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Project Admins:

• Christian Tatarau

[Christian Tatarau]

1 Start the volume exploration tool
Type the following line into the Matlab window at session start:

addpath(genpath('[path]'))

Then start the program by typing:

batForm

for example:

addpath(genpath('D:\BatViewer_Data\batViewer'))
batForm

[Christian Tatarau]

2 Usage
2.1 Main Window
There are three main tabs: myData, Matching and Preferences

• myData: here you can load a CT volume, load a skull scan and load the atlas or any other volume related to the CT data

• Matching: allows you to correct the spatial position of the skull

• Preferences: here you can set some GUI preferences and set the origin and voxel size of your CT data. Without this information, the program is not able to compute any spatial information

2.2 myData

• Button "Load Volume": loads a set of frontal slices or a DICOM file and creates a 3D volume

• Button "Show Volume": starts the volume exploring tool and shows the three cutting planes – frontal, transversal and saggital

• Button "Load Scan": loads the skull scan. You generate this file in the VEE program.

• Button "Show Scan": displays the scan data on the CT images

• Edit field "resize factor for atlas": lets you resize the atlas images. As anatomical images may be very detailed and have a high resolution, the available RAM may be too small. In this case you need to scale the images down. Type a number between 0 and 1 in order to produce smaller images. Use the point "." as decimal separator.

• Button "Load Atlas": loads a set of image files and builds a volume

• Button "Show Atlas": opens a window and shows a frontal cutting plane within the atlas volume

• Upper text field: shows the path and the size of the CT volume

• Lower text field: shows information about the scan data

2.3 Matching:

• Box "matching": contains six edit fields, one for each transformation along the X, Y and Z axis. Change the value and press enter.

• Button "Atlas ↔ Real Coordinates": opens a window where you can convert atlas coordinates into the real coordinates. You can do the same for electrode paths. In the latter case you need to set two points: the target point and the starting point. Both define the electrode path in the brain.

• List box "Auxiliary Points": if you have stored additional points after the skull scan, you can access them from this list box. One click on a point will move the volume explorer to the specified coordinates

2.4 Preferences

Box "Scan Data"

• "show scan data": uncheck it if you don't want the scanned skull to be displayed on the volume slices.

Interpolation method:

• "Raw Data": will show only the measured skull points on the slices, without any interpolation. By that you see exactly what you have measured, but as the distance between scan rows can be high, it may happen that you don't see any points if you are just between the existing data lines.

• "grid data": this option builds a grid with constant grid size by interpolating the measured points.

• Origin: here you can set the origin of your CT volume and the voxel size. The program cannot read this information from DICOM and image files usually do not contain such information. thereforee you need to set manually this data for every new volume. The data will be saved in a file named "volume_properties.txt" int he same folder as the data. There is one file per folder, therefore you cannot save several volume files (such as DICOM) in the same folder, otherwise the volume information will be overwritten.

• Button "set origin and voxel size": writes the data into the file

• "show origin": check this option if you want to see the volume origin on the slices

• "enable cross hairs": shows cross hairs at the cutting planes at the current coordinates

Graphic options:

• Color map: chooses which color map to use for the CT slices

• "Erase mode": xor: the cross hairs are superposed on the slice image and computated with xor so that you still can see the background

normal: the cross hairs are opaque

• "line width": here you can choose between thin and thick cross hairs

[Christian Tatarau]

Dear users: I will upload a set of data samples as soon as I can. For now, you have to be patient and just browse or use the code.