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The brain image to be analyzed is called Input. In the user interface the related label occasionally appears capitalized INPUT for clarity.

The processing steps, reflected by the user interface, are the following:

1.Brain Atlas Adjustment page, INPUT layout:

a.Loading of the Input image series which may be static or dynamic.

b.Dynamic  case: Averaging of the series in a specified frame range. The averaged image will be used in all following steps except for the final statistics calculation and parametric mapping.

c.Cropping of the (averaged) Input image to retain mainly the brain part, potentially with some neighboring tissue which helps the normalization (e.g. Harderian glands for PET).

2.Brain Atlas Adjustment page, NORMALIZATION layout:

a.Configuration of the atlas template and the normalization method.

b.Start of the normalization procedure which matches the (averaged) Input image to the selected atlas template.

3.Brain Atlas Adjustment page, NORMALIZED layout:

a.Visual assessment of the normalization.

b.In case of a bad match, return to the NORMALIZATION layout, change the normalization approach, and normalize again. Repeat until a satisfactory match is obtained. If no automatic procedure works, resort to manual rigid matching.

c.Start transformation of the atlas brain regions so that they can be overlaid on the (average) Input image as segments.

4.Brain Atlas Adjustment page, BRAIN SEGMENTS layout:

a.Visual assessment of the overlaid segments.

b.Selection of the image space (Atlas or Subject) where the VOIs are generated.

c.Start generation of the outline VOIs in the result space.

5.Brain Atlas Adjustment page, VOIS layout:

a.Visual assessment of the brain VOI outlines overlaid on the (average) Input image by the user. If the match is not satisfactory, return to step 3 and try to improve the normalization.

b.If needed, manually adjust the whole VOI set or individual structures. For instance, all VOIs can be scaled at once.

c.Start calculation of the VOI statistics on the Input image.

6.Results statistics page:

a.Inspect the results.

b.Save the statistics table (or time curves in dynamic case).

c.In the dynamic case transfer the curves (usually PET tissue time-activity curves) to the PKIN tool (option) and continue there with modeling.

7.Save the complete configuration of the processing with Save protocol icon in the top line.

Parametric Mapping of Dynamic Data (PXMOD Option)

In the case of a dynamic Input series, return to

8.Brain Atlas Adjustment page, VOIs layout:

a.Select an appropriate parametric mapping method.

b.Proceed to parametric mapping.

9.Parametric Mapping page:

a.Perform the Parametric Mapping workflow as in PXMOD.

b.Save the parametric maps.

10.Save the complete configuration of the processing including parametric mapping with Save protocol icon in the top line.