SPM Normalization Pipeline

Description

This small pipeline will use SPM to perform an anatomical normalization, and then convert the SPM normalization matrix into a Morphologist-compatible one. If needed and allowed, it can also reorient the initial anatomica image if it was incorrectly oriented.

Please read the docs of the SPM normalization processes for details and possible issues.

Parameters

t1mri: Raw T1 MRI ( input )

transformation: Transform Raw T1 MRI to Talairach-MNI template-SPM ( output )

spm_transformation: SPM2 normalization matrix ( output )

normalized_t1mri: Raw T1 MRI ( output )

template: anatomical Template ( input )

allow_flip_initial_MRI: Boolean ( input )

allow_retry_initialization: Boolean ( input )

reoriented_t1mri: Raw T1 MRI ( output )

init_translation_origin: Choice ( input )

voxel_size: Choice ( input )

cutoff_option: Integer ( input )

nbiteration: Integer ( input )

Technical information

Toolbox : Morphologist

User level : 1

Identifier : SPMnormalizationPipeline

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

Supported file formats :

t1mri :

NIFTI-1 image, NIFTI-1 image, SPM image, gz compressed NIFTI-1 image

transformation :

Transformation matrix, Transformation matrix

spm_transformation :

Matlab file, Matlab file

normalized_t1mri :

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

template :

NIFTI-1 image, MINC image, NIFTI-1 image, gz compressed NIFTI-1 image

reoriented_t1mri :

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