[MINC-users] making slices using mincreshape

[Andrew Janke]

Hi Lisa,

On 10 February 2012 06:39, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> I have been using mincresample to slice up MINC images into individual
> axial MINC slice files using the following command options:
> mincreshape -clobber -dimrange zspace=${slice},1 orig.mnc orig_${slice}.mnc;
>
> However, I am getting slices with a lot of white noise on slices that
> should be completely black according to what I see
> in that slice location on the original image. I get these odd outputs for
> axial slices superior of the head/skull.
> These issues aren't present for black slices containing no tissue inferior
> of the head.

My guess would be that there is indeed noise in these slices (with no
real data). as part of its operation mincreshape will set the min and
max of an output image (slice) to the range of the data in it.

So, if your image data ranges between 0 and 5000 and the noise in the
background between 0 and 10 then a slice in the middle will have an
output range of 0-5000 and you won't see the noise much as it is well
down in the colourmap of tools like register/Display.

If instead you pick a slice position with no data then the output
range will be 0-10 and you will see the noise now. So, I'd be checking
the output range of your slices with white noise in them. (mincstats
will do).

This also might not be the case!, if not a screenshot of what is going
on will help.

Thanks


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