From 54ee23e15891cf2adca20e27e2cb407eb8062249 Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Mon, 9 Nov 2009 13:29:10 +0000
Subject: [PATCH] 4D Timeseries mode for SS and MJ
---
fslstats.cc | 50 ++++++++++++++++++++++++++++++++------------------
1 file changed, 32 insertions(+), 18 deletions(-)
diff --git a/fslstats.cc b/fslstats.cc
index 92a96ef..7f43953 100644
--- a/fslstats.cc
+++ b/fslstats.cc
@@ -14,7 +14,8 @@
using namespace NEWIMAGE;
void print_usage(const string& progname) {
- cout << "Usage: fslstats <input> [options]" << endl << endl;
+ cout << "Usage: fslstats [-t] <input> [options]" << endl << endl;
+ cout << "-t will give a separate output line for each 3D volume of a 4D timeseries" << endl;
cout << "Note - options are applied in order, e.g. -M -l 10 -M will report the non-zero mean, apply a threshold and then report the new nonzero mean" << endl << endl;
cout << "-l <lthresh> : set lower threshold" << endl;
cout << "-u <uthresh> : set upper threshold" << endl;
@@ -120,31 +121,38 @@ int generateNonZeroMask(const volume4D<float> &mask, volume4D<float> &masknz, co
return 0;
}
-int generate_masks(volume4D<float> &mask, volume4D<float> &masknz, const volume4D<float> &input,float& lthr, float& uthr)
+int generate_masks(volume4D<float>& mask, volume4D<float>& masknz, const volume4D<float>& input, const float& lthr, const float& uthr)
{
mask = binarise(input,lthr,uthr,exclusive);
return generateNonZeroMask(mask,masknz,input);
}
-int fmrib_main_float(int argc, char* argv[])
+int fmrib_main_float(int argc, char* argv[],const bool timeseriesMode)
{
-
cout.setf(ios::dec);
cout.setf(ios::fixed, ios::floatfield);
cout.setf(ios::left, ios::adjustfield);
cout.precision(6);
- volume4D<float> vol, mask, masknz;
- read_volume4D(vol,argv[1]);
-
- float lthr(vol.min()-1);
- float uthr=(vol.max()+1);
+ int nTimepoints(1);
+ volume4D<float> vol, inputMaster;
+ if ( timeseriesMode) {
+ read_volume4D(inputMaster,argv[1]);
+ nTimepoints=inputMaster.tsize();
+ } else
+ read_volume4D(vol,argv[1]);
- int narg=2;
- string sarg;
+ for ( int timepoint=0; timepoint < nTimepoints ; timepoint++ )
+ {
+ if ( timeseriesMode )
+ vol=inputMaster[timepoint];
+ volume4D<float> mask, masknz;
+ float lthr(vol.min()-1);
+ float uthr=(vol.max()+1);
+ int narg(2);
while (narg<argc) {
- sarg=argv[narg];
+ string sarg(argv[narg]);
if (sarg=="-n") {
for (int t=vol.mint(); t<=vol.maxt(); t++)
for (int z=vol.minz(); z<=vol.maxz(); z++)
@@ -461,8 +469,8 @@ int fmrib_main_float(int argc, char* argv[])
narg++;
}
-
cout << endl;
+ }
return 0;
}
@@ -472,16 +480,22 @@ int main(int argc,char *argv[])
{
Tracer tr("main");
-
- int retval;
+ string progname(argv[0]);
+ int retval(-1);
+ bool timeseriesMode(false);
+ if ( argc > 2 && string(argv[1])=="-t" ) {
+ argv++;
+ argc--;
+ timeseriesMode=true;
+ }
+
try {
- string progname=argv[0];
- if (argc<3) {
+ if (argc < 3 ) {
print_usage(progname);
return 1;
}
- retval = fmrib_main_float(argc,argv);
+ retval = fmrib_main_float(argc,argv,timeseriesMode);
} catch(std::exception &e) {
cerr << e.what() << endl;
} catch (...) {
--
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