int main(int argc, char **argv)
{
std::cout << "/-------------------------------/" << std::endl;
std::cout << "| Subtool |" << std::endl;
std::cout << "/-------------------------------/" << std::endl;
BrainIO *brainio = new BrainIO();
/*--- Init ---*/
std::cout << "\t-------------------------------" << std::endl;
std::cout << "\t Init " << std::endl;
std::cout << "\t-------------------------------" << std::endl;
// We check the input parameters
FileNameType baselineFolderName, baselineImagesFolderName, baselineTransformsFolderName, baselineSegmentationFolderName;
FileNameType followupFolderName, followupImagesFolderName, followupTransformsFolderName, followupSegmentationFolderName;
FileNameType subtractionFolderName;
switch (argc) {
case 3:
baselineFolderName = argv[1];
followupFolderName = argv[2];
baselineImagesFolderName = baselineFolderName + "preprocessed/";
followupImagesFolderName = followupFolderName + "preprocessed/";
baselineTransformsFolderName = baselineFolderName + "transforms/";
followupTransformsFolderName = followupFolderName + "transforms/";
baselineSegmentationFolderName = baselineFolderName + "segmentation/";
followupSegmentationFolderName = followupFolderName + "segmentation/";
subtractionFolderName = followupFolderName + "subtraction/";
break;
case 4:
baselineFolderName = argv[1];
followupFolderName = argv[2];
baselineImagesFolderName = baselineFolderName + argv[3];
followupImagesFolderName = followupFolderName + argv[3];
baselineTransformsFolderName = baselineFolderName + "transforms/";
followupTransformsFolderName = followupFolderName + "transforms/";
baselineSegmentationFolderName = baselineFolderName + "segmentation/";
followupSegmentationFolderName = followupFolderName + "segmentation/";
subtractionFolderName = followupFolderName + "subtraction/";
break;
case 5:
baselineFolderName = argv[1];
followupFolderName = argv[2];
baselineImagesFolderName = baselineFolderName + argv[3];
followupImagesFolderName = followupFolderName + argv[3];
baselineTransformsFolderName = baselineFolderName + argv[4];
followupTransformsFolderName = followupFolderName + argv[4];
baselineSegmentationFolderName = baselineFolderName + "segmentation/";
followupSegmentationFolderName = followupFolderName + "segmentation/";
subtractionFolderName = followupFolderName + "subtraction/";
case 6:
baselineFolderName = argv[1];
followupFolderName = argv[2];
baselineImagesFolderName = baselineFolderName + argv[3];
followupImagesFolderName = followupFolderName + argv[3];
baselineTransformsFolderName = baselineFolderName + argv[4];
followupTransformsFolderName = followupFolderName + argv[4];
baselineSegmentationFolderName = baselineFolderName + argv[5];
followupSegmentationFolderName = followupFolderName + argv[5];
subtractionFolderName = followupFolderName + "subtraction/";
case 7:
baselineFolderName = argv[1];
followupFolderName = argv[2];
baselineImagesFolderName = baselineFolderName + argv[3];
followupImagesFolderName = followupFolderName + argv[3];
baselineTransformsFolderName = baselineFolderName + argv[4];
followupTransformsFolderName = followupFolderName + argv[4];
baselineSegmentationFolderName = baselineFolderName + argv[5];
followupSegmentationFolderName = followupFolderName + argv[5];
subtractionFolderName = followupFolderName + argv[6];
default:
std::cerr << "Incorrect number of parameters." << std::endl << "Correct usage: SubtractionTool baseline_folder followup_folder [images_folder] [transforms_folder] [segmentation_folder] [subtraction_folder]" << std::endl;
return EXIT_FAILURE;
break;
}
#ifdef WIN32
CreateDirectory(subtractionFolderName.c_str(),NULL);
#else
mkdir(subtractionFolderName.c_str(), 0777);
#endif
/*--- Image reading ---*/
