Re: [Freesurfer] FSGD Contrast Setup Question

Hi Josh, there is not a way that I know of to do the paired analysis if some are missing a scan. A "real" statistician might know of a way theoretically, and I might be able to implement that theory, but I don't know myself. So does that mean you want to do an unpaired test? doug

Roffman, Joshua L.,M.D. wrote:

Hi Doug, Thanks for weighing in. For this study, while most subjects have 2 sets of good scan data (pre and post treatment), a number have only one set (pre or post). We're hoping to use all of the data given that it's overall a pretty small study. Is it possible to run the paired analysis if we are missing pre or post data for some subjects? Best, Josh

-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thu 9/15/2011 4:54 PM To: Adam Nitenson Cc: freesurfer@nmr.mgh.harvard.edu; Roffman, Joshua L.,M.D. Subject: Re: [Freesurfer] FSGD Contrast Setup Question

Hi Adam, you have a "repeated measures" design. In your case, this is best handled using a paired analysis. You can search for "paired" on the wiki to get instructions. The easiest way to do this is to run mris_preproc with the --paired-diff option, then follow the instructions for the "standard" one or two group analysis (search for "fsgd").

doug

Adam Nitenson wrote:

...

Hi Freesurfers,

 I am trying to set up both a 2 Group 1 Covariate and a 4 Group 1

Covariate analysis but just want to make sure I'm using the correct contrast option.

 For the first analyis, the two groups are Drug Pre and Drug Post,

with folate-serum level as a covaraite. We want to keep the covariate under consideration in our analyses, but we really want to look at the difference between the Drug Pre and Drug Post activation (so folate-serum level is more of a nuisance variable). It seems that the first option under the 2G1V Page "Null Hypothesis: is there a difference between the group intercepts? Is there a difference between groups regressing out the effect of age? 1 -1 0 0" reflects this idea best.

  For the second analysis, the 4 Groups are Drug Pre, Drug Post,

Placebo Pre, and Placebo Post, with the same folate-serum level covariate. We are intersted in the double subtraction of (Drug Post

• Drug Pre) MINUS (Placebo Post - Placebo Pre), but again wish to

covary by folate level. For this it seems like contast 7 on the 4G1V page "is there an interaction between gender and handedness regressing out the effects of age? 0.5 -0.5 -0.5 0.5 0 0 0 0" is best.

Is this the best way to go about analyzing these two questions?

Thanks,

Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson@nmr.mgh.harvard.edu Phone: 617-643-3215 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer