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Documentation.Quality History
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scalarGrid -target input.df.nii.gz -grid 0
scalarGrid -target input.df.nii.gz -grid 1
scalarGrid -target input.df.nii.gz -grid 2
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SVtool -target input.df.nii.gz -grid
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!!Overview
Visualizing spatial transformations is an important quality assurance step. This tutorial describes how to create uniform grid images and how to visualize a spatial transformation by viewing the warped grid images.
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->[@ scalarGrid -target input.df.nii.gz -grid 0 to:
->[@
scalarGrid -target input.df.nii.gz -grid 0 Changed lines 21-22 from:
->[@deformationScalarVolume -in gridx.nii.gz -out wgridx.nii.gz -trans input.df.nii.gz -target input.df.nii.gz to:
->[@
deformationScalarVolume -in gridx.nii.gz -out wgridx.nii.gz -trans input.df.nii.gz -target input.df.nii.gz
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To visualize the deformation field input.df.nii.gz, simply apply this warp to the three grid images and visualize the warped grid (wgridx.nii.gz, wgridy.nii.gz, and wgridz.nii.gz) using an image viewer such as MRIcro.
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To visualize the deformation field input.df.nii.gz, simply apply this warp to the three grid images and visualize the warped grid (''wgridx.nii.gz'', ''wgridy.nii.gz'', and ''wgridz.nii.gz'') using an image viewer such as [[http://www.cabiatl.com/mricro/mricron/index.html|MRIcro]].
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The movies below, from left to right, illustrate the result of browsing through each of these images in MRIcro, along sagittal for wgridx.nii.gz, coronal for wgridy.nii.gz, and axial for wgridz.nii.gz.
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The movies below, from left to right, illustrate the result of browsing through each of these images in [[http://www.cabiatl.com/mricro/mricron/index.html|MRIcro]], along sagittal for ''wgridx.nii.gz'', coronal for ''wgridy.nii.gz'', and axial for ''wgridz.nii.gz''.
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%center%[Attach:gridx.png Attach:wgridy.png Attach:wgridz.png to:
%center%Attach:gridx.png Attach:wgridy.png Attach:wgridz.png
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!!Visualize Deformation Fields
To visualize the deformation field input.df.nii.gz, simply apply this warp to the three grid images and visualize the warped grid (wgridx.nii.gz, wgridy.nii.gz, and wgridz.nii.gz) using an image viewer such as MRIcro.
->[@deformationScalarVolume -in gridx.nii.gz -out wgridx.nii.gz -trans input.df.nii.gz -target input.df.nii.gz
deformationScalarVolume -in gridy.nii.gz -out wgridy.nii.gz -trans input.df.nii.gz -target input.df.nii.gz
deformationScalarVolume -in gridz.nii.gz -out wgridz.nii.gz -trans input.df.nii.gz -target input.df.nii.gz
@]
The movies below, from left to right, illustrate the result of browsing through each of these images in MRIcro, along sagittal for wgridx.nii.gz, coronal for wgridy.nii.gz, and axial for wgridz.nii.gz.
%center%[Attach:gridx.png Attach:wgridy.png Attach:wgridz.png
%center%Click on each image to look at it in its original resolution
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%center%[[Attach:Attach:gridx.png]] Attach:gridy.png Attach:gridz.png to:
%center%[[Attach|Attach:gridx.png]] Attach:gridy.png Attach:gridz.png
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%center%Attach:[[Attach|gridx.png]] Attach:gridy.png Attach:gridz.png to:
%center%[[Attach:Attach:gridx.png]] Attach:gridy.png Attach:gridz.png
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%center%Attach:gridx.png Attach:gridy.png Attach:gridz.png to:
%center%Attach:[[Attach|gridx.png]] Attach:gridy.png Attach:gridz.png
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%center%Attach:gridx.png Attach:gridy.png Attach:gridz.png to:
%center%Attach:gridx.png Attach:gridy.png Attach:gridz.png
%center%Click on each image to look at it in its original resolution
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Attach:gridx.png
Attach:gridy.png Attach:gridz.png to:
%center%Attach:gridx.png Attach:gridy.png Attach:gridz.png
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Attach:gridx.png Attach:gridy.png Attach:gridz.png to:
Attach:gridx.png
Attach:gridy.png Attach:gridz.png
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(:noleft:) (:notitle:)(:title Visualize Spatial Transformation:)
! Visualization of Spatial Transformation
!!Create Grid Images
The three commands below use the tool ''scalarGrid'' to create the grid images along x, y and z axes.
->[@ scalarGrid -target input.df.nii.gz -grid 0
scalarGrid -target input.df.nii.gz -grid 1
scalarGrid -target input.df.nii.gz -grid 2
@]
An example of the grid images are illustrated in the figures below. From left to right are ''gridx.nii.gz'' (need to be in sagittal view), ''gridy.nii.gz'' (need to be in coronal view), and ''gridz.nii.gz'' (in axial view). In this example, the voxel space, specified by ''input.df.nii.gz'', is 192x224x144 voxels with 1x1x1 mm spatial resolution.
Attach:gridx.png Attach:gridy.png Attach:gridz.png
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