[Insight-users] Re: how to select all the slices in the same frame?

[kingaza at gmail.com]

Hi Luis

I am so sorry, for i just thought it is the question many people would
encounter, and i also thought a little short words are enough.

now i should discribe the details
the series is a 4D dataset with the size 512*512*40*6 (3D: 512*512*40,
time: 6), and all the files are 2D slices, that means 240 files in a
folder.
now i want to get all the slices in the time t, for example, t = 0,
1,...5, so at the end i should get 6 volumes in size of 512*512*40.

could you tell me how could I implement it?


btw, after your previous email, I have tried the filter
ExtractImageFilter, but I don't know how to read the series data set
accurately, and the result is not what i expect: it told me that the
size is 512*512*240

here are my codes:

typedef itk::Image<unsigned char, 4> BinaryImage4DType;
typedef itk::ImageFileReader<BinaryImage4DType> BinaryReader4DType;
typedef itk::ImageSeriesReader<BinaryImage4DType>	BinaryReader4DSeriesType;
typedef itk::GDCMImageIO DicomImageIOType;
typedef itk::GDCMSeriesFileNames DicomSeriesFileNames;

DicomImageIOType::Pointer dcmIO = DicomImageIOType::New();
DicomSeriesFileNames::Pointer	series = DicomSeriesFileNames::New();
typedef vector<string> FileNamesContainer;
BinaryReader4DSeriesType::Pointer reader4d = BinaryReader4DSeriesType::New();
series->SetInputDirectory( "E:\\series" );
FileNamesContainer filenames = series->GetInputFileNames();

reader4d->SetFileNames( filenames );
reader4d->SetImageIO( dcmIO );

try
{
	reader4d->Update();
}
catch (itk::ExceptionObject &excp)
{
	cerr << "Exception thrown while writing the image" << endl;
	cerr << excp << endl;
}

typedef itk::ExtractImageFilter< BinaryImage4DType, BinaryImage3DType
> FilterType;
FilterType::Pointer filter = FilterType::New();

BinaryImage4DType::RegionType inputRegion =
reader4d->GetOutput()->GetLargestPossibleRegion();

BinaryImage4DType::SizeType size = inputRegion.GetSize();
BinaryImage4DType::IndexType start = inputRegion.GetIndex();



On 5/19/05, Luis Ibanez <luis.ibanez at kitware.com> wrote:
> 
> 
> Hi Kingaza,
> 
> 
> Thanks for the additional bit of information.
> 
> 
>     Five more emails like this one and we
>     will be able to figure out what you need .    :-)
> 
> 
> 
> You see... when you write short emails...
> you end up writing many of them.
> 
> It will be wiser to provide a full description of
> your problem in a single shot so we don't have to
> go in "interrogatory mode".
> 
> 
> 
> How about you let us know if you are reading this
> time series from DICOM files or from other means ?
> 
> 
> ---
> 
> 
> ITK will allow you to proces 4D datasets in a native
> way.  In principle, getting a 3D frame at a time "t"
> out of a 4D dataset is as simple as instantiating
> the ExtractImageFilter and just setting the region
> to be extracted.
> 
> 
> However,
>     chances are that you are by now just trying
> to bring your 4D data set from disk into memory.
> 
> 
> Hopefully we will know that in the next episode
> of your problem description      :-)
> 
> 
> 
>    Please let us know,
> 
> 
> 
>        Thanks
> 
> 
> 
>           Luis
> 
> 
> 
> 
> --------------------------
> kingaza at gmail.com wrote:
> 
> > Hi Luis,
> >
> > yes, i mean time series (3D+t), and i want to seek out all the slices
> > in a certain t0
> >
> > Regards,
> > Kingaza
> >
> > On 5/19/05, Luis Ibanez <luis.ibanez at kitware.com> wrote:
> >
> >>Hi Kingaza,
> >>
> >>Please provide more information regarding your problem.
> >>
> >>ITK in itself doesn't have a notion of "frames".
> >>
> >>Are you talking about visualization ?
> >>or about time series ?
> >>
> >>
> >>
> >>    Thanks
> >>
> >>
> >>       Luis
> >>
> >>
> >>
> >>-------------------------
> >>kingaza at gmail.com wrote:
> >>
> >>
> >>>Hi all
> >>>
> >>>I wonder if there is such a method...
> >>>
> >>>Regards,
> >>>Kingaza
> >>>_______________________________________________
> >>>Insight-users mailing list
> >>>Insight-users at itk.org
> >>>http://www.itk.org/mailman/listinfo/insight-users
> >>>
> >>>
> >>
> >>
> >>
> >>
> >
> >
> 
> 
> 
>