Dear Ged, Jeff,
what is the data type of your images? Did you have a look at scaling
factors and possible intensity offsets encoded in SPM parts of the analyze
header? This information should be available in the .pinfo field of
spm_vol's output.
Volkmar
On Thu, 12 Apr 2007, Ged Ridgway wrote:
> Hi all,
>
> Just to clarify the situation, and the query,
>
> Jeff Browndyke, Ph.D. wrote:
>> I posted a couple of days ago about apparent image intensity changes
>> following reslicing with Ged's modified resize_img script. Discussion
>> with
>> Ged backchannel revealed that the script was detecting negative intensity
>> values in the data, which were then being scaled to zero and resulting in
>> high intensities in non-negative voxels.
>
> The reslicing isn't really detecting and zeroing negative voxels; it was just
> that they were isolated negative voxels surrounded by reasonably strongly
> positive ones, so when interpolating for the reslice, they happened to end up
> positive.
>
> The concern was partly just a display issue, and partly due to padding around
> the resliced image. The presence of negative voxels in the originals makes
> the image display a little brighter (e.g. -26 maps to black, rather than 0 to
> black, and other intensities get shifted up a little too). In terms of
> means/medians etc. the issue here was that the resliced image includes more
> zeros around the edge (the world bounding box is fixed, but in voxel space,
> the reorientation means the resliced image requires a bigger voxel BB). The
> mean/median/etc of the *non-zero* voxels in the original and resliced images
> match very well --- the reslicing isn't doing anything peculiar.
>
>> I went back to our original image
>> data and found that the original files did not contain negative intensity
>> values. These only appeared after undergoing the SPM2 Realign procedure.
>
> This however, sounds very peculiar to me... Jeff assures me that only realign
> is being used, not reslice, in which case, my understanding is that only a
> new .mat is created --- intensities shouldn't be altered at all. Can anyone
> see anything obvious I'm missing?
>
> Thanks,
> Ged.
>
>
--
Volkmar Glauche
-
Department of Neurology [log in to unmask]
Universitaetsklinikum Freiburg Phone 49(0)761-270-5331
Breisacher Str. 64 Fax 49(0)761-270-5416
79106 Freiburg http://fbi.uniklinik-freiburg.de/
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