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Add documentation (#8)
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‎.github/ISSUE_TEMPLATE/feature_request.yml

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For information on how to contribute, please refer to our [contributing guidelines](https://www.nipreps.org/community/CONTRIBUTING/).
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options:
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- "Yes"
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- Yes, but I would need guidance
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- "Yes, but I would need guidance"
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- "No"
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validations:
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required: true

‎.github/config.yml

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# Configuration for new-pr-welcome - https://github.com/behaviorbot/new-pr-welcome
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# Comment to be posted to on PRs from first time contributors in your repository
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newPRWelcomeComment: >
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Welcome, new contributor!
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We ask you to read through the Contributing Guide:
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https://github.com/nipreps/fmripost-template/blob/main/CONTRIBUTING.md
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These are guidelines intended to make communication easier by describing a consistent process, but
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don't worry if you don't get it everything exactly "right" on the first try.
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To boil it down, here are some highlights:
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1) Consider starting a conversation in the issues list before submitting a pull request. The discussion might save you a
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lot of time coding.
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2) Please use a descriptive title for your pull request.
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Please remember to set your pull request as a "draft" if it is not ready for review.
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3) Any code you submit will be licensed under the same terms (Apache License 2.0) as the rest of fMRIPost-template.
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4) We invite every contributor to add themselves to the `.zenodo.json` file
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(https://github.com/nipreps/fmripost-template/blob/main/.zenodo.json), which will result in your being listed as an author
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at the next release. Please add yourself as the next-to-last entry, just above Russ.
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A pull request is a conversation. We may ask you to make some changes before accepting your PR,
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and likewise, you should feel free to ask us any questions you have.

‎.github/pull_request_template.md

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<!--
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Text in these brackets are comments, and won't be visible when you submit your pull request.
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If this is your first contribution, please take the time to read these, in particular the comment
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beginning "Welcome, new contributors!".
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-->
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Closes .
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## Changes proposed in this pull request
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<!--
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Please describe here the main features / changes proposed for review and integration in fMRIPost-template
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If this PR addresses some existing problem, please use GitHub's citing tools
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(eg. ref #, closes # or fixes #).
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(e.g., ref #, closes # or fixes #).
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If there is not an existing issue open describing the problem, please consider opening a new
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issue first and then link it from here (so the *fMRIPost-template* community has a better understanding
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of ongoing development efforts and possible overlaps between contributions).
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<!--
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Please summarize here the main changes to the documentation that the reviewers should be aware of.
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-->
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<!--
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Welcome, new contributors!
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We ask you to read through the Contributing Guide:
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https://github.com/nipreps/fmripost-template/blob/main/CONTRIBUTING.md
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These are guidelines intended to make communication easier by describing a consistent process, but
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don't worry if you don't get it everything exactly "right" on the first try.
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To boil it down, here are some highlights:
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1) Consider starting a conversation in the issues list before submitting a pull request. The discussion might save you a
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lot of time coding.
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2) Please use descriptive prefixes in your pull request title, such as "ENH:" for an enhancement or "FIX:" for a bug fix.
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(See the Contributing guide for the full set.) And consider adding a "WIP" tag for works-in-progress.
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3) Any code you submit will be licensed under the same terms (Apache License 2.0) as the rest of fMRIPost-template.
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4) We invite every contributor to add themselves to the `.zenodo.json` file
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(https://github.com/nipreps/fmripost-template/blob/main/.zenodo.json), which will result in your being listed as an author
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at the next release. Please add yourself as the next-to-last entry, just above Russ.
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A pull request is a conversation. We may ask you to make some changes before accepting your PR,
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and likewise, you should feel free to ask us any questions you have.
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-->

‎.mailmap

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Christopher J. Markiewicz <[email protected]>
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Christopher J. Markiewicz <[email protected]> <[email protected]>
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Christopher J. Markiewicz <[email protected]> <[email protected]>
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Taylor Salo <[email protected]>
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Taylor Salo <[email protected]> <[email protected]>
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Taylor Salo <[email protected]> <[email protected]>

‎.zenodo.json

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"affiliation": "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland",
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"name": "Esteban, Oscar",
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"orcid": "0000-0001-8435-6191"
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},
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{
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"name": "Ferrer, Vicente"
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},
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{
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"name": "Uruñuela, Eneko"
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},
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{
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"name": "Pedregosa, Fabian"
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},
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{
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"name": "Caballero Gaudes, Cesar"
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}
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],
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"creators": [
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"neuroimaging",
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"workflow",
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"pipeline",
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"preprocessing",
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"postprocessing",
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"fMRI",
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"BIDS"
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],

