[MINC-users] minctoraw

[Stephen Smith]

sorry - forgot to add that the MINC images are being created by gyrotominc
- I guess it is possible that gyrotominc is doing something nasty to the
global intensity scaling?

Thanks.


On Wed, 28 Aug 2002, Peter NEELIN wrote:

> On Wed, 28 Aug 2002, Stephen Smith wrote:
>
> > hello - I've just found a gotcha in "minctoraw -normalise" (which I use to
> > convert to analyze). It seems to me that without the -normalise option you
> > get the "arbitrary" scaling of each slice's intensity, which you clearly
> > don't want in the final raw image - right? So my conversion program has
> > always used the -normalise flag. However I have just discovered that there
> > is still some overall intensity scaling that gets lost this way, because
> > when I compare two MINC files their subtraction makes sense - but when
> > comparing two converted analyze files, they are somehow scaled relative to
> > eachother, so the subtraction is not now sensible
>
> Yes. I am afraid that I never got around to replacing minctoraw (the
> original, rather primitive program with the helpful name) with mincextract
> (the later, more featureful program with a less obvious name). Between
> being afraid of breaking things and general inertia, I never fixed
> that problem and so people still end up using the rather limited
> minctoraw.
>
> mincextract has the option -image_range that allows you to specify the
> normalization of the output data (combined with the valid_range, one can
> calculate a scale from real values to the dumped voxel values). Note also
> that mincextract has -normalize turned on by default. You will need to
> specify the output type, however (probably something like
> "-short -signed -range 0 4095" for analyze files). If your original data
> was integer data and that scaling was preserved in the conversion to minc,
> then you can get the original integer values back with something like
>
>    mincextract -short -signed -range 0 4095 -image_range 0 4095 file.mnc
>
> (completely untested - just working from memory). The important point is
> that using the same -range and -image_range will give a scaling of 1 and
> offset of 0 when converting real values back to voxel values.
>
> 'Hope this helps.
>
>             Peter
> ----
>             Peter Neelin (neelin@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