auto_warp.py


#++ auto_warp.py version: 0.04

    ===========================================================================
    auto_warp.py     - Nonlinear regisration

    Basic Usage:
      auto_warp.py -base TT_N27+tlrc -input anat.nii  \
                   -skull_strip_input yes

    ---------------------------------------------
    REQUIRED OPTIONS:

    -base   : name of reference or template volume
    -input  : name of dataset to be registered

    MAJOR OPTIONS:

    -help       : this help message

    OTHER OPTIONS:

    -qblur bB bS : specify 3dQwarp blurs for base and source volumes
    -qworkhard i0 i1: set the two values for 3dQwarp's -workhard option
    -qw_opts 'OPTS': Pass all of OPTS as extra options directly to 3dQwarp

A full list of options for auto_warp.py:

   -base
      use:                Template volume.
   -input
      use:                dataset to be aligned to the template
   -keep_rm_files
      use:                Don't delete any of the temporary files created here
   -prep_only
      use:                Do preprocessing steps only without alignment
   -help
      use:                The main help describing this program with options
   -limited_help
      use:                The main help without all available options
   -option_help
      use:                Help for all available options
   -version
      use:                Show version number and exit
   -ver
      use:                Show version number and exit
   -verb
      use:                Be verbose in messages and options
   -save_script
      use:                save executed script in given file
   -skip_affine
      use:                Skip the affine registration process
                          Equivalent to -affine_input_xmat ID
                          (apply identity transformation)

      allowed:            yes, no
      default:            no
   -skull_strip_base
      use:                Do not skullstrip base/template dataset
      allowed:            yes, no
      default:            no
   -skull_strip_input
      use:                Do not skullstrip input dataset
      allowed:            yes, no
      default:            no
   -ex_mode
      use:                Command execution mode.
                          quiet: execute commands quietly
                          echo: echo commands executed
                          dry_run: only echo commands

      allowed:            quiet, echo, dry_run, script
      default:            script
   -overwrite
      use:                Overwrite existing files
   -suffix
      default:            _al
   -child_anat
      use:                Names of child anatomical datasets
   -qblur
      use:                3dQwarp base and source blurs (FWHM)

   -qw_opts
      use:                3dQwarp miscellaneous options.
                          Parameters will get passed directly to 3dQwarp.

   -qworkhard
      use:                3dQwarp -workhard values

      default:            [0, 1]
   -warp_dxyz
      use:                Resolution used for computing warp (cubic only)

      default:            [0.0]
   -affine_dxyz
      use:                Resolution used for computing initial transform (cubic only)

      default:            [0.0]
   -affine_input_xmat
      use:                Affine transform to put input in standard space.
                          Special values are:
                              'AUTO' to use @auto_tlrc
                              'ID' to do nothing
                              'FILE.1D' for a pre-computed matrix FILE.1D will
                                        get applied to the input before Qwarping

      default:            AUTO
   -smooth_anat
      use:                Smooth anatomy before registration

   -smooth_base
      use:                Smooth template before registration

   -unifize_input
      use:                To unifize or not unifize the input

      allowed:            yes, no
      default:            y e s
   -output_dir
      use:                Set directory for output datasets

      default:            awpy
   -followers
      use:                Specify follower datasets

   -affine_followers_xmat
      use:                Specify follower datasets' affine transforms

   -skullstrip_opts
      use:                3dSkullstrip miscellaneous options.
                          Parameters will get passed directly to 3dSkullstrip.

   -at_opts
      use:                @auto_tlrc miscellaneous options.
                          Parameters will get passed directly to @auto_tlrc.