Thresholding a t-map does not require additional information. However, its hard to get SPM to threshold a t-map computed outside of the SPM.mat structure.

In terms of thresholding the t-map:

(1) using voxel p-value and cluster extent requires no additional information [although you'd want to say how you came up with the cluster extent (e.g. 3dClustSim);

(2) using voxel-wise FDR correction requires no additional information; and

(3) using any RFT correction (tFDR, cluster FDR, cluster FWE) requires knowing the FWHM that is computed from the residuals or residual image or another source.

With that being said, computing the t-map in SPM is the best approach and can be done by setting the variance of the groups to be equal. The unequal variance option will cause the model to fail.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Fri, Dec 27, 2013 at 8:14 PM, Vladimir Litvak <[log in to unmask]> wrote:

Dear Amy,

1) You can do this kind of t-test if you set the variance to be equal. This is one of the options when specifying the design.

2) There is no simple way to threshold a t-image computed outside SPM. You need additional information (e.g. the residuals) to use RFT correction.

Best,

Vladimir

On 28 Dec 2013, at 00:03, Amy Kuceyeski <[log in to unmask]> wrote:

> Hi all!
>
> I am performing an unpaired t-test in SPM where one of the "groups" is a single individual. It seems as though this is equivalent to performing the Crawford modified t-test, which is exactly what I want. However, when I try to implement this in SPM8, it throws an error when I enter only one subject for group 2. In particular, the contrast definition in the Results section that fails to complete. Has anyone out there had success with doing this sort of analysis? I would eventually like to be able to do this command line or with batch script.
>
> On a related note, is there a way for me to use the results section on a t-map that I create myself? For example, I could calculate the t-map using the Crawford modified t-test formula and then use SPM for the thresholding. Or does the thresholding involve the other images that are created along the way (beta_0001/beta_0002, etc)?
>
> Thanks for any help you can give and Happy new year!
>
> Amy