AC/PC Or Normalization

A switch process which allows to use either the standard manual AC/PC PrepareSubject, or a normalization process as the T1 pipeline first step

Description

This process aims at writing the commissure coordinates file, containing AC, PC and IH points, either using the classical, manual way, or by normalizing the input volume and using normalization information to set AC,PC and IH points.

Note that the normalization will not override the input volume: all following T1 segmentation will still be performed in the native subject space, but normalization information will be used for inter-subject links.

Note also that when normalization is used, this process also replaces the T1 pipeline Talairach Transformation process, because normalization allows to get the full Talairach transformation, without the need of brain segmentation, and in a more robust way.

For now, only FSL normalization is taken into account. SPM normalization will follow soon...

Parameters

T1mri: Raw T1 MRI ( input )

commissure_coordinates: Commissure coordinates ( output )

allow_flip_initial_MRI: Boolean ( input )

reoriented_t1mri: Raw T1 MRI ( output )

Technical information

Toolbox : Morphologist

User level : 0

Identifier : acpcOrNormalization

File name : brainvisa/toolboxes/morphologist/processes/segmentationpipeline/components/acpcOrNormalization.py

Supported file formats :

T1mri :

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

commissure_coordinates :

Commissure coordinates, Commissure coordinates

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