {
usage_SUMA_ConvertSurface(ps, strlen(argv[kar]) > 3 ? 2:1);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
SUMA_TO_LOWER(argv[kar]);
if (!brk && (strcmp(argv[kar], "-seed") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need 1 integer after -seed\n");
exit (1);
}
randseed = atoi(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-xyzscale") == 0)) {
kar ++;
if (kar+2 >= argc) {
fprintf (SUMA_STDERR, "need 3 values after -XYZscale\n");
exit (1);
}
sc[0] = strtod(argv[kar], NULL); kar ++;
sc[1] = strtod(argv[kar], NULL); kar ++;
sc[2] = strtod(argv[kar], NULL);
xmat_name = "Scale";
Doxmat = YUP;
Doinv = 0;
brk = YUP;
}
if (!brk && ( (strcmp(argv[kar], "-xmat_1d") == 0) ||
(strcmp(argv[kar], "-xmat_1D") == 0) ) ) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need 1 argument after -xmat_1D\n");
exit (1);
}
xmat_name = argv[kar];
Doxmat = YUP;
Doinv = 0;
brk = YUP;
}
if (!brk && ( (strcmp(argv[kar], "-ixmat_1d") == 0) ||
(strcmp(argv[kar], "-ixmat_1D") == 0) ) ) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need 1 argument after -ixmat_1D\n");
exit (1);
}
xmat_name = argv[kar];
Doxmat = YUP;
Doinv = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-polar_decomp") == 0)) {
Do_PolDec = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-merge_surfs") == 0)) {
Domergesurfs = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-pc_proj") == 0)) {
kar ++;
if (kar+1 >= argc) {
fprintf (SUMA_STDERR, "need 2 argument after -pc_proj\n");
exit (1);
}
if (!strcmp(argv[kar],"PC0_plane")) Do_PCproj = E1_PLN_PRJ;
else if (!strcmp(argv[kar],"PC1_plane")) Do_PCproj = E2_PLN_PRJ;
else if (!strcmp(argv[kar],"PC2_plane")) Do_PCproj = E3_PLN_PRJ;
else if (!strcmp(argv[kar],"PCZ_plane")) Do_PCproj = EZ_PLN_PRJ;
else if (!strcmp(argv[kar],"PCY_plane")) Do_PCproj = EY_PLN_PRJ;
else if (!strcmp(argv[kar],"PCX_plane")) Do_PCproj = EX_PLN_PRJ;
else if (!strcmp(argv[kar],"PC0_dir")) Do_PCproj = E1_DIR_PRJ;
else if (!strcmp(argv[kar],"PC1_dir")) Do_PCproj = E2_DIR_PRJ;
else if (!strcmp(argv[kar],"PC2_dir")) Do_PCproj = E3_DIR_PRJ;
else if (!strcmp(argv[kar],"PCZ_dir")) Do_PCproj = EZ_DIR_PRJ;
else if (!strcmp(argv[kar],"PCY_dir")) Do_PCproj = EY_DIR_PRJ;
else if (!strcmp(argv[kar],"PCX_dir")) Do_PCproj = EX_DIR_PRJ;
else {
SUMA_S_Err("Bad value of %s for -pca_proj", argv[kar]);
exit(1);
}
++kar;
if (argv[kar][0] == '-') {
SUMA_S_Err("Prefix for -pc_proj should not start with '-'.\n"
"Could it be that %s is another option and \n"
"the prefix was forgtotten?", argv[kar]);
exit(1);
}
PCprojpref = argv[kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-node_depth") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need a prefix argument after -node_depth\n");
exit (1);
