Registration of 3D serial MR brain images

London University (March, 2001)

Mark Holden,

Radiological Sciences, GKT, Guy's Hospital, London, SE1 9RT, UK.



This thesis investigates automatic registration to detect and quantify small structural changes in brain anatomy; and also to rectify scanner geometrical distortion. Five treated growth hormone (GH) patients, six normals and a cube phantom were imaged serially at 0, 3 and 6 months using a Siemens 3D FLASH T1 weighted gradient echo MR sequence. Eight voxel similarity measures were quantitatively evaluated for rigid-body registration of the serial brain scans by measuring registration consistency. The serial images were rigidly registered, with and without brain pre-segmentation and scaling error correction (obtained from the nine degrees of freedom registration of phantom images), and interpolated using a sinc kernel to produce sixty-six difference images. These difference images were randomised and visually assessed for structural change by two neuro-radiologists. Structural change was also quantified with a non-rigid registration algorithm based on a tensor product of cubic B-splines and optimisation of normalised mutual information. The geometrical distortion of a Philips ACS2 scanner was investigated with a phantom consisting of a 3D matrix of 427 spherical reference structures. Distortion was determined by point-based non-rigid registration, with a fourth order polynomial, of imaged and modelled sphere centre point-sets. The evaluation of similarity measures indicated that mutual information was significantly (p < 0.01, n=33) more consistent than the other six measures. The blinded visual assessment of difference images indicated a significant (p < 0.01) increase in brain/CSF volume ratio for five GH patients compared to six normals. Quantitative measurements gave a mean ventricular volume change over 6 months of: -1.2cc for GH patients compared to +0.18cc for normals with a significant (p=0.013) difference between the two groups. There was high correlation (rho ~ 0.7, n=11) of the quantitative and visual measurements. Distortion measurements indicated large shear and second order components and negligible distortion change over 11 weekly scans.

Thesis in PDF format:

  • Thesis in pdf (available to researchers on request)
    Mark Holden
    Last modified: 4 May, 2001.