Thanks for the answer. I am sorry if I confused you that I am hacking the
code. I want to generate a Pseudo-T map using another image rendering
software called BrainSuite2 which read in analyze format files. I prefer
using uint16 format. So I was trying to see if I could read in the file
and convert to uint16, then use it for display. Actually, could I just
use the SPMt.img directly? Does it contain the Pseudo-T statistic if I
setup the program using variance smoothing? Thanks!
Xue
Quoting Thomas E Nichols <[log in to unmask]>:
> Xue,
>
> > I am using SnPM and I have a quick question with SnPMt.mat
> > file. According to the comment, SnPMt.mat contains a 1xS matrix of
> > the statistic of interest (either t or pseudo-t) supplied for all S
> > voxels at locations XYZ. I assume this the statistic for the correct
> > permutation. The matrix size for the file is 1 x 1923595. This does
> > not conform to my image matrix size (199x199x199=7880599) I fed into
> > the program. Does the SPM program chop off some of the peripheral
> > regions? How could I translate the result back into my original
> > image matrix? Thanks a lot for your time and help!
>
> S is the number of voxels within the brain mask, which will generally
> be quite smaller than the total number of possible voxels in the 3D
> volume.
>
> To work with SnPMt use the XYZ variable. XYZ is a 3xS matrix, giving
> you the x,y,z location of each column of SnPMt.
>
> Hope this helps! Happy hacking!
>
> -Tom
>
>
> -- Thomas Nichols -------------------- Department of
> Biostatistics
> http://www.sph.umich.edu/~nichols University of Michigan
> [log in to unmask] 1420 Washington Heights
> -------------------------------------- Ann Arbor, MI 48109-2029
>
>
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