SCI Seg3D Mailing List

Text archives Help

Re: [Seg3D] Seg3D Image Origin/Spacing

Chronological Thread 
  • From: Ayla Khan <>
  • To: "Stoner, Kirsten E" <>
  • Cc: "" <>
  • Subject: Re: [Seg3D] Seg3D Image Origin/Spacing
  • Date: Fri, 16 Sep 2016 17:05:37 -0600

Hi Kirsten,

The Seg3D GDCM importer has some custom code that compares the DICOM header slice thickness to the distance between the first and second slices in the DICOM stack and reports the warning you’re seeing if they don’t match to within a given tolerance. If I understand correctly, your DICOM images have different spacing between the first 2 slices than between the slices in the rest of the stack? Which spacing is Seg3D using for the imported image volume?



On Sep 13, 2016, at 11:40 AM, Stoner, Kirsten E <> wrote:

Hi All,
I’ve been having some inconsistences with the image origins of my images. If I load the same DICOM image in 3DSlicer and ITKsnap I get the same origin and voxel spacing (LPS vs RAS accounted for). However if I load this DICOM image into SEG3D I get a warning that states:  Slice spacing in DOCME header is inconsistent, using patient slice location to derive z spacing, and the origin is not the same as that reported by 3DSlicer or ITKSnap. I have checked the slice location in the DICOM metadata and from the first to second slice the difference in slice location is 7.2mm were it should be 0.8mm but it is 0.8 for all of the other slices. Is this causing the error? And do you have any idea why this is not causing an issue in ITKSnap or 3DSlicer? Thanks!
Seg3d mailing list:
To unsubscribe, email with the "unsubscribe seg3d" in the message body.

Archive powered by MHonArc 2.6.18.

Top of page