CRUISE/software/docs

CRUISE Control Documentation

CRUISE quick-start guide

Install the

1.	Open MIPAV v4.1.2 and check the Plugins menu to ensure that the CRUISE plugin has been installed (MedIC Downloads). If not yet installed, install iacl-plugins.jar and maps4mipav.jar like a standard plugin.
2.	Open a stripped image, then open the CRUISE plugin. The interface will automatically open to the TOADS 2007 tab.	CRUISE plugin
3.	In the drop-down menu in the Image to segment section, choose the image you want to work with. The list provided here will include any images you currently have open. If you want to open another image, you may either open it through the MIPAV file menu or browse to the image within the CRUISE interface using the Browse button under the Image to segment area.	Image to segment
4.	Under Image modality, make sure the proper type of image is selected.	Image modality
5.	Under Atlas file, input the path for the template you wish to use. You may use the text file from the TOADS atlas to begin with [1], or input another atlas text file of your choice.	Atlas file
6.	Modify any other parameters you wish to change (link to extended guide). You should be able to get a decent result without changing any other options.	All necessary options filled
7.	Click on the OK button at the base of the plugin interface to begin processing. A window will pop up in which you may indicate where you want to save the output files. Once you have chosen a location, press the Save button in this window, and the processing will begin.	Choose output directory TOADS progress bar
8.	You will immediately see a very large jump in memory use by MIPAV. If you have enough memory that is not allocated to MIPAV, you may use your computer with the process running in the background. If you find your processes are lagging, leave your computer alone until the iterations are complete.
9.	After processing has finished, there should be several output folders, all within a folder named cruise which will be in the same directory as your input file. These folders should include ace, crop, gvf, tgdm, Toads07, and topo_correct. Please see the extended guide for more information on the output files in each of these folders (link to extended guide).	cruise output directory Folders within cruise
10.	To view a topological reconstruction of the extracted cortical surfaces, you may look at the files within the tgdm folder.	tgdm contents

CRUISE extended guide

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 1. Install ParaView 3.2.1. 2. Open Paraview Paraview 3. 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. Select .vtk file to view 4. The filename of the image you have chosen will appear in the upper left side of the interface. Surface file loaded 5. 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. 3d surface view 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. 1. Open MIPAV and your source image, and go to the Volume Converter plugin. Volume Converter 2. 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. Select source image 3. 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. Select File Type 4. 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. Select output directory 5. A box will appear when the plugin has finished converting your source image to a vtk file. Conversion is complete Viewing Nested Surfaces in Paraview 1. Open Paraview. Paraview 2. Use the File menu to browse to the output folder for the Volume Converter, which will be named volconvert. Volume Converter output folder 3. Select the .vtk file inside the volconvert folder and press the OK button. Select .vtk file 4. Your selected .vtk file will be visible in the upper left side of the Paraview interface. .vtk file loaded 5. 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. Volume display 6. Scroll up in the Display tab to the Color area. Click on the Edit Color Map button. Edit Color Map 7. 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. Preset Color Scales 8. 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. Color Scale Color Scale adjustment 9. 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. Load outer surface file 10. 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. Load inner surface file 11. 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. Surface files loaded Group Datasets 12. 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. Cut 13. 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. Reset orientation Viewing Labeled Surfaces in Paraview 1. Label your CRUISE surface. There are many ways to do this. A brief overview can be found here. 2. Open Paraview. Paraview 3. 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. Edit Color Map 4. Click on the Choose Preset button to bring up the preset color range selector. Select the Import option to choose a custom Color Scale. Preset Color Scales 5. 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 Paraview Striped LUT 6. 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. Labeled CRUISE Surface Creating Animations in Paraview 1. 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. 2. Open Paraview and load the surfaces or volumes you would like to animate. Paraview 3. Use Paraview's tools to create the visualization you would like. Here, we took an axial slice through an inner cortical surface. Edit Color Map 4. 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'. Preset Color Scales 5. 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. Paraview Striped LUT 6. 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. Animation keyframes 7. 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. Animation settings