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Software @ CIS : lddmm-landmark : Validationmanual | faq | input formats | validation | credits | changelog | feedbackContent OverviewThe LDDMM Validation section provides input data, processing and visualization examples for LDDMM to ensure correctness of the resultant data. These examples are useful tests when LDDMM is run on new environments or platforms. Examples are displayed with available visualization software. A sample lddmm-landmark command is posted with each example (or type lddmm-landmark --help for more lddmm-landmark usage information).X to H TestInput: input.tar.gz Output: output.tar.gz DTIStudio Files: dtistudio.tar.gz Command: lddmm-landmark -s 7.5 -j -m -c -w LDDMMMatrix.hdr -p ThreeLayerX.txt ThreeLayerX.txt ThreeLayerH.txt This test matches landmarks on an "X" to landmarks on an "H" using lddmm-landmark on a Unix platform. The original landmarks are then flowed according to the lddmm results, and a volume transformation (*.xfm file) is created. This matching can similarly be performed in Landmarker. The H image and the associated landmarks are loaded as the template, and the X is loaded as the subject. The user selects Transformation->Landmark Based LDDMM from the menu, then performs a 2D transformation with 3 slices and a 1 pixel interval, and a sigma of 7.5. The following figures show the results of matching as displayed in Landmarker. The first figure is the input data before matching. The second is after the X has been deformed by lddmm-landmark matching in Landmarker. The third shows the X image after the transform computed on the Linux platform is applied.
Sphere to Ellipse TestInput: input.tar.gzOutput: output.tar.gz Image Files: images.tar.gz Command: lddmm-landmark -s 10.0 -j -m -c -A smallSphereImage.vti -p largeSphere.lmk templateSphere.lmk targetEllipse.lmk This test matches landmarks on a sphere to corresponding landmarks on an ellipse using lddmm-landmark on a Unix platform. After matching, first a larger file of points randomly uniformly distributed on the sphere are flowed according to the lddmm-landmark results. The sphere is deformed into the elliptical shaped object. Second, image data that represents a sphere is deformed. The sphere is also deformed to the shape of an ellipse. The following figures show first the results of matching as displayed in CAWorks. Pictured first are the spherical points (blue) input into lddmm-landmark, the elliptical points (yellow) they are matched with.
Monkey Brain TestInput: input.tar.gz Output: output.tar.gz DTIStudio Files: dtistudio.tar.gz Command: lddmm-landmark -s 7.5 -j -m -c -w LDDMMMatrix.hdr monkey1.lmk monkey2.lmk This test matches landmarks on two monkey brains using lddmm-landmark on a Unix platform. A volume transformation (monkey1.lmk_monkey2.lmk.xfm) is created during the matching. After matching, the monkey brain Analyze image files are loaded into DTIStudio Landmarker (monkey2 = template, monkey1 = subject). The VolumeTransformation file is loaded onto the subject file, and the target landmarks superimposed on the image. The following figures show the results of matching as displayed in DTIStudio Landmarker. Pictured here are the image and landmark data before and after the volume transformation is applied.
Last Modified: Tuesday, 30-Jun-2009 15:10:08 EDT |
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