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Re: [Seg3D] Pediatric Torso CT DICOM Files will not Properly Import

Chronological Thread 
  • From: Rob MacLeod <>
  • To: Bradley Due <>
  • Cc: Rob MacLeod <>,, Jess Tate <>
  • Subject: Re: [Seg3D] Pediatric Torso CT DICOM Files will not Properly Import
  • Date: Wed, 4 Jan 2017 15:10:15 -0700

HI Brad,

Given your application, I also want to be sure you know about our research on this specific topic:

• J.D. Tate, T. Pilcher, K. Aras, B. Burton, R.S. MacLeod. Verification of a Defibrillation Simulation Using Internal Electric Fields in a Human Shaped Phantom. Comp. in Cardiol. 41:689-692, 2014.
• M. Jolley, J. Stinstra, J. Tate, S. Pieper, R. Macleod, L. Chu, P. Wang, and J.K. Triedman. Finite element modeling of subcutaneous implantable defibrillator electrodes in an adult torso. Heart Rhythm. 7(5):692–698, 2010.
• J.K. Triedman, M. Jolley, J. Stinstra, D.H. Brooks, and R. MacLeod. Predictive modeling of defibrillation using hexahedral and tetrahedral finite element models: recent advances. J. Electrocardiol. 41(6):483–486, 2008.
• M. Jolley and J. Stinstra, S. Pieper, R.S. MacLeod, D.H. Brooks, F. Cecchin, and J.K. Tried- man. A Computer Modeling Tool for Comparing Novel ICD Electrode Orientations in Chil- dren and Adults. Heart Rhythm, 5(4): 565–572, 2008.

So there are all the tools you need in our suite:

• R.S.Macleod,J.G.Stinstra,S.Lew,R.T.Whitaker,D.J.Swenson,M.J.Cole,J.Kruger,D.H. Brooks, and C.R. Johnson. ”Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examples. Phil. Trans. Royal Soc. 367(1896):2293–2310, 2009.


On Jan 2, 2017, at 12:15 , Jess Tate <> wrote:

Hi Brad,

Dicoms have many different formats that can encode images many different ways.  Seg3d usually does a pretty good job getting the right format, but it does struggle with data that includes inconsistent slice thicknesses, tie dependent data, and data that includes multiple axes in a slice.  I suspect your data is the last example.  You can use a dicom viewer such as osirix to view and export data in a format that may be better for Seg3D.  

There are some example dicom datasets in the Sed3DData directory.  It is available at  There are some example segmentations in the SCIRunData directory (saved as nrrd files), available at


On Jan 1, 2017, at 11:09 PM, Bradley Due <> wrote:


I am a biomedical engineering student at Texas A&M University and I am working on a project that requires I be able to model defibrillation of pediatric patients. I have a working knowledge of SciRun, however I have been unable to successfully import pediatric CT scans to Seg3D in order to generate a 3D mesh of a pediatric torso. 

I have access to CT scans that I would like to import into Seg3D, but when I import them as an image series, the order of the images seem to become mixed up and generate an incoherent image. For example, some coronal images seem to get mixed with in with Sagittal images and vice versa. Other times the images fail to import entirely.

Is this a common issue? If so how may I fix this problem? I can attach images showing the results of the scans improperly importing on a follow up email if that would help elucidate the issue I'm having.

Also are there any online resources where I could download dicom files of deidentified pediatric torso CT scans that can be successfully imported into Seg3D? I am looking to model defibrillation of patients aging from 6 months to 2 years of age.

Best regards,
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