PowerMap User’s Manual

Laboratory for Complex Brain Networks

Wake Forest University
http://lcbn.wakehealth.edu

Last Revised 12/15/2011

Table of Contents
Disclaimer....................................................................................................................................................3
1. Getting Started.......................................................................................................................................3
1.1 Installation and Compatibility......................................................................................................3
2. Power and Sample Size Image Generation..............................................................................................4
2.1 Selecting Image Files and Specifying Options....................................................................................4
2.2 One-Sample T and Linear Regression................................................................................................5
2.3 Two-Sample T....................................................................................................................................7
2.4 One-Way ANOVA...............................................................................................................................8
2.5 Power or Sample Size Image Output...............................................................................................10
2.6 Repeat Analyses...............................................................................................................................10

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 Disclaimer

The PowerMap software tool comes with ABSOLUTELY NO WARRANTY. Although we are confident
that the algorithm and processing functions included in PowerMap are theoretically valid, we also
would like to warn users that statistical power calculation rarely can account for all the variability
present in data yet to be collected. Consequently, we cannot guarantee the accuracy of the power
or sample size calculation results. We claim no responsibility for PowerMap suggesting fewer or
more study subjects than actually needed in a study. In addition, we claim no responsibility in
success or failure of research funding proposals planned using PowerMap. We provide no formal
statistical consulting or formal technical support for PowerMap. Thus users should use PowerMap
at their own risk.

1. Getting Started
PowerMap is a software tool specifically designed for neuroimaging studies. PowerMap allows its
users to calculate statistical power and sample sizes for future studies based on pilot study results.
The power calculation method used in PowerMap can account for massive multiple comparisons
among correlated voxels often present in neuroimaging data. Results are in the form of 3D power
images or sample size images, enabling visual representation of spatially varying sensitivity within
the brain. PowerMap is a self-contained package, and does not require any other neuroimage
analysis software tools.

1.1 Installation and Compatibility

PowerMap has been tested with MATLAB R2009 running on Windows and Linux machines, and is
compatible with statistic images generated using SPM5 or later, or any other package that produces
statistical images in NIfTI or ANALYZE format with a NIfTI-compatible header file. MATLAB R2009 (or
later) is required, with the Statistic Toolbox installed. To install, download the PowerMap package
from https://sourceforge.net/projects/powermap/. Unpack the files and place them in a directory.
Add that directory to your MATLAB path by opening MATLAB, selecting File>Set Path, and choosing
the PowerMap install directory. Save the new MATLAB path file.

PowerMap does not include an image viewer. A user can use their preferred image viewing
software tool to view power and/or sample size images. Image viewing tools include SPM, FSL, and
MRIcro.

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2. Power and Sample Size Image Generation
2.1 Selecting Image Files and Specifying Options
Run PowerMap by typing pm_gui at the MATLAB prompt. Make sure you have added the installed
directory to your MATLAB path ahead of time. The main PowerMap GUI screen will appear, as
shown in Figure 1. Use the Browse buttons to select a statistic image (for example a T-statistic map).
The statistic image refers to a statistic image generated from an analysis of pilot data. PowerMap
can handle statistic images generated by one of four simple study designs: one-sample T, two-
sample T, linear regression T-test for slope, and one-way ANOVA. Also select a mask image and an
output directory. The mask image can include all brain voxels to analyze the entire brain, or
alternatively the mask can include only voxels in a particular area if there is an a priori hypothesis
for that brain area. Create a unique output directory each time you run PowerMap to avoid
overwriting previous power or sample size images. Finally, select the test-type based on the statistic
image and click the Next button.

Figure 1. The main PowerMap GUI screen.

A screen for specifying map options will appear, as shown in Figure 2. To generate a power image or
a sample size image, select the corresponding option under the Map Type panel. Select the
correction method, either FDR (false discovery rate) or FWE (family wise error) and indicate the
desired level of significance in the correction threshold box. One of the crucial pieces of information
for the FWE-based power is the image smoothness. If smoothness information (i.e. the full-width at
half-maximum or FWHM) of the statistic image is known this can be entered manually in the next
screen (Figure 3), or if unknown it can be estimated from the data. Note that this estimation
procedure is not guaranteed to be accurate, and in fact may not be as accurate as other estimation
methods, such as the one used by SPM. Please use at your own risk. Click the Next button. If you
indicated that the smoothness information was known, enter the X-Y-Z dimensions and select the

Last Revised 12/15/2011

 units as voxels or millimeters. Click Next to continue, and follow the appropriate directions in
sections 2.2 – 2.4 depending on the test type selected.

Figure 2. Selecting map type and specifying options.

Figure 3. Specifying the smoothness information, if known.

2.2 One-Sample T and Linear Regression

For a one-sample T test or a linear regression, PowerMap assumes that there is a single group in the
analysis. A window will appear (Figure 4) in which the group size associated with the statistic image
can be entered.

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 Figure 4. Indicating group size of pilot study.

Click OK when done entering the group size, and a window for entering the degrees of freedom will
appear (Figure 5). Enter the degrees of freedom for the T-statistic image selected earlier. Typically
for a one-sample T test, this is the group size minus 1. For a linear regression model, this is the
group size minus the number of regression parameters. If there is an intercept term in the
regression model, don’t forget to count the intercept in the above calculation.