std::cout << "\t-------------------------------" << std::endl;
std::cout << "\t Image reading " << std::endl;
std::cout << "\t-------------------------------" << std::endl;
//------> PD
//-- Baseline
FileNameType pdBaselineName = baselineImagesFolderName + "pd_corrected_matched.nii.gz";
ProbabilityImage pdBaseline = brainio->ReadProbabilityImage(pdBaselineName);
//-- FollowUp
FileNameType pdFollowupName = followupImagesFolderName + "pd_corrected.nii.gz";
ProbabilityImage pdFollowup = brainio->ReadProbabilityImage(pdFollowupName);
//------> T2
//-- Baseline
FileNameType t2BaselineName = baselineImagesFolderName + "t2_corrected_matched.nii.gz";
ProbabilityImage t2Baseline = brainio->ReadProbabilityImage(t2BaselineName);
//-- FollowUp
FileNameType t2FollowupName = followupImagesFolderName + "t2_corrected.nii.gz";
ProbabilityImage t2Followup = brainio->ReadProbabilityImage(t2FollowupName);
//------> FLAIR
//-- Baseline
FileNameType flairBaselineName = baselineImagesFolderName + "flair_corrected_matched.nii.gz";
ProbabilityImage flairBaseline = brainio->ReadProbabilityImage(flairBaselineName);
FileNameType flairBaselineTransformName = baselineTransformsFolderName + "affineFLAIRtoSpace.tfm";
AffineTransform flairBaselineAffine;
if (pdBaseline != (ProbabilityImage)NULL)
flairBaselineAffine = brainio->ReadAffineTransform(flairBaselineTransformName);
//-- FollowUp
FileNameType flairFollowupName = followupImagesFolderName + "flair_corrected.nii.gz";
ProbabilityImage flairFollowup = brainio->ReadProbabilityImage(flairFollowupName);
FileNameType flairFollowupTransformName = followupTransformsFolderName + "affineFLAIRtoSpace.tfm";
if (pdFollowup != (ProbabilityImage)NULL) {
AffineTransform flairFollowupAffine = brainio->ReadAffineTransform(flairFollowupTransformName);
flairFollowup = BrainRegistration::ResampleImage<AffineTransformType>(pdFollowup, flairFollowup, flairFollowupAffine);
}
//------> Segmentation files
//-- Baseline
MaskImage baselineWMMask = brainio->ReadMaskImage(baselineSegmentationFolderName + "wm_mask.nii.gz");
//-- FollowUp
MaskImage followupWMMask = brainio->ReadMaskImage(followupSegmentationFolderName + "wm_mask.nii.gz");
/*--- Registration + subtraction ---*/
std::cout << "\t-------------------------------" << std::endl;
std::cout << "\t Registration " << std::endl;
std::cout << "\t-------------------------------" << std::endl;
// We set the fixed and moving images we just preprocessed
std::cout << "\t/-- Affine registration" << std::endl;
FileNameType affineName = baselineTransformsFolderName + "baseline2followup.tfm";
AffineTransform affine = brainio->ReadAffineTransform(affineName);
if (affine == (AffineTransform)NULL) {
if ((pdFollowup != (ProbabilityImage)NULL) && (pdBaseline != (ProbabilityImage)NULL)) {
affine = BrainRegistration::AffineRegistration(pdFollowup, pdBaseline, 3000);
brainio->WriteAffineTransform(
baselineTransformsFolderName + "baseline2followup.tfm",
affine
);
} else if ((pdFollowup != (ProbabilityImage)NULL) && (flairBaseline != (ProbabilityImage)NULL)) {
affine = BrainRegistration::AffineRegistration(pdFollowup, flairBaseline, 3000);
brainio->WriteAffineTransform(
baselineTransformsFolderName + "baseline2followup.tfm",
affine
);
}
else {
std::cerr << "The aren't any images to perform subtraction" << std::endl;
return EXIT_FAILURE;
}
}
std::cout << "\t/-- Image resampling" << std::endl;
std::cout << "\t -- WM mask" << std::endl;
MaskImage baselineWMMaskMoved = BrainRegistration::ResampleImage<AffineTransformType>(followupWMMask, baselineWMMask, affine);
ProbabilityImage pdMoved;
if ((pdFollowup != (ProbabilityImage)NULL) && (pdBaseline != (ProbabilityImage)NULL)) {
pdMoved = BrainRegistration::ResampleImage<AffineTransformType>(pdFollowup, pdBaseline, affine);
