missing '-R' argument preceding reference_image in ComposeMultiTransform

[grandjeanlab]

Summary

ANTs2.3.5 ComposeMultiTransform function takes the following format ComposeMultiTransform Dimension outwarp.nii -R template.nii ExistingWarp.nii ExistingAffine.nii.

nipype.interfaces.ants.ComposeMultiTransform omits the -R before the tempalte.nii where template.nii is specified with compose_transform.inputs.reference_image = tempalte leading to ERROR.

Actual behavior

Curent output of compose_transform.cmdline

ComposeMultiTransform 3 transform1Warp_composed.nii.gz ../output/template/template.nii.gz ../output/o2High15/AnatSynQuick_node/transform1Warp.nii.gz ../output/o2High15/AnatSynQuick_node/transform0GenericAffine.mat

Expected behavior

ComposeMultiTransform 3 transform1Warp_composed.nii.gz -R ../output/template/template.nii.gz ../output/o2High15/AnatSynQuick_node/transform1Warp.nii.gz ../output/o2High15/AnatSynQuick_node/transform0GenericAffine.mat

How to replicate the behavior

from nipype.interfaces.ants import ComposeMultiTransform compose_transform = ComposeMultiTransform() compose_transform.inputs.dimension = 3 compose_transform.inputs.reference_image = tempalte compose_transform.inputs.transforms = [myWarp, myAffine] compose_transform.cmdline

Script/Workflow details

Trying to combine the FUNC to ANAT and ANAT to Template transforms into a single file.

Platform details:

python -c "import nipype; from pprint import pprint; pprint(nipype.get_info())" {'commit_hash': '54f502940', 'commit_source': 'installation', 'networkx_version': '2.5', 'nibabel_version': '3.1.0', 'nipype_version': '1.6.0', 'numpy_version': '1.19.2', 'pkg_path': '/home/gjoanes/.local/lib/python3.8/site-packages/nipype', 'scipy_version': '1.4.1', 'sys_executable': '/usr/bin/python3', 'sys_platform': 'linux', 'sys_version': '3.8.5 (default, Jul 28 2020, 12:59:40) \n[GCC 9.3.0]', 'traits_version': '6.1.1'}

Execution environment

• My python environment outside container