diff --git a/fslorient.cc b/fslorient.cc
index 3e4166ba21d6fcf8ddfb5841f16be3a560cb2fd7..d66704afcc29410c186e2a21f69829ca55550f52 100644
--- a/fslorient.cc
+++ b/fslorient.cc
@@ -17,16 +17,30 @@ void print_usage() {
cout << "Usage: " << progname << " <main option> <filename>" << endl;
cout << endl;
cout << " where the main option is one of:" << endl;
- cout << " -forceradiological (makes radiological header)" << endl;
- cout << " -forceneurological (makes neurological header - not Analyze)" << endl;
- cout << " -swaporient (swaps radiological and neurological)" << endl;
- cout << " -getorient (prints left-right orientation)" << endl;
- cout << " -deleteorient (removes orient info from header - not Analyze)" << endl;
+ cout << " -getorient (prints FSL left-right orientation)" << endl;
+ cout << " -getsform (prints the 16 elements of the sform matrix)" << endl;
+ cout << " -getqform (prints the 16 elements of the qform matrix)" << endl;
+ cout << " -setsform <m11 m12 ... m44> (sets the 16 elements of the sform matrix)" << endl;
+ cout << " -setqform <m11 m12 ... m44> (sets the 16 elements of the qform matrix)" << endl;
+ cout << " -getsformcode (prints the sform integer code)" << endl;
+ cout << " -getqformcode (prints the qform integer code)" << endl;
+ cout << " -setsformcode <code> (sets sform integer code)" << endl;
+ cout << " -setqformcode <code> (sets qform integer code)" << endl;
+ cout << " -copysform2qform (sets the qform equal to the sform - code and matrix)" << endl;
+ cout << " -copyqform2sform (sets the sform equal to the qform - code and matrix)" << endl;
+ cout << " -deleteorient (removes orient info from header)" << endl;
+ cout << " -forceradiological (makes FSL radiological header)" << endl;
+ cout << " -forceneurological (makes FSL neurological header - not Analyze)" << endl;
+ cout << " -swaporient (swaps FSL radiological and FSL neurological)" << endl;
cout << endl;
- cout << " Note: The stored data order is never changed here - only the header info." << endl;
+ cout << " Note: ANALYZE files are NOT modified by any of the commands" << endl;
+ cout << " - they are for NIFTI files ONLY!" << endl;
+ cout << " For NIFTI: the stored data order is never changed here - only the header info." << endl;
cout << " To change the data storage use avwswapdim." << endl;
cout << endl;
cout << " e.g. " << progname << " -forceradiological myimage" << endl;
+ cout << " " << progname << " -copysform2qform myimage" << endl;
+ cout << " " << progname << " -setsform -2 0 0 90 0 2 0 -126 0 0 2 -72 0 0 0 1 myimage" << endl;
cout << endl;
}
@@ -42,51 +56,144 @@ void swaporient(volume4D<T>& invol) {
invol.set_qform(invol.qform_code(),invol.qform_mat() * swapmat);
}
+
+template <class T>
+int getorient(const volume4D<T>& invol)
+{
+ if (invol.left_right_order()==FSL_RADIOLOGICAL) {
+ cout << "RADIOLOGICAL" << endl;
+ } else {
+ cout << "NEUROLOGICAL" << endl;
+ }
+ return 0;
+}
+
+
+template <class T>
+int getorient(const string& filename)
+{
+ volume4D<T> invol;
+ read_volume4D(invol,filename);
+ return getorient(invol);
+}
+
+
+int showmat(const Matrix& mat) {
+ for (int a=1; a<=4; a++) {
+ for (int b=1; b<=4; b++) {
+ cout << mat(a,b) << " ";
+ }
+ }
+ cout << endl;
+ return 0;
+}
+
+
+int testminargs(int argnum, int argc) {
+ if (argc < (argnum + 1)) {
+ print_usage();
+ exit(EXIT_FAILURE);
+ }
+ return 0;
+}
+
+
template <class T>
int fmrib_main(int argc,char *argv[])
{
+ bool modified=false;
int retval=0;
- string option=argv[1], filename=argv[2];
+ string option=argv[1], filename;
volumeinfo volinfo;
volume4D<T> invol;
+
+ filename=argv[argc-1];
read_volume4D(invol,filename,volinfo);
- if (option=="-forceradiological") {
+ if (option=="-getorient") {
+ getorient(invol);
