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.. _ahelp_adjunct_deob_around_origin:

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adjunct_deob_around_origin
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.. contents:: :local:


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Overview
========

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    This is a simple program to wrap around the 3drefit functionality to 
    remove obliquity from a dataset whilst preserving its origin.
    
    In many cases, this is very useful to run on oblique anatomicals
    before processing.
    
    ver  = 1.0
    auth = PA Taylor, RC Reynolds (SSCC, NIMH, NIH)
    

Options
=======

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    -input                 : (req) input volumetric dataset name
    -prefix                : (req) output dataset name
    -oblique_origin        : style of preserving origin, via 3drefit (def)
    -oblique_recenter      : style of preserving origin, via 3drefit (def)
    -oblique_recenter_raw  : style of preserving origin, via 3drefit (def)
    -workdir               : working directory name (just name, no path;
                             will be subdirectory of the output location)
    -overwrite             : when writing output, overwrite any preexisting
                             dataset (def: do not overwrite)
    -no_clean              : when done, do not remove temporary working
                             directory (def: do remove woroking directory
    -echo                  : run very verbosely (with 'set echo' on)
    -ver                   : display program version
    -help                  : show help
    -hview                 : show help in text editor
    
    

Examples
========

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    1) Basic usage:
         adjunct_deob_around_origin                       \
             -input   sub-001_T1w.nii.gz                  \
             -prefix  sub-001_T1w_DEOB.nii.gz
    
    2) Different origin-preservation choice:
         adjunct_deob_around_origin                       \
             -oblique_recenter_raw                        \
             -input   sub-001_T1w.nii.gz                  \
             -prefix  sub-001_T1w_DEOB.nii.gz