}
Do_NodeDepth = 1;
if (argv[kar][0] == '-') {
SUMA_S_Err("Prefix for -node_depth should not start with '-'.\n"
"Could it be that %s is another option and \n"
"the prefix was forgtotten?", argv[kar]);
exit(1);
}
NodeDepthpref = argv[kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-make_consistent") == 0)) {
Do_wind = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-flip_orient") == 0)) {
Do_flip = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-xcenter") == 0)) {
kar ++;
if (kar+2>= argc) {
fprintf (SUMA_STDERR, "need 3 arguments after -xcenter\n");
exit (1);
}
xcen[0] = atof(argv[kar]); ++kar;
xcen[1] = atof(argv[kar]); ++kar;
xcen[2] = atof(argv[kar]);
Docen = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-native") == 0)) {
Do_native = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-orient_out") == 0)) {
kar ++;
if (kar>= argc) {
fprintf (SUMA_STDERR, "need 1 argument after -orient_out\n");
exit (1);
}
snprintf(orcode, 4*sizeof(char), "%s", argv[kar]);
if (!SUMA_ok_orstring(orcode)) {
fprintf (SUMA_STDERR, "%s is a bad orientation string\n", orcode);
exit (1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-radial_to_sphere") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need 1 argument after -radial_to_sphere\n");
exit (1);
}
DoR2S = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-patch2surf") == 0)) {
Do_p2s = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-xml_ascii") == 0)) {
oFormat = SUMA_XML_ASCII_SURF;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-xml_b64") == 0)) {
oFormat = SUMA_XML_B64_SURF;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-xml_b64gz") == 0)) {
oFormat = SUMA_XML_B64GZ_SURF;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-tlrc") == 0)) {
Do_tlrc = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-acpc") == 0)) {
Do_acpc = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-mni_rai") == 0)) {
Do_mni_RAI = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-mni_lpi") == 0)) {
Do_mni_LPI = YUP;
brk = YUP;
}
if (!brk && !ps->arg_checked[kar]) {
fprintf (SUMA_STDERR,
"Error %s: Option %s not understood. Try -help for usage\n",
FuncName, argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else {
brk = NOPE;
kar ++;
}
}
if (argc < 3) {
SUMA_S_Err("Too few options");
usage_SUMA_ConvertSurface (ps, 0);
exit (1);
}
/* transfer info from ps structure (backward compat) */
if (ps->o_N_surfnames) {
of_name = ps->o_surfnames[0];
of_name2 = ps->o_surftopo[0];
oType = ps->o_FT[0];
if (oFormat == SUMA_FF_NOT_SPECIFIED) {
oFormat = ps->o_FF[0];
}
}
if (ps->i_N_surfnames) {
if_name = ps->i_surfnames[0];
if_name2 = ps->i_surftopo[0];
iType = ps->i_FT[0];
iForm = ps->i_FF[0];
}
