load_ants_h5 error when using --multi-step-reg

[madisoth]

What happened?

@moser297 and I both got the below error on 25.0.0a1 using the new --multi-step-reg option. I think part of the issue is the new concatenated xfm for anat -> MNIInfant -> MNI152 is collapsed into a single nonlinear transform, instead of the usual with antsRegistration outputting a composite .h5 transform with an affine xform[0] and a nonlinear xform[1]

What command did you use?

/opt/conda/envs/nibabies/bin/nibabies /data /out participant --participant-label 0011 --derivatives /bibsnet --fs-license-file /opt/freesurfer/license.txt --cifti-output 91k --omp-nthreads 8 --nprocs 8 --project-goodvoxels --surface-recon-method mcribs --fd-radius 45 --age-months 1 --multi-step-reg --norm-csf -vv -w /work --output-spaces MNI152NLin6Asym:res-2

What version of NiBabies are you using?

25.0.0a1

Relevant log output

Node: nibabies_24_2_wf.single_subject_sub-0011_ses-MENORDIC_wf.bold_ses_MENORDIC_task_oddball_acq_3T2mm_run_12_echo_1_wf.bold_std_wf.resample
Working directory: /work/nibabies_24_2_wf/single_subject_sub-0011_ses-MENORDIC_wf/bold_ses_MENORDIC_task_oddball_acq_3T2mm_run_12_echo_1_wf/bold_std_wf/_in_tuple_MNI152NLin6Asym.res2/resample

Node inputs:

cval = 0.0
fieldmap = <undefined>
in_file = <undefined>
inverse = [False]
jacobian = True
mode = constant
num_threads = 8
order = 3
output_data_type = float32
pe_dir = <undefined>
prefilter = True
ref_file = <undefined>
ro_time = <undefined>
transforms = <undefined>

Traceback (most recent call last):
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 66, in run_node
    result["result"] = node.run(updatehash=updatehash)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
    result = self._run_interface(execute=True)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
    return self._run_command(execute)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node resample.

Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 401, in run
	    runtime = self._run_interface(runtime)
	              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/interfaces/resampling.py", line 186, in _run_interface
	    transforms = load_transforms(self.inputs.transforms, self.inputs.inverse)
	                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/interfaces/resampling.py", line 51, in load_transforms
	    xfm = load_ants_h5(path)
	          ^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/interfaces/resampling.py", line 90, in load_ants_h5
	    transforms = [nt.Affine(xform[0].to_ras())]
	                            ~~~~~^^^
	IndexError: list index out of range

Add any additional information or context about the problem here.

No response

[effigies]

With the latest nitransforms, there should be no further need for this function. It can be gotten rid of.

See nipreps/fmriprep#3378.