[Insight-developers] ImageFileReader Bug 0007520 and some considerations/ideas about ImageSeriesReader/Writer

[Iván Macía]

Dear all,

 

We are trying to read slice by slice a DICOM series. We cannot use
ImageSeriesReader because the series is heterogeneus in size and it does not
correspond to a 3D volume. When trying to read the last image with
ImageFileReader an exception occurs in
ImageFileReader::EnlargeOutputRequestedRegion()

 

“ImageIO returns IO region that does not fully contain the requested region”


 

Having a look at the source of the problem, ImageFileReader fails when
trying to read a second image that is smaller that the previous image read.
The problem is that the LargestPossibleRegion is assigned the new smaller
size but the RequestedRegion is not. Having a look at Mantis I found a
related bug 

 

Bug 0007520: failed propagation of largestPossibleRegion to
requestedPossibleRegion

 

Probably this can be solved with a call to
output->SetRequestedRegionToLargestPossibleRegion() at the end of
ImageFileReader::GenerateOutputInformation() after setting
output->SetLargestPossibleRegion().

 

On the other hand, I wanted to know if there are some plans to extend the
capabilities of ImageSeriesReader and ImageSeriesWriter. We are developing a
viewer for a DICOM PACS and found many different types of series that does
not correspond to the usual ITK concept of a series consisting of slices of
a 3D images. For example, we have found:

 

-          Series of 2D images as a time series (cine) or single images with
multiple frames (these all can be considered as multi-frame).

-          Series with intermixed volumes, such as those that show different
times of a contrast-enhanced volume. These could also be considered as 3D+t.

-          Series that represent a reslicing of the original volume and show
a preview image.

 

and even more exotic series such as those consisting of

 

-          Intermixing of multi-frame and non-multiframe 2D images in the
same series.

-          Series with different pixel types (for example the preview image
of the reconstruction can be RGB whereas the rest is short for CT or ushort
for MR).

-          Images of type RGB<short>.

 

I have found some methods in GDCM 1.x that can deal with some of these
features, such as gdcm::SerieHelper::SplitOnOrientation() and we had to
develop some of heuristics by our own, but wanted to know if there were some
plans to add functionality for this analysis in ITK. One idea could be to
develop a class that could take the file names of a series and analyse them
in order to split them in groups according to some property.

 

Thanks in advance

 

Iván Macía

 

 

____________________________________________________________________
Iván Macía Oliver
Investigador / Researcher

Aplicaciones Biomédicas / Biomedical Applications

 

VICOMTech - Visual Interaction and Communication Technologies Center
Mikeletegi Pasealekua, 57 - Parque Tecnológico
E-20009 Donostia - San Sebastián, Spain
Tel: +[34] 943 30 92 30
Fax: +[34] 943 30 93 93
e-mail: imacia at vicomtech.org
http://www.vicomtech.org

 

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