#++ auto_warp.py version: 0.02
auto_warp.py - Non-linear 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
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 Qwarpingdefault: 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