CRUISE/software/docs

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CRUISE Control Documentation

CRUISE quick-start guide

1.	Open MIPAV v4.1.2 and check the Plugins menu to ensure that the CRUISE plugin has been installed (MedIC Downloads).
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

|valign="top"|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 6. To view individual slices with nested surfaces, it is necessary to use the Volume Converter plugin in MIPAV. Why can't I make another subheading here? When I try to add it, it shows up under Instructions for viewing the surface images with Paraview, which is not where I want it to be. Grrrr. 3d surface view 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