Hi Linda

> If I can use the" 3dcalc" to calculate the
> subject.niml.dset file, so that I can get mean
> value at each node from a group of subjects.
> Is it right to use it as followed:
> 3dcalc -a Subject1.niml.dset[6] \
> -b Subject2.niml.dset[6] \
> .
> .
> .
> -expr mean(a,b,...)
> -prefix mean_suject.niml.dset
Yes, that would be OK for computing the cross subject mean for 'sub-brick #6'. A better program to use for this would be 3dMean.

> I want to know if I need to get the certain
> columns as the input or just use
> Subject1.niml.dset. as the input. And if I want to
> do the 3dttest, at this time, the input is
> Subject1.niml.dset.?

If you wanted the mean to perform a t-test, you should definitely use 3dttest++ instead. 3dttest++ will take surface data much like it takes volumetric data.

Note that the old SUMA.doc is quite old, it is best you use the suma.pdf document I mentioned in earlier posts to get more updated information.

cheers,
Ziad