[VoxBo] resampling issue

[Daniel Y Kimberg]

Benjamin Greené wrote:
> Hello, I would like to display functional data from a group analysis
> on a colin brain of different dimensions in mricro. How can I align
> these using the resample command? The details are below. I appreciate
> your help.  Cheers, Ben
>
[doing some trimming below]
> Functional .cub file:
> On Wernicke: /data/benc/NV/RFX/NVB-VVB_GLM/NVB-VVB.cub
> VoxDims(XYZ):	53	63	46
> VoxSizes(XYZ):	1.0000	1.0000	1.0000
> Origin(XYZ):	88	124	70
...
> Anatomical .cub file:
> VoxDims(XYZ):	181	217	181
> VoxSizes(XYZ):	1.0000	1.0000	1.0000
> Origin(XYZ):	88	124	70

The origin and voxel sizes on your functional are obviously wrong.
Voxel sizes should be 3x3x3, you might have to look up the origin
somewhere (there's a great page, maybe attached to the CARET software,
that lists a lot of standard origins, make sure you subtract 1 from
the SPM origin because VoxBo indexes from 0).  Then you should be able
to use resample with the -rr option.  You might need to fiddle a bit,
but let me know if something doesn't work as expected.  The arguments
to resample need to be overhauled.

You might also consider not resampling at all.  MRIcro should be able
to align things that are sliced differently as long as you get the
origin and voxel sizes right.  Double-check all your origins both
visually and (since these are standard bounding boxes) according to
some reference.

dan