:orphan:

.. _ahelp_SurfLayers:

**********
SurfLayers
**********

.. contents:: :local:


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Overview
========

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    This is a program to compute intermediate surfaces between two boundary surfaces
    
    SurfLayers computes new surfaces for a given number of cortical divisions
    at intermediate distances by simple computation of the fraction 
    between the inner and outer-most surfaces (aka "equi-distant"). 
    A single dividing surface would be halfway between the two surfaces.
    

Options
=======

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      -spec SPEC_DSET      :dataset that is the SUMA specification file
                            describing input surfaces 
    
      -outdir DIRNAME      :new directory for output (default: surflayers)
    
      -states IN OUT       :typically smoothwm, pial states to describe inner
                            and outer surfaces (default: "smoothwm pial")
    
      -hemi  HH            :choose hemisphere: "lh", "rh" or "lh rh" (for both)
    
      -n_intermed_surfs N  :total number of intermediate surfaces to create
    
      -surf_A      SB      :inner boundary surface by filename (e.g. smoothwm.gii)
    
      -surf_B      SA      :outer boundary surface by filename (e.g. pial.gii)
    
      -surf_intermed_pref SIP  :name for interpolated surfaces 
                            (default: isurf)
      
      -echo                :run script with 'set echo' (i.e., verbosely)
    
      -no_clean            :do not remove temp files (probably just for testing)
    

Notes
=====

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    Output includes a new directory containing:
    + isurf.lh.01...n.gii -  interpolated surfaces numbered 1 to n
    + other files too if -spec option was utilized
    + a run*tcsh script to view the output directly
    
    See also the quickspecSL program for creating a *.spec file.
    
    For more information or questions, please contact:
      Salvatore (Sam) Torrisi (torrisi@berkeley.edu)
      Daniel Glen (glend@mail.nih.gov)
    

Examples
========

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      1) 
    
      SurfLayers                       \
          -spec std.60.myspec.lh.spec  \
          -states "white pial"         \
          -n_intermed_surfs 3
    
      2) 
    
      SurfLayers                       \
          -surf_A lh.white.gii         \
          -surf_B lh.pial.gii          \
          -n_intermed_surfs 3