Quick manual

The program works in Java sand-box mode. In three occasions the program will try to get access to local files: loading MRI images, loading 3DS models and save results. The program implements these functions via Java, presenting a warning message indicating which files will be accessed. The user has the chance to decide the files to be loaded into the program. However, the result file will only be generated by the program and be stored in Desktop (Windows)/Home directory (Linux). I guarantee that it is just a text file and will do no harm to the system.

Open MRI data: Choose MRI files in Analysis format in IMG/HDR pairs. However, the program will not try to recognize whether the two files are from the same subjects, so it is user’s responsibility to make sure the IMG/HDR pair is from the same subject.

Load 3DS model: Choose 3DS files or OBJ files. However, there are some many file formats end with OBJ, so be sure it is WaveFront 3D model format.

Load default headpost: That is the headpost used in our lab. If it is exactly the same size/shape, the users will have to create 3D models for their own and use them instead of the default one.

Load default chamber: It is the 6-ICO-J0 from Crist Instrument Co., Inc. Again, the users need to make their own chamber models if this is not the one they use.

Fly around: The whole view of the program works as a kind of flight simulator. That is, as flying on the surface of earth, the user will use LEFT, RIGHT, UP and DOWN arrow keys to move around. Using R and T to change flight direction, so it looks like a rotation. Using PAGE UP and PAGE DOWN to zoom in/out.

Moving focus point: Try A/Z, W/S and E/D keys to move focus point, which will change the planes showing in standard view. The users need these keys to surfing in MRI matrix, if the MRI images have been loaded.

Moving/Rotating 3D models: If the model has been selected in the MessageWindow, try mouse drag to move it. However, since mouse drag can only give 2D information, it will take several combinations of changing view direction by arrow keys and mouse drag before get the model to desired position. Try X/C, V/B, N/M keys to rotate the model, especially when it looks not fit with the outer surface of the skull.

Moving Key Points: Again, combination of mouse drag and arrow keys. However, if the key points are linked with a model, they will change their position with the model accordingly unless the user breaks the linkage in the MessageWindow.

Defining Markers: To defining coordinate markers, the user should load MRI images in, moving focus point (A/Z, W/S and E/D keys) to marker positions (left ear bar, right ear bar, center plane, IOP or frontal area, superior area) and select the corresponding checkbox in MessageWindow. A small colored sphere will be place at the focus point/corrected position (see Markers and Coordinates for details).

Image intensity parameters: The program will try automatically to choose the display intensity parameters for best gray/white matter contrast, after loading the MRI images. However, these parameters may change the image intensity parameters in Misc tab in MessageWindow. It is especially necessary during the procedure of defining markers, if the images are obtained by a surface coil and has relatively low intensity in areas around ear bars. Change the numbers in Min/Max edit box and press Apply button to see what happens.

Segmentation parameters: This is one of the core parts of the program. The program will try its best guess of the parameters. Get a glance of the Threshold/Eraser Size/Volume Size parameters in Misc tab and press Apply button to see what happens. The program will try to segment the outer surface of the skull from the image data, without any assumption. It will take a fairly long time, if the dataset is large. However, it may fail or not optimized. Click Message tab and check internal messages. A line starts with MaxCluster will give some clues. Thresold will decide the value above which data could be treated as part of the brain, instead of air/noise. Eraser Size will define the cubic size of erasers to delete small noise clusters. The idea is that if a cluster could be isolated within the size of the eraser, it could be deleted as noise. Volume Size will decide the reserved final cluster size. Clusters with size smaller than this parameter will be deleted while remaining cluster/clusters will be treated as outer surface of the skull.

Radial View: After segmentation, an outer surface of skull will be generated. Using F/G keys to change the radius for this view, the user could have the chance to look into the brain, as if brain is an onion, which may get a better experience of the position of interested area, compared to standard 2D plane view.

Message tab: Some internal messages. Most of them are nonsense, kept for debugging purpose, but some may useful.

Menu->View->Radial View: Change to Radial View, if the segmentation has been done.

Menu->View->Standard View->Sagittal View / AxialView / CoronalView, etc.: Change to standard view, including possible combinations of the three traditional planes.

Menu->Window->Message Window On: Bring back the message window, if by chance it has been closed, although I don’t suggest so.