AddScannerBasedReferential

Process to manage the scanner based referential which is sometimes stored in the header of data files.

Description

This process is especially useful in the case of freesurfer data, to manage raw input data (mri/orig.nii) and resampled data (mri/ori/001.nii) with correspondance between their coordinate systems.

This process adds new referentials in the brainvisa manager of transformations and creates a transformation from the volume to the scanner based referential.

Then, in order to link two scanner based referentials between them, see the MergeReferentials process.

Parameters

volume_input: T1 MRI ( input )

referential_volume_input: Referential of Raw T1 MRI ( output )

T1_TO_Scanner_Based: Transformation to Scanner Based Referential ( output )

new_referential: Scanner Based Referential ( output )

Technical information

Toolbox : Tools

User level : 2

Identifier : AddScannerBasedReferential

File name : brainvisa/toolboxes/tools/processes/registration/AddScannerBasedReferential.py

Supported file formats :

volume_input :

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

referential_volume_input :

Referential, Referential

T1_TO_Scanner_Based :

Transformation matrix, Transformation matrix

new_referential :

Referential, Referential