[VoxBo] normalization using SPM procedures

[Daniel Y Kimberg]

Joonkoo Park wrote:
> I normalized my functional image(s) [dimension 64*64*30] using EPI.nii
> template [dimension 91*109*91] in SPM5. But then the normalized image
> has a dimension of 79*95*69, when my common sense expects the dimension
> of the normalized data to be the same as the template. And in fact some
> edges of the brain are cut off. Would this be something normal?

With SPM normalization, you get to pick your voxel sizes and bounding
box, which collectively determine how many voxels you get.  The
default bounding box has changed between versions of SPM in the past,
but looking in spm_defaults.m, you can see it's currently this:

[[-78 -112 -50];[78 76 85]]

which is consistent with the dimensions you got.  You can certainly
set these variables (e.g., normalise.write.bb) to whatever you like.

> I also noticed that if I want to normalize a .tes file with 150 time
> points, then I first convert .tes into 150 different .img files and
> transfer them to SPM, then normalize, then possibly convert them
> back into a .tes file. Would this be a normal procedure? It seems
> like a LOT of grunt work (for all runs of every subject), and
> thought there's gotta be a way around it.

VoxBo jobtypes are intended to make this easy, if you want to use our
scripting system.  We don't have jobtypes written for SPM5, but it
wouldn't be too hard to adapt the ones for SPM2.  Then in your script
you just tell it to spm_norm your tes files, and the conversion back
and forth happens behind the scenes.  The jobtype currently only works
if your files start in tes format, but it would be easy to adapt as
needed.

We're almost done with a cool new scripting system that we hope will
make these things even easier.

dan