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I have sets of .dcm files of an MRI scan. I am trying to convert them into 3d formats like obj (preferably) or fbx to import them into Unity 3d. I used the following open source software dcmtk to convert .dcm file into text file.

Converting DICOM files to text files

However, the dcm files lack the needed information. Is it even possible to convert .dcm files to obj and fbx. if so, could you suggest something? Thanks

(Edit) I would like to put my question more precisely: I want to visualize MRI data as a 3D model in Unity 3d. This is possible only when I it stored as .obj or .fbx format. Which format of MRI medical data should I start with to convert to these formats?

Thanks

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Sunil Nair
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  • When you say "the dcm files lack the needed information", what kind of information are you referring to? DICOM files have plenty of information into their Data Elements (header attributes). – jap1968 Mar 07 '15 at 20:20
  • The data contained in dcm files ncludes the patients name, date, id etc. I am looking for a .obj format. .obj format is one with: # List of Vertices v 0.123 0.234 0.345 # Texture coordinates, in (u, v [,w]) coordinates, vt 0.500 1 [0] vt ... # Normals in (x,y,z) form; normals might not be unit. vn 0.707 0.000 0.707 f 3/1 4/2 5/3 Do I need to start with a different format instead of dcm to get to the obj format? – Sunil Nair Mar 09 '15 at 04:47
  • What you want to do is much more complex than just a conversion. Think of getting a SVG vector image from a raw BMP. This is the same. DICOM contains raw images from every slice (a TC for example) so you can end up having a 3D matrix of values. If you want some vectorial information you will have to do the segmentation process for yourself. You could start looking for "DICOM segmentation howto" in your favorite search engine. – jap1968 Mar 09 '15 at 07:49
  • the image data in a dicom image is compressed and I am not able to retrieve the vertex values from the dicom file. I am not interested in the metadata but in the point co-ordinates. How do I do that? – Sunil Nair Mar 09 '15 at 18:21

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According to your previous comments you are looking for the necessary information in order to obtain the geometrical information of a DICOM series representing volumetric information (RM, TC, PET, ...)

In this case, you should have a look at the Roni Zaharia web site where he explains very clearly the concepts related to orientation and geometry of the DICOM images: DICOM is easy: Getting oriented

In this particular page you will find information about Pixel Spacing, Image Orientation, Image Position, Slice Thickness, and Slice Location, as well as additional information references.

jap1968
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