CRUISE/software/docs
<meta name="title" content="CRUISE Control Documentation"/>
CRUISE Control Documentation
CRUISE quick start guide
1) Open MIPAV [1] and check the Plugins menu to ensure that the CRUISE plugin has been installed ([2]).
2) Open a stripped image, then open the CRUISE plugin. The interface will automatically open to the TOADS 2007 tab.
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.
4) Under Image Modality, make sure the proper type of image is selected.
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 [3], or input another atlas text file of your choice.
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.
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.
IMAGE 6
IMAGE 7
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).
IMAGE 8
IMAGE 9
10) To view a topological reconstruction of the extracted cortical surfaces, you may look at the files within the tgdm folder.
IMAGE 11
11) Instructions for viewing in MIPAV...
12) Instructions for viewing the surface images with Paraview [4].
a) Install the Paraview plugin
b) Open Paraview
IMAGE 12
c) 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.
IMAGE 13
d) The filename of the image you have chosen will appear in the upper left side of the interface.
IMAGE 14
e) 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.
IMAGE 15
f) To view all of the .vtk output files as one image with nested surfaces… (actually, I don’t know how to do this, unfortunately, so I will need some more help with that).
