T1 Bias Correction

Correct for the spatial bias in usual MR images

Description

This new bias correction is based on a method that should deal much better with low grey/white contrast and high bias magnitude.

Parameters

t1mri: Raw T1 MRI ( input )

commissure_coordinates: Commissure coordinates ( optional, input )

sampling: Float ( input )

field_rigidity: Float ( input )

weight for the field rigidity constraint

zdir_multiply_regul: Float ( input )

wridges_weight: Float ( input )

ngrid: Integer ( input )

background_threshold_auto: Choice ( input )

delete_last_n_slices: OpenChoice ( input )

t1mri_nobias: T1 MRI Bias Corrected ( output )

mode: Choice ( input )

write_field: Choice ( input )

field: T1 MRI Bias field ( optional, output )

write_hfiltered: Choice ( input )

hfiltered: T1 MRI Filtered For Histo ( output )

write_wridges: Choice ( input )

white_ridges: T1 MRI White Matter Ridges ( output )

variance_fraction: Integer ( input )

write_variance: Choice ( input )

variance: T1 MRI Variance ( output )

edge_mask: Choice ( input )

write_edges: Choice ( input )

edges: T1 MRI Edges ( output )

write_meancurvature: Choice ( input )

meancurvature: T1 MRI Mean Curvature ( optional, output )

fix_random_seed: Boolean ( input )

modality: Choice ( input )

use_existing_ridges: Boolean ( input )

Technical information

Toolbox : Morphologist

User level : 0

Identifier : T1BiasCorrection

File name : brainvisa/toolboxes/morphologist/processes/segmentationpipeline/components/T1BiasCorrection.py

Supported file formats :

t1mri :

gz compressed NIFTI-1 image, Aperio svs, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, Ventana bif, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

commissure_coordinates :

Commissure coordinates, Commissure coordinates

t1mri_nobias :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

field :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

hfiltered :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

white_ridges :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

variance :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

edges :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

meancurvature :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image