Hi Derbin, I have not thought about doing a power calc with FDR before, but what you propose seems reasonable. Maybe someone else on the list has more experience with this.

doug

Derin Cobia wrote:

Hi Doug,

To follow up on this question, we were able to calculate effect sizes for every vertex on the surface using the gamma(var).mgh files, as well as an average effect size across each hemisphere surface using the equation below. In determining alpha, would the most appropriate method be to use the FDR-corrected alpha level that results from our pilot analysis? For example, for a two-group comparison we FDR at 0.05, which results in a corrected /p/ (alpha) of 0.001, and we use that for the power analysis calculation (#3 below), thanks.

-Derin

On Mar 22, 2011, at 4:55 PM, Douglas N Greve wrote:

...

For the power analysis, you need four things:

1. Effect Size
2. Number of Subjects
3. Target False Positive Rate (alpha)
4. Target False Negative Rate (beta)

Given any 3, you can compute the 4th. You can get the Effect Size from the output of the QDEC analysis. Each analysis creates a GLM directory, and there is a directory for each contrast in the GLM dir. In the contrast dir, you will find several files, but the important ones for this are the gamma.mgh and the gammavar.mgh. The gammavar is the square of the error bar (ie, t=gamma/sqrt(gammavar)). The gamma will not change as you add subjects (at least in expectation). The gammavar will drop linearly with the number of subjects (again in expectation). The effect size will then be gamma/sqrt(gammavar*Npilot), where Npilot is the number subjects in the pilot study. In a new study with Nnew subjects, the expected t will be tnew = gamma/sqrt(gammavar*Npilot/Nnew)

doug

Emily Rogalski wrote:

...

How would you complete a power analysis for a whole brain group comparison qdec analysis?

Thanks, Emily

-- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogalski@gmail.com mailto:erogalski@gmail.com

mailto:erogalski@gmail.com

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.