Figure 5. Entering the degrees of freedom for the statistic image.

Click Next in the degrees of freedom window. If you selected to generate a power image on the
previous screen, an additional screen will appear for specifying the number of subjects anticipated
to participate in the full-scale study (Figure 6). Enter the number of subjects, and click OK. If you
selected to generate a sample size image on the previous screen, an additional screen will appear
for inputting the desired level of power (Figure 7). If so, specify the power and click Run. Continue
to section 2.5 on PowerMap output images.

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 Figure 6. Indicating anticipated group size for full-scale study.

Figure 7. Specifying the desired power of full-scale study.

2.3 Two-Sample T
For a two-sample T test, PowerMap assumes that there are two groups in the analysis. A window
will appear for the group size associated with each group in the pilot study (Figure 8). Enter the size
of group 1 and click OK. Another window will appear to enter the size of group 2. Click OK again and
a window for entering the degrees of freedom will appear (Figure 9).

Figure 8. Specifying group size for each group.

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 Enter the degrees of freedom for the T-statistic image selected previously. Typically for a two-
sample T test this is the sum of the group sizes minus 2.

Figure 9. Entering the degrees of freedom for the statistic image.

Click Run, and if you selected to generate a power image on the previous screen, an additional
screen will appear for specifying the number of subjects anticipated to participate in the full-scale
study (Figure 10). Enter the number of subjects and click OK for each group. If you selected to
generate a sample size image on the previous screen, an additional screen will appear for inputting
the desired level of power (Figure 11). If so, specify the power and click Run. It should be noted
that, for the calculation of a sample size image, a balanced design (i.e., equal number of subjects
per group) is assumed. Continue to section 2.5 on PowerMap output images.

Figure 10. Indicating anticipated group size for full-scale study.

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 Figure 11. Specifying the desired power of full-scale study.

2.4 One-Way ANOVA

A window will appear for specifying the number of groups in the ANOVA (Figure 12).

Figure 12. Specifying the number of groups in the ANOVA.

Enter the number of groups and click Next. A window will appear for the group size associated with
each group in the pilot study (Figure 13). Enter the size of each group and click OK between groups.

Figure 13. Specifying group size for each group.

After the group size for each group has been entered, a window for specifying the degrees of
freedom will appear (Figure 14). Enter the numerator and denominator degrees of freedom
associated with the F-statistic image selected previously. Typically the numerator is the number of
groups minus 1, and the denominator is the sum of the number of subjects in all groups minus the
number of groups.

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 Figure 14. Entering the degrees of freedom for the statistic image.

Click Next, and if you selected to generate a power image on the previous screen, an additional
screen will appear for specifying the number of subjects anticipated to participate in the full-scale
study (Figure 15). Enter the number of subjects and click OK for each group. If you selected to
generate a sample size image on the previous screen, an additional screen will appear for inputting
the desired level of power (Figure 16). If so, specify the power and click Run. It should be noted
that, for the calculation of a sample size image, a balanced design (i.e., equal number of subjects
per group) is assumed. Continue to section 2.5 on PowerMap output images.

Figure 15. Indicating anticipated group size for full-scale study.

Figure 16. Specifying the desired power of full-scale study.

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2.5 Power or Sample Size Image Output
After PowerMap has finished running, a power surface image will be displayed on screen (Figure
17). In the output directory there will be a file called precalcFDR.mat or precalcFWE.mat, depending
on the type of correction. This file contains the power surface data used to generate the power map
and the sample size map. Note that if a precalcFDR.mat or precalcFWE.mat file was found in the
output directory, it is assumed that the user is repeating an analysis previously run, but wishes to
change the level of power or anticipated sample size. If so, this precalc file is used for the analysis.
Also present in the output directory is an effect size image.

Figure 17. An example power surface automatically displayed after the analysis is complete.

If you are generating a power image, an image file named PowerImg.img will be created for the
power map image. If you are generating a sample size image, an image file called NImg.img will be
created containing the sample size map image. In the sample size map image for a two-sample T-
test or a one-way ANOVA, the voxel value corresponds to the number of necessary subjects per
group to achieve the desired power in a balanced design. Image files can be viewed using any
imaging viewing software such as MRIcro(n), FSL, or SPM. Examples of power and sample size
images that would be generated are shown in Figure 18 (power) and Figure 19 (sample size).

Figure 18. An example power map.

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 Figure 19. An example sample size map.

2.6 Repeat Analyses

Sometimes a user may wish to repeat an analysis previously run, but with different input
parameters. If you wish to re-run an analysis and are changing only the level of power or
anticipated sample size, back up to the appropriate screen (either power or sample size) and enter
the new values. Continue through the remaining screens to run the analysis. In either of these
cases, if the precalc and effect size image files are in the output directory, PowerMap will not
calculate a new precalc file and the analysis will run faster. However, if you wish to change
something else (e.g. the FWHM), you must remove or rename the precalc and effect size image
files, and then continue from the screen you wish to edit and through all subsequent screens. All
data entered into PowerMap GUI screens that are still open are retained in memory, so it is only
necessary to continue from the last edited screen. If you do not wish to overwrite old images, be
sure to rename those before re-running PowerMap.

Last Revised 12/15/2011