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Commit b5303651 authored by Stephen Smith's avatar Stephen Smith
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*** empty log message ***

parent 480a0d9b
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...@@ -107,9 +107,6 @@ void FilmGlsOptions::parse_command_line(int argc, char** argv, Log& logger) ...@@ -107,9 +107,6 @@ void FilmGlsOptions::parse_command_line(int argc, char** argv, Log& logger)
if ( arg == "-ms") { if ( arg == "-ms") {
gopt->ms = atoi(argv[n+1]); gopt->ms = atoi(argv[n+1]);
n+=2; n+=2;
} else if ( arg == "-sp" ) {
gopt->susanpath = argv[n+1];
n+=2;
} else if ( arg == "-rn" ) { } else if ( arg == "-rn" ) {
gopt->datadir = argv[n+1]; gopt->datadir = argv[n+1];
n+=2; n+=2;
...@@ -154,7 +151,6 @@ void FilmGlsOptions::print_usage(int argc, char *argv[]) ...@@ -154,7 +151,6 @@ void FilmGlsOptions::print_usage(int argc, char *argv[])
cout << "Usage: " << argv[0] << " [options] <groupfile> [optional:<paradigmfile>] <thresh>\n\n" cout << "Usage: " << argv[0] << " [options] <groupfile> [optional:<paradigmfile>] <thresh>\n\n"
<< " Available options are:\n" << " Available options are:\n"
<< " -sa (smooths auto corr estimates)\n" << " -sa (smooths auto corr estimates)\n"
<< " -sp <path> (susan path)\n"
<< " -ms <num> (susan mask size)\n" << " -ms <num> (susan mask size)\n"
<< " -epith <num> (set susan brightness threshold - otherwise it is estimated)\n" << " -epith <num> (set susan brightness threshold - otherwise it is estimated)\n"
<< " -v (outputs full data)\n" << " -v (outputs full data)\n"
......
...@@ -30,7 +30,6 @@ class FilmGlsOptions { ...@@ -30,7 +30,6 @@ class FilmGlsOptions {
string paradigmfname; string paradigmfname;
string epifname; string epifname;
string datadir; string datadir;
string susanpath;
string neffsfname; string neffsfname;
...@@ -79,7 +78,6 @@ inline FilmGlsOptions::FilmGlsOptions() ...@@ -79,7 +78,6 @@ inline FilmGlsOptions::FilmGlsOptions()
// set up defaults // set up defaults
neffsfname = "neffs"; neffsfname = "neffs";
datadir = "results"; datadir = "results";
susanpath = "/usr/local/fsl/bin/susan_smooth";
epifname = "epivolume"; epifname = "epivolume";
thresh = 0; thresh = 0;
inputfname = ""; inputfname = "";
......
...@@ -120,10 +120,6 @@ void FilmGlsOptionsRes::parse_command_line(int argc, char** argv, ofstream& logf ...@@ -120,10 +120,6 @@ void FilmGlsOptionsRes::parse_command_line(int argc, char** argv, ofstream& logf
gopt->ms = atoi(argv[n+1]); gopt->ms = atoi(argv[n+1]);
logfile << argv[n+1] << " "; logfile << argv[n+1] << " ";
n+=2; n+=2;
} else if ( arg == "-sp" ) {
gopt->susanpath = argv[n+1];
logfile << argv[n+1] << " ";
n+=2;
} else if ( arg == "-iters") { } else if ( arg == "-iters") {
gopt->numiters = atoi(argv[n+1]); gopt->numiters = atoi(argv[n+1]);
logfile << argv[n+1] << " "; logfile << argv[n+1] << " ";
......
...@@ -28,7 +28,6 @@ class FilmGlsOptionsRes { ...@@ -28,7 +28,6 @@ class FilmGlsOptionsRes {
string contrastfname; string contrastfname;
string epifname; string epifname;
string datadir; string datadir;
string susanpath;
string neffsfname; string neffsfname;
string zscoresfname; string zscoresfname;
...@@ -84,7 +83,6 @@ inline FilmGlsOptionsRes::FilmGlsOptionsRes() ...@@ -84,7 +83,6 @@ inline FilmGlsOptionsRes::FilmGlsOptionsRes()
zscoresfname = "zstats"; zscoresfname = "zstats";
neffsfname = "neffs"; neffsfname = "neffs";
datadir = "results"; datadir = "results";
susanpath = "/usr/local/fsl/bin/susan_smooth";
epifname = "epivolume"; epifname = "epivolume";
thresh = 0; thresh = 0;
contrastfname = ""; contrastfname = "";
......