if (ps->ipar_N_surfnames) {
ifpar_name = ps->ipar_surfnames[0];
ifpar_name2 = ps->ipar_surftopo[0];
iparType = ps->ipar_FT[0];
iparForm = ps->ipar_FF[0];
}
if (ps->N_sv) sv_name = ps->sv[0];
if (ps->N_vp) vp_name = ps->vp[0];
/* sanity checks */
if (Do_native && orcode[0] != '\0') {
SUMA_S_Err("Options -native and -orient_out are mutually exclusive");
exit(1);
}
if (Do_mni_LPI && Do_mni_RAI) {
SUMA_S_Err("\nCombining -MNI_lpi and -MNI_rai options.\nNot good.");
exit(1);
}
if (!if_name) {
SUMA_S_Err("input surface not specified.\n");
exit(1);
}
if (!of_name && (Do_PCproj < 0 && !Do_NodeDepth) ) {
SUMA_S_Err("output surface or projection PREFIX not specified.\n");
exit(1);
}
if (iType == SUMA_FT_NOT_SPECIFIED) {
SUMA_S_Err("input type not recognized.\n");
exit(1);
}
if (oType == SUMA_FT_NOT_SPECIFIED && (Do_PCproj < 0 && !Do_NodeDepth) ) {
SUMA_S_Err("output type not recognized.\n");
exit(1);
}
if ( oType != SUMA_GIFTI &&
oFormat >= SUMA_XML_SURF &&
oFormat <= SUMA_XML_B64GZ_SURF &&
(Do_PCproj < 0 && !Do_NodeDepth) ){
SUMA_S_Err("XML output options only valid with -o_gii\n");
exit(1);
}
if (iType == SUMA_SUREFIT) {
if (!if_name2) {
SUMA_S_Err("input SureFit surface incorrectly specified.\n");
exit(1);
}
if (sv_name && !vp_name) {
SUMA_S_Err("VolParent needs the -sv option for SureFit surfaces.");
exit(1);
}
}
if (iType == SUMA_VEC) {
if (!if_name2) {
SUMA_S_Err("Input vec surface incorrectly specified.\n");
exit(1);
}
}
if (( Do_mni_RAI || Do_mni_LPI) && !Do_tlrc) {
SUMA_SL_Warn ( "I hope you know what you're doing.\n"
"The MNI transform should only be applied to a\n"
"Surface in the AFNI tlrc coordinate space.\n");
}
if (Do_acpc && Do_tlrc) {
SUMA_S_Err("You can't do -tlrc and -acpc simultaneously.");
exit(1);
}
if ((Doxmat || Docen) && (Do_acpc || Do_tlrc)) {
SUMA_S_Err("You can't do -tlrc or -acpc with -xmat_1D and -xcenter.\n");
exit(1);
}
if ((!Doxmat && Docen)) {
SUMA_S_Err("You can't use -xcenter without -xmat_1D.\n");
exit(1);
}
if (oType == SUMA_SUREFIT) {
if (!of_name2) {
SUMA_S_Err("output SureFit surface incorrectly specified. \n");
exit(1);
}
}
if (oType == SUMA_VEC) {
if (!of_name2) {
SUMA_S_Err("output vec surface incorrectly specified. \n");
exit(1);
}
}
if ( ps->i_N_surfnames > 1 && !Domergesurfs) {
SUMA_S_Err("Multiple surfaces specified without -merge_surfs option\n"
"Nothing to do for such an input\n");
exit(1);
}
/* test for existence of input files */
if (!SUMA_is_predefined_SO_name(if_name, NULL, NULL, NULL, NULL) &&
!SUMA_filexists(if_name)) {
SUMA_S_Errv("if_name %s not found.\n", if_name);
exit(1);
}
if (if_name2) {
if (!SUMA_filexists(if_name2)) {
SUMA_S_Errv("if_name2 %s not found.\n", if_name2);
exit(1);
}
}
if (ifpar_name2) {
if (!SUMA_filexists(ifpar_name2)) {