‎Dockerfile

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#
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# MIT License
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#
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# Copyright (c) The NiPreps Developers
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# Copyright (c) 2024 The NiPreps Developers
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#
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# Permission is hereby granted, free of charge, to any person obtaining a copy
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# of this software and associated documentation files (the "Software"), to deal

‎NOTICE

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src/fmripost_aroma/data/NOTICE
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src/fmripost_template/data/NOTICE

‎README.md

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‎README.rst

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#################
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fMRIPost-template
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#################
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A generic fMRIPost workflow.
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********
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Overview
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********
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fMRIPost-template is a template repository that can be used to create new fMRIPost workflows.
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The workflows and functions in this repository are designed to implement the majority of
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general-purpose steps in an fMRIPost pipeline.
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Here are a few of the key features:
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1. Configuration files to define expected BIDS derivatives from the preprocessing pipeline.
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2. Functions to collect and organize data from the BIDS derivatives.
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3. The ability to work with the following preprocessing configurations:
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- fMRIPrep with ``--level full`` and the required output space for the fMRIPost workflow.
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For example, fMRIPost-AROMA requires outputs in ``MNI152NLin6Asym`` space with
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2x2x2 mm voxels.
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- fMRIPrep with ``--level full`` and boldref-space outputs,
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along with transforms to the required output space for the fMRIPost workflow.
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- fMRIPrep with ``--level full`` and boldref-space outputs,
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along with transforms to spaces that can be combined with existing transforms to
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required spaces.
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For example, users may apply fMRIPost-AROMA to boldref derivatives with transforms to
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MNI152NLin2009cAsym space.
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In this case, the fMRIPost-AROMA workflow will pull a transform from MNI152NLin2009cAsym
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to MNI152NLin6Asym from TemplateFlow and apply it,
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along with the boldref-to-MNI152NLin2009cAsym transform, to the boldref-space derivatives.
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.. warning::
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Currently, minimal- and resampling-level fMRIPrep derivatives are not supported,
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as fMRIPost workflows typically require confounds that are only generated with
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``--level full``.
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4. General NiPreps infrastructure for running a BIDS App, such as a config file,
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a command-line interface, and tools to generate HTML reports.

‎docs/Makefile

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = .
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BUILDDIR = _build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎docs/_static/theme_overrides.css

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/* override table width restrictions */
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@media screen and (min-width: 767px) {
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.wy-table-responsive table td {
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/* !important prevents the common CSS stylesheets from overriding
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this as on RTD they are loaded after this stylesheet */
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white-space: normal !important;
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}
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.wy-table-responsive {
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overflow: visible !important;
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}
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}
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/* Fix parameter type style */
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.function .classifier {
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margin: 0 0 0 5px;
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padding: 3px;
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background: rgba(0, 0, 0, .1);
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}

‎docs/api.rst

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.. include:: links.rst
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================
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Developers - API
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================
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The *NiPreps* community and contributing guidelines
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---------------------------------------------------
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*fMRIPost-template* is a *NiPreps* application, and abides by the
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`NiPreps Community guidelines <https://www.nipreps.org/community/>`__.
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Please, make sure you have read and understood all the documentation
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provided in the `NiPreps portal <https://www.nipreps.org>`__ before
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you get started.
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Setting up your development environment
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---------------------------------------
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We believe that *fMRIPost-template* must be free to use, inspect, and critique.
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Correspondingly, you should be free to modify our software to improve it
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or adapt it to new use cases and we especially welcome contributions to
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improve it or its documentation.
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We actively direct efforts into making the scrutiny and improvement processes
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as easy as possible.
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As part of such efforts, we maintain some
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`tips and guidelines for developers <https://www.nipreps.org/devs/devenv/>`__
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to help minimize your burden if you want to modify the software.
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Internal configuration system
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-----------------------------
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.. automodule:: fmripost_template.config
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:members: from_dict, load, get, dumps, to_filename, init_spaces
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Workflows
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---------
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.. automodule:: fmripost_template.workflows.base

‎docs/changes.rst

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.. include:: links.rst
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----------
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What's new
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----------
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.. include:: ../CHANGES.rst

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