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| = Create a scene using the virtual family = | | = Virtual Family = |
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| First convert two members of the virtual family
| | For more information on the <b>Virtual Family</b>, please visit the IT'IS foundation website: |
| | * [http://www.itis.ethz.ch/news-events/news/latest-news/ http://www.itis.ethz.ch/news-events/news/latest-news/] |
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| VirtualFamilyTxtToMhdCsv Duke_34y_v5_2mm.txt Duke_34y_v5_2mm.raw Duke.mhd Duke.csv
| | They have an outstanding collection of anatomical models that are available for scientific purposes: |
| VirtualFamilyTxtToMhdCsv Ella_26y_v2_2mm.txt Ella_26y_v2_2mm.raw Ella.mhd Ella.csv
| | * [http://www.itis.ethz.ch/services/anatomical-models/virtual-population/ http://www.itis.ethz.ch/services/anatomical-models/virtual-population/] |
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| This produces representations in the .mhd format.
| | The models from the Virtual Population have been segmented based on the image data of volunteers. Whole-body models that represent a broad range of ages, body shapes and sizes, and both genders are available. The imaging resolution and segmentation details are excellent. Users must agree to the terms and conditions to use those data, in order to respect the privacy of the volunteers. |
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| One wacky thing, the man is imaged head-first while the woman is imaged feet-first. This can be made consistent by adding an orientation matrix and origin to the woman's header file.
| | = Maverick = |
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| vi Ella.mhd
| | [[Maverick]] and the application mentioned on this page is no longer available. Interested people should contact the IT'IS foundation (above) for more information and consider the use of [http://www.slicer.org Slicer] for viewing medical images. |
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| Add the two lines below so that they appear before the last line of the file.
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| Origin = 0 0 1680
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| Orientation = 1 0 0 0 1 0 0 0 -1
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| This Orientation field is specifying a transform matrix for the data. It must be a 3x3 matrix. It can be used to swap right/left and front/back and (shown) top/bottom and to permute the axis (e.g., swap x-axis and y-axis) of the data. In this case, the final -1 causes the z-axis to be flipped.
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| The flipping now cause Ella to span the space from 0 to -1680 (she has 840 z-slices, each 2mm thick). However, the virutal man is on the positive side of the z-axis (0 to 1900 or so). So, we shift Ella's origin in the positive z direction to compensate for the z-axis flip.
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| The new Ella.mhd should look like this:
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| NDims = 3
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| DimSize = 265 150 840
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| HeaderSize = -1
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| ElementType = MET_UCHAR
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| ElementByteOrderMSB = True
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| ElementSpacing = 2 2 2
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| Origin = 0 0 1680
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| Orientation = 1 0 0 0 1 0 0 0 -1
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| ElementDataFile = Ella_26y_V2_2mm.raw
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| The current release of Maverick, however, requires the images to be in the .mha format. So, perform the conversion using imageMath
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| imageMath Duke.mhd -W 3 Duke.mha
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| imageMath Ella.mhd -W 3 Ella.mha
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| Now Merlin can be used to create a scene containing these labelmaps and indexed via those .csv files. Use the standard labelmap import process of Merlin to achieve this.
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| = Create a new version of the woman that is shaped somewhat like the man =
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| To simulate different size people, the virtual woman (Ella) can be registered with the virtual man (Duke) using a deformable (BSpline) transform. In this manner, the woman will take on aspects of the shape of the man. The RegisterImages module accomplishes this
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| RegisterImages Duke.mha Ella.mha
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| --registration PipelineBSpline --interpolation NearestNeighbor
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| --minimizeMemory --controlPointSpacing 100 --bsplineSamplingRatio 0.02
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| --resampledImage TallElla.mha --saveTransform TallElla.tfm
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| All of the above should be on one line. Processing time will vary from 30 minutes to 1 hour, depending on the PC. The result should be two new files: TallElla.mha and TallElla.tfm
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| Regretfully, this output image, while a .mha image, uses compression that isn't well supported by Maverick applications at this time. So, the TallElla.mha file must be run-thru imageMath
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| imageMath TallElla.mha -W 3 TallElla.mha
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| The new version of the TallElla.mha file can be imported into Merlin.
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| == BEFORE Registration: Ella-to-Duke ==
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| [[Image: Maverick-VirtualFamily-ManWomanRegistration-before.jpg]] | |
| == AFTER Registration: Ella-to-Duke ==
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| [[Image: Maverick-VirtualFamily-ManWomanRegistration-after.jpg]]
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| == Notes ==
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| You can control how closely the woman is deformed into the man by controlling how many BSpline control points are used. More points means more flexibility and ultimately a closer match. The two relevant command-line arguments are --controlPointSpacing and --bsplineSamplingRatio. A smaller controlPointSpacing value means that more bspline control points will be used to span the image. When more control points are used, more samples should be taken to evaluate the metric, i.e., the bsplineSamplingRatio should be increased. Note that computation time can quickly become multiple hours.
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| = View the short and tall Ella next to one another in the same volume =
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| First move TellElla 600 mm to the right by editing the file TallElla.mha using vi or another text editor.
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| vi TallElla.mha
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| Change line containing the keyword <em>Offset</em> to induce the shift
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| Offset = 600 0 -100
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| Note: the -100 was added to the z-axis after some trial and error. It is needed to align the bottom of their feet.
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| Now we will use the MultipleVolumesToVolume function to merge these women into a single volume.
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| First create a text file (call it ellaTwins.txt) that lists these files
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| Ella.mha
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| TallElla.mha
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| Then run the MultipleVolumesToVolume program
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| MultipleVolumesToVolume ellaTwins.txt 0,0,0 300,128,465 4,4,4 1,0,0,0,1,0,0,0,1 EllaTwins.mha
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| This file can be directly imported into Merlin and other Maverick applications.
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| [[Image:Maverick-EllaTwins.jpg]]
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