cteRegisterThicknessImageToAtlas.sh

(Note: This page is automatically generated. Please do not attempt to edit it!)

This script registers a T1 image to an atlas, and then calculates stats for each atlas region.

Usage: cteRegisterThicknessImageToAtlas.sh t1.nii thickness.nii name [options] 

Mandatory Arguments:

  t1.nii                   : The T1 image to register to an atlas.
  
  thickness.nii            : The thickness image in the T1 image space, that the stats are calculated over.
  
  name                     : Basename for the output. Output files are:
              
                             <name>_native_to_atlas_affine.txt - The affine transformation.
                             <name>_native_to_atlas_cpp.nii    - The non-rigid FFD control point transformation.
                             <name>_image_in_atlas.nii         - Original T1 image in atlas space.
                             <name>_data_in_atlas.nii          - Thickness image in Atlas space.
                             <name>_atlas_stats_*.csv          - Statistics for each region.

Options:

  -atlas     image.nii     : An alternative atlas image.

  -atlas_regions image.nii : An alternative set of regions, that should match the atlas.
  
  -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 non-rigid registration, pass in the 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 2.
  
  -regions 1,2,3,4,5       : Comma separated list of region numbers.
  
                             NOTE: You are advised to specify which regions you want, or else the output may have too many columns.