Hello SPM users:

I have several questions regarding VBM in SPM. I am using VBM to compare the grey and white matter volume of 3 groups of subjects (ALS, PLS, and normals) pairwise (a total of 3 separate tests) using two-sided t-test since I do not know how to perform the analysis using one design matrix.

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.

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.

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?

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?

Thank you for your generous time,

Aaron J. Shapiro

Biomedical Engineer

Human Spinal Physiology Unit

NINDS, NIH