/// <summary>
/// Uses the ANTS implementation of the N4 bias correction algorithm to correct the given file.
/// </summary>
/// <param name="inputFile">Path to input nifti file.</param>
/// <param name="updates">Event handler for updates from the process</param>
/// <returns>Path for output nifti file.</returns>
public static string AntsN4(string inputFile, DataReceivedEventHandler updates = null)
{
string niftiInPath = Path.GetFullPath(inputFile);
string niftiOutPath = Path.GetFullPath(inputFile + ".antsN4.out.nii");
var args = $"-i \"{niftiInPath}\" -o \"{niftiOutPath}\"";
Log.GetLogger().Info(" --Starting AntsN4..");
ProcessBuilder.CallExecutableFile(CapiConfig.GetConfig().Binaries.N4BiasFieldCorrection, args, outputDataReceived: updates, errorOccuredInProcess: updates);
return(niftiOutPath);
}
public static void ConvertBmpToDicom(string bmpFilepath, string dicomFilePath, string dicomHeadersFilePath = "")
{
var arguments = string.Empty;
if (!string.IsNullOrEmpty(dicomHeadersFilePath))
{
arguments = $"-df \"{dicomHeadersFilePath}\" "; // Copy dicom headers from dicom file: -df = dataset file
}
arguments += $"-i BMP \"{bmpFilepath}\" \"{dicomFilePath}\"";
ProcessBuilder.CallExecutableFile(CapiConfig.GetConfig().Binaries.img2dcm, arguments);
}
/// <summary>
/// Uses the BrainSuite BSE tool to extract the brain from the given Nifti file path.
/// </summary>
/// <param name="inputFile">Path to .nii file which needs a brain extractin'</param>
/// <param name="updates">Event handler to accept progress updates from the tool.</param>
/// <returns>The path of the output file.</returns>
public static string BrainSuiteBSE(string inputFile, DataReceivedEventHandler updates = null)
{
string niftiInPath = Path.GetFullPath(inputFile);
string niftiOutPath = Path.GetFullPath(inputFile + ".bse.out.nii");
var args = $"--auto --trim -i \"{niftiInPath}\" -o \"{niftiOutPath}\"";
ProcessBuilder.CallExecutableFile(CapiConfig.GetConfig().Binaries.bse, args, outputDataReceived: updates);
return(niftiOutPath);
}
public static string CMTKResliceUsingPrevious(string floatingFile, string niftiRefPath, DataReceivedEventHandler updates = null)
{
Environment.SetEnvironmentVariable("CMTK_WRITE_UNCOMPRESSED", "1");
string niftiOutPath = floatingFile + ".cmtkrego.out.nii";
string regOutPath = "reg";
var args = $"-o \"{niftiOutPath}\" --floating \"{floatingFile}\" \"{niftiRefPath}\" \"{regOutPath}\"";
ProcessBuilder.CallExecutableFile(CapiConfig.GetConfig().Binaries.reformatx, args, outputDataReceived: updates);
return(niftiOutPath);
}
public static string ANTSApplyTransforms(string floatingFile, string referenceFile, DataReceivedEventHandler updates = null)
{
floatingFile = Path.GetFullPath(floatingFile);
referenceFile = Path.GetFullPath(referenceFile);
string niftiOutPath = Path.Combine("warped.nii");
string args = $"-d 3 --float 1 -i \"{floatingFile}\" -r \"{referenceFile}\" -o \"{niftiOutPath}\" -n Linear -t \"{niftiOutPath}0GenericAffine.mat\"";
ProcessBuilder.CallExecutableFile(CapiConfig.GetConfig().Binaries.antsApplyTransforms, args, outputDataReceived: updates);
return(niftiOutPath);
}
/// <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);
}
public static string ANTSRegistration(string floatingFile, string fixedFile, DataReceivedEventHandler updates = null)
{
string niftiOutPath = floatingFile + "warped.nii";
// ANTS didn't like me splitting args into a nicely tabbed string so it's all one big line.
