User Tools
Overlay and Alignment
In order to analyse the data properly, its important that the functional and anatomical image sets are correctly aligned to prevent innaccurate results. Selecting the anatomical image, display it in the 3-plane view (the icon is in the View Taskbar). The brightness of the image can be adjusted by using the brighten/darken icons in the View Taskbar, or by toggling the up and down arrows.
Overlay
Also see Overlay
The next step to align the data is the 'Overlay' function. Opening the Overlay Taskbar, click the image you wish to overlay first and then click the image you want as an underlay. In this case, the overlay should be a functional image, and the underlay one of the anatomical images (see images in workspace files). Then click the icon for overlay. The two windows should superimpose, overlay on top of underlay. To distinguish the superimposition, assign a different color for overlay then for underlay (ex: red for overlay, green for underlay). To adjust the brightness of the overlay, toggle the brighten/darken icons, or the up and down arrows. To adjust the brightness of the underlay, select the icon for underlay only, and toggle the brighten/darken icon or the up and down arrows. Then select the icon for both overlay and underlay again.
Align
Also see Align
When the two images are suitably brightened or darkened, select the 'Align' icon in the Overlay Taskbar. Another tab will open, the Alignment Taskbar, and allow adjustments to be made. There are several four different forms of adjustment: forward/back, left/right, up/down, and grow/shrink. Depending on what sort of adjustment needs to be made, click the appropriate icon, and right-click to see which arrow keys corresponds with that adjustment (adjustment references).
To make sure the adjustments have been made comprehensively, it is necessary to check the overlay of the other functional image sets. Go to the Cortmap Tab in the Taskbar Menu, and select the icon that says 'Copy Alignment'. The alignment matrix created with the initial overlay will be copied to all the other functional images. After copying the alignment, overlay the other images to make sure this aligment is satisfactory across the board. Make adjustments as necessary, and click 'Copy Alignment' again. Continue this with all the functional images until the alignment is satisfactory. Alternatively, checking the alignment of the first and last functional images should yield the greatest discrepancies and fitting alignment to both images should make checking the alignment of all the images in between unnecessary.
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