User Tools
Threshold and Overlay
Threshold
See Also Thresholding
After opening an activation map in fScan using the behavioral and functional files (see how here), it is important to adjust the threshold of the image for more clarity. Press the f key to filter the image, and then press F7 to set the threshold to '-4.0,4.0', which should eliminate most of the extraneous activity. The resulting image will be primarily in green or yellow, yellow showing all the activation of the first task in the command:
- -r run1list.txt delay 4.5 -ttest 1 2
In this case it is 1.
The green indicates all the additional activation of the second task in the command (2) which does not overlap with the first.
Overlay
The next step in analysing the behavioral data is to overlay the activation map over the anatomical rendition of the subject. Opening the anatomical image, select the '3-plane' icon from the View Taskbar. Following the overlay procedure (see how in Overlay and Alignment), the colored behavioral map will be transposed onto the anatomical image. No adjustments should be necessary if the alignment of functional and anatomical files were already made.
Multiple Overlays
A useful tool in comparing scans, a multiple overlay involves some manipulation of the color and threshold of the activation map. A single overlay can show the comparison between two tasks in the same scan. To compare with other tasks from different scans, it is necessary to make certain adjustments.
Open two activation maps from two different scans involves the same process as seen here, and changing the threshold as demonstrated above. Then select which tasks to compare. If one activation map is comparing task 1 and task 2, it is possible to eliminate one task from the map by increasing or decreasing the threshold. The first task (in this case 1) will be the yellow, and by increasing the threshold (using the up arrow key) it will disappear. The opposite is true for the second task (in this case 2), which will disappear by decreasing the threshold. Generally no more than -5.0 or 5.0 is needed, but there is some variability. Once there is only one task remaining, the color can be changed by simply selecting a different color icon in the Threshold Taskbar. Now the activation maps have different color schemes, allowing them to both be overlayed without confusing which task is which. The resulting activation map can compare various tasks from various scans.
See Also:
