#++ auto_warp.py version: 0.06
===========================================================================
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.
