From 46437f42a717ad4d8f33ce193ccc85f241c00da7 Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Fri, 19 Oct 2018 11:15:53 +0000
Subject: [PATCH] Fixes to more closely match previous version
---
fslcreatehd.cc | 59 +++++++++++++++++++++++++-------------------------
1 file changed, 30 insertions(+), 29 deletions(-)
diff --git a/fslcreatehd.cc b/fslcreatehd.cc
index 43dd194..ef4f97b 100755
--- a/fslcreatehd.cc
+++ b/fslcreatehd.cc
@@ -1,7 +1,7 @@
// fslcreatehd.cc - Copy certain parts of an AVW header
// Mark Jenkinson, Steve Smith and Matthew Webster, FMRIB Image Analysis Group
-// Copyright (C) 2001-2005 University of Oxford
-// CCOPYRIGHT
+// Copyright (C) 2001-2005 University of Oxford
+// CCOPYRIGHT
#include "newimage/newimageall.h"
#include <fstream>
@@ -9,12 +9,15 @@
using namespace NEWIMAGE;
-void print_usage(const string& progname)
+void print_usage(const string& progname)
{
cout << endl;
cout << "Usage: fslcreatehd <xsize> <ysize> <zsize> <tsize> <xvoxsize> <yvoxsize> <zvoxsize> <tr> <xorigin> <yorigin> <zorigin> <datatype> <headername>" << endl;
cout << " fslcreatehd <nifti_xml_file> <headername>" << endl;
cout << " Datatype values: " << DT_UNSIGNED_CHAR << "=char, " << DT_SIGNED_SHORT << "=short, " << DT_SIGNED_INT <<"=int, " << DT_FLOAT << "=float, " << DT_DOUBLE<< "=double" << endl;
+ cout << " In the first form, a radiological image will be created, the origin being given as voxel co-ordindates," << endl;
+ cout << " if the output file already exists, its data ( but not geometric information ) will be copied if it has" << endl;
+ cout << " a matching number of elements."
cout << " In the second form, an XML-ish form of nifti header is read (as output by fslhd -x)" << endl;
cout << " Note that stdin is used if '-' is used in place of a filename" << endl;
@@ -30,10 +33,10 @@ int fslcreatehd_main(int argc, char *argv[])
string filename;
int fileread(1);
bool existingImage(false);
-
+
if (argc==3) /* use the XML form of header specification */
filename = string(argv[2]);
- else
+ else
filename = string(argv[13]);
/* check if file already exists and if so, read the image contents */
@@ -43,11 +46,11 @@ int fslcreatehd_main(int argc, char *argv[])
header=reader.loadImage(filename,buffer,extensions);
originalHeader=header;
}
-
+
if (argc>3) {
/* set uninteresting defaults */
- if (!existingImage)
+ if (!existingImage)
header.datatype=atoi(argv[12]);
header.dim[0]=4;
for (int i=1;i<=4;i++)
@@ -57,40 +60,40 @@ int fslcreatehd_main(int argc, char *argv[])
if ( atoi(argv[9]) != 0 || atoi(argv[10]) != 0 || atoi(argv[11]) != 0 ) {
- header.sX[3]=atoi(argv[9]);
- header.sY[3]=atoi(argv[10]);
- header.sZ[3]=atoi(argv[11]);
- header.sX[0]=atoi(argv[5]);
- header.sY[1]=atoi(argv[6]);
- header.sZ[2]=atoi(argv[7]);
+ header.sX[0]=-header.pixdim[1];
+ header.sY[1]=header.pixdim[2];
+ header.sZ[2]=header.pixdim[3];
+ header.sX[3]=-header.pixdim[1]*(header.dim[1]-1.0-atoi(argv[9]));
+ header.sY[3]=-header.pixdim[2]*atoi(argv[10]);
+ header.sZ[3]=-header.pixdim[3]*atoi(argv[11]);
}
} else {
/* read XML form */
char *newstr, *oldfname, *oldiname;
ifstream inputfile;
vector<string> settings;
-
+
if (strcmp(argv[1],"-")==0) {fileread=0;}
newstr = (char *)calloc(10000,1);
oldfname = (char *)calloc(10000,1);
oldiname = (char *)calloc(10000,1);
- if (fileread)
+ if (fileread)
{
- inputfile.open (argv[1], ifstream::in | ifstream::binary);
+ inputfile.open (argv[1], ifstream::in | ifstream::binary);
if (!inputfile.is_open())
- {
+ {
cerr << "Cannot open file " << argv[1] << endl;
return EXIT_FAILURE;
}
}
-
- do
+
+ do
{
- if (fileread)
+ if (fileread)
{
inputfile.getline(newstr,9999); // maybe use > for delimiting character remove while increase size
- }
- else
+ }
+ else
{
if (fgets(newstr,9999,stdin)==NULL) break;
}
@@ -99,7 +102,7 @@ int fslcreatehd_main(int argc, char *argv[])
header=NiftiHeader(settings);
- if (fileread)
+ if (fileread)
inputfile.close();
}
@@ -117,7 +120,7 @@ int fslcreatehd_main(int argc, char *argv[])
fill(buffer,buffer+header.nElements(),0);
}
- int filetype=FslGetEnvOutputType();
+ int filetype=FslGetEnvOutputType();
if(!existingImage) {
filename=make_basename(filename)+outputExtension(filetype);
}
@@ -132,12 +135,10 @@ int fslcreatehd_main(int argc, char *argv[])
int main(int argc,char *argv[])
{
- if (argc != 14 && argc != 3)
+ if (argc != 14 && argc != 3)
{
print_usage(string(argv[0]));
- return 1;
+ return 1;
}
- return fslcreatehd_main(argc,argv);
+ return fslcreatehd_main(argc,argv);
}
-
-
--
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