SUMA_S_Errv("ifpar_name2 %s not found.\n", ifpar_name2);
exit(1);
}
}
if (ifpar_name) {
if (!SUMA_filexists(ifpar_name)) {
SUMA_S_Errv("ifpar_name %s not found.\n", ifpar_name);
exit(1);
}
}
if (xmat_name) {
if (!strstr(special_xmats,xmat_name) && !SUMA_filexists(xmat_name)) {
SUMA_S_Errv("xmat file %s not found.\n", xmat_name);
exit(1);
}
} else {
if (Do_PolDec) {
SUMA_S_Err("-polar_decomp is useless without -xmat_1D");
exit(1);
}
}
if (sv_name) {
char *head = NULL, view[10];
head = SUMA_AfniPrefix(sv_name, view, NULL, &volexists);
if (!SUMA_AfniExistsView(volexists, view) && !SUMA_filexists(sv_name)) {
fprintf (SUMA_STDERR,
"Error %s: volume %s not found.\n", FuncName, head);
exit(1);
}
if (head) SUMA_free(head); head = NULL;
}
if ((Do_tlrc || Do_acpc) && (!sv_name)) {
fprintf (SUMA_STDERR,
"Error %s: -tlrc must be used with -sv option.\n", FuncName);
exit(1);
}
if (vp_name) {
if (!SUMA_filexists(vp_name)) {
fprintf (SUMA_STDERR,
"Error %s: %s not found.\n", FuncName, vp_name);
exit(1);
}
}
/* check for existence of output files */
if ((Do_PCproj < 0 && !Do_NodeDepth) ) {
if (of_name2) {
SUMA_SFname *SFname;
SO_name = SUMA_2Prefix2SurfaceName (of_name, of_name2, NULL,
vp_name, oType, &exists);
SFname = (SUMA_SFname *)SO_name;
OF_name2 = SUMA_copy_string(SFname->name_topo);
OF_name = SUMA_copy_string(SFname->name_coord);
} else {
SO_name = SUMA_Prefix2SurfaceName (of_name, NULL, vp_name,
oType, &exists);
OF_name = SUMA_copy_string((char *) SO_name);
}
if (exists && !THD_ok_overwrite()) {
if (OF_name2)
fprintf (SUMA_STDERR,
"Error %s: output file(s) %s and/or %s exist already.\n",
FuncName, OF_name, OF_name2);
else fprintf ( SUMA_STDERR,
"Error %s: output file %s exists already.\n",
FuncName, OF_name);
exit(1);
}
}
/* now for the real work */
if (Doxmat) {
MRI_IMAGE *im = NULL;
double *far=NULL;
int nrow, ncol;
if (!strcmp(xmat_name,"RandRigid")) {
SUMA_FillRandXform(xform, randseed, 2);
} else if (!strcmp(xmat_name,"RandAffine")) {
SUMA_FillRandXform(xform, randseed, 3);
} else if (!strcmp(xmat_name,"RandShift")) {
SUMA_FillRandXform(xform, randseed, 1);
} else if (!strcmp(xmat_name,"Scale")) {
SUMA_FillScaleXform(xform, sc);
} else if (!strcmp(xmat_name,"NegXY")) {
SUMA_FillXYnegXform(xform);
} else {
im = mri_read_double_1D (xmat_name);
if (!im) {
SUMA_SLP_Err("Failed to read 1D file");
exit(1);
}
far = MRI_DOUBLE_PTR(im);
nrow = im->nx;
ncol = im->ny;
if (nrow == 1) {
if (ncol != 12) {
SUMA_SL_Err("Mat file must have\n"
"one row of 12 columns.");
mri_free(im); im = NULL; /* done with that baby */
exit(1);
}
i = 0;
while (i < 12) {
xform[i/4][0] = far[i]; ++i;
xform[i/4][1] = far[i]; ++i;
xform[i/4][2] = far[i]; ++i;
xform[i/4][3] = far[i]; ++i;
}
