[VoxBo] normalization question

[Daniel Y Kimberg]

Ranjani wrote:
>  I'm trying to normalize my tes files using a version of the bigprep script that
>  creates both normalized and non-normalized tes files.
>
>  My question is this:  Should the origin of the normalized tes files be in the
>  same location as the nFunctional.cub and nAnatomical. cub files?  Because when
>  I check the origin of my nrunX.tes files, the origin is off (at the edge of
>  a ventricle) rather than in the middle of the AC.

Ultimately, yes -- the normalized tes file should end up with the
standard origin.  One thing to check is that your tes files and your
Functional.cub have the same dimensions.  This can occasionally mess
things up.  I'm also not sure if the value for adir in your dataset
already has a trailing slash, but you might want to change
$adir$paramfile to $adir/$paramfile, just to be safe.  Have you
checked visually to make sure the tes files were actually getting
normalized?

>  I checked the origin of my nAnatomical.cub and nFunctional.cub files and they
>  both look correct (in the middle of the AC).  And my Anatomical.cub and
>  Functional.cub files seem to have the origin in the same place, though not in
>  the AC (because I never specified for it to be in the AC for these files in my
>  pre-processing script).  And the origin of the nrunX.tes files doesn't look
>  like it's in the same place as the Anatomical.cub and Functional.cub files -
>  though the script is copying the origin from the Functional.cub file onto the
>  nrunX.tes files.

Sounds like everything's reasonably normal leading up to the SPM2
normalization.  Incidentally, the origin of the nAnatomical and
nFunctional should actually be a slice or two superior to the anterior
commisure.  For whatever reason, that's the standard SPM origin.

>  So, I'm wondering if the origin of the nrunX.tes files should match the origin
>  of the nFunctional.cub (that is, should the origin of the nrunX.tes files be in
>  the middle of the AC)?  If so, I can modify the script to copy the origin from
>  nFunctional.cub rather than Functional.cub.

It should but if it's not happening automatically, I'd worry that the
normalization didn't work properly.

dan