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

This script will take a FreeSurfer subject (that has already been run successfully)
and then run a voxel based analysis, and generate a replacement thickness file.

Usage: fsVoxelBasedGenerateThickness.sh [ options ] ALLFR ALLHA CCCCC DDDDD etc.

All arguments after the options are FreeSurfer directories under the current directory.

Options:

-regbased : Use registration based method: S. R. Das et. al., NeuroImage 45 (2009) 867-879
without which we default to : IEEE TMI Vol. 22, No. 10, Oct 2003

-old : As of 29/01/2009, I have two versions of this cortical thickness.
old = itkRegistrationBasedCTEFilter.h
new = itkRegistrationBasedCorticalThicknessFilter.h

new is default.

-time <int> : Number of time steps for Das method. Use 1 or 2 on a workstation,
and more on a 64 bit machine, memory permitting. Default is 1.

-vmf : Voxel multiplication factor for voxel based method.

************************************************************************************************
* NOTE: In order to get the averaging to work, the thickness file must still be called *
* lh.thickness and rh.thickness. So, this script will overwrite the existing ones. *
* So you are advised to run FreeSurfer 'as per normal', then take a copy of all your patients, *
* and run this script on the copy. *
************************************************************************************************