[Insight-users] Truncating DICOM Series

[Neil Panjwani]

I'm running into a few problems when reading select DICOM images from a
dataset.

I followed the example in the software guide to read a DICOM series a while
back and wrapped it in a function. I used the ImageSeriesReader and
GDCMImageIO. However, I could not get the GDCMSeriesFileNames to work
properly. I figured it was due to my filenames
(mr10_092_13p_i0001.dcm, mr10_092_13p_i0002.dcm...etc), so I found a
solution using RegularExpressionSeriesFileNames and the match
"[^.]*i([0-9]+).dcm". Since then I haven't had many problems with DICOM.

Today, however, I tried to use the Adaptive Threshold filter from the
insight journal. I am trying to test the filter on 5 slices, so after the
file names are retrieved, I truncate the vector to only include a few
slices. Then I apply my algorithm on that input. These 5 slices output
perfectly fine.However, after this filter, I get the following error:

Error:
itk::ExceptionObject (000000000126FB50)
Location: "void __cdecl itk::DataObject::PropagateRequestedRegion(void)
throw(class itk::InvalidRequestedRegionError)"
File: ..\..\..\Code\Common\itkDataObject.cxx
Line: 397
Description: Requested region is (at least partially) outside the largest
possible region.

The strangest part is that when I read the DICOM series in ImageJ, truncate
it to 5 slices manually, write to Nifti, and then apply the filter to that
input, it works just fine. This makes me believe my DICOM truncation isn't
working right (even though I can clearly see the truncated output just
fine...). Any idea on how to fix this?

BTW, I output my files in the Nifti format (.nii) and view them using Fiji.

Thanks,
Neil
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