MRITOTAL: Automatic Volumetric Registration

In both diagnostic and research applications, the interpretation of magnetic resonance (MR) images of the human brain is facilitated when different data sets can be compared by visual inspection of equivalent anatomical planes. Quantitative analysis with pre-defined atlas templates often requires the initial alignment of atlas and image planes. Unfortunately, the axial planes acquired during separate scanning sessions are often different in their relative position and orientation, and these slices are not coplanar with those in the atlas.

I have developed a completely automatic method, based on multi-scale, three dimensional (3D) cross-correlation, to register a given volumetric data set to an average MRI brain (n=305) aligned with the Talairach stereotaxic coordinate system. Once the data set is resampled by the transformation recovered by the algorithm, atlas slices can be directly super-imposed on the corresponding slices of the resampled volume (see below). The use of such a standardized space also allows the direct comparison, voxel-to-voxel, of two or more data sets brought into stereotaxic space.

How to do this here at the MNI:

The script mritotal can be used to register a T1-weighted MRI volume to the standard stereotaxic space. To run the script, simply type:

mritotal volume.mnc transform.xfm

and the program will run for 20-30 minutes. It will take the input volume volume.mnc and calculate the best transformation that fits the volume onto the average MRI model, used here to define stereotaxic space. This transformation will be written out in transform.xfm and can be used by mincresample to resample the input volume into the stereotaxic space.

Minctracc:

The routine mritotal relies on the program minctracc to accomplish the registration. If you are interested in using mritotal to fit other types of data such as PET to PET or PET to MR, read on. The following documentation is available (this data is pretty out of date... will be updated soon):