Visible Human Project Data Utilization and Explaination

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Okay. READ THESE CAREFULLY if you wish to utilize the VHP dataset for any reconstructions

Root refers to the folder VHPfemale or VHPmale, whichever you wish to load up

Remember: all scan numbers have THREE copies... (in terms of CM) as a b c is the 1

For full color RAW

(pre-processed image data)

   * Check \Fullcolor and all the sections of the VHP projects will be there
         o If no has has messed up with the existing structures, it should list as many as these:
         o VHP Female:
               + \fullbody: 1001abc~2730abc
               + \head: 1001abc~1285abc, 856 slices
               + \thorax: 1262abc~1488abc, 680 slices
               + \abdomen:1432abc~1909abc, 1434 slices
               + \pelvis: 1703abc~1953abc, 753 slices
               + \thighs: 1703abc~2300abc,1794 slices
               + \legs: 2200abc~2730abc,1589 slices
         o VHP Male:

For full color PNG

  • For graphic formats, make sure when you load it, select the appropriate setting in the color channel setting to convert it into black and white images and allow labeling.
  • Make sure you know the dimension and set it properly to stack it well
  • X and Y dimensions are defined by the 2D slices or pictures you acquired.
  • Z dimension is defined via the number of pictures you stacked together.
  • However, you still need to take the VOXEL dimension into consideration.
    • If the readme files tell you that the XYZ resolutions are IDENTITICAL, then you have a CUBIC voxel. X = 0.33mm, Y = 0.33mm, Z = 0.33mm then X:Y:Z ratio = 1:1:1
    • If the readme files tell you that XYZ resolution are NOT identical, they you have a NON-cubic voxel and you need to adjust Z-stacking accordingly. X = 0.33mm, Y = 0.33mm, Z = 4mm then X:Y:Z ratio = 1:1:12
  • Example 1:
    • You have a stack of 50 images with dimension 900*1000
    • The voxel is a CUBE, eg. x:y:z = 1:1:1
    • To define boundary: X = 900, Y = 1000, Z = 50
  • Example 2:
    • You have a stack of 200 images with dimension 130*300
    • The voxel is NOT a cube but with ratio of X,Y,Z = 1:1:2

on=load(str)

    • To define the boundary: X = 130, Y = 300, Z = 400

For MRI

   * Look under Root\Radiologicla\MRI\
   * T1, T2, POC and PD all have different meanings
   * All files are in RAW format when reading from Amira.
   * They are taken from every 4mm where as PNG or RAW scans are taken every 0.33mm
   * Read the mriHeaders folder for detailed explanation on each individual files
   * Dimensions:
         o X = 256
         o Y = 256
         o Z = how many slices you selected to load up
         o Header = 7900 most of the time. "Requested" does not match "filesize" then use "filesize" - "requested" when no "header" = 0
         o Anyway, your goal to load things up properly, is to make requested = filesize.
   * Datatype: most of the time leave it at ushort or short.
   * Voxel size is usually:
         o X = 0.859375 mm
         o Y = 0.859375 mm
         o Z = 4 mm
         o  

For CT

0.00033m = 0.33mm