[MINC-users] making slices using mincreshape

[Gang Liang]

Andrew is right.

mincresample and mincreshape do not always keep the original range. to keep
the original range, use this option:

mincresample -keep_real_range
or
mincreshape -valid_range min max
where you can get min and max using mincinfo or mincheader minc_file|grep
range

Hope this help.


On Thu, Feb 9, 2012 at 5:51 PM, Andrew Janke <a.janke at gmail.com> wrote:

> 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
>
>
> a
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