cteRegisterAtlasToImage.sh

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This script registers an atlas to an MR image, and resamples the atlas regions into MR native space.

Usage: cteRegisterAtlasToImage.sh image.nii name [options] 

Mandatory Arguments:

  image.nii                  : The image that the atlas should register to.
  
  name                       : Basename for the output. Output files are:
              
                               <name>_atlas_to_native_affine.txt     - The affine transformation.
                               <name>_atlas_to_native_cpp.nii        - The non-rigid FFD control point transformation.
                               <name>_atlas_in_native.nii            - Atlas in native image space.
                               <name>_regions_in_native.nii          - Atlas regions in native image space.

Options:

  -mask      mask.nii        : A binary mask image to apply to the target image.
  
  -dilations                 : Dilations to apply to mask.
  
  -atlas     atlas.nii       : An alternative atlas image.

  -affine    affine.txt      : If you have already done an affine registration, pass in the affine transformation.
  
  -cpp       cpp.nii         : If you have already done the FFD registration, pass in the FFD control points transformation.
  
  -tmproot <directory>       : Define a root directory for temporary files. Default /tmp
                               The difference between this option and the next, is that this
                               one takes the root directory (eg. /tmp) and creates a sub directory
                               with a process ID in it. (eg. /tmp/seg.1234) whereas the next option
                               just uses exactly what you give it.
                            
  -tmpdir <directory>        : Set temporary workspace directory.

  -keeptmp                   : Keep temporary workspace directory.
  
  -gpu                       : Use -gpu option for nifty_reg.

  -levels <int>              : The number of Free-Form Deformation multi-resolution levels in pyramid. Default 3.
  
  -levels_to_perform <int>   : The number of Free-Form Deformation multi-resolution levels to actually optimise. Default 3.