The brain was shrunken within the volume - the dimensions were exactly the
same. I think your second suggestion is correct - normalizing with bilinear
interpolation does not result in the same shrinking. Your answer would seem to
suggest that the brains are not really shrunken, but rather that the outer
edges are eroded by the interpolation procedure (leaving the internal voxels
accurately registered) - do you think that's correct?
does this problem argue that zeros, rather than NaN's, should be inserted into
the masked-out voxels in the next version of SPM99 (or alternatively, that the
sinc interpolation procedure be made more robust to NaN's)?
thanks,
russ
John Ashburner wrote:
> When you say smaller, do you mean that the actual dimensions (numbers
> of voxels) are smaller, or that the brains in the image volumes have
> shrunk. If you mean the volume dimensions, then check the bounding boxes.
>
> If you are referring to the brains within the volume shrinking, then
> I have my suspicians about the source of the problem. My first
> thought was that SPM was picking up wrong .hdr or .mat information,
> but renaming the file and trying different .hdr files didn't fix it,
> so I guess that this is not the source.
>
> I think what could be the problem is related to the masking that is done
> to define voxels who's values are not known. Floating point format images
> have values of NaN (Not a Number, normally generated by 0/0) inserted into
> these voxels. There is no NaN representation for most of the other image
> data types, so zero is used instead. I am also assuming that you are
> using sinc interpolation to resample the images. The interpolation routines
> don't cope to well with NaNs, so if you use sinc interp, then any voxels
> that are within half a sinc kernel from a NaN will come out as NaN. With
> bilinear interpolatin, then only the closest voxels will come out this way.
>
> Good luck,
> -John
--
Russell A. Poldrack, Ph. D.
MGH-NMR Center
Building 149, 13th St.
Charlestown, MA 02129
Phone: 617-726-4060
FAX: 617-726-7422
Email: [log in to unmask]
Web Page: http://www.nmr.mgh.harvard.edu/~poldrack
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