MMM Co-Registration
Table of Contents
Co-Registration of Rat Brains
Assumptions
You have an MR and a PET image of the same rat. The MR image contains only the brain. The PET image contains the whole head of the rat from nose to about the ears. The MR image, as shown in reset position, shows the rat on its back in the TRANSAXIAL OrthoPart, or equivalently the back on the right side of the SAGITTAL OrthoPart. The PET image, on the contrary, shows the rat with the back upwards in the TRANSAXIAL OrthoPart, or equivalently the back on the left side of the SAGITTAL OrthoPart.
Pre-requisites
You need a file that conatins a rat brain and nothing else as target for the registration. Internally, we use “good_rsl100.v_clipped_brain_ref__mr” and variants with different pixel size to represent rats of 90 % and 95 % size.
The new Rat Schemes
MMM uses a set of new schemes to handle rat images.
MR -> Reference Brain
This scheme first rotates the MR by 180° around the z-axis, then it co-registrates the MR to the reference brain. You can switch off the pre-rotation temporarily in the MMM tool itself, or permanently by editing the scheme.
PET -> Reference Brain
This scheme first first co-registrates the PET image with a rat head mask (using the scheme below), then it co-registrates the PET to the reference brain.
- PET -> Head Mask
This scheme first first co-registrates the PET image with a rat head mask. It brings the rat head roughly in a postion where the brain is about right, so that other mutual information minima are no longer attractive for the algorithm, when co-registrating with the reference brain.
PET -> MR, norm. position
This scheme co-registrates the PET image to the MR. It will only work when MR as well as PET are already positioned about right using the co-registration to the reference brain, see above.
X- to X-modality
This scheme co-registrates one image to another image of the same modality. You can use it to transport a manual co-registration of one image to all the other images of a series and thus bring the PETs to a position about right to start the MR -> PET scheme.
X- to Y-modality
This scheme co-registrates one image to another image of a different modality but of the same rat to another image of the same modality but of a different rat. You can use it to transport a manual co-registration of one image to all the other images of a series and thus bring the PETs to a position about right to start the MR -> PET scheme.