Conducting Level 2 Analysis
To begin level 2 data analysis, click on the “SPM level 2” option in the “Data Analysis” dox. This will open “Statistical Parametric Mapping for level 2”.
In the “Multiple data specification” box, you are able to set up the parameters for your analysis by selecting the number of groups as well as the number of subjects in each group. For example, if there were two groups with 8 subjects in each group, the notation for number of subjects would be [8,8].
After the number of groups and subjects have been selected, begin loading the hemoglobin SPM file of your desired subjects. Note that when the level two load option is clicked, this will bring up the most recently opened window, be sure to confirm the folder that was opened contains the desired SMP subject file. An example of a pathway to an SPM file can be seen in the image.
Navigate to and load all of the desired SPM files that are specific to the desired subject and hemoglobin characteristic. Once all the subjects have been loaded in, the load window will close itself, returning to the SPM level two menu.
The next step is to specify the contrast for the data files selected. Click “Specify contrast” in the “Constrast specification, result visualization” box, the design matrix may look different depending on the group or subject numbers). This will open the SPM contrast manager window.
From this window it is possible to select t-contrast or F-contrast. This selection will depend on the statistical needs of a specific analysis. To begin, enter the name of the test in the first box below the contrast selection box.
The next step is to define the contrast, to do this, click “define new contrast” in the lower portion of the window. In the new window, enter a name in the designated box and check which type of contrast is desired. In the image, the specified contrast is examining a motor task with a t-contrast. R>L means that when right tapping occurs, it is expected that there will be a greater amount of oxyHb in the left hemisphere motor cortex compared to the right hemisphere motor cortex. The contrast weight values tell the program how to weight and compare events during the test. The notation in which this is written can be described as follows. Events with equal weight will be considered part of the same ‘categoty’ and compared against weighted of equal but opposite sign. In the image, the values “1” indicate components of the right finger tap event, specifically the canonical temporal and dispersion wave forms taken together. The “-1” values indicate the same waveforms but for the left finger tap event. The zeros at the end of the notation indicate constants, or baseline. When the submit button is clicked the program will determine if the notation is valid. This will be indicated by a green copy of the notation followed by the word “ok”. After inputing the desired contrast parameters, click “ok”. (Image: contrast manager) After entering the contrast parameters, chose the desired contrast and click “Done”.
In the level 2 SPM window, chose the “view” option from”Contrast speficication, result visualization” box. This will open the “SPM result Viewr” window (Image: SPM result viewer) From this window it is possble to chose the statistical context the results may be viewed in from as well as load previous results. To view resutls simply chose the a statistic from the dropdown window and click “view”.
The beta values for the hemoglobin type you have specified have now been compared across trials according to the parameters you have set. This concludes level 2 analysis of the data.