xform[3][0] = 0.0;
xform[3][1] = 0.0;
xform[3][2] = 0.0;
xform[3][3] = 1.0;
} else {
if (ncol < 4 ) {
SUMA_SL_Err("Mat file must have\n"
"at least 4 columns.");
mri_free(im); im = NULL; /* done with that baby */
exit(1);
}
if (nrow < 3 ) {
SUMA_SL_Err("Mat file must have\n"
"at least 3 rows.");
mri_free(im); im = NULL; /* done with that baby */
exit(1);
}
if (ncol > 4) {
SUMA_SL_Warn( "Ignoring entries beyond 4th \n"
"column in transform file.");
}
if (nrow > 3) {
SUMA_SL_Warn( "Ignoring entries beyond 3rd\n"
"row in transform file.\n");
}
for (i=0; i < 3; ++i) {
xform[i][0] = far[i];
xform[i][1] = far[i+nrow];
xform[i][2] = far[i+2*nrow];
xform[i][3] = far[i+3*nrow];
}
xform[3][0] = 0.0;
xform[3][1] = 0.0;
xform[3][2] = 0.0;
xform[3][3] = 1.0;
}
}
if (LocalHead) {
fprintf(SUMA_STDERR,"\n++ ConvertSurface xform:\n");
for (i=0; i < 4; ++i) {
fprintf(SUMA_STDERR," %+.5f\t%+.5f\t%+.5f\t%+.5f\n",
xform[i][0], xform[i][1],
xform[i][2], xform[i][3]);
}
fprintf(SUMA_STDERR,"\n");
}
mri_free(im); im = NULL;
if (Doinv) {
mat44 A, A0;
LOAD_MAT44( A0, \
xform[0][0], xform[0][1], xform[0][2], xform[0][3], \
xform[1][0], xform[1][1], xform[1][2], xform[1][3], \
xform[2][0], xform[2][1], xform[2][2], xform[2][3] );
A = nifti_mat44_inverse(A0);
UNLOAD_MAT44(A, \
xform[0][0], xform[0][1], xform[0][2], xform[0][3], \
xform[1][0], xform[1][1], xform[1][2], xform[1][3], \
xform[2][0], xform[2][1], xform[2][2], xform[2][3] );
}
if (Do_PolDec) {
#ifdef USE_DECOMPOSE_SHOEMAKE
/* a little something to do a polar decomposition on M into M = Q*S*/
{
float det, m[4][4], q[4][4], s[4][4];
char *stmp = SUMA_append_string("QS_",xmat_name);
FILE *fout = fopen(stmp,"w"); SUMA_free(stmp); stmp = NULL;
SUMA_S_Note("FixMe! #include above and if(1) here ...");
det = polar_decomp(M, q,s);
fprintf(fout,"#[M][D]: (D is the shift)\n");
for (i=0;i<3; ++i)
fprintf(fout, "#%.5f %.5f %.5f %.5f\n",
M[i][0], M[i][1], M[i][2], M[i][3]);
fprintf(fout,"#Q:\n");
for (i=0;i<3; ++i)
fprintf(fout, "#%.5f %.5f %.5f %.5f\n",
q[i][0], q[i][1], q[i][2], q[i][3]);
fprintf(fout,"#S:\n");
for (i=0;i<3; ++i)
fprintf(fout, "#%.5f %.5f %.5f %.5f\n",
s[i][0], s[i][1], s[i][2], s[i][3]);
fprintf(fout,"#det: %f\n", det);
fprintf(fout, "#[Q][D]: A close xform to [M][D], "
"without scaling.\n#M = Q*S\n");
for (i=0;i<3; ++i)
fprintf(fout, "%.5f %.5f %.5f %.5f\n",
q[i][0], q[i][1], q[i][2], M[i][3]);
fclose(fout); SUMA_free(stmp); stmp = NULL;
}
/* replace user's xform with orthogonal one: */
fprintf(SUMA_STDOUT,"Replacing matrix:\n");
for (i=0;i<3; ++i)
fprintf( SUMA_STDOUT,
" %.5f %.5f %.5f %.5f\n",
M[i][0], M[i][1], M[i][2], M[i][3]);
fprintf(SUMA_STDOUT," with matrix:\n");
for (i=0;i<3; ++i)
fprintf(SUMA_STDOUT,
" %.5f %.5f %.5f %.5f\n",
