Import MNI CIVET Segmentation

None

Parameters

input_raw_t1_mri: Raw T1 MRI ( optional, input )

input_bias_corrected: T1 MRI Bias Corrected ( optional, input )

input_brain_mask: T1 Brain Mask ( optional, input )

input_grey_white: Grey White Mask ( optional, input )

use_civet_segmentations_in_mni_space: Boolean ( input )

input_T1_to_MNI_transformation: MINC transformation matrix ( optional, input )

input_white_mesh_left: Hemisphere White Mesh ( optional, input )

input_white_mesh_right: Hemisphere White Mesh ( optional, input )

input_pial_mesh_left: Hemisphere Mesh ( optional, input )

input_pial_mesh_right: Hemisphere Mesh ( optional, input )

grey_white_classif_from_meshes: Boolean ( input )

output_raw_t1_mri: Raw T1 MRI ( output )

output_bias_corrected: T1 MRI Bias Corrected ( output )

output_T1_to_Talairach_transformation: Transform Raw T1 MRI to Talairach-AC/PC-Anatomist ( optional, output )

output_ACPC: Commissure coordinates ( optional, output )

output_brain_mask: T1 Brain Mask ( optional, output )

output_left_grey_white: Left Grey White Mask ( optional, output )

output_right_grey_white: Right Grey White Mask ( optional, output )

use_t1pipeline: Choice ( input )

transform_Talairach_to_MNI: Transformation matrix ( input )

Technical information

Toolbox : Morphologist

User level : 3

Identifier : importMNIcivetSegmentation

File name : brainvisa/toolboxes/morphologist/processes/import/importMNIcivetSegmentation.py

Supported file formats :

input_raw_t1_mri :

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

input_bias_corrected :

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

input_brain_mask :

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

input_grey_white :

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

input_T1_to_MNI_transformation :

MINC transformation matrix, MINC transformation matrix

input_white_mesh_left :

GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh

input_white_mesh_right :

GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh

input_pial_mesh_left :

GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh

input_pial_mesh_right :

GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh

output_raw_t1_mri :

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

output_bias_corrected :

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

output_T1_to_Talairach_transformation :

Transformation matrix, Transformation matrix

output_ACPC :

Commissure coordinates, Commissure coordinates

output_brain_mask :

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

output_left_grey_white :

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

output_right_grey_white :

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

transform_Talairach_to_MNI :

Transformation matrix, Transformation matrix