[MINC-users] minctoraw

[Stephen Smith]

Hi - thanks for this. In fact, using the normalise option DOES make all
the slices have the right intensity _relative to eachother_ but the
overall 3D intensity scaling is in general lost - unless you use the
normalise option with the output datatype set as float in which case all
is well. It is a pain to have to use floats but that seems the only thing
that works....hohum :)

	Thanks, Steve.



On Thu, 5 Sep 2002, Andrew Janke wrote:

> On Thu, 29 Aug 2002, Stephen Smith wrote:
>
> > Hi - thanks for the reply, though I couldn't quite follow what the range
> > options are really doing. I have tried that and sadly it gives junk output
> > - most values being set to 32767...
> >
> > The intensity range parts of mincheader are below - does that tell you
> > anything useful about what the options should be to mincextract?
>
> Time for me to add my 2c + 15% GST worth.
>
> >  image-min = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> >  image-max = 5896592.46886447, 6089528.00976801, 5860417.05494506,
>
> What peter is elluding to is that your images have probably been rescaled (per
> slice) along the way. This can be viewed as either an unfortunate or fortunate
> thing... :)
>
> Peter also is taking a stab at your input and output data range being 12-bit.
> (something that we all know is very common of certain unnamed manufacturers).
>
> The problem as you describe it sounds like you are writing out data that is
> scaled per slice and getting "zippering" between slices. Unfortunately minctoraw
> and mincextract don't appear to have an option to "normalize" just between
> slices although peter will correct me here if I am wrong.
>
> As such what you need to do is make sure a MINC image has only one max and min
> value before doing a minctoraw/mincextract.  Most programs that use volume_io
> and set_volume_real_range have the side-effect of doing this.. :)
>
> On this note, I have been meaning to write a quick volume_io proggie to do this.
> Stay tuned (or email me again in a week) and I'll have a fix for you.
>
>
> andrew
>
>
>
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> MINC-users@bic.mni.mcgill.ca
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>

 Stephen M. Smith
 Head of Image Analysis, FMRIB

 Oxford University Centre for Functional MRI of the Brain
 John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
 +44 (0) 1865 222726  (fax 222717)

 steve@fmrib.ox.ac.uk  http://www.fmrib.ox.ac.uk/~steve