q[i][0], q[i][1], q[i][2], M[i][3]);
for (i=0;i<3; ++i) {
M[i][0] = q[i][0]; M[i][1] = q[i][1]; M[i][2] = q[i][2];
}
#else
{/* use the NIFTI polar decomposition function
(same results as above)*/
mat33 Q, A;
for (i=0;i<3;++i) {
A.m[i][0] = xform[i][0];
A.m[i][1] = xform[i][1];
A.m[i][2] = xform[i][2];
}
Q = nifti_mat33_polar( A );
/* replace user's xform with orthogonal one: */
fprintf(SUMA_STDOUT,"Replacing matrix:\n");
for (i=0;i<3; ++i)
fprintf( SUMA_STDOUT,
" %.5f %.5f %.5f %.5f\n",
xform[i][0], xform[i][1],
xform[i][2], xform[i][3]);
fprintf(SUMA_STDOUT," with matrix:\n");
for (i=0;i<3; ++i)
fprintf( SUMA_STDOUT,
" %.5f %.5f %.5f %.5f\n",
Q.m[i][0], Q.m[i][1], Q.m[i][2], xform[i][3]);
for (i=0;i<3; ++i) {
xform[i][0] = Q.m[i][0];
xform[i][1] = Q.m[i][1];
xform[i][2] = Q.m[i][2];
}
}
#endif
}
}
if ( ps->i_N_surfnames == 1) {
/* load that one surface */
SO = SUMA_Load_Surface_Object_Wrapper ( if_name, if_name2, vp_name,
iType, iForm, sv_name, 1);
if (!SO) {
SUMA_S_Err("Failed to read input surface.\n");
exit (1);
}
} else if ( ps->i_N_surfnames > 1 && Domergesurfs) {
SUMA_SurfaceObject **SOar=NULL;
int ii;
SUMA_S_Notev("Merging %d surfaces into 1\n", ps->i_N_surfnames);
SOar = (SUMA_SurfaceObject **)
SUMA_calloc(ps->i_N_surfnames, sizeof(SUMA_SurfaceObject *));
if (ps->N_sv > 1 || ps->N_vp > 1) {
SUMA_S_Errv("Cannot handle multiple (%d) -sv or multiple (%d) -vp\n",
ps->N_sv, ps->N_vp);
exit(1);
}
for (ii = 0; ii<ps->i_N_surfnames; ++ii) {
SOar[ii] = SUMA_Load_Surface_Object_Wrapper(ps->i_surfnames[ii],
ps->i_surftopo[ii],
vp_name,
ps->i_FT[0], ps->i_FF[0],
sv_name, 1);
}
if (!(SO = SUMA_MergeSurfs(SOar, ps->i_N_surfnames))) {
SUMA_S_Err("Failed to merge");
exit(1);
}
for (ii = 0; ii<ps->i_N_surfnames; ++ii) {
SUMA_Free_Surface_Object(SOar[ii]);
SOar[ii]=NULL;
} SUMA_free(SOar); SOar=NULL;
}
if (DoR2S > 0.0000001) {
if (!SUMA_ProjectSurfaceToSphere(SO, NULL , DoR2S , NULL)) {
SUMA_S_Err("Failed to project to surface");
exit(1);
}
}
if (ifpar_name) {
SOpar = SUMA_Load_Surface_Object_Wrapper ( ifpar_name, ifpar_name2,
vp_name, iparType, iparForm, sv_name, 1);
if (!SOpar) {
SUMA_S_Err("Failed to read input parent surface.\n");
exit (1);
}
/* need edge list */
if (!SUMA_SurfaceMetrics_eng (SOpar,"EdgeList", NULL, 0,
SUMAg_CF->DsetList)) {
SUMA_SL_Err("Failed to create edgelist for parent");
exit(1);
}
}
/* if Do_wind */
if (Do_wind) {
fprintf (SUMA_STDOUT,
"Checking and repairing mesh's winding consistency...\n");
/* check the winding, but that won't fix the normals,
you'll have to recalculate those things, if need be ... */
if (!SUMA_SurfaceMetrics_eng (SO, "CheckWind", NULL, 0,
SUMAg_CF->DsetList)) {
SUMA_S_Err("Failed in SUMA_SurfaceMetrics.\n");
exit(1);
}
}