...@@ -105,10 +105,6 @@ void FilmOlsOptions::parse_command_line(int argc, char** argv, ofstream& logfile ...@@ -105,10 +105,6 @@ void FilmOlsOptions::parse_command_line(int argc, char** argv, ofstream& logfile
gopt->ms = atoi(argv[n+1]); gopt->ms = atoi(argv[n+1]);
logfile << argv[n+1] << " "; logfile << argv[n+1] << " ";
n+=2; n+=2;
} else if ( arg == "-sp" ) {
gopt->susanpath = argv[n+1];
logfile << argv[n+1] << " ";
n+=2;
} else if ( arg == "-rn" ) { } else if ( arg == "-rn" ) {
gopt->datadir = argv[n+1]; gopt->datadir = argv[n+1];
logfile << argv[n+1] << " "; logfile << argv[n+1] << " ";
...@@ -150,8 +146,6 @@ void FilmOlsOptions::print_usage(int argc, char *argv[]) ...@@ -150,8 +146,6 @@ void FilmOlsOptions::print_usage(int argc, char *argv[])
<< " -det (detrend data as preprocessing step)\n" << " -det (detrend data as preprocessing step)\n"
<< " -rn <dir> (directory name to store results in, default is " << " -rn <dir> (directory name to store results in, default is "
<< gopt->datadir << ")\n" << gopt->datadir << ")\n"
<< " -sp <path> (path for SUSAN executable, default is "
<< gopt->susanpath << ")\n"
<< " -help\n\n"; << " -help\n\n";
} }
......
...@@ -27,7 +27,6 @@ class FilmOlsOptions { ...@@ -27,7 +27,6 @@ class FilmOlsOptions {
string paradigmfname; string paradigmfname;
string datadir; string datadir;
string epifname; string epifname;
string susanpath;
bool verbose; bool verbose;
bool detrend; bool detrend;
...@@ -71,7 +70,6 @@ inline FilmOlsOptions::FilmOlsOptions() ...@@ -71,7 +70,6 @@ inline FilmOlsOptions::FilmOlsOptions()
epifname = "epivolume"; epifname = "epivolume";
inputfname = ""; inputfname = "";
paradigmfname = ""; paradigmfname = "";
susanpath = "/usr/local/fsl/bin/susan_smooth";
thresh = 0; thresh = 0;
ms = 4; ms = 4;
......
...@@ -143,7 +143,7 @@ int main(int argc, char *argv[]) ...@@ -143,7 +143,7 @@ int main(int argc, char *argv[])
// Smooth raw estimates: // Smooth raw estimates:
if(globalopts.smoothACEst) if(globalopts.smoothACEst)
{ {
acEst.spatiallySmooth(logger.getDir() + "/" + globalopts.epifname, epivol, globalopts.ms, globalopts.epifname, globalopts.susanpath, globalopts.epith); acEst.spatiallySmooth(logger.getDir() + "/" + globalopts.epifname, epivol, globalopts.ms, globalopts.epifname, globalopts.epith);
} }
if(globalopts.tukeysize == 0) if(globalopts.tukeysize == 0)
globalopts.tukeysize = (int)(2*sqrt(sizeTS))/2; globalopts.tukeysize = (int)(2*sqrt(sizeTS))/2;
...@@ -159,7 +159,7 @@ int main(int argc, char *argv[]) ...@@ -159,7 +159,7 @@ int main(int argc, char *argv[])
// Smooth raw estimates: // Smooth raw estimates:
if(globalopts.smoothACEst) if(globalopts.smoothACEst)
{ {
acEst.spatiallySmooth(logger.getDir() + "/" + globalopts.epifname, epivol, globalopts.ms, globalopts.epifname, globalopts.susanpath, globalopts.epith); acEst.spatiallySmooth(logger.getDir() + "/" + globalopts.epifname, epivol, globalopts.ms, globalopts.epifname, globalopts.epith);
} }
acEst.pava(); acEst.pava();
......
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