How to select a ROI on dicomseries?

Beginner Questions
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1

Hi everyone,
I want to know how to select a ROI on dicomseries? I knew how to read dicomseries and did it for a single dicom. but for dicomseries i have no idea.
For example i have a dicom series,now i want to select a ROI for all of them ,each slice will set the same ROI ,then save as new dicom series. I have readed the example RegionOfInterestImageFilter
It help me work on single dicom .For series I try to change the “reader and writer” to ImageSeriesReader and ImageSeriesWriter,but not work .There must be something here that I don’t know. Someone give me some hits? Thanks!

btw, the example RegionOfInterestImageFilter has a BUG ,it’s missing a line of code: reader->update(). when the pointer reader after getting data

2

Hello everyone!
I know my problem description is wordy and bad.So here is my new description:
I want to know How to use the “RegionOfInterestImageFilter” on DicomSeries. There is the example for Single Dicom image. And for Series i have no idea about how to set the index and size for region. Or this filiter can` t work on 3D ?Someone give me some hits? Thanks!

3

RoI filter can be used with 3D images:

start[0] = std::stoi( argv[3] );
start[1] = std::stoi( argv[4] );
start[2] = std::stoi( argv[5] );
size[0] = std::stoi( argv[6] );
size[1] = std::stoi( argv[7] );
size[2] = std::stoi( argv[8] );

Here is an example of how to read a DICOM series as a 3D image and write it as a DICOM series. You need to insert some processing in the middle: add reader->Update(); and then use reader->GetOutput().

4

Thanks a lot! it works ,but i also have a question.
I was used 2 Points, One Point start[] and another is end[] point .both is 3D point. then set region.SetIndex(start);andregion.SetUpperIndex(end); without using region.setsize(size). It didnt work before.
That means if i use the RoI filter i must set the size argument?

5

Modify the Size of the ImageRegion so that the provided index will be the upper corner index.

So you don’t have to modify the size directly if you call SetUpperIndex.

6

Here is the code . The whole code is too long so i pick the ROI Part.

///////////////////////////////////ROI//////////////////////////////////////////////////////////

using FilterType = itk::RegionOfInterestImageFilter< ImageType, ImageType >;//imagetype is 3D

FilterType::Pointer filter = FilterType::New();
filter->SetInput(reader->GetOutput());//reader is Seriesreader

CoordinanteTrans(StartPosition[0], StartPosition[1],size, WindowSize);
CoordinanteTrans(EndPosition[0], EndPosition[1],size, WindowSize);
std::cout <<"After CoordinanteTrans:"<< StartPosition[0] <<","<<StartPosition[1]<<std::endl << EndPosition[0] << "," << EndPosition[1] << std::endl;

const auto startx = static_cast<itk::IndexValueType>(StartPosition[0]);
const auto endx = static_cast<itk::IndexValueType>(EndPosition[0]);
const auto starty = static_cast<itk::IndexValueType>(StartPosition[1]);
const auto endy = static_cast<itk::IndexValueType>(EndPosition[1]);

ImageType::IndexType start;
start[0] = startx;
start[1] = starty;
start[2] = 0;        //always from the first Slice z=0

ImageType::IndexType end;
end[0] = endx;
end[1] = endy;
end[2] = size[2];//size[2] is the number of Slices from reader

ImageType::SizeType size2;

//size2[0] = abs(end[0] - start[0]) + 1;
//size2[1] = abs(end[1] - start[1]) + 1;
//size2[2] = size[2];

region.SetIndex(start);
region.SetUpperIndex(end);
//region.SetSize(size2);

filter->SetRegionOfInterest(region);
filter->Update();

const unsigned int firstSlice = start[2];
const unsigned int lastSlice = start[2] + size[2] - 1;
nameGenerator->SetStartIndex(firstSlice);
nameGenerator->SetEndIndex(lastSlice);
nameGenerator->SetIncrementIndex(1);

using WriterType = itk::ImageSeriesWriter<ImageType, Image2DType>;
WriterType::Pointer writer = WriterType::New();
writer->SetInput(filter->GetOutput());
writer->SetImageIO(gdcmImageIO);
writer->SetFileNames(nameGenerator->GetFileNames());
writer->SetMetaDataDictionaryArray(reader->GetMetaDataDictionaryArray());
try
{
	writer->Update();
}
catch (itk::ExceptionObject & error)
{
	std::cerr << "Error: " << error << std::endl;
	return EXIT_FAILURE;
}

return EXIT_SUCCESS;
}

If i invoke the region.SetSize(size2); not call the SetUpperIndex then it works…
Do you know why? Thank you again!

7

I think size2 is greater by +1 than SetUpperIndex. You could inspect it in the debugger.