Anatomy Normalization (using SPM)
Anatomy Normalization (using SPM)BE CAREFUL : This process can not be iterated. It is constructed to launch the correction for all images successively.
This process calls SPM to perform anatomical normalization. So SPM must be present, installed and available, to run. If you encounter problems with SPM, you can check the SPM configuration options in the preferences.
In case of problems: SPM takes into account any transformation to a scanner-based coordinates system present in NIFTI files. Typically it may contain at least an origin translation, or an additional rotation. If such a transformation is present, SPM uses it to initialize the normalization process. In some cases, this transformation is not correct. Especially if you need to flip the image, you can do it using the AC/PC "Prepare subject" process, but the transformation to the scanner-based referential will be combined, and will still be present in the NIFTI file. In such case, you may need to reset the internal transformations using the Reset internal image transformation process, before using this normalization process.
There is a variant of this normalization process, which will try to run SPM normalization first, and, if it fails (that is, if it does not write the output transformation), then any internal transformation is reset from the NITFI file (using the Reset internal image transformation process), and SPM normalization is tried again: this is the Anatomy normalization using SPM with reinitiailization process.
anatomy_data: Raw T1 MRI ( input )The anatomical data to normalize
anatomical_template: anatomical Template ( optional, input )The template on which the normalisation will be done. If there is no specified template, the T1 MRI template of SPM5 is chosen.
job_file: SPM2 parameters ( optional, output )The Matlab file containing the SPM5 job that will be launched
voxel_size: Choice ( input )The size of each voxel of the volume
cutoff_option: Integer ( input )The type of transformation (Inf = rigid transformation)
nbiteration: Integer ( input )The number of iteration for the normalization
transformations_informations: SPM2 normalization matrix ( output )The resulting transformation writen by SPM 5
normalized_anatomy_data: Raw T1 MRI ( output )
Toolbox : Morphologist
User level : 2
Identifier :
Normalization_SPMFile name :
brainvisa/toolboxes/morphologist/processes/registration/Normalization_SPM.pySupported file formats :
anatomy_data :NIFTI-1 image, NIFTI-1 image, SPM imageanatomical_template :NIFTI-1 image, MINC image, NIFTI-1 image, SPM imagejob_file :Matlab file, Matlab filetransformations_informations :Matlab file, Matlab filenormalized_anatomy_data :NIFTI-1 image, NIFTI-1 image, SPM image