[MINC-users] in plane

[Andrew Janke]

Hi Soren,

>  I am trying to correct some dynamic perfusion CT data for motion.
> The slices are relatively thick at 12 mm and there are only 2 of them
> so coverage is sparse. It seems the main components of the motion are
> around the z axis so I am trying to constrain the registration to
> in-plane rotations
>
> I am not sure if there is any straightforward way to do this with the
> MINC tools so I tried to add some lines to mritoself to pass through
> w_translations and w_rotations to minctracc.
>
> I would think that setting the following should achieve in plane
> translations and rotations only
> -w_rotations 0 0 0.017
> -w_translations 1 1 0
>
> The rotation bit seemed to work - but not translation.
> So where am I going wrong - and is there a way to do what I want?

You certainly are on the right track and if you mess about with the
weights enough it will eventually work... That said minctracc really
is optimised for 3D only. So another approach I have used in these
cases is to fake 3D data.

In your case simply making the slices a whole lot thicker than they
are and adding a blank slice top and bottom should make minctracc do
what you want.  (just run it as is without weights).

The blank slices top and bottom are actually very important as it will
give minctracc a bounds to work to. It may even work by simply doing
this to your volumes:

   $ mincresample -dimrange zspace=-1,4 in.mnc out.mnc

Once this is done then just pull the bits out the xfm that you want
using xfm2param and make another using param2xfm.

Another approach if you have single slice data is to duplicate the
slice to make a "cylinder" of data.


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883