Anat and stim images must have the same planar field of view and orientation, however, their slice spacing may differ. When the slice spacing does differ between the Anat and the Stim, the Map images generated from the Stim images will not be aligned to the Anat. To approximate the map values at the anat slices, linear interpolation between the nearest slice above and below are used to generate the color overlays. By pressing the Show Align button (4-1), an alignment report is printed out to the standard output (i.e. the shelltool window where stimulate was invoked).
An example of an alignment report is given in Figure 6. First the planar offset and corresponding slice position in centimeters is given for both the stim and anat images. Then the percentages used for the linear interpolation are given. For example, the anat image slice at offset 1 is located at -1.0 centimeters. There is no stim image slice located at this position. However, there is a stim image slice above and below it; specifically, stim offset of 0 at location -2.67 centimeters and stim offset of 1 at location 0.0 centimeters. To generate a map for this anat slice, 37.5% of the map intensity from the stim slice offset 0 and 62.5% of the map intensity from the stim slice offset 1 are used.
Figure 6: Example Alignment output.