header correcting util

fslcorrecthd.cc

+//     fslcorrecthd.cc - check and correct a nifti file for bad vox-offset
+//     Matthew Webster, FMRIB Image Analysis Group
+//     Copyright (C) 2007 University of Oxford  
+//     COPYRIGHT  
+
+#include "newimage/newimageall.h"
+#include <iostream>
+using namespace NEWIMAGE;
+
+void print_usage(const string& progname) 
+{
+  cout << endl;
+  cout << "Usage: fslcorrecthd <input> <output>" << endl;
+}
+
+int main(int argc,char *argv[])
+{
+  if (argc < 3) 
+  {
+    print_usage(string(argv[0]));
+    return 1; 
+  }
+  FSLIO* fslio=NULL;
+  fslio = FslOpen(FslMakeBaseName(argv[1]),"rb");
+  FslClose(fslio);
+  int ft;
+  struct dsr *hdr;
+  ft = FslGetFileType(fslio);
+  hdr = (struct dsr *)calloc(1,sizeof(struct dsr));
+  FslReadRawHeader(hdr,fslio->niftiptr->fname);
+  if (fslio->niftiptr->byteorder != nifti_short_order()) 
+  {
+    cout << "Byte swapping" << endl;
+    AvwSwapHeader(hdr);
+  } 
+  //check nifti-libs output versus raw header info
+  ft = fslio->niftiptr->iname_offset - hdr->dime.vox_offset;
+  int minft=MIN(fslio->niftiptr->iname_offset,hdr->dime.vox_offset);
+  cerr << "number of bytes wrong: " << ft << endl;
+  cerr << "start at byte location: " << minft << endl;
+
+ ifstream input_file;
+ ofstream output_file;
+ char byte[1];
+ input_file.open(argv[1],ios::in | ios :: binary);
+ output_file.open(argv[2],ofstream::out | ofstream::binary);
+ for(int i=1;i<=minft;i++)
+ {
+   input_file.read(byte,1);
+   if (input_file.eof()) break;
+   output_file.write(byte,1);
+ }
+
+ for(int i=1;i<=abs(ft) && ft>0;i++)
+ {
+   byte[0]=0;
+   output_file.write(byte,1);
+   }
+
+ for(int i=1;i<=abs(ft) && ft<0;i++)
+ {
+   input_file.read(byte,1);
+ }
+
+ while(true)
+ {
+   input_file.read(byte,1);
+   if (input_file.eof()) break;
+   output_file.write(byte,1);
+ }  
+ output_file.close();
+ input_file.close();
+  return 0;
+}
+
+