[MINC-users] Variations on normalization of minc volumes in minc-toolkit

[Andrew Janke]

Hi Gabriel,

I'll comment on the one I know.

inormalize was written by Alex Z and yes it does require volumes to be
aligned to a model. There are a few different ways it can be used to
calculate the map between the two volumes (or even between slices
within one file). These are detailed in the "Solution options" section
of inormalize -help.

I tend to use it like this (I've simplified a bit):

      # calculate normalisation
      map="map.txt"
      if [ ! -e $map ]
      then
         inormalize \
            -nonormalize -print -quiet \
            -model model.mnc \
            -mask model_mask.mnc \
            $infile |\
            sed -e 's/^\ \ //' -e 's/(//' -e 's/\,//' -e 's/)//' |\
            tee $map
      fi

      # apply it
      scale=$(grep medianOfRatios $map | cut -f2 -d\ )
      offset=$(grep medianOfRatios $map | cut -f3 -d\ )
      minccalc -clobber \
         -expression "$offset + $scale*A[0]" \
         $infile $outfile


Note that I separate out the calculation and the subsequent
application of the normalization via minccalc, at the time inormalize
was written I don't think minccalc existed so I doubt you'll find this
method in any of the examples!


a


On 19 November 2014 05:49, Gabriel A. Devenyi <gdevenyi at gmail.com> wrote:
> Hi All,
>
> I'm working on streamlining a
> parallel grid-aware
> preprocessing pipeline using bpipe (see https://code.google.com/p/bpipe/
> and https://github.com/CobraLab/bpipe-library) and I've come across these
> normalization tools within minc-toolkit:
>
> minc_nuyl - documented at http://www.ncbi.nlm.nih.gov/pubmed/10784285
> volume_pol - no documentation?
> inormalize - no documentation?
> normalize_mri - wrapper for inormalize
>
> Is there any documentation out there regarding these tools (what they do,
> and how they do it).
>
> Additionally, are there any details on the requirements to apply these
> tools?
>
> For example, the source header in inormalize.cc I think indicates that the
> volumes must be registered, is that correct?
>
>
> Can anyone provide any insights on these tools? Thanks!
>
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
> _______________________________________________
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