Inter volumes slice coregistration

This process can be used after the anatomical volume has been made spatially consistent in 3D by running the Intra volume propagative slice registration process. It enables you to obtain a 3D consistent functional volume by using the previously registered anatomical volume as a reference.

Each 2D autoradiographic slice in the stacked functional volume is directly co-registered with its corresponding registered histological slice from the anatomical volume using the same block-matching method as in the process Intra volume propagative slice registration.

NOTE: To perform such an anatomo-functional co-registration, anatomical and functional volumes must have exactly the same number of slices. However, the two volumes can have different resolutions (voxel sizes).

Parameters

Input_3dImage: 3D Volume ( input )

Click on .
Select the initial reconstructed volume you have obtained by stacking the individualized coronal autoradiographic slices in the direction orthogonal to the cut-plane (output file from the process Stacking individual slice or Individualizing and stacking multiple slices), for instance Test_volume_rat1_autoradio.ima.

Input_3dImage_Preprocessed: 3D Volume ( optional, input )

Channel: Choice ( input )

Input_3dImage_Reference: 3D Volume ( input )

Click on .
Select the 3D reconstructed anatomical volume used as a reference (output file from the Intra volume propagative slice registration process), for instance Test_volume_rat1_cresyl_aligned.ima.

Channel_Reference: Choice ( input )

Rigid_Activated: Boolean ( input )

Rigid_Start_Level: Integer ( input )

Rigid_Stop_Level: Integer ( input )

Affine_Activated: Boolean ( input )

Affine_Start_Level: Integer ( input )

Affine_Stop_Level: Integer ( input )

High_Threshold_Reference: Integer ( optional, input )

High_Threshold_Test: Integer ( optional, input )

Init_Transfo_Reference: Choice ( optional, input )

Init_Ratio_Reference: Float ( optional, input )

Percent_Kept: Float ( optional, input )

Resize: Choice ( optional, input )

Output_Directory: Directory ( optional, output )

Output_3dImage: 3D Volume ( output )

Click on .
Specify the output directory and enter the output file name, for instance Test_volume_rat1_autoradio_coaligned.ima.

Centered_3dImage: 3D Volume ( optional, output )

Verbose: Boolean ( input )

Technical information

Toolbox : BrainRAT

User level : 0

Identifier : InterVolumesSliceCoregistration

File name : brainvisa/toolboxes/brainrat/processes/2d-3dpmi/InterVolumesSliceCoregistration.py

Supported file formats :

Input_3dImage :

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

Input_3dImage_Preprocessed :

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

Input_3dImage_Reference :

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

Output_Directory :

Directory, Directory

Output_3dImage :

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

Centered_3dImage :

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