Visible Human Project Data Utilization and Explaination
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
- To define the boundary: X = 130, Y = 300, Z = 400
For more detailed information, you can access the readme file here
* 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
0.00033m = 0.33mm