// --dimensionality 3 :: we have a 3-d image
// --float 1 :: we want to keep things floating point
// --interpolation Linear :: using linear interpolation for the warped image
// --use-histogram-matching 0 :: histogram matching is pre-normalisation (we're avoiding this in case we have hyper-intense fat on one and not the other)
// --initial-moving-transform [{fixedFile},{floatingFile}, 1] :: inputs
// --transform Rigid[0.1] :: using an rigid transform (6 degrees of freedom, linear)
// --metric MI[{fixedFile},{floatingFile},1,32,Regular,0.25] :: metric is mutual information, although we could use cross correlation so long as we're registering the same sequence type
// --convergence [1000x500x250x100,1e-6,10] :: convergence is the iterations at each level and the threashold for imporovement in the metric
// --shrink-factors 8x4x2x1 :: shrink factors control the resolution at each level
// --smoothing-sigmas 3x2x1x0vox :: not really sure what smoothing sigmas do but the values should be fine
// --output [_, {niftiOutPath}] :: output the transform value + our sweet nifti file.
var args = $" --dimensionality 3 --float 1 --interpolation Linear --use-histogram-matching 0 --initial-moving-transform [\"{fixedFile}\",\"{floatingFile}\", 1] --transform Affine[0.1] --metric MI[\"{fixedFile}\",\"{floatingFile}\",1,32,Regular,0.25] --convergence [1000x500x250x100,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox --output [\"{niftiOutPath}\", \"{niftiOutPath}\"]";
ProcessBuilder.CallExecutableFile(CapiConfig.GetConfig().Binaries.antsRegistration, args, outputDataReceived: updates);
return(niftiOutPath);
}
/// <summary>
/// Converts the given Dicom path to a nifti file which is loaded and returned as a nifti object.
/// </summary>
/// <param name="dicomPath">Path to the DICOM</param>
/// <param name="updates">Event handler to handle updates.</param>
/// <returns></returns>
public static string Dcm2Nii(string dicomPath, string name, DataReceivedEventHandler updates = null)
{
if (!FileSystem.DirectoryIsValidAndNotEmpty(dicomPath))
{
Log.GetLogger().Error("Directory " + dicomPath + " does not seem to exist, or is empty.");
return(null);
}
var niftiPath = Path.GetFullPath(Path.Combine(Path.GetDirectoryName(dicomPath), name));
var tmpDir = Path.GetFullPath(Path.Combine(Path.GetDirectoryName(niftiPath), "tmp"));
if (Directory.Exists(tmpDir))
{
Directory.Delete(tmpDir, true);
}
FileSystem.DirectoryExistsIfNotCreate(tmpDir);
var args = $" -o \"{tmpDir}\" \"{dicomPath}\"";
ProcessBuilder.CallExecutableFile(CapiConfig.GetConfig().Binaries.dcm2niix, args, outputDataReceived: updates);
if (!Directory.Exists(tmpDir))
{
throw new DirectoryNotFoundException("dcm2niix output folder does not exist!");
}
var outFiles = Directory.GetFiles(tmpDir);
// Rather than cracking a tanty when we have more than one nii in the stack, we're just going to use the biggest one.
// This is in case we have a reference slide at the front or end of the dicom stack, which can happen.
var nims = outFiles.Where(f => Path.GetExtension(f) == ".nii").OrderByDescending(f => new FileInfo(f)?.Length);
var nim = nims.FirstOrDefault();
if (nim == null)
{
if (!File.Exists(CapiConfig.GetConfig().Binaries.dcm2niix))
{
Log.GetLogger().Error("Could not find dcm2niix at: " + CapiConfig.GetConfig().Binaries.dcm2niix);
}
var log = Log.GetLogger();
log.Error("Could not find valid output for dcm2niix. Files output were: ");
foreach (var of in outFiles)
{
log.Error($"[{of}]");
}
throw new FileNotFoundException("Could not find output of dcm2niix");
}
if (File.Exists(niftiPath))
{
File.Delete(niftiPath);
}
File.Move(nim, niftiPath);
Directory.Delete(tmpDir, true);
return(niftiPath);
}