brainio->WriteProbabilityImage(
followupImagesFolderName + "pd_moved.nii.gz",
pdMoved
);
}
std::cout << "\t -- T2" << std::endl;
ProbabilityImage t2Moved;
if (t2Baseline != (ProbabilityImage)NULL) {
t2Moved = BrainRegistration::ResampleImage<AffineTransformType>(pdFollowup, t2Baseline, affine);
brainio->WriteProbabilityImage(
followupImagesFolderName + "t2_moved.nii.gz",
t2Moved
);
}
std::cout << "\t -- FLAIR" << std::endl;
ProbabilityImage flairMoved;
if (flairBaseline != (ProbabilityImage)NULL) {
if ((pdBaseline != (ProbabilityImage)NULL) && (pdFollowup != (ProbabilityImage)NULL)) {
std::cout << "\t /-- PD in baseline and followup" << std::endl;
AffineTransform flairAffine = AffineTransformType::New();
affine->Compose(flairBaselineAffine, true);
flairMoved = BrainRegistration::ResampleImage<AffineTransformType>(pdFollowup, flairBaseline, affine);
brainio->WriteProbabilityImage(
followupImagesFolderName + "flair_moved.nii.gz",
flairMoved
);
}
else if (pdFollowup != (ProbabilityImage)NULL) {
std::cout << "\t /-- PD only in followup" << std::endl;
flairMoved = BrainRegistration::ResampleImage<AffineTransformType>(pdFollowup, flairBaseline, affine);
brainio->WriteProbabilityImage(
followupImagesFolderName + "flair_moved.nii.gz",
flairMoved
);
}
else {
std::cout << "\t /-- No PD" << std::endl;
flairMoved = BrainRegistration::ResampleImage<AffineTransformType>(flairFollowup, flairBaseline, affine);
brainio->WriteProbabilityImage(
followupImagesFolderName + "flair_moved.nii.gz",
flairMoved
);
}
}
// Final ROI
MaskImage wmMask = BrainSegmentation::Union(baselineWMMaskMoved, followupWMMask);
brainio->WriteMaskImage(
followupSegmentationFolderName + "union_wm_mask.nii.gz",
wmMask
);
// The last step is to apply the subtraction
std::cout << "\t/-- Subtractions" << std::endl;
ProbabilityImage subtractionPD = brainio->ReadProbabilityImage(subtractionFolderName + "pd_subtraction.nii.gz");
if ((subtractionPD == (ProbabilityImage)NULL) && (pdFollowup != (ProbabilityImage)NULL) && (pdMoved != (ProbabilityImage)NULL)) {
subtractionPD = BrainSegmentation::Subtraction(pdFollowup, pdMoved);
brainio->WriteProbabilityImage(
subtractionFolderName + "pd_subtraction.nii.gz",
subtractionPD
);
}
ProbabilityImage subtractionT2 = brainio->ReadProbabilityImage(subtractionFolderName + "t2_subtraction.nii.gz");
if ((subtractionT2 == (ProbabilityImage)NULL) && (t2Followup != (ProbabilityImage)NULL) && (t2Moved != (ProbabilityImage)NULL)) {
subtractionT2 = BrainSegmentation::Subtraction(t2Followup, t2Moved);
brainio->WriteProbabilityImage(
subtractionFolderName + "t2_subtraction.nii.gz",
subtractionT2
);
}
ProbabilityImage subtractionFLAIR = brainio->ReadProbabilityImage(subtractionFolderName + "flair_subtraction.nii.gz");
if ((subtractionFLAIR == (ProbabilityImage)NULL) && (flairFollowup != (ProbabilityImage)NULL) && (flairMoved != (ProbabilityImage)NULL)) {
subtractionFLAIR = BrainSegmentation::Subtraction(flairFollowup, flairMoved);
brainio->WriteProbabilityImage(
subtractionFolderName + "flair_subtraction.nii.gz",
subtractionFLAIR
);
}
// Masking with brainmask
ProbabilityImage maskedSubtractionPD = brainio->ReadProbabilityImage(subtractionFolderName + "pd_masked_subtraction.nii.gz");
if ((maskedSubtractionPD == (ProbabilityImage)NULL) && (subtractionPD != (ProbabilityImage)NULL)) {
maskedSubtractionPD = BrainPreprocessing<ProbabilityImageType>::MaskImage(subtractionPD, wmMask);
brainio->WriteProbabilityImage(
subtractionFolderName + "pd_masked_subtraction.nii.gz",
maskedSubtractionPD
);
}
ProbabilityImage maskedSubtractionT2 = brainio->ReadProbabilityImage(subtractionFolderName + "t2_masked_subtraction.nii.gz");
