:orphan:

.. _ahelp_@djunct_overlap_check:

*********************
@djunct_overlap_check
*********************

.. contents:: :local:


| 

    

OVERVIEW
========

.. code-block:: none

    
    More helpful helpfile description coming (some day...)
    
    This is just a helper script for other things.
    
    written by PA Taylor, modelled heavily on RW Cox's '@snapshot_volreg'
    script
    
    # --------------------------------------------------------------------
    

COMMAND OPTIONS
===============

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    -hview
    -help
    -ver
    -echo
    -ulay              ULAY
    -olay              OLAY
    -prefix            PREFIX
    -box_focus_slices  DSET_BFS
    -montgap           MG
    -montcolor         MC
    -cbar              CBAR
    -opacity           OPA
    -zerocolor         ZC
    -set_dicom_xyz     XX YY ZZ
    -ulay_range        umin umax
    -ulay_range_nz     umin umax
    -montx             MX
    -monty             MY
    -montx_cat         MX2
    -monty_cat         MY2
    -label_mode        LM
    -pbar_posonly_off
    -edgy_ulay
    -set_dicom_xyz_off
    -no_cor
    -no_axi
    -no_sag
    -no_clean
    

NOTES TO SELF
=============

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    This is mostly useful if the olay has no skull and the ulay has a
    skull, in terms of being able to see overlap well.
    
    If using -box_focus_slices, don't use the AMASK_FOCUS_OLAY keyword,
    but instead repeat the name of the olay explicitly.  This is because
    this program creates an edgified version of the olay, which gets
    passed into @chauffeur_afni, and then using the AMASK* functionality
    would try to 'automask' that dset, typically leaves no voxels and
    leads to an error.  Repeating the name of the input olay leads to
    correct behavior.  (Ask me how I discovered *this* tidbit of
    knowledge?)