if (Do_flip) {
fprintf (SUMA_STDOUT,
"Flipping triangle winding...\n");
SUMA_FlipSOTriangles(SO);
}
if (Do_tlrc) {
fprintf (SUMA_STDOUT,"Performing talairach transform...\n");
/* form the tlrc version of the surface volume */
tlrc_name = (char *) SUMA_calloc (strlen(SO->VolPar->dirname)+
strlen(SO->VolPar->prefix)+60,
sizeof(char));
sprintf (tlrc_name, "%s%s+tlrc.HEAD",
SO->VolPar->dirname, SO->VolPar->prefix);
if (!SUMA_filexists(tlrc_name)) {
fprintf (SUMA_STDERR,"Error %s: %s not found.\n", FuncName, tlrc_name);
exit(1);
}
/* read the tlrc header */
aset = THD_open_dataset(tlrc_name) ;
if( !ISVALID_DSET(aset) ){
SUMA_S_Err("%s is not a valid data set.\n", tlrc_name) ;
exit(1);
}
if( aset->warp == NULL ){
SUMA_S_Err("tlrc_name does not contain a talairach transform.\n");
exit(1);
}
warp = aset->warp ;
/* now warp the coordinates, one node at a time */
if (!SUMA_AFNI_forward_warp_xyz(warp, SO->NodeList, SO->N_Node)) {
SUMA_S_Err("Failed in SUMA_AFNI_forward_warp_xyz.\n");
exit(1);
}
}
if (Do_acpc) {
fprintf (SUMA_STDOUT,"Performing acpc transform...\n");
/* form the acpc version of the surface volume */
acpc_name = (char *) SUMA_calloc (strlen(SO->VolPar->dirname)+
strlen(SO->VolPar->prefix)+60,
sizeof(char));
sprintf (acpc_name,
"%s%s+acpc.HEAD", SO->VolPar->dirname, SO->VolPar->prefix);
if (!SUMA_filexists(acpc_name)) {
fprintf (SUMA_STDERR,"Error %s: %s not found.\n", FuncName, acpc_name);
exit(1);
}
/* read the acpc header */
aset = THD_open_dataset(acpc_name) ;
if( !ISVALID_DSET(aset) ){
fprintf (SUMA_STDERR,
"Error %s: %s is not a valid data set.\n",
FuncName, acpc_name) ;
exit(1);
}
if( aset->warp == NULL ){
fprintf (SUMA_STDERR,
"Error %s: acpc_name does not contain an acpc transform.\n",
FuncName);
exit(1);
}
warp = aset->warp ;
/* now warp the coordinates, one node at a time */
if (!SUMA_AFNI_forward_warp_xyz(warp, SO->NodeList, SO->N_Node)) {
fprintf (SUMA_STDERR,
"Error %s: Failed in SUMA_AFNI_forward_warp_xyz.\n", FuncName);
exit(1);
}
}
if (Do_mni_RAI) {
fprintf (SUMA_STDOUT,"Performing MNI_RAI transform...\n");
/* apply the mni warp */
if (!SUMA_AFNItlrc_toMNI(SO->NodeList, SO->N_Node, "RAI")) {
fprintf (SUMA_STDERR,
"Error %s: Failed in SUMA_AFNItlrc_toMNI.\n", FuncName);
exit(1);
}
sprintf(orsurf,"RAI");
}
if (Do_mni_LPI) {
fprintf (SUMA_STDOUT,"Performing MNI_LPI transform...\n");
/* apply the mni warp */
if (!SUMA_AFNItlrc_toMNI(SO->NodeList, SO->N_Node, "LPI")) {
fprintf (SUMA_STDERR,
"Error %s: Failed in SUMA_AFNItlrc_toMNI.\n", FuncName);
exit(1);
}
sprintf(orsurf,"LPI");
}
if (Doxmat) {
fprintf (SUMA_STDOUT,"Performing affine transform...\n");
if (LocalHead) {
for (i=0; i<3 ; ++i) {
fprintf (SUMA_STDERR,
"M[%d][:] = %f %f %f %f\n",
