[VoxBo] normalization question

[Ranjani Prabhakaran]

Hi,

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.

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.

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.

I've pasted the part of the bigprep script that creates normalized tes files
below.

Thanks so much!

Ranjani


# process the data
shellcommand "mkdir -p $run"
shellcommand "vb2tes $rawdir/$src $run/$run.tes -e $dummies"
slicecorrect $run/$run.tes $run/$run.tes 1
orient $run/$run.tes $run/$run.tes RPI
runonce extractref $firstrun $adir/FirstEPI.cub
shellcommand "setorigin -c Anatomy/Functional.cub $run/$run.tes"
spm2_realign $run $adir/Functional.cub $run.tes

#create normalized 4D file too
spm2_norm_apply4d $DIR/$run $adir$paramfile $run.tes n$run.tes $xf $yf $zf
$bb_func
smooth $run/n$run.tes $run/n$run.tes 2.67 2.67 2.67
threshold $run/n$run.tes $run/n$run.tes $thresh
calcgs $run/n$run.tes $run/n$run.tes
calcps $run/n$run.tes $run/n$run.tes