Anatomy Normalization (using SPM) with Re-initialization

Description

This process is similar to the Anatomy normalization using SPM process, but will try a second time in case of failure: if the output normalization matrix cannot be output, it will reset any internal transformation to a scanner-based referential in the NIFTI file, using the Reset internal transformation process, before trying again the SPM normalization. It may solve cases when the internal transformation is wrong.

Warning: However in some cases SPM will actually write a normalization matrix, but will be wrong because of a wrong initialization due to a bad internal transformation to a scanner-based referential. In that case, BrainVisa cannot detect the problem easily, so you may need to run Reset internal transformation by hand first.

Parameters

anatomy_data: Raw T1 MRI ( input )

anatomical_template: anatomical Template ( optional, input )

job_file: SPM2 parameters ( optional, output )

voxel_size: Choice ( input )

cutoff_option: Integer ( input )

nbiteration: Integer ( input )

transformations_informations: SPM2 normalization matrix ( output )

normalized_anatomy_data: Raw T1 MRI ( output )

allow_retry_initialization: Boolean ( input )

init_translation_origin: Choice ( input )

Technical information

Toolbox : Morphologist

User level : 0

Identifier : Normalization_SPM_reinit

File name : brainvisa/toolboxes/morphologist/processes/registration/Normalization_SPM_reinit.py

Supported file formats :

anatomy_data :

NIFTI-1 image, NIFTI-1 image, SPM image

anatomical_template :

NIFTI-1 image, MINC image, NIFTI-1 image, SPM image

job_file :

Matlab file, Matlab file

transformations_informations :

Matlab file, Matlab file

normalized_anatomy_data :

NIFTI-1 image, NIFTI-1 image, SPM image