i, xform[i][0], xform[i][1], xform[i][2], xform[i][3]);
}
fprintf (SUMA_STDERR,"Cen[:] %f %f %f\n", xcen[0], xcen[1], xcen[2]);
}
if (Docen) {
if (!SUMA_Apply_Coord_xform( SO->NodeList, SO->N_Node, SO->NodeDim,
xform, 0, xcen)) {
SUMA_SL_Err("Failed to xform coordinates"); exit(1);
}
} else {
if (!SUMA_Apply_Coord_xform( SO->NodeList, SO->N_Node, SO->NodeDim,
xform, 0, NULL)) {
SUMA_SL_Err("Failed to xform coordinates"); exit(1);
}
}
SUMA_Blank_AfniSO_Coord_System(SO->aSO);
}
if (orcode[0] != '\0') {
SUMA_LHv("Changing coordinates from %s to %s\n", orsurf, orcode);
if (!SUMA_CoordChange(orsurf, orcode, SO->NodeList, SO->N_Node)) {
SUMA_S_Err("Failed to change coords.");
exit(1);
}
SUMA_Blank_AfniSO_Coord_System(SO->aSO);
}
if (Do_p2s) {
SUMA_SurfaceObject *SOold = SO;
SUMA_LH("Changing patch to surface...");
SO = SUMA_Patch2Surf(SOold->NodeList, SOold->N_Node,
SO->FaceSetList, SO->N_FaceSet, 3);
if (!SO) {
SUMA_S_Err("Failed to change patch to surface.");
exit(1);
}
/* get rid of old surface object */
SUMA_Free_Surface_Object(SOold);
}
if (Do_native) {
if (!SUMA_Delign_to_VolPar (SO, NULL)) {
SUMA_S_Err("Failed to transform coordinates to native space");
exit(1);
}
}
if (Do_NodeDepth) {
float *dpth=NULL, mx=0.0;
SUMA_PC_XYZ_PROJ *pcp=NULL;
if (SUMA_NodeDepth(SO->NodeList, SO->N_Node, E1_DIR_PRJ, &dpth,
0.0, NULL, &mx, &pcp) < 0) {
SUMA_S_Err("Failed to compute node depth");
exit(1);
} else {
if (!SUMA_WriteNodeDepth(NodeDepthpref,pcp,dpth, mx)) {
SUMA_S_Err("Failed to write node depth");
exit(1);
}
}
SUMA_ifree(dpth);
pcp = SUMA_Free_PC_XYZ_Proj(pcp);
}
if (Do_PCproj > NO_PRJ) {
SUMA_PC_XYZ_PROJ *pcp=NULL;
pciref = 0; pcxyzref = NULL;
if (!(pcp = SUMA_Project_Coords_PCA(SO->NodeList, SO->N_Node,
pciref, pcxyzref, Do_PCproj, Do_PCrot, 1))) {
SUMA_S_Err("Failed to project");
exit(1);
} else {
if (!SUMA_Write_PC_XYZ_Proj(pcp, PCprojpref)) {
SUMA_S_Err("Failed to write out projections");
exit(1);
} else {
pcp = SUMA_Free_PC_XYZ_Proj(pcp);
}
exit(0);
}
}
/* write the surface object */
if (SO_name) {
if (LocalHead) SUMA_Print_Surface_Object (SO, stderr);
fprintf (SUMA_STDOUT,"Writing surface...\n");
if (!(SUMA_Save_Surface_Object ( SO_name,
SO, oType, oFormat, SOpar))) {
fprintf (SUMA_STDERR,
"Error %s: Failed to write surface object.\n",
FuncName);
exit (1);
}
}
if (of_name_strip) of_name_strip = SUMA_Free_Parsed_Name (of_name_strip);
if (of_name2_strip) of_name2_strip = SUMA_Free_Parsed_Name (of_name2_strip);
if (OF_name) SUMA_free(OF_name);
if (OF_name2) SUMA_free(OF_name2);
if (SF_name) SUMA_free(SF_name);
if (SO_name) SUMA_free(SO_name);
if (SO) SUMA_Free_Surface_Object(SO);
if (SOpar) SUMA_Free_Surface_Object(SOpar);
if (ps) SUMA_FreeGenericArgParse(ps); ps = NULL;
return (0);
}
