cmind.pipeline.ants_applywarp

utility for calling antsApplyTransforms

Functions

ants_applywarp(transform_list, fixed, ...[, ...]) utility for calling antsApplyTransforms
cmind.pipeline.ants_applywarp.ants_applywarp(transform_list, fixed, moving, output_warped, ANTS_path=None, dim=3, interp_type='', nopng=False, inverse_flag=False, extra_ANTS_args='', is_timeseries=False, verbose=False, logger=None)[source]

utility for calling antsApplyTransforms

Parameters:

transform_list : list

a list of the transformations to apply

fixed : str

image filename for the “fixed” image (registration target)

moving : str

image filename for the “moving” image

output_warped : str

image filename for the output

ANTS_path : str

path to the ants binaries

dim : {2, 3},optional

number of image dimensions

interp_type : str,optional

nopng : bool,optional

if False, generate overlay images summarizing the registration

inverse_flag : bool,optional

if True, apply the inverse of the transforms in transform_list

extra_ANTS_args : str, optional

optional string containing additional ANTs command line arguments

is_timeseries : bool, optional

if true, input_name corresponds to timeseries data. the transformation will be applied to all time frames (adds ‘ –input-image-type 3 ‘ to the antsApplyTransform command line)

verbose : bool, optional

print additional output (to terminal and log)

logger : logging.Logger or str, optional

logging.Logger object (or string of a filename to log to)

Notes

if inverse_flag, then fixed is registered to moving instead of the other way around

Possible interp_type strings are:
  • HammingWindowedSinc
  • NearestNeighbor
  • BSpline[<order=3>]
  • MultiLabel[<sigma=imageSpacing>,<alpha=4.0>]
  • Gaussian[<sigma=imageSpacing>,<alpha=1.0>]
  • CosineWindowedSinc
  • WelchWindowedSinc
  • LanczosWindowedSinc
  • “”