[BUG]: compute_epi_mask fails for data in native space

[synchon]

Is there an existing issue for this?

• I have searched the existing issues

Current Behavior

I want to compute the epi mask on native space. Junifer fails with the following trace:

Traceback (most recent call last):
  File "/home/fraimondo/miniforge3/envs/junifer_dev/bin/junifer", line 8, in <module>
    sys.exit(cli())
             ^^^^^
  File "/home/fraimondo/miniforge3/envs/junifer_dev/lib/python3.12/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fraimondo/miniforge3/envs/junifer_dev/lib/python3.12/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/fraimondo/miniforge3/envs/junifer_dev/lib/python3.12/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fraimondo/miniforge3/envs/junifer_dev/lib/python3.12/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fraimondo/miniforge3/envs/junifer_dev/lib/python3.12/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fraimondo/dev/tbox/junifer/junifer/cli/cli.py", line 185, in run
    cli_func.run(
  File "/home/fraimondo/dev/tbox/junifer/junifer/api/functions.py", line 223, in run
    mc.fit(datagrabber_object[t_element])
  File "/home/fraimondo/dev/tbox/junifer/junifer/pipeline/marker_collection.py", line 103, in fit
    data = preprocessor.fit_transform(data)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fraimondo/dev/tbox/junifer/junifer/pipeline/pipeline_step_mixin.py", line 232, in fit_transform
    return self._fit_transform(input=input, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fraimondo/dev/tbox/junifer/junifer/preprocess/base.py", line 181, in _fit_transform
    t_out = self.preprocess(input=t_input, extra_input=extra_input)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fraimondo/dev/tbox/junifer/junifer/preprocess/_temporal_filter.py", line 148, in preprocess
    mask_img = get_data(
               ^^^^^^^^^
  File "/home/fraimondo/dev/tbox/junifer/junifer/data/_dispatch.py", line 160, in get_data
    return registry().get(
           ^^^^^^^^^^^^^^^
  File "/home/fraimondo/dev/tbox/junifer/junifer/data/masks/_masks.py", line 483, in get
    warper_spec = get_native_warper(
                  ^^^^^^^^^^^^^^^^^^
  File "/home/fraimondo/dev/tbox/junifer/junifer/data/utils.py", line 120, in get_native_warper
    raise_error(
  File "/home/fraimondo/dev/tbox/junifer/junifer/utils/logging.py", line 267, in raise_error
    raise klass(msg)
RuntimeError: Could not find correct warping specification

Indeed, the error comes from the _masks.py file, when it tries to get the warp spec to go from native (?) to native:

        # Extra data type requirement check if target space is native
        if target_space == "native":
            # Check for extra inputs
            if extra_input is None:
                raise_error(
                    "No extra input provided, requires `Warp` and `T1w` "
                    "data types in particular for transformation to "
                    f"{target_data['space']} space for further computation."
                )
            # Get native space warper spec
            warper_spec = get_native_warper(
                target_data=target_data,
                other_data=extra_input,
            )

Expected Behavior

I expect that the EPI mask is computed in native space

Steps To Reproduce

1. With junifer latest dev
2. Run:

workdir: /tmp

with:
  ./external/juni-private-farm/datagrabbers/juseless_ukb_bold.py
datagrabber:
    kind:  JuselessUKBBoldDataGrabber

preprocess:
    kind: TemporalFilter
    detrend: true
    standardize: true
    low_pass: 0.08
    high_pass: 0.01
    masks:
      - compute_epi_mask

markers:
  - name: Schaefer200x17-TianxS2x3TxMNInonlinear2009cAsym_FC
    kind: FunctionalConnectivityParcels
    parcellation: 
        - Schaefer200x17
        - TianxS2x3TxMNInonlinear2009cAsym
    masks:
      - inherit
storage:
  kind: HDF5FeatureStorage
  uri: /data/group/riseml/fraimondo/ukb_fcprediction/feature_storage/ukb_fc_features.h5

queue:
  jobname: EXTRACT_FC_UKB
  kind: HTCondor
  env:
    kind: conda
    name: junifer_dev
  mem: 8G

Environment

junifer:
  version: 0.0.7.dev301
python:
  version: 3.12.7
  implementation: CPython
dependencies:
  click: 8.1.7
  numpy: 1.26.4
  scipy: 1.14.1
  datalad: 1.1.4
  pandas: 2.2.3
  nibabel: 5.3.2
  nilearn: 0.10.4
  sqlalchemy: 2.0.36
  ruamel.yaml: 0.18.6
  templateflow: 24.2.2
  lazy_loader: '0.4'
  looseversion: None
  junifer_data: None
  structlog: 25.5.0
system:
  platform: Linux-6.12.9+bpo-amd64-x86_64-with-glibc2.36
environment:
  PATH: 
    /home/fraimondo/miniforge3/envs/junifer_dev/bin:/home/fraimondo/.local/bin:/home/fraimondo/miniforge3/condabin:/usr/local/bin:/home/fraimondo/miniforge3/condabin:/home/fraimondo/.cargo/bin:/usr/local/bin:/usr/bin:/bin:/usr/games

Relevant log output

Anything else?

No response

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2026-01-28 15:35 UTC