Hi David,

Thanks for sending along that link, I think I understand all that, I'm trying to answer 
slightly different questions that aren't addressed by the standard 4D global normalization.  
In particular, 1) I'd like to compare activity changes between drug levels in terms of 
percent signal changes (where the percentage is computed relative to the local voxel 
mean for each run), and 2) I would also like to use flame12 to detect any region-specific 
changes in mean BOLD signal.

I tried a work around for (1) where I scaled the first level copes by 100/(mean_func) and 
varcopes by (100/mean_func)^2, but for some reason that gave identical results to the 
unscaled case (is there some scaling/normalization that happens when copes are passed 
up to 2nd level?), and for (2) I'm wondering if there's an easy way to get a mean BOLD 
image and its variance from the standard FSL output (I know how I'd do this from scratch, 
but am hoping there's a way to get it for free from what FSL already computes).

Any ideas FSL experts?  Thanks for your help!

--P

PS-- In case it isn't clear, when I scaled the first level copes to "convert" them to percent 
signal change units, what I did was:

scaled_cope(x,y,z) = 100*cope(x,y,z)/mean_func(x,y,z);

(the reason I did this is so that the resulting 2nd level pe's and copes would be in terms 
of percentage signal changes)


On Tue, 12 May 2009 21:22:50 -0400, David V. Smith <[log in to unmask]> 
wrote:

>Hi Patrick,
>
>Somebody will probably have to correct me on this, but I don't think you
>really need to do any normalization here for two reasons. In fact, depending
>on how you do it, normalizing may create spurious deactivations in your data
>(see Laurienti, 2004, JoCN).
>
>1) I think only relative changes matter, so the mean intensity shouldn't
>affect your stats
>
>2) All of the data are scaled to a preset mean. You can see some of the FSL
>course slides for more info on this.
>http://www.fmrib.ox.ac.uk/fslcourse/lectures/feat1_part1.pdf
>
>Hopefully I'm not steering you in the wrong direction. I defer to the
>experts on this one...
>
>Cheers,
>David
>
>
>-----Original Message-----
>From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
>Of Patrick Purdon
>Sent: Tuesday, May 12, 2009 5:52 PM
>To: [log in to unmask]
>Subject: [FSL] Adjusting Global Intensity Normalization? Group Analysis on
>Mean BOLD signal?
>
>Hi FSL'ers,
>
>I'm analyzing data from a drug study, where the drug is likely to change the
>mean BOLD signal in a region-specific manner, in addition to altering
>functional responses to stimulation.  To account for any possible
>region-specific mean BOLD signal changes as a function of drug level, I
>would like to:
>
>1. Normalize each data set (or cope image) by its temporal mean (like
>"mean_func.nii.gz"), essentially creating a "percent signal change image."
>This would allow me to compare drug-level effects in my group analysis in
>terms of percent signal changes.
>     --I tried doing this on some simulated data by scaling the first-level
>"cope1" by 100/mean_func and varcope1 by (100/mean_func)^2, but the flame12
>2nd-level pe's and copes ended up being identical to the unscaled case
>(????).  What could be happening here?  Is there a straightforward way to
>accomplish this?
>
>2. Run a flame12 analysis on the mean BOLD signal as a function of drug
>level.
>     --Is there an easy way to get an unscaled temporal mean and variance
>from the first-level analysis that can be passed up to flame12?
>
>Any suggestions on how to do this?  Thanks a lot for your help!
>
>--Patrick