+ } else if (option=="-getsformcode") {
+ cout << invol.sform_code() << endl;
+ } else if (option=="-getqformcode") {
+ cout << invol.qform_code() << endl;
+ } else if (option=="-getqform") {
+ showmat(invol.qform_mat());
+ } else if (option=="-getsform") {
+ showmat(invol.sform_mat());
+ } else if (option=="-setsformcode") {
+ testminargs(3,argc);
+ modified=true;
+ int code = (int) atof(argv[2]);
+ invol.set_sform(code,invol.sform_mat());
+ } else if (option=="-setqformcode") {
+ testminargs(3,argc);
+ modified=true;
+ int code = (int) atof(argv[2]);
+ invol.set_qform(code,invol.qform_mat());
+ } else if ( (option=="-setqform") || (option=="-setsform") ) {
+ testminargs(18,argc);
+ modified=true;
+ Matrix mat(4,4);
+ for (int a=1; a<=4; a++) {
+ for (int b=1; b<=4; b++) {
+ mat(a,b)=atof(argv[a*4+b-3]);
+ }
+ }
+ // override the last line
+ mat(4,1)=0; mat(4,2)=0; mat(4,3)=0; mat(4,4)=1;
+ if (option=="-setqform") {
+ invol.set_qform(invol.qform_code(),mat);
+ }
+ if (option=="-setsform") {
+ invol.set_sform(invol.sform_code(),mat);
+ }
+ } else if (option=="-copysform2qform") {
+ modified=true;
+ invol.set_qform(invol.sform_code(),invol.sform_mat());
+ } else if (option=="-copyqform2sform") {
+ modified=true;
+ invol.set_sform(invol.qform_code(),invol.qform_mat());
+ } else if (option=="-swaporient") {
+ modified=true;
+ swaporient(invol);
+ } else if (option=="-deleteorient") {
+ modified=true;
+ invol.set_sform(NIFTI_XFORM_UNKNOWN,invol.sform_mat());
+ invol.set_qform(NIFTI_XFORM_UNKNOWN,invol.qform_mat());
+ } else if (option=="-forceradiological") {
+ modified=true;
if (invol.left_right_order()==FSL_NEUROLOGICAL) {
swaporient(invol);
}
} else if (option=="-forceneurological") {
+ modified=true;
if (invol.left_right_order()==FSL_RADIOLOGICAL) {
swaporient(invol);
}
- } else if (option=="-swaporient") {
- swaporient(invol);
- } else if (option=="-getorient") {
- if (invol.left_right_order()==FSL_RADIOLOGICAL) {
- cout << "RADIOLOGICAL" << endl;
+ } else{
+ // does the first arg exist as an image file?
+ if (fsl_imageexists(string(argv[1]))) {
+ getorient<T>(string(argv[1]));
} else {
- cout << "NEUROLOGICAL" << endl;
+ cerr << "Unrecognised option: " << option << endl;
+ print_usage();
+ retval = -1;
}
- return 0;
- } else if (option=="-deleteorient") {
- invol.set_sform(NIFTI_XFORM_UNKNOWN,invol.sform_mat());
- invol.set_qform(NIFTI_XFORM_UNKNOWN,invol.qform_mat());
- } else{
- cerr << "Unrecognised option: " << option << endl;
- print_usage();
- retval = -1;
}
- if (FslBaseFileType(FslGetFileType(&volinfo))!=FSL_TYPE_ANALYZE) {
- FslSetOverrideOutputType(FslGetFileType(&volinfo));
- write_volume4D(invol,filename,volinfo);
- FslSetOverrideOutputType(-1); // restore to default
- } else {
- cerr << "Cannot modify orientation for Analyze files" << endl;
- cerr << " All Analyze files are treated as radiological" << endl;
- cerr << " To change the data storage use avwswapdim" << endl;
- retval=-1;
+
+ if (modified) {
+ if (FslBaseFileType(FslGetFileType(&volinfo))!=FSL_TYPE_ANALYZE) {
+ FslSetOverrideOutputType(FslGetFileType(&volinfo));
+ write_volume4D(invol,filename,volinfo);
+ FslSetOverrideOutputType(-1); // restore to default
+ } else {
+ cerr << "Cannot modify orientation for Analyze files" << endl;
+ cerr << " All Analyze files are treated as radiological" << endl;
+ cerr << " To change the data storage use avwswapdim" << endl;
+ retval=-1;
+ }
}
return retval;
}
@@ -94,12 +201,13 @@ int fmrib_main(int argc,char *argv[])
int main(int argc,char *argv[])
{
- if (argc<3) {
+ if (argc<2) {
print_usage();
return -1;
}
- string inname = argv[2];
+ string inname;
+ inname = argv[argc-1];
// call the templated main
return call_fmrib_main(dtype(inname),argc,argv);
}