[MINC-users] interpolating missing slices?

[Andrew Janke]

Hi Alex,

> I have a stack of image slices with some slices missing, and I would
> like to stitch those together into a volume by interpolating the
> missing slices. Does anybody have a suggestion on what would be an
> efficient way to do this? I initially thought volregrid would do this
> sort of thing but it seems not (or if it does, I have not been able to
> figure out how to use it :)

Well volregrid will do it but it's probably not the most straight
forward way. I do this:

1. hack the volume up into a series of 1 slice images and skip the blank ones.

   for i in `seq 1 200`; do
      mincreshape -dimrange zspace=$i,1 in.mnc tmp/$i.mnc
   done

   # remove the dud ones
   rm tmp/<blah>mnc

2. put it all back together

   mincconcat tmp/*.mnc concat.mnc

3. You will not have a volume with irregular spacing.  so make it regular:

   mincresample -sync -zstep 1 concat.mnc concat-reg.mnc

This is a little script of mine that will figure out a good step size
for step 3 in you are interested. It also makes the volume isotropic
so perhaps not what you want

  http://packages.bic.mni.mcgill.ca/scripts/voliso

If however your data is label data, then I'd use morphological
interpolation, I am writing code to do this now for some mouse mapping
labels that I can make available.

ta


a