From d12fdfd5f214bcc8e6701485d9062a2b4ee43ab3 Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Mon, 12 Nov 2007 13:57:50 +0000
Subject: [PATCH] header correcting util
---
fslcorrecthd.cc | 76 +++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 76 insertions(+)
create mode 100755 fslcorrecthd.cc
diff --git a/fslcorrecthd.cc b/fslcorrecthd.cc
new file mode 100755
index 0000000..d69604d
--- /dev/null
+++ b/fslcorrecthd.cc
@@ -0,0 +1,76 @@
+// 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;
+}
+
+
--
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