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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2013 SRI International
//
// This file is part of the Computational Morphometry Toolkit.
//
// http://www.nitrc.org/projects/cmtk/
//
// The Computational Morphometry Toolkit is free software: you can
// redistribute it and/or modify it under the terms of the GNU General Public
// License as published by the Free Software Foundation, either version 3 of
// the License, or (at your option) any later version.
//
// The Computational Morphometry Toolkit is distributed in the hope that it
// will be useful, but WITHOUT ANY WARRANTY; without even the implied
// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License along
// with the Computational Morphometry Toolkit. If not, see
// <http://www.gnu.org/licenses/>.
//
// $Revision: 326 $
//
// $LastChangedDate: 2009-07-29 15:08:42 -0700 (Wed, 29 Jul 2009) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#include <cmtkconfig.h>
#include <System/cmtkCommandLine.h>
#include <System/cmtkExitException.h>
#include <System/cmtkConsole.h>
#include <System/cmtkProgressConsole.h>
#include <IO/cmtkVolumeIO.h>
#include <Segmentation/cmtkAtlasSegmentation.h>
#include <list>
#include <string>
int
doMain( const int argc, const char* argv[] )
{
bool fast = false;
std::string targetImageName;
std::string outImageName;
std::string channelSRI24( "spgr" );
std::string labelsSRI24( "tzo116plus" );
try
{
cmtk::CommandLine cl( cmtk::CommandLine::PROPS_XML );
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Segmentation using SRI24 atlas" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "Register a target image to a selected channel of the SRI24 human brain atlas, then reformat one of the atlas label maps to the target image. "
"Note: it is assume that the target image is skull-stripped, i.e., contains only the brain." );
cl.SetProgramInfo( cmtk::CommandLine::PRG_CATEG, "CMTK.Segmentation" );
typedef cmtk::CommandLine::Key Key;
cl.AddSwitch( Key( 'f', "fast" ), &fast, true, "Fast mode." );
cmtk::CommandLine::EnumGroup<std::string>::SmartPtr channelGroup =
cl.AddEnum( "registration-channel", &channelSRI24, "The SRI24 channel used for registration to the target image." );
channelGroup->AddSwitch( Key( "spgr" ), "spgr", "SPGR (T1-weighted) structural channel" );
channelGroup->AddSwitch( Key( "early-fse" ), "erly", "Early-echo (PD-weighted) fast spin echo channel" );
channelGroup->AddSwitch( Key( "late-fse" ), "late", "Late-echo (T2-weighted) fast spin echo channel" );
channelGroup->AddSwitch( Key( "fa" ), "fa", "Fractional anisotropy channel, derived from diffusion tensor images" );
cmtk::CommandLine::EnumGroup<std::string>::SmartPtr labelsGroup =
cl.AddEnum( "label-map", &labelsSRI24, "The SRI24 label map that is reformatted to the target image." );
labelsGroup->AddSwitch( Key( "tzo116plus" ), "tzo116plus", "Extended cortical parcellation template based on Tzourio-Mazoyer AAL 116 region template." );
labelsGroup->AddSwitch( Key( "lpba40" ), "lpba40", "Template based on the 40 subject LONI Probabilistic Brain Atlas segmentation." );
labelsGroup->AddSwitch( Key( "tissue" ), "tissue", "SRI24 maximum likelihood three compartment (GM, WM, CSF) tissue segmentation map." );
cl.AddParameter( &targetImageName, "TargetImage", "Target image path. This is the image to be segmented." )
->SetProperties( cmtk::CommandLine::PROPS_IMAGE );
cl.AddParameter( &outImageName, "OutputImage", "Output image path. This is where the reformatted label map is written." )
->SetProperties( cmtk::CommandLine::PROPS_IMAGE | cmtk::CommandLine::PROPS_LABELS | cmtk::CommandLine::PROPS_OUTPUT );
cl.Parse( argc, argv );
}
catch ( const cmtk::CommandLine::Exception& e )
{
cmtk::StdErr << e << "\n";
throw cmtk::ExitException( 1 );
}
// Instantiate programm progress indicator.
cmtk::ProgressConsole progressIndicator( "Segmentation Using the SRI24 Atlas" );
cmtk::UniformVolume::SmartPtr targetImg( cmtk::VolumeIO::ReadOriented( targetImageName ) );
if ( !targetImg )
{
cmtk::StdErr << "ERROR: could not read target image " << targetImageName << "\n";
throw cmtk::ExitException( 1 );
}
std::string atlasImageName = std::string( CMTK_ROOT_PATH_SRI24 ) + "/" + channelSRI24 + ".nii";
cmtk::UniformVolume::SmartPtr atlasImg( cmtk::VolumeIO::ReadOriented( atlasImageName ) );
if ( !atlasImg )
{
cmtk::StdErr << "ERROR: could not read atlas image " << atlasImageName << "\n";
throw cmtk::ExitException( 1 );
}
std::string atlasLabelName = std::string( CMTK_ROOT_PATH_SRI24 ) + "/" + labelsSRI24 + ".nii";
cmtk::UniformVolume::SmartPtr atlasLbl( cmtk::VolumeIO::ReadOriented( atlasLabelName ) );
if ( !atlasLbl )
{
cmtk::StdErr << "ERROR: could not read atlas labels " << atlasLabelName << "\n";
throw cmtk::ExitException( 1 );
}
cmtk::AtlasSegmentation segment( targetImg, atlasImg, atlasLbl );
segment.SetFast( fast );
cmtk::VolumeIO::Write( *(segment.GetLabelMap()), outImageName );
return 0;
}
#include "cmtkSafeMain"
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