FSL Normalization Pipeline

Anatomical normalization using FSL and conversion of the normalization information into BrainVisa/Aims compatible information

Description

This process chains the FSL anatomical normalization process, and the conversion of FSL normalization matrix into BrainVisa transformations framework.

Parameters

t1mri: Raw T1 MRI ( input )

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

template: anatomical Template ( input )

alignment: Choice ( input )

set_transformation_in_source_volume: Boolean ( input )

allow_flip_initial_MRI: Boolean ( input )

allow_retry_initialization: Boolean ( input )

reoriented_t1mri: Raw T1 MRI ( output )

Technical information

Toolbox : Morphologist

User level : 1

Identifier : FSLnormalizationPipeline

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

Supported file formats :

t1mri :

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

transformation :

Transformation matrix, Transformation matrix

template :

NIFTI-1 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