Improve handling of low timepoint BOLDs

What happened?

Running nibabies with freesurfer using this command. During reference scan, crashed out on each scan. Scan protocol and dicom -> bids conversion unchanged from previous runs. Only difference is using freesurfer and not mcribs or infant-freesurfer.

What command did you use?

nipreps/nibabies:unstable
        /input /output participant -v
        -w /work
        --participant-label 006 
        --session-id 01
        --fs-license-file /opt/freesurfer/license.txt
        --derivatives /seg
        --age-months 29
        --surface-recon-method freesurfer
        --cifti-output 91k
        --debug registration
        --project-goodvoxels
        --multi-step-reg
        --norm-csf
        --output-spaces fsLR MNIInfant:cohort-9 MNI152NLin6Asym:res-2 T2w
        --omp-nthreads 8
        --mem 300000
        --nprocs 8
        --stop-on-first-crash
        --skip_bids_validation

What version of NiBabies are you using?

unstable

Relevant log output

Node: nibabies_26_0_wf.single_subject_sub-006_ses-01_wf.bold_ses_01_task_rest_run_06_wf.bold_fit_wf.hmc_boldref_wf.select_frames
Working directory: /work/nibabies_26_0_wf/single_subject_sub-006_ses-01_wf/bold_ses_01_task_rest_run_06_wf/bold_fit_wf/hmc_boldref_wf/select_frames

Node inputs:

dummy_scans = <undefined>
function_str = def _select_frames(
    in_file: str, ref_frame_start: int, dummy_scans: int | None
) -> tuple[int, list]:
    import warnings

    import nibabel as nb
    import numpy as np

    img = nb.load(in_file)
    img_len = img.shape[3]

    # Ensure start index is the largest of the two
    # Will usually be `ref_frame_start`
    start_frame = max(ref_frame_start, dummy_scans) if dummy_scans else ref_frame_start

    if start_frame >= img_len:
        warnings.warn(
            f'Caculating the BOLD reference starting on frame {start_frame} but only {img_len} '
            'volumes in BOLD file, so using last volume.',
            stacklevel=1,
        )
        start_frame = img_len - 1

    t_mask = np.array([False] * img_len, dtype=bool)
    t_mask[start_frame:] = True
    return start_frame, list(t_mask)

in_file = <undefined>
ref_frame_start = 16

Traceback (most recent call last):
  File "/opt/conda/envs/nibabies/lib/python3.12/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
    result = self._run_interface(execute=True)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
    return self._run_command(execute)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.12/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 select_frames.

Traceback:
        Traceback (most recent call last):
          File "/opt/conda/envs/nibabies/lib/python3.12/site-packages/nipype/interfaces/base/core.py", line 401, in run
            runtime = self._run_interface(runtime)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/opt/conda/envs/nibabies/lib/python3.12/site-packages/nipype/interfaces/utility/wrappers.py", line 139, in _run_interface
            out = function_handle(**args)
                  ^^^^^^^^^^^^^^^^^^^^^^^
          File "<string>", line 10, in _select_frames
        IndexError: tuple index out of range

Add any additional information or context about the problem here.

No response