adjunct_deob_around_origin

Overview

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

-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

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