| As soon as I have finished more of the extended guide, there will be a short description and link to it here.
Cortical surface viewing instructions
Instructions for viewing in MIPAV
| As soon as this is possible, I will put instructions here.
Instructions for viewing the surface images with ParaView
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Install ParaView 3.2.1.
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Open Paraview
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Browse to the .vtk output images using the File menu. When you have selected the surface file you would like to view (inner, middle, or outer surface), click on the OK button at the bottom of the file selection window.
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The filename of the image you have chosen will appear in the upper left side of the interface.
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To visualize the surface, press the Apply button under the Properties tab in the lower left side of the interface. This will result in a three-dimensional display of the image you have chosen in the large grey box on the lower right side of the interface.
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Using the Volume Converter Plugin in MIPAV
To view individual slices with nested surfaces, it is necessary to use the Volume Converter plugin in MIPAV.
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Open MIPAV and your source image, and go to the Volume Converter plugin.
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Under the Volume area of the interface, use the drop-down menu to choose your source image. If you want to open another image, you may do so using the Browse button.
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Use the drop-down menu under File Type to select the type of output file you wish to generate. In this case, you should choose vtk, which is all the way at the bottom of the option list.
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Press the OK button at the bottom of the interface. Next, you will be required to input a target directory for saving the output file. When you have selected this directory, press the Save button.
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A box will appear when the plugin has finished converting your source image to a vtk file.
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Viewing Nested Surfaces in Paraview
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Open Paraview.
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Use the File menu to browse to the output folder for the Volume Converter, which will be named volconvert.
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 Volume Converter output folder |
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Select the .vtk file inside the volconvert folder and press the OK button.
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Your selected .vtk file will be visible in the upper left side of the Paraview interface.
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On the lower left side of the interface, click on the Display tab. Scroll down to the Style section, and use the menu to the right of Representation to Volume.
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Scroll up in the Display tab to the Color area. Click on the Edit Color Map button.
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Click on the Choose Preset button to bring up the preset color range selector. You will probably want to choose to have your image represented in Grayscale.
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If you choose the Grayscale preset, you may want to adjust the color scale to get a better contrast. When you are happy with the contrast, click on the Close button.
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Use the File menu to browse to the outer surface vtk file. Press the OK button once you have selected the file. Once it is loaded in Paraview, press the Apply button.
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Use the File menu to browse to the inner surface vtk file. Press the OK button once you have selected the file. Once it is loaded in Paraview, press the Apply button.
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Once the surface files are loaded, click on the Group Datasets icon, which is the second button from the right on the toolbar immediately above the upper left side window containing the loaded filenames (this icon is marked with a red circle on the Group Datasets image). After you have clicked on this icon, press the Apply button.
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Next, locate the Cut icon. This is the fourth button from the left on the toolbar immediately above the upper left side window containing the loaded filenames (this icon is marked with a red circle on the Cut image). Press the Apply button after using the Cut tool.
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Go to the Properties tab and locate the Normal subsection of the Slice Type: Plane area. Modify these values according to the acquisition orientation of your source image. For example, if you have used an axial image, change to values in the Normal section to 0,0,1.
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Viewing Labeled Surfaces in Paraview
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Label your CRUISE surface. There are many ways to do this. A brief overview can be found here.
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Open Paraview.
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It is often useful to change the look-up-table (LUT) used to color the surface. To do this, scroll up in the Display tab to the Color area. Click on the Edit Color Map button.
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Click on the Choose Preset button to bring up the preset color range selector. Select the Import option to choose a custom Color Scale.
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Paraview color scales are stored as .xml files. A good choice for surfaces with discrete labels is the striped Color Scale, and xml file for which can be found here. Click Ok to choose a custom color scale
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Select the Color Scale you would like from the menu, and click Ok. Click Close to exit the color scale editor. Your labeled surface should now have a different color for every label.
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Creating Animations in Paraview
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Here we will briefly walk through the steps in creating a simple animation in Paraview. The example shown will create an animation showing axial cuts of a cortical surface for a number of axial slices.
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Open Paraview and load the surfaces or volumes you would like to animate.
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Use Paraview's tools to create the visualization you would like. Here, we took an axial slice through an inner cortical surface.
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Click View > Animation Inspector to open the Animation Inspector. Under 'Track Selection' change the 'Selected Object', and 'Propery To Animate' drop down menus to select the objects and properties you would like to animate. In this example, we would like the plane which cuts the surface to move in the z direction. We choose 'Slice2' as our selected object, and 'Slice Type - Origin(2)' which refers to the slice plane's z-coordinate as the 'Propery To Animate'.
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Next, we need to specify the keyframes for our animation. In this example we will need two keyframes. In the 'Animation Inspector' scroll down to the 'Key Frame Editor' and click on 'Add Key Frame' once. You will see that the key frame options are now active. Change the 'Key Frame Value' to the value you would like the 'Property to Animate' to take at time=0. We chose a value of 50 for our axial slice. Click the up arrow to the right of 'Key Frame Index' to edit the parameters for the second key frame. We chose a value of 135 for our axial slice.
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To bring up an overview of the current animation, click View>Animation View. This should open a panel showing the objects and properties currently being animated. In our example, Slice2 - Slice Type - Origin(2) is being animated. Double clicking the object name will open a window as shown in the figure to the right. It shows that this objects properties start at 50 and end at 135. Also displayed is the interpolation. The default, ramp, creates a linear change in the property with time.
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Close the Animation Keyframes window. Again in the Animation Inspector, change play mode to 'Real Time'. This allows you to specify the duration of the animation. Choosing 'Sequence' allows you to specify the number of frames in the animation. Once this is done select File>Save Animation and specify the framerate, duration, and resolution of the animation. When you are finished, click ok. Note: Paraview may automatically change the resolution of the animation depending on your settings.
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