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FYI...this issue was address by Tom Nichols et al a few years ago as
well....we implemented their solution in spm5 (happy to share, probably
would work fine for spm8 as well) and it works quite well.  For details see
the poster below:

http://www.sph.umich.edu/~nichols/Docs/HBM2007-Huang-MissingData.pdf



> -----Original Message-----
> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On
> Behalf Of Jonathan Peelle
> Sent: Thursday, May 05, 2011 12:43 PM
> To: [log in to unmask]
> Subject: Re: [SPM] Deletion of Voxels in Group Analyses
> 
> Dear Bob,
> 
> > From what I understand, during second-level estimation (e.g., one-sample
> > t-test) SPM performs the test only for voxels in which ALL subjects have
> > data. In areas of the brain in which signal quality is highly variable
from
> > subject-to-subject (e.g., high susceptibility areas such as ventral
frontal
> > and temporal), this procedure is quite problematic, especially for large
> > samples. Has any one customized the SPM algorithm to bypass the
all-or-none
> > exclusion procedure? I imagine this would require also producing a
> > degrees-of-freedom image (e.g., to use when reporting statistics).
> 
> I'm not aware of anyone who has dealt with this, although some folks
> (like Donald) are working on solving this in an elegant fashion.
> 
> In the meantime, I imagine you could get around this by adjusting the
> threshold SPM uses on the 1st level to be less restrictive to the
> voxels it includes in the analysis; see, for example:
> 
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1104&L=SPM&P=R65987
> 
> If there are subjects for whom you don't think you have useful data,
> you could include additional regressors in your second level design to
> remove their contribution, which should also appropriately adjust the
> degrees of freedom (although this would obviously get tricky if it
> varied across voxels/regions that you are interested in).  If there
> are specific areas you care about, you could also extract the values
> and do statistics outside of SPM, which may offer you some additional
> flexibility in how you model things.
> 
> Best regards,
> Jonathan
> 
> --
> Dr. Jonathan Peelle
> Department of Neurology
> University of Pennsylvania
> 3 West Gates
> 3400 Spruce Street
> Philadelphia, PA 19104
> USA
> http://jonathanpeelle.net/