IntensityVolumeNormalization

This process enables to investigate regional differences in cerebral glucose uptake between groups of animals independent of global differences in the absolute amount of radiotracer delivered to the brain. For that purpose, the voxel values of each 3D reconstructed autoradiographic volume are normalized to a reference value by applying a multiplicative or additive coefficient so that the mean intensity for each brain is the same. For example, this reference value can be calculated as the mean of the mean activity values measured in each respective brain.

Parameters

Input_3dImage: 3D Volume ( input )

Click on .
Select the 3D reconstructed autoradiographic volume to be normalized. Make sure the grey level values of this volume have been previously converted to activity or CMRGlu values.

Multiplicative_Coefficient: Float ( input )

Enter the multiplicative coefficient.
A default value of 1.0 is automatically assigned.

Additive_Coefficient: Float ( input )

Enter the additive coefficient.
A default value of 0.0 is automatically assigned.

Output_3dImage: 3D Volume ( optional, output )

Click on .
Specify the output directory and enter the output file name. This parameter is optional. If you do not complete it, you will be notified by a warning message that the process will be going to overwrite the input volume.

Technical information

Toolbox : BrainRAT

User level : 0

Identifier : IntensityVolumeNormalization

File name : brainvisa/toolboxes/brainrat/processes/toolbox/IntensityVolumeNormalization.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

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