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

Chronological Thread 
  • From: Jess Tate <>
  • To: Bradley Due <>
  • Cc:
  • Subject: Re: [Seg3D] Pediatric Torso CT DICOM Files will not Properly Import
  • Date: Mon, 2 Jan 2017 12:15:59 -0700

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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