Dear Aaron,

> 1)      First, how does one go about calculating Total Intracranial
> Volume (TIV) in SPM8? I read that it is possible to use NewCalc_tivs.m
> in SPM5, but this script is not in SPM8. Also to calculate TIV should
> one use modulated warped segmented images, or should you use segmented
> images in native space and what are the file denotations for the two
> kinds of segmented images? How do I go about adding TIV as a nuisance
> variable.

The following should get you started:

> 2)      In the authoritative VBM methods paper on VBM from 2000
> Ashburner and Friston assert that “voxel-based extent statistics should
> not be used in VBM” because of the “highly nonstationary nature of the
> underlying neuroanatomy.” Does that mean I should leave the cluster
> extent at “0” when in the interactive statistical results GUI? I am
> confused because I was told by other researchers to set this between 25
> and 50.

No, that value is 'just' a threshold on the cluster extent (as defined
by the number of voxels constituting a cluster). The correction will
still assume stationarity (uniform smoothness). If you want to do non
stationary cluster extent correction, have a look at:
and rule number 5 of Ged's "Ten simple rules for reporting VBM studies":

> 3)      To perform a two-sampled two sided t test (two-tailed t test) do
> I just use the [-1 1] for my contrast and set the type to F?

Sounds good to me.

> 4)      Also, I noticed that SPM8 does not have the option for False
> Discovery Rate (FDR) correction for multiple comparisons, but this is
> included in SPM5. Is my SPM8 missing a toolbox or a particular update or
> is this not available when using an F contrast?

FDR correction is still there in SPM8 but in its topological
instantiation, see:;pxeBbw;20090406192205%2B0100
If you want to use the voxel-wise FDR as implemented in SPM5, edit
spm_defaults.m so that, l.42:
defaults.stats.topoFDR  = 0;

All the best,

Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG