Preprocessing : image field of view

This process can be used to homogenize field of view on a list of images that have different voxel sizes.

Output volumes field of view can be processed using many different methods :

• Using manually defined sizes
• Using minimum sizes
• Using maximum sizes

Parameters

ListOf_Input_Image: ListOf( 3D Volume ) ( input )

Click on .
Select input images for which it is necessary to homogenize field of view, for instance Test_volume_rat1_cresyl.ima, Test_volume_rat2_cresyl.ima

Resize_Policy: Choice ( input )

Select the policy to use during filed of view resize.
Policy can be selected among :

• Using manually defined sizes. In that case Size_X (in mm), Size_Y (in mm) and Size_Z (in mm) will be used if they are set. Otherwise field of view size will not be modified in the corresponding dimension (X, Y, Z)
• Using minimum sizes. In that case Size_X (in mm), Size_Y (in mm) and Size_Z (in mm) will be used if they are set. Otherwise, field of view size will be modified using the smaller field of view size, for the corresponding dimension, among images.
• Using maximum sizes. In that case Size_X (in mm), Size_Y (in mm) and Size_Z (in mm) will be used if they are set. Otherwise, field of view size will be modified using the larger field of view size, for the corresponding dimension, among images.

Resize_Alignment: Choice ( input )

Select how field of view alignment is defined among :

• Centered. If output field of view is larger than input field of view. Content will be centered in the output image for the corresponding dimension (X, Y, Z). If output field of view is smaller than input field of view. Content will be cropped symetrically in the output image for the corresponding dimension (X, Y, Z).
• Using origin. If output field of view is larger than input field of view. Content will be aligned using the origin of output image for the corresponding dimension (X, Y, Z). If output field of view is smaller than input field of view. Content will be cropped only at the end in the output image for the corresponding dimension (X, Y, Z).

Size_X: Float ( optional, input )

Size of output field of view in the X dimension.

Size_Y: Float ( optional, input )

Size of output field of view in the Y dimension.

Size_Z: Float ( optional, input )

Size of output field of view in the Z dimension.

Resampling_Mode: Choice ( input )

Select resampling mode to use :

• Linear interpolates values in the image using linear interpolation
• Cubic interpolates values in the image using cubic spline interpolation
• Quadratic interpolates values in the image using quadratic spline interpolation
• Nearest does not interpolate values in the image, but uses neighbors to set values in the output image

Border_Interpolation_Method: Choice ( input )

Select the method to use to generate border value :

• Maximum interpolates image border using the maximum value in input image border
• Majority interpolates image border using the majority value in input image border
• Mean interpolates image border using the mean value in input image border
• Median interpolates image border using the median value in input image border

ListOf_Output_Image: ListOf( 3D Volume ) ( output )

Click on .
Specify the output images directory and enter the output file names, for instance Test_volume_rat1_cresyl_fov.ima, Test_volume_rat2_cresyl_fov.ima

NOTE: Name choice is important to identify the content of an image and distinguish it of each other.

Technical information

Toolbox : Bioprocessing

User level : 3

Identifier : FovPreprocessing

File name : brainvisa/toolboxes/bioprocessing/processes/research/toolbox/FovPreprocessing.py

Supported file formats :

ListOf_Input_Image :

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

ListOf_Output_Image :

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