AxialSlicesPermutation

This process inverts the order of two slices which have been incorrectly disposed on the glass slide during the cryostat sectioning process.

Parameters

Input_3dImage: 3D Volume ( input )

Click on .
Select the volume to be processed, for instance Test_volume_rat1_cresyl.ima.

Permutation_Slice_Number_1: Integer ( input )

Enter the number of the first slice to be inverted, for instance 62.

Permutation_Slice_Number_2: Integer ( input )

Enter the number of the second slice to be inverted, for instance 63.

Output_3dImage: 3D Volume ( optional, output )

Click on .
Specify the output directory and enter the output file name, for instance Test_perm62-63_volume_rat1_cresyl.ima.
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 : AxialSlicesPermutation

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