cteRunLongitudinal.sh

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This script runs longitudinal cortical thickness estimation for a single subject, using voxel based methods.

Usage: cteRunLongitudinal.sh [options] 

Mandatory Options:

  -i image.nii              : An image
  -m mask.nii               : A mask
  
                              You should have as many masks as images, and can repeatedly specify -i and -m.
                     
                              For example:
                     
                              -i image1.nii -m mask1.nii -i image2.nii -m mask2.nii
                     
                              Clearly, you need at least two masks and at least two images.
                              The ordering of masks should be the same as the images.

 -name <string>             : Prefix for the name of the output files
                       
Options:

  -initialize <int>         : Initialize the atlas based on this image number. Default to 1.

  -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
  
  -affineiters <int>        : Number of affine iterations in groupwise registration. Default 2.
  
  -nonrigiditers <int>      : Number of non-rigid iterations in groupwise registration Default 10.
  
  -usepreviouscpp           : Non-rigid registration picks up the previous control points each time

  -spm <directory>          : SPM directory, which if specified is added
                              onto the front of the MATLABPATH variable

  -levels                   : The number of multi-resolution levels in pyramid. Default 3.
  
  -levels_to_perform        : The number of multi-resolution levels to actually optimise. Default 2.

  -reg                      : Default is to use Acosta's method for cortical thickness [1]
                              -reg will switch to Das's method [2]. 
  
    
[1] Oscar Acosta, Pierrick Bourgeat, Maria A. Zuluaga, Jurgen Fripp, Olivier Salvado
Sebastien Ourselin, and the Alzheimer's Disease NeuroImaging Initiative.
"Automated voxel-based 3D cortical thickness measurement in a combined Lagrangian-
Eulerian PDE approach using partial volume maps"
Medical Image Analysis 13 (2009) 730-743: doi:10.1016/j.media.2009.07.003
   
[2] Sandhitsu R. Das, Brian B. Avants, Murray Grossman, James C. Gee
"Registration based cortical thickness measurement" 
NeuroImage 45 (2009) 867-879: doi:10.1016/j.neuroimage.2008.12.016