public static INifti <float> ANTSRegistration(INifti <float> floating, INifti <float> reference, DataReceivedEventHandler updates = null)
{
// Setup our temp file names.
string niftiInPath = Path.GetFullPath(Tools.TEMPDIR + floating.GetHashCode() + ".antsrego.in.nii");
string niftiRefPath = Path.GetFullPath(Tools.TEMPDIR + floating.GetHashCode() + ".antsrego.ref.nii");
floating.WriteNifti(niftiInPath);
reference.WriteNifti(niftiRefPath);
string niftiOutPath = Path.GetFullPath(ANTSRegistration(niftiInPath, niftiRefPath, updates));
var output = floating.DeepCopy();
output = output.ReadNifti(niftiOutPath);
return(output);
}
/// <summary>
/// Uses the CMTK registration and reformatx tools to register and reslice the floating nifti to match the reference nifti.
/// </summary>
/// <param name="floating">Nifti to be registered</param>
/// <param name="reference">Reference nifti</param>
/// <param name="updates">Event handler for updates from the toolchain...</param>
/// <returns></returns>
public static INifti <float> CMTKRegistration(INifti <float> floating, INifti <float> reference, DataReceivedEventHandler updates = null)
{
// Setup our temp file names.
string niftiInPath = Tools.TEMPDIR + floating.GetHashCode() + ".cmtkrego.in.nii";
string niftiRefPath = Tools.TEMPDIR + floating.GetHashCode() + ".cmtkrego.ref.nii";
string niftiOutPath = Tools.TEMPDIR + floating.GetHashCode() + ".cmtkrego.out.nii";
// Write nifti to temp directory.
floating.WriteNifti(niftiInPath);
reference.WriteNifti(niftiRefPath);
niftiOutPath = CMTKRegistration(niftiInPath, niftiRefPath, updates);
//INifti output = floating.DeepCopy();
floating.ReadNifti(niftiOutPath);
return(floating);
}
/// <summary>
/// Uses the BrainSuite BSE tool to extract the brain from a given INifti.
/// </summary>
/// <param name="input">Nifti which contains the brain to be extracted</param>
/// <param name="updates">Data handler for updates from the BSE tool.</param>
/// <returns>The INifti containing the extracted brain.</returns>
public static INifti <float> BrainSuiteBSE(INifti <float> input, DataReceivedEventHandler updates = null)
{
// Setup our temp file names.
string niftiInPath = Path.GetFullPath(Tools.TEMPDIR + input.GetHashCode() + ".bse.in.nii");
string niftiOutPath = Path.GetFullPath(Tools.TEMPDIR + input.GetHashCode() + ".bse.out.nii");
// Write nifti to temp directory.
input.WriteNifti(niftiInPath);
var args = $"--auto --trim -i \"{niftiInPath}\" -o \"{niftiOutPath}\"";
ProcessBuilder.CallExecutableFile(CapiConfig.GetConfig().Binaries.bse, args, outputDataReceived: updates);
var output = input.DeepCopy(); // Sometimes this messes with the header and gives us a 4-up???
output.ReadNifti(niftiOutPath);
return(output);
}
/// <summary>
/// Uses the ANTS implementation of the N4 bias correction algorithm.
/// </summary>
/// <param name="input">The input nifti to be corrected</param>
/// <param name="updates">Event handler for updates from the process</param>
/// <returns>New, corrected nifti</returns>
public static INifti <float> AntsN4(INifti <float> input, DataReceivedEventHandler updates = null)
{
// Setup our temp file names.
string niftiInPath = Path.GetFullPath(Tools.TEMPDIR + input.GetHashCode() + ".antsN4.in.nii");
string niftiOutPath = Path.GetFullPath(Tools.TEMPDIR + input.GetHashCode() + ".antsN4.out.nii");
// Write nifti to temp directory.
input.WriteNifti(niftiInPath);
var args = $"-i \"{niftiInPath}\" -o \"{niftiOutPath}\"";
ProcessBuilder.CallExecutableFile(CapiConfig.GetConfig().Binaries.N4BiasFieldCorrection, args, outputDataReceived: updates);
var output = input.DeepCopy();
output.ReadNifti(niftiOutPath);
output.RecalcHeaderMinMax();
return(output);
}