[Insight-users] Reading DICOM time series study

[Martin Kavec]

Mathieu,

On Tuesday 12 July 2005 15:07, Mathieu Malaterre wrote:
> Martin,
>
> 	I'll repeat what Mark just told you: I never saw those tags before.
> I'll double check what 3.3 says about wether or not those tags are
> compulsory, but I would rather order the files using the usual Date/Time
> tags. Those I am pretty sure to find everywhere and I am also pretty
> sure that they are correct :)
>
> 	BTW is this a dual echo sequences ?

Why would you say that? I could find some reasons to have dual echo in time 
series (bolus tracking perfusion), but hardly in fMRI. "Number of Temporal 
Positions" reflects the number, how many times was each slice/volume  
acquired during the activation experiment and Temporal Position Identifier is 
an actual volume number of the volume in time series. Did you mean anything 
else?

> I'd would like to know how they increment the number in this case ?

Sorry, I am a newbie in DICOM standards.
:)

Cheers,
Martin

>
> Thanks,
> Mathieu
>
> Martin Kavec wrote:
> > Thanks for the reply, Karthik.
> >
> > Your code may, for sure, be a valid solution. However, after I read your
> > message, I told myself there must be an information related to the time
> > series in the DICOM header of an image. So I randomly grabbed an image
> > from an fMRI time series and found following two (correct) tags
> >
> > 0020,0100  Temporal Position Identifier: 52
> > 0020,0105  Number of Temporal Positions: 120
> >
> > Everything what's needed to construct the 4D image is there, so why not
> > to use it? Quoting myself: Is this a limitation of ITK's DICOM image
> > reader implementation? I would still be tempted to say: yes.
> >
> > What do you say?
> >
> > Regards,
> > Martin
> >
> > On Monday 11 July 2005 14:45, Karthik Krishnan wrote:
> >>I don't think it is not a limitation of the dicom image reader. You need
> >>to do that with your code.
> >>
> >>You could for instance read all the dicom series in the directory and
> >>use the JoinSeriesImageFilter to create a 4D image from the 3D images
> >>you just read. It is not a limitation of the dicom reader because a
> >>dicom file is  a 2D file. So the ImageSeriesReader which passes the set
> >>of filenames to the GDCMImageIO has to be instantiated over an image of
> >>dimension 2+1.
> >>
> >>You could do something like
> >>    const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
> >>    SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
> >>    SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
> >>    while( seriesItr != seriesEnd )
> >>      {
> >>      seriesReader->SetFileNames( nameGenerator->GetFileNames(
> >>seriesItr->c_str() ) );
> >>      seriesReader->Update();
> >>      joinSeriesFilter->SetInput( i++, seriesReader->GetOutput() );
> >>      seriesItr++;
> >>      }
> >>
> >>my4DImage = joinSeriesFilter->GetOutput();
> >>
> >>Thanks
> >>karthik
> >>
> >>Martin Kavec wrote:
> >>>Hi,
> >>>
> >>>I have a time series (fMRI, bolus tracking) studies in DICOM format,
> >>> which I am trying to read in. I gave a brief trial test to
> >>>DicomSeriesReadImageWrite2.cxx from Examples/IO. Although I changed the
> >>>Dimension = 4, the output Analyze format image is 3D only. I assume that
> >>>internal itkImage dimension is also 3D.
> >>>
> >>>Is this a limitation of ITK's DICOM image reader implementation?
> >>>
> >>>Regards.
> >>>
> >>>Martin
> >>>_______________________________________________
> >>>Insight-users mailing list
> >>>Insight-users at itk.org
> >>>http://www.itk.org/mailman/listinfo/insight-users
> >
> > _______________________________________________
> > Insight-users mailing list
> > Insight-users at itk.org
> > http://www.itk.org/mailman/listinfo/insight-users

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