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.. _ahelp_3dLocalUnifize:

**************
3dLocalUnifize
**************

.. contents:: :local:


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OVERVIEW
========

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    This program takes an input and generates a simple "unifized" output
    volume.  It estimates the median in the local neighborhood of each
    voxel, and uses that to scale each voxel's brightness.  The result is
    a new dataset of brightness of order 1, which still has the
    interesting structure(s) present in the original.
    
    This program's output looks very useful to help with dataset alignment
    (esp. EPI-to-anatomical) in a wide array of cases.
    
    ver   : 1.1
    date  : July 4, 2022
    auth  : PA Taylor (SSCC, NIMH, NIH)
    
    

USAGE
=====

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    This program is generall run as:
    
        3dLocalUnifize [options] -prefix DSET_OUT -input DSET_IN
    
    where the following options exist:
    
      -input     DSET_IN  :(req) input dataset
      
      -prefix   DSET_OUT  :(req) output dataset name, including path
    
      -wdir_name WD       :name of temporary working directory, which 
                           should not contain any path information---it will be
                           created in the same directory as the final dataset
                           is created
                           (def: __wdir_LocalUni_, plus a random alphanumeric str)
    
      -echo               :run this program very verbosely (def: don't do so)
    
      -no_clean           :do not remove the working directory (def: remove it)
    
     ... and the following are 'tinkering' options, likely not needed in
         most cases:
    
      -local_rad LR       :the spherical neighborhood's radius for the 
                           3dLocalStat step (def: -3)
    
      -local_perc LP      :the percentile used in the 3dLocalStat step,
                           generating the scaling volume 
                           (def: 50)
    
      -local_mask LM      :provide the masking option to be used in the
                           3dLocalStat step, which should be enclosed in
                           quotes for passing along to the internal
                           program call.  To remove any masking, put "None" as
                           the option value.
                           (def: "-automask")
    
      -filter_thr FT      :put a ceiling on values in the final, scaled dataset,
                           whose values should be of order 1; setting FT to be a
                           value <=0 turns off this final filtering
                           (def: 1.5)
    
    

NOTES
=====

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      This program is designed to not need a lot of tinkering with
      options, such as the '-local_* ..' ones.  In most cases, the default
      scaling will be useful.
    
    

EXAMPLES
========

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      1. Basic local unifizing:
         3dLocalUnifize                                                  \
            -prefix  vr_base_LU                                          \
            -input   vr_base_min_outlier+orig.HEAD
    
      1. Same as above, without masking:
         3dLocalUnifize                                                  \
            -prefix      vr_base_LU_FOV                                  \
            -input       vr_base_min_outlier+orig.HEAD                   \
            -local_mask  None