From 148f2211d51fd5f25082a44a3fdc6c5503b456ac Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Mon, 3 Sep 2018 13:46:04 +0000
Subject: [PATCH] wrong value for default\!
---
fslmerge.cc | 54 ++++++++++++++++++++++++++---------------------------
1 file changed, 26 insertions(+), 28 deletions(-)
diff --git a/fslmerge.cc b/fslmerge.cc
index 2099f54..b7214a3 100755
--- a/fslmerge.cc
+++ b/fslmerge.cc
@@ -1,13 +1,13 @@
// fslmerge.cc concatenate AVW files into a single output
// Steve Smith, David Flitney, Stuart Clare and Matthew Webster, FMRIB Image Analysis Group
-// Copyright (C) 2000-2010 University of Oxford
-// CCOPYRIGHT
+// Copyright (C) 2000-2010 University of Oxford
+// CCOPYRIGHT
#define EXPOSE_TREACHEROUS
#include "newimage/newimageall.h"
#include "newimage/fmribmain.h"
using namespace NEWIMAGE;
-void print_usage(const string& progname)
+void print_usage(const string& progname)
{
cout << endl;
cout << "Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds]" << endl;
@@ -27,18 +27,18 @@ int fmrib_main(int argc, char *argv[])
NiftiIO reader;
NiftiHeader header(reader.loadHeader(return_validimagefilename(string(argv[3]))));
- float newTR(header.pixdim[3]);
-
+ float newTR(header.pixdim[4]);
+
if (!strcmp(argv[1], "-t")) direction=0;
else if (!strcmp(argv[1], "-x")) direction=1;
else if (!strcmp(argv[1], "-y")) direction=2;
- else if (!strcmp(argv[1], "-z")) direction=3;
+ else if (!strcmp(argv[1], "-z")) direction=3;
else if (!strcmp(argv[1], "-a")) direction=4;
else if (!strcmp(argv[1], "-tr")) {
direction=0;
newTR=atof(argv[--argc]);
}
- else
+ else
{
print_usage(string(argv[0]));
return(1);
@@ -53,27 +53,27 @@ int fmrib_main(int argc, char *argv[])
}
for(int vol = 4; vol < argc; vol++)
- {
+ {
header=reader.loadHeader(return_validimagefilename(string(argv[vol])));
if (direction==0) tdimtot+=header.dim[4];
- if (direction==1) xdimtot+=header.dim[1];
+ if (direction==1) xdimtot+=header.dim[1];
if (direction==2) ydimtot+=header.dim[2];
if (direction==3) zdimtot+=header.dim[3];
}
volume4D<T> output_volume(xdimtot,ydimtot,zdimtot,tdimtot);
- read_volume4D(input_volume,string(argv[3]));
+ read_volume4D(input_volume,string(argv[3]));
output_volume.copyproperties(input_volume);
for(int vol = 3; vol < argc; vol++)
- {
+ {
if (vol>3) {
- read_volume4D(input_volume,string(argv[vol]));
+ read_volume4D(input_volume,string(argv[vol]));
// sanity check on valid orientation info (it should be consistent)
if ((output_volume.sform_code()!=NIFTI_XFORM_UNKNOWN) || (output_volume.qform_code()!=NIFTI_XFORM_UNKNOWN)) {
if ((input_volume.sform_code()!=NIFTI_XFORM_UNKNOWN) || (input_volume.qform_code()!=NIFTI_XFORM_UNKNOWN)) {
float rms = rms_deviation(output_volume.newimagevox2mm_mat(),input_volume.newimagevox2mm_mat());
if ( rms > 0.5 && direction == 0 ) { // arbitrary 0.5mm rms diff threshold - maybe too sensitive?
- cerr << endl << "WARNING:: Inconsistent orientations for individual images when attempting to merge." <<endl;
+ cerr << endl << "WARNING:: Inconsistent orientations for individual images when attempting to merge." <<endl;
cerr <<" Merge will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!" <<endl<<endl;
}
}
@@ -81,24 +81,24 @@ int fmrib_main(int argc, char *argv[])
}
if (direction == 0 && (input_volume.xsize() != xdimtot || input_volume.ysize() != ydimtot || input_volume.zsize() != zdimtot)) dimerror=1;
if (direction == 1 && (input_volume.ysize() != ydimtot || input_volume.zsize() != zdimtot || input_volume.tsize() != tdimtot)) dimerror=1;
- if (direction == 2 && (input_volume.xsize() != xdimtot || input_volume.zsize() != zdimtot || input_volume.tsize() != tdimtot)) dimerror=1;
+ if (direction == 2 && (input_volume.xsize() != xdimtot || input_volume.zsize() != zdimtot || input_volume.tsize() != tdimtot)) dimerror=1;
if (direction == 3 && (input_volume.xsize() != xdimtot || input_volume.ysize() != ydimtot || input_volume.tsize() != tdimtot)) dimerror=1;
if (dimerror)
{
- cerr << "Error in size-match along non-concatenated dimension for input file: " << string(argv[vol]) << endl;
+ cerr << "Error in size-match along non-concatenated dimension for input file: " << string(argv[vol]) << endl;
return 1;
}
-
- for(int t=0;t<input_volume.tsize();t++)
+
+ for(int t=0;t<input_volume.tsize();t++)
for(int k=0;k<input_volume.zsize();k++)
- for(int j=0;j<input_volume.ysize();j++)
+ for(int j=0;j<input_volume.ysize();j++)
for(int i=0;i<input_volume.xsize();i++)
output_volume.value(i+xoffset,j+yoffset,k+zoffset,t+toffset)=input_volume.value(i,j,k,t);
- if (direction==0) toffset+=input_volume.tsize();
- if (direction==1) xoffset+=input_volume.xsize();
- if (direction==2) yoffset+=input_volume.ysize();
- if (direction==3) zoffset+=input_volume.zsize();
+ if (direction==0) toffset+=input_volume.tsize();
+ if (direction==1) xoffset+=input_volume.xsize();
+ if (direction==2) yoffset+=input_volume.ysize();
+ if (direction==3) zoffset+=input_volume.zsize();
}
output_volume.setTR(newTR);
save_volume4D(output_volume,string(argv[2]));
@@ -108,12 +108,10 @@ int fmrib_main(int argc, char *argv[])
int main(int argc,char *argv[])
{
- if (argc < 4)
- {
+ if (argc < 4)
+ {
print_usage(string(argv[0]));
- return 1;
+ return 1;
}
- return call_fmrib_main(dtype(string(argv[3])),argc,argv);
+ return call_fmrib_main(dtype(string(argv[3])),argc,argv);
}
-
-
--
GitLab