Outputs and matrices

At any step of the registration process you can save the current moving image by pressing this button. If no extension is given by the user then the image is saved in ITK Analyze format (.hdr/.img).
IMPORTANT : Note that the image is saved resampled and registered : ``as you are seeing it in the views''.

Again at any step of the registration process, you can save the current registration matrix in a text file by pressing ``save matrix''. This corresponds to the linear transformation. Considering a fixed image and a moving image , a 3D coordinate point , the output matrix can be written (in homogeneous coordinates, mm) as follows : . Dimensions and spacings of the input images are written respectivly in voxels and mm. The output file is a text file were are written these information :

• Moving image information

  movdimX, movdimY, movdimZ, movspacingX, movspacingY, movspacingZ,

• Fixed image information

  fixdimX, fixdimY, fixdimZ, fixspacingX, fixspacingY, fixspacingZ,

• Affine matrix coefficients

  M11, M12, M13, M21, M22, M23, M31, M32, M33, M41, M42, M43

where M is the affine matrix used for registration :

You can save the deformation field reuslting of a non-linear registration in ITK metafile format (.mha) thanks to this button. The deformation field maps the moving image onto the fixed image. A deformation field is represented as an image whose pixel type is some vector type with N elements, where N is the dimension of the fixed image. Note that you currently cannot save and load deformation field for 2D image non-linear registration.

You can use these outputs again : As soon as you open the same set of input images, you can load either the corresponding matrix file or the corresponding deformation field. You can access these buttons in the advanced tab of the control panel. Loading a specific affine matrix or a specific deformation field overrides any previous registration step.

Note that he affine matrix format fits the format that is needed by the DTI track module (see related documentation and MedINRIA appendix for details). Hence you can register a volume into the diffusion weighted images, output the resulted rigid matrix, and input it in a DTI study so that the fiber tracks fit the desired volume (e.g. a T1 image) geometry.

These two buttons might be useful in order to manually set the image spacing (in mm), for very specific cases where the scaling information is wrong (3D reconstructed volumes from jpeg 2D images for instance).