if ((maskedSubtractionT2 == (ProbabilityImage)NULL) && (subtractionT2 != (ProbabilityImage)NULL)) {
maskedSubtractionT2 = BrainPreprocessing<ProbabilityImageType>::MaskImage(subtractionT2, wmMask);
brainio->WriteProbabilityImage(
subtractionFolderName + "t2_masked_subtraction.nii.gz",
maskedSubtractionT2
);
}
ProbabilityImage maskedSubtractionFLAIR = brainio->ReadProbabilityImage(subtractionFolderName + "flair_masked_subtraction.nii.gz");
if ((maskedSubtractionFLAIR == (ProbabilityImage)NULL) && (subtractionFLAIR != (ProbabilityImage)NULL)) {
maskedSubtractionFLAIR = BrainPreprocessing<ProbabilityImageType>::MaskImage(subtractionFLAIR, wmMask);
brainio->WriteProbabilityImage(
subtractionFolderName + "flair_masked_subtraction.nii.gz",
maskedSubtractionFLAIR
);
}
/*--- Lesion detection ---*/
std::cout << "\t-------------------------------" << std::endl;
std::cout << "\t Lesion detection " << std::endl;
std::cout << "\t-------------------------------" << std::endl;
// Subtraction smoothing
ProbabilityImage gaussSubtractionPD = brainio->ReadProbabilityImage(subtractionFolderName + "pd_smoothed_subtraction.nii.gz");
if ((gaussSubtractionPD == (ProbabilityImage)NULL) && (maskedSubtractionPD != (ProbabilityImage)NULL)) {
gaussSubtractionPD = BrainPreprocessing<ProbabilityImageType>::GaussianFiltering(maskedSubtractionPD, 0.5);
brainio->WriteProbabilityImage(
subtractionFolderName + "pd_smoothed_subtraction.nii.gz",
gaussSubtractionPD
);
}
ProbabilityImage gaussSubtractionT2 = brainio->ReadProbabilityImage(subtractionFolderName + "t2_smoothed_subtraction.nii.gz");
if ((gaussSubtractionT2 == (ProbabilityImage)NULL) && (maskedSubtractionT2 != (ProbabilityImage)NULL)) {
ProbabilityImage gaussSubtractionT2 = BrainPreprocessing<ProbabilityImageType>::GaussianFiltering(maskedSubtractionT2, 0.5);
brainio->WriteProbabilityImage(
subtractionFolderName + "t2_smoothed_subtraction.nii.gz",
gaussSubtractionT2
);
}
ProbabilityImage gaussSubtractionFLAIR = brainio->ReadProbabilityImage(subtractionFolderName + "flair_smoothed_subtraction.nii.gz");
if ((gaussSubtractionFLAIR == (ProbabilityImage)NULL) && (maskedSubtractionFLAIR != (ProbabilityImage)NULL)) {
ProbabilityImage gaussSubtractionFLAIR = BrainPreprocessing<ProbabilityImageType>::GaussianFiltering(maskedSubtractionFLAIR, 0.5);
brainio->WriteProbabilityImage(
subtractionFolderName + "flair_smoothed_subtraction.nii.gz",
gaussSubtractionFLAIR
);
}
// Simple thresholding of the smoothed subtractions
MaskImage positiveActivityPD = brainio->ReadMaskImage(subtractionFolderName + "pd_positive_activity.nii.gz");
if ((positiveActivityPD == (MaskImage)NULL) && (gaussSubtractionPD != (ProbabilityImage)NULL)) {
MaskImage positiveActivityPD = BrainSegmentation::GetPositiveActivity(gaussSubtractionPD);
brainio->WriteMaskImage(
subtractionFolderName + "pd_positive_activity.nii.gz",
positiveActivityPD
);
}
MaskImage positiveActivityT2 = brainio->ReadMaskImage(subtractionFolderName + "t2_positive_activity.nii.gz");
if ((positiveActivityT2 == (MaskImage)NULL) && (gaussSubtractionT2 != (ProbabilityImage)NULL)) {
MaskImage positiveActivityT2 = BrainSegmentation::GetPositiveActivity(gaussSubtractionT2);
brainio->WriteMaskImage(
subtractionFolderName + "t2_positive_activity.nii.gz",
positiveActivityT2
);
}
MaskImage positiveActivityFLAIR = brainio->ReadMaskImage(subtractionFolderName + "flair_positive_activity.nii.gz");
if ((positiveActivityFLAIR == (MaskImage)NULL) && (gaussSubtractionFLAIR != (ProbabilityImage)NULL)) {
MaskImage positiveActivityFLAIR = BrainSegmentation::GetPositiveActivity(gaussSubtractionFLAIR);
brainio->WriteMaskImage(
subtractionFolderName + "flair_positive_activity.nii.gz",
positiveActivityFLAIR
);
}
delete(brainio);
return EXIT_SUCCESS;
}
