Convert image to nii with mipav

ResaveVolume.java

package mipavProject;

import java.io.File;
import java.io.IOException;

import gov.nih.mipav.model.file.FileIO;
import gov.nih.mipav.model.file.FileNIFTI;
import gov.nih.mipav.model.file.FileUtility;
import gov.nih.mipav.model.file.FileWriteOptions;
import gov.nih.mipav.model.structures.ModelImage;
import gov.nih.mipav.view.ViewUserInterface;

public class ResaveVolume
{
	public static void main( String[] args ) throws IOException
	{
		String in = args[ 0 ];
		String out = args[ 1 ];
		
		File inF = new File( in );
		String imgDir = inF.getParent();
		
		File outF = new File( out );
		String outDir = outF.getParent();
		String outName = outF.getName();
		
		if( !imgDir.endsWith( File.separator ))
			imgDir = imgDir + File.separator;
		
		if( !outDir.endsWith( File.separator ))
			outDir = outDir + File.separator;
		

		ViewUserInterface vui = ViewUserInterface.create();
		vui.setDefaultDirectory( imgDir );
		
		FileIO fio = new FileIO();
		fio.setQuiet( true );
		
		
		System.out.println("reading: " + in );
		ModelImage img = fio.readImage( in );
		System.out.println( img );
		
		System.out.println("writing");
		FileWriteOptions opts = new FileWriteOptions( outName, outDir, true );
		opts.setFileType( FileUtility.NIFTI );
		opts.setNIFTIExtension( ".nii" );
		opts.setBeginSlice( 0 );
		opts.setEndSlice( img.getExtents()[ 2 ] - 1 ); // subtract one since EndSlice seems to be inclusive
		opts.setMultiFile( false );

		FileNIFTI niif = new FileNIFTI( outName, outDir );
		niif.writeImage( img, opts );
		
		System.out.println("done");
		System.exit( 0 );
	}
}