Merge branch 'skeleton'

Author: effigies

.git-blame-ignore-revs

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+# Tue Apr 1 10:16:12 2025 -0400 - [email protected] - sty: ruff format [ignore-rev]
+3577bfbbac45ca1e2f9d8b6dd3c036eba5dcd7d2

.github/config.yml

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+# Configuration for new-pr-welcome - https://github.com/behaviorbot/new-pr-welcome
+
+# Comment to be posted to on PRs from first time contributors in your repository
+newPRWelcomeComment: >
+  :wave: Welcome, and thank you for your first contribution!
+
+  We ask you to take a moment to read through our Contributing Guide:
+
+  :point_right: https://github.com/nipreps/fmripost-aroma/blob/main/CONTRIBUTING.md
+
+  These guidelines help us maintain a consistent and collaborative workflow.
+  But don't worry — you don't have to get everything perfect on the first try!
+
+  :mag: Here are a few quick tips:
+
+  1. **Start a conversation**: Consider opening an issue to discuss your idea
+     before submitting a pull request. It might save you time.
+  1. **Descriptive titles**: Please use a clear, descriptive title for your
+     pull request. If it is still a work in progress, mark it as a "Draft".
+  1. **Licensing**: All contributions will be licensed under the Apache 2.0
+     license — the same as the rest of the project.
+  1. **Authorship**: You're invited to add yourself to the `.zenodo.json` file.
+     file. This will credit you as a co-author in the next release. Please add
+     your name as the second-to-last entry, just above the last author.
+
+  A pull request is a conversation. We may suggest changes before merging,
+  and likewise, you should feel free to ask us any questions you have.
+
+  :rocket: We're happy to have you here!

README.rst

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+#################
+fMRIPost-template
+#################
+
+A generic fMRIPost workflow.
+
+********
+Overview
+********
+
+fMRIPost-template is a template repository that can be used to create new fMRIPost workflows.
+
+The workflows and functions in this repository are designed to implement the majority of
+general-purpose steps in an fMRIPost pipeline.
+Here are a few of the key features:
+
+1.  Configuration files to define expected BIDS derivatives from the preprocessing pipeline.
+2.  Functions to collect and organize data from the BIDS derivatives.
+3.  The ability to work with the following preprocessing configurations:
+
+    -   fMRIPrep with ``--level full`` and the required output space for the fMRIPost workflow.
+        For example, fMRIPost-AROMA requires outputs in ``MNI152NLin6Asym`` space with
+        2x2x2 mm voxels.
+    -   fMRIPrep with ``--level full`` and boldref-space outputs,
+        along with transforms to the required output space for the fMRIPost workflow.
+    -   fMRIPrep with ``--level full`` and boldref-space outputs,
+        along with transforms to spaces that can be combined with existing transforms to
+        required spaces.
+        For example, users may apply fMRIPost-AROMA to boldref derivatives with transforms to
+        MNI152NLin2009cAsym space.
+        In this case, the fMRIPost-AROMA workflow will pull a transform from MNI152NLin2009cAsym
+        to MNI152NLin6Asym from TemplateFlow and apply it,
+        along with the boldref-to-MNI152NLin2009cAsym transform, to the boldref-space derivatives.
+    -   fMRIPrep with ``--level full`` and raw BOLD data.
+        In this case, the fMRIPost workflow will apply minimal preprocessing steps internally
+        to generate the required derivatives.
+        This will rarely be used, but may be useful for fMRIPost workflows that require raw data,
+        like fMRIPost-phase.
+
+    .. warning::
+
+        Currently, minimal- and resampling-level fMRIPrep derivatives are not supported,
+        as fMRIPost workflows typically require confounds that are only generated with
+        ``--level full``.
+
+4.  General NiPreps infrastructure for running a BIDS App, such as a config file,
+    a command-line interface, and tools to generate HTML reports.
+
+
+*****
+Usage
+*****
+
+If you use this template to create a new fMRIPost workflow, you will need to:
+
+1.  Replace all instances of ``fmripost_aroma`` with the name of your new workflow.
+2.  Replace all instances of ``fMRIPost-template`` with the name of your new workflow.
+3.  Modify the workflows and interfaces to apply your desired processing steps.
+4.  Update the documentation to reflect the new workflow.
+
+Please also include something like the following in your boilerplate:
+
+> Data were postprocessed using *fMRIPost-<name>*,
+> which is based on *fMRIPost-template* ([cite fMRIPost-template version and DOI here]).

src/fmripost_aroma/interfaces/__init__.py

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+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2024 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Nipype interfaces for the fMRIPost-template workflow."""
+
+from . import bids, reportlets
+
+__all__ = ['bids', 'reportlets']

src/fmripost_aroma/reports/__init__.py

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+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2024 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Tools for generating reports."""
+
+from . import core
+
+__all__ = ['core']

src/fmripost_aroma/tests/data/README

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+Test data that can be bundled in the GitHub repository.

src/fmripost_aroma/utils/__init__.py

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+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2024 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Utility functions for fMRIPost-template."""
+
+from . import bids, utils
+
+__all__ = ['bids', 'utils']