Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Office: (773) 406-2464
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On Fri, Jun 10, 2011 at 12:10 PM, Pamela LaMontagne
<[log in to unmask]> wrote:
I am preparing to do a PPI analysis and have some fairly basic questions.
1) Identifying the VOI of interest: This Is based off of the group GLM analysis and a priori predictions, correct?
Either one is justifiable. I have used both for past projects.
2) Defining the VOI: Although identified through group analysis, the eigenvariate is extracted on a subject by subject basis. Correct?
2b) If a subject does not have activity in that are do you exclude them from the analysis?
If you threshold the data, and there is no activity, then no voxels will be extracted. However, I like to set the threshold to .999 and grab all voxels in my VOI so I know I am comparing the same brain regions. NOTE: gPPI does not allow a threshold. Darren and others would argue that you should only look at voxels with significant activity. My argument has always been that the connectivity could be important and significant even if the activity does not reach significance. Also, you can get significant group effects in activity without the individual subjects being significant -- although rare.
3) Contrasts for VOI identification & extraction vs. Contrasts for creating PPI variable: The example uses a VOI extracted for the Motion contrast while the Attention contrast is used in the creation of the PPI variable. Is it acceptable to use the same contrast for both steps?
This is fine. But as I said above, a threshold of .999 will grab all voxels.
3b) VOI Batch vs. Results window: when using the VOI utility in the batch window there is not an option for contrast or thresholding, only adjust for effects of interest. Are these necessary or is the eigenvariate calculated despite this information?
Not sure. I always use my own program.
3c) When using the results window clicking on eigenvariate moves the coordinates to the nearest active voxel but in the batch this nearest voxel could be included in the sphere. Is it correct to have the region fixed or to go with the nearest active voxel? This could potentially be a different region so I am hesitant to move the sphere.
I prefer a fixed region and using the mean.
Thanks
Pamela
