[MINC-users] making slices using mincreshape

[Lisa F. Akiyama]

Hi Andrew and Gang,

Thank you for your advice.
Yes, what both of you had suspected was the case and I was able to create
slice files with the original intensity range intact.

Is there an option in mnc2nii to preserve the original intensity range when
converting from MINC to NIFTI (or ANALYZE)?
When I try to convert a MINC file that has a range of 0-100 (according to
mincinfo) to NIFTI, I am getting a NIFTI while with a mere range of 0-2.


Thank you.


Best,
Lisa



On Thu, Feb 9, 2012 at 4:18 PM, Gang Liang <gang.liang.2011 at gmail.com>wrote:

> 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
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
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