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Re: [Seg3D] Files in image stack are loading in wrong order


Chronological Thread 
  • From: Chris Butson <butson@sci.utah.edu>
  • To: seg3d@sci.utah.edu
  • Subject: Re: [Seg3D] Files in image stack are loading in wrong order
  • Date: Sat, 15 Nov 2014 11:21:29 -0700
Well this is interesting: The patient is identified in the original data, so I anonymized it before sending. On a hunch I loaded the anonymized dataset into Seg3D and the slices are ordered correctly!

I note that there are many ways to store conflicting information in DICOM headers, and I suspect that this is the case with these files and that some of the conflicting information is somehow getting erased during anonymization.

Ayla: I can't send the identifiable data or copy it to the server, but I can show you if you stop by my office one day next week. Thanks.

Chris

Christopher R. Butson, PhD
Director of Neuromodulation Research
Faculty, Scientific Computing & Imaging (SCI) Institute
Associate Professor, Departments of Biomedical Engineering, Neurology & Neurosurgery
University of Utah

Warnock Engineering Building
72 South Central Campus Drive, Room 3686
Salt Lake City, Utah 84112
butson@sci.utah.edu

On Nov 14, 2014, at 9:58 AM, Ayla Khan <ayla@sci.utah.edu> wrote:

Hi Chris,

I think these issues may be related. It's possible that the GDCM library (takes care of DICOM import) is processing these tags incorrectly. Would it be possible for me to have a look at some data?

Ayla

On Nov 13, 2014, at 2:21 PM, Christopher Butson, PhD wrote:

I also note that Seg3D is incorrectly reading the slice thickness, which is specified as 5mm in the DICOM header but about 29mm in Seg3D. However, this is easily corrected using the Transform tool. I only mention it in case it is connected to the slice ordering issue.

Chris

I am loading a stack of 47 DICOM CT files into Seg3D. This mostly works, but I note that about every 10th or 11th file is in the wrong order when I scroll through the axial slices. 
I suspect this is a file ordering problem during load, but I don’t know how to fix it. Any ideas? Thanks, Chris

Christopher R. Butson, PhD
Director of Neuromodulation Research
Faculty, Scientific Computing & Imaging (SCI) Institute
Associate Professor, Departments of Biomedical Engineering, Neurology & Neurosurgery
University of Utah

Warnock Engineering Building
72 South Central Campus Drive, Room 3686
Salt Lake City, Utah 84112
butson@sci.utah.edu





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