Rigid registration with mutual information

Interface AimsMIRegister

Description

This process interfaces registration command AimsMIRegister and proposes to compute (or not) new resampled image.

Method of registration is based on an iconic approach, based on voxels grey levels. It uses mutual information (statistical dependence between 2 variables) to compute the registration.

A rigid transformation is calculated between the reference image and source image (translation and matrix rotation) with similar field of view.

If images are 4D Volume, then an automatic sum of all the frames is made to obtain a 3D Volume.

Matrix transformation:

The format file of matrix transformation is .trm and its syntax is:

*TO*.trm (* indicates all types of characters or character string).





Format files

Initialization of registration:

There are 2 modes for initialization of registration:

• init_with_gravity_center=yes -> initialization with gravity center: this is the default mode. It works with reference_threshold and source_threshold options. These thresholds preserve a percentage of intensity according to the maximun intensity.
• init_with_gravity_center=no -> initialization with coordinates (or a starting transformation): to initialize coordinates with Tx, Ty .....

Sub-resolution of reference image:

Reference image can be damaged with a reduction factor according to the principle of a pyramid.

value 1 --> 1 voxel out of 2 in the 3 directions --> reduction by a factor of 8

value 1 --> 1 voxel out of 4 in the 3 directions --> reduction by a factor of 64





Registration of source image:

The AimsMIRegister command allows the determination of a matrix transformation file. You can choose to apply this matrix transformation to the source image. Then you must indicate the name of the registred image for resampled_image. You can then choose the method of interpolation with resampled_interpolation.



Example:
Here is a registration of a source image (fonc.ima) with a reference image (anat.ima). The output files are refTOtest.trm, testTOref.trm and resampfonc.ima (registred image). Ouput files for this process are not currently managed by database. Thus you must use icon to indicate output files.



Process BrainVISA: Rigid registration with mutual information

Parameters

source_image: 4D Volume ( input )

reference_image: 4D Volume ( input )

source_to_reference: Transformation matrix ( output )

reference_to_source: Transformation matrix ( output )

init_with_gravity_center: Boolean ( input )

reference_threshold: Float ( input )

source_threshold: Float ( input )

reference_reduction_factor: Integer ( input )

initial_translation_x: Float ( optional, input )

initial_translation_y: Float ( optional, input )

initial_translation_z: Float ( optional, input )

initial_rotation_x: Float ( optional, input )

initial_rotation_y: Float ( optional, input )

initial_rotation_z: Float ( optional, input )

step_translation_x: Float ( optional, input )

step_translation_y: Float ( optional, input )

step_translation_z: Float ( optional, input )

step_rotation_x: Float ( optional, input )

step_rotation_y: Float ( optional, input )

step_rotation_z: Float ( optional, input )

error_epsilon: Float ( input )

gray_level: Integer ( input )

index_optimized: Choice ( input )

resampled_image: 4D Volume ( optional, output )

resampled_interpolation: Choice ( input )

Technical information

Toolbox : Tools

User level : 0

Identifier : Register3DMutualInformation

File name : brainvisa/toolboxes/tools/processes/registration/Register3DMutualInformation.py

Supported file formats :

source_image :

gz compressed NIFTI-1 image, Aperio svs, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIF image, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, VIDA image, Ventana bif, XBM image, XPM image, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

reference_image :

gz compressed NIFTI-1 image, Aperio svs, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIF image, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, VIDA image, Ventana bif, XBM image, XPM image, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

source_to_reference :

Transformation matrix, Transformation matrix

reference_to_source :

Transformation matrix, Transformation matrix

resampled_image :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image