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.. _ahelp_asymm_report.csh:

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asymm_report.csh
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.. contents:: :local:


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Overview
========

.. code-block:: none

    
    This is a script to compute volumes, surface areas, patch
    surface areas and asymmetry ratios between
    left and right regions from labeled datasets. These can be in a 
    native subject space or in a standard template space, as for an atlas.
    

Usage Example
=============

.. code-block:: none

    
       asymm_report.csh                                 \
          -input HCA_lr_v0.9.nii.gz                     \
          -right_range 1 21                             \
          -left_range 31 51                             \
          -isosurf_dir ~/HCA_subjects/sub-101/surfs     \
          -isosurf_base HCA                             \
          -reportfile HCA_asymm_report.txt
    
       Note only the input dset and the left and right ranges are *required*.
    
    

Options
=======

.. code-block:: none

    
      -input input_dset    :required input dataset for relative region sizes
    
      Provide index values either by range or by list files:
      -right_range min max :minimum and maximum index values for right regions
      -left_range  min max :minimum and maximum index values for left regions
    
      with list files (columns or rows of numbers)
      -right_list rightlist.1D : list of index values for right regions
      -left_list  leftlist.1D : list of index values for left regions
    
      -isosurf_dir dir      :directory with gifti surface files for regions 
                             (default current directory)
      -isosurf_base prefix  :beginning part of gifti file names shared across 
                             regions   
      -make_isosurfs        :make isosurfaces from all regions in input volume
                             uses isosurf_dir for directory and isosurf_base for
                             prefix for output, e.g. isosurf_base.gii
      -surf_patch           :compute areas of patches on surfaces
      -surf_patch_surface surfdset :use one isosurface from labeled volume 
                             for patches (different than isosurfaces for 
                             individual regions)
      -make_patch_surface   :generate new surface for patch area computations
      -reportfile textout   :specify filename for text output (default is stdout)
      -use_left_labels      :default is to use labels from right index regions in
                             output report. This option switches to use left labels
      -surf_patch_prefix ppp:prefix for output labelled patch dset prefix.niml.dset
      -surf_patch_smooth nn :neighborhood size for modal smoothing on surface 
                             (2mm default). Check surface with smoothed data for
                             reasonableness
      -method LI            :use method for comparison
                             LI (laterality index) = (L-R)/(L+R)
                             (negative values have right symmetry, 
                              positive values have left symmetry
                              zero values are symmetric)
                             or 
                             RL (right to left ratio) = R/L (Default)