[MINC-users] minctracc on 2D volumes?

[Andrew Janke]

> Soren said:
>  Adding to that, you may want to try padding with two all-zero slices in
> each z-extreme (on top of what Mallar suggested).
> I had to do that to force and in-plane registration only.

> Mallar said:
>> It’s tricky to get minctracc to work on 2D slices in linear mode.  I would
>> suggest using the -w_translations and -w_rotations options that you
>> basically “turn off” the out of plane components by using an absurdly small
>> value.

I'll bow to Mallars experience with this here...  But to add a bit of
"practicality" here's how I would approach using this advice.

First, remember that minctracc expects a 3D volume, so let's give it one.

Make your z slice big and thick so that rotations out of plane
are penalised by minctracc:
(beware! minc_modify_header modifies your file in place!)

   $ minc_modify_header -dinsert zspace:step 20 xtrue_rot45deg.mnc

Then add a "blank" slice either side to further penalise minctracc for
doing out of plane rotations:

   $ mincreshape -dimrange zspace=-1,3 xtrue_rot45deg.mnc expanded.mnc

And not run minctracc using the arguments that Mallar suggests:

   $ minctracc -lsq6 -w_translations 1 1 0.0001 \
         -w_rotations 0.00001 0.00001 0.017453 \
         expanded.mnc expanded2.mnc out.xfm

(you will have to apply the same treatment to your target file to make
expanded2.mnc)

Let us know how it goes, this seems to be a recurring question so it'd
be nice to put this up on wikibooks somewhere if this recipie works
well.

Thanks


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