LLN, le 24/06/05

Dear Florence,

I cannot comment on your "strange" deactivations, but here are some 
quotes extracted from the list concerning scaling at first/second 
level.

Hope this helps,

Mauro.

--------------
- From Jesper Andersson

Global scaling: Is used to remove global signal drifts/trends across 
an indidividual time-series (session). It is largely a remnant from 
the PET days where differences in injected activity could be a large 
part of the scan-scan variance. For fMRI a) most of the "global" 
changes are removed by the high-pass filter and b) the "estimator" of 
"global" intensity that is commonly used can be biased by true 
activations. For that reason it is typically not recommended.

Grand mean scaling: Simply means putting all time series on a common 
scale by normalising the mean of all voxels (over space and time)t to 
100. Doesn't change first-level stats at all (though its application 
at first level will change second level results). Should always (I 
think) be used at first level unless data are somehow "quantitative". 
For second level analysis it is less clear if it should be applied or 
not. Its application at the second level doesn't change the 2nd level 
stats. Neither do I think it helps interpretation. The "grand mean 
scaling" is applied automatically if "global normalisation" isn't 
selected. This means that the effects you observe at a second level 
all have a common scale (as common as it gets with BOLD).
The purpose of "grand mean scaling" is to facilitate interpretation 
of the betas and of any plots that you might do. Say for example you 
have a scanner where BOLD data are arbitrarily scaled so that 
"normal" intensity values are in the range 10e-6. This means your 
betas and the y-axis of any plots will be in the same range, and it 
would take a bit of experience with that particular data until you 
"know" what is a "big" beta. If the data are scaled prior to any 
analysis so that the mean (across voxels and time) voxel intensity is 
100, then interpretation is easier and you can think of it as "sort 
of" % change (N.B. it is _not_ really % change).  What is meant by 
"quantitative" is if your data consist of for example calculated rCBF 
values (using PET) in which case each voxel value has an absolute 
value in terms of ml/(min*100ml) (typically around 70-80 in gray 
matter). Then one would typically _not_ want to do either global 
normalisation nor grand mean scaling.

Global normalisation at the second level would change results at the 
second level. If you have two groups and you find that BOLD signal is 
vastly different in one group compared to the other regardless of 
type of task, then your data will always be very difficult to 
interpret. One _possible_ way would be to model each subjects signal 
with the subjects own HRF (including its height) as assessed by a 
separate scan with some very basic sensory task (e.g. rev. 
checkerboard). When then applying that to some task of interest it 
might be possible to assess if there are differences over an above 
those due to some overall BOLD response difference. The big problem 
here would be how to select the set of voxels in the basic scan over 
which to assess the height of the HRF (would be VERY dependent on 
which voxels are chosen).

Thresholding at the second level will simpy affect what parts of the 
brain that are being included in the calculations 



- From Karsten Specht, PhD
Department of Biological and Medical Psychology , University of 
Bergen, Norway, <[log in to unmask]>

"Global scaling" should be skipped on the first level, and skipped 
definitely on the second level:

The session/subject regressor, assuming that there are no scaling 
differences within one session, captures the different baselines on 
the first level.

The scaling on the second level is only useful when analysing other 
images than con_images (MRI-Perfusion images or PET images, for 
example). Here, it is necessary, that the global mean is the same 
across subjects.In case of a 'classical' second level analysis, 
con-images are already appropriately scaled, i.e. positive values are 
reflecting a signal increase, negative values a decrease and the 
value itself represents somewhat like the strength of the effect.


- From Stephen J. Form:

A few years ago it was common for people to do global scaling in SPM 
fMRI analyses. Nowadays the advice is that, in most situations, it 
shouldn't be done. SPM does grand mean scaling implicitly. The 
purpose of grand mean scaling is to attempt to deal with scaling 
differences, without doing something as strong as global scaling. In 
grand mean scaling, the mean over all (intracerebral, essentially) 
voxels in all volumes in the session is computed.  Then all voxels in 
all volumes in that session are scaled by this mean (and perhaps then 
multiplied by something like 100). This takes care of scaling 
differences between *sessions*.  It doesn't address the issue of 
scaling differences between volumes within a *session*. The 
presumption is that those latter differences aren't that high.





>Dear SPM experts,
>
>I have run an fMRI study on 12 subjects with (among others) the 
>following 3 conditions:
>
>(1) a motor coordination task
>(2) a visual search task
>(3) tasks 1 and 2 performed simultaneously (dual-task condition)
>
>Using RFX analysis for group results, I have observed some "strange" 
>deactivations in 3 different areas of the prefrontal cortex during 
>the dual-task condition, i.e. the prefrontal areas are activated in 
>single tasks 1 and 2, and deactivated in dual-task.
>As I have used proportional scaling at first-level analysis, I was 
>wondering whether these deactivations could be explained by a 
>relative increase of the global signal in the dual-task condition 
>relative to other conditions? and if this makes sense, should 
>proportional scaling be used in my particular experiment?
>
>Any help or advice would be greatly appreciated.
>
>Florence Remy, Ph.D.
>Motor Control Lab
>KULeuven, Belgium


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Mauro PESENTI
Research Associate, National Fund for Scientific Research (Belgium)
Unite de Neurosciences Cognitives
Departement de Psychologie
Universite Catholique de Louvain
Place Cardinal Mercier, 10
B-1348 Louvain-la-Neuve

tel.: +32 (0)10 47 88 22
fax:  +32 (0)10 47 37 74
E-mail:  [log in to unmask]
http://www.nesc.ucl.ac.be
http://www.nesc.ucl.ac.be/mp/pesentiHomepage.htm