View source for DICOM CD workflow

A description of the workflow to produce the medical image rendered in X3DOM [http://www.kshell.com/pages/MedDICOMDemo20161018/index.xhtml here], from the CD containing results of MRI scans.

[http://www.kshell.com/pages/MedDICOMDemo20161018/index.xhtml  Complete Image Set]
[http://www.kshell.com/pages/MedDICOMDemo20161018/index2.xhtml Truncated Image Set]

==Workflow==
The workflow to prepare an X3DOM volume rendering from a set of DICOM images contains these steps:

===1. Selection of Images===
From the set of DICOM images select a set of images which represent a sequence of parallel slices taken  at uniform spacing through the imaged volume. Each image in the set should have compatible (equivalent) imaging characteristics and image size.

===2. Generating 3D Texture===
* [http://www.web3d.org/documents/specifications/19775-1/V3.3/Part01/components/volume.html#VolumeData VolumeData] node. The geometric size of the rendered volume is defined in the dimensions attribute of this node. This node combines volumetric data represented by a 3D texture (abstract node [http://www.web3d.org/documents/specifications/19775-1/V3.3/Part01/components/texture3D.html#X3DTexture3DNode X3DTexture3DNode]) and volume rendering style information as an abstract [http://www.web3d.org/documents/specifications/19775-1/V3.3/Part01/components/volume.html#X3DVolumeRenderStyleNode X3DVolumeRenderStyleNode]
* [http://doc.x3dom.org/author/Texturing/ImageTextureAtlas.html ImageTextureAtlas] is an X3DOM extension node. It is not part of the X3D v 3.3 standard but has the attributes required to be considered a descendand node of X3DTexture3DNode. This node contains an attribute url which is a link to a standard 2D image which through tiling contains a  sequence of the 2D slices. 
===3. Creating X3DOM web content===



===Software===
*[http://www.python.org Python 2.7] , with additional libraries
**[http://www.numpy.org NumPy] - numerical analysis library
**[http://www.scipy.org SciPy]   - companion to NumPy with additional analysis functions
**[http://www.pythonware.com/products/pil PIL]      - Python Imaging Library
**[http://pydicom.readthedocs.io/en/latest/getting_started.html pydicom] A python library for reading DICOM files.

*[http://www.osirix-viewer.com/download_form/download_form.php Osirix-Lite] : This free demo version of the [http://www.osirix-viewer.com/ Osirix] software for viewing DICOM image files, for Mac OS. Similar [http://technologyadvice.com/blog/healthcare/5-dicom-viewers/ DICOM viewers] are available for Windows OS

==Scans==
The original data set was flat collection of DICOM files as provided on CD by a hospital. The contents of this folder were imported into the Osirix Lite viewing software. The viewing software organized the file set by patient name (there was only one patient) and into three series of scans. The thumbnail images for one such series is shown:
[[File:DWI_NEW_NOGOP_1.jpg | 1080px | center | MRI scan series from DICOM folder generated by Osirix software]]