Merge remote-tracking branch 'upstream/main' into fix_762

ME-ICA · Jan 4, 2022 · 129abd6 · 129abd6
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -225,6 +225,15 @@
         "code",
         "doc"
       ]
+    },
+    {
+      "login": "manfredg",
+      "name": "Manfred G Kitzbichler",
+      "avatar_url": "https://avatars.githubusercontent.com/u/1173430?v=4",
+      "profile": "https://github.com/manfredg",
+      "contributions": [
+        "code"
+      ]
     }
   ],
   "contributorsPerLine": 5,

diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -14,7 +14,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Generate environment
           command: |
@@ -24,7 +24,7 @@ jobs:
               pip install .[tests]
             fi
       - save_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
           paths:
               - /opt/conda/envs/tedana_py37
 
@@ -35,7 +35,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py36-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py36-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Generate environment
           command: |
@@ -54,7 +54,7 @@ jobs:
             mkdir /tmp/src/coverage
             mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.py36
       - save_cache:
-          key: conda-py36-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py36-v2-{{ checksum "tedana/info.py" }}
           paths:
               - /opt/conda/envs/tedana_py36
       - persist_to_workspace:
@@ -69,7 +69,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Running unit tests
           command: |
@@ -91,7 +91,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py38-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py38-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Generate environment
           command: |
@@ -110,7 +110,7 @@ jobs:
             mkdir /tmp/src/coverage
             mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.py38
       - save_cache:
-          key: conda-py38-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py38-v2-{{ checksum "tedana/info.py" }}
           paths:
               - /opt/conda/envs/tedana_py38
       - persist_to_workspace:
@@ -125,7 +125,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py39-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py39-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Generate environment
           command: |
@@ -144,7 +144,7 @@ jobs:
             mkdir /tmp/src/coverage
             mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.py39
       - save_cache:
-          key: conda-py39-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py39-v2-{{ checksum "tedana/info.py" }}
           paths:
               - /opt/conda/envs/tedana_py39
       - persist_to_workspace:
@@ -159,7 +159,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Style check
           command: |
@@ -175,7 +175,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Run integration tests
           no_output_timeout: 40m
@@ -200,7 +200,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Run integration tests
           no_output_timeout: 40m
@@ -225,7 +225,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Run integration tests
           no_output_timeout: 40m
@@ -250,7 +250,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Run integration tests
           no_output_timeout: 40m
@@ -277,7 +277,7 @@ jobs:
           at: /tmp
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Merge coverage files
           command: |

diff --git a/.gitignore b/.gitignore
@@ -108,7 +108,6 @@ ENV/
 
 # jupyter notebooks
 .ipynb_checkpoints/
-*.ipynb
 
 # vim swap files
 *.swp
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -132,7 +132,7 @@ Make sure to always [keep your fork up to date][link_updateupstreamwiki] with th
 To test a change, you may need to set up your local repository to run a `tedana` workflow.
 To do so, run
 ```
-pip install -e .[all]
+pip install -e .'[all]'
 ```
 from within your local `tedana` repository. This should ensure all packages are correctly organized and linked on your user profile.
 

diff --git a/README.md b/README.md
@@ -1,13 +1,9 @@
 # tedana: TE Dependent ANAlysis
 
-The ``tedana`` package is part of the ME-ICA pipeline, performing TE-dependent
-analysis of multi-echo functional magnetic resonance imaging (fMRI) data.
-``TE``-``de``pendent ``ana``lysis (``tedana``) is a Python module for denoising
-multi-echo functional magnetic resonance imaging (fMRI) data.
-
 [![Latest Version](https://img.shields.io/pypi/v/tedana.svg)](https://pypi.python.org/pypi/tedana/)
 [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/tedana.svg)](https://pypi.python.org/pypi/tedana/)
-[![DOI](https://zenodo.org/badge/110845855.svg)](https://zenodo.org/badge/latestdoi/110845855)
+[![JOSS DOI](https://joss.theoj.org/papers/10.21105/joss.03669/status.svg)](https://doi.org/10.21105/joss.03669)
+[![Zenodo DOI](https://zenodo.org/badge/110845855.svg)](https://zenodo.org/badge/latestdoi/110845855)
 [![License](https://img.shields.io/badge/License-LGPL%202.0-blue.svg)](https://opensource.org/licenses/LGPL-2.1)
 [![CircleCI](https://circleci.com/gh/ME-ICA/tedana.svg?style=shield)](https://circleci.com/gh/ME-ICA/tedana)
 [![Documentation Status](https://readthedocs.org/projects/tedana/badge/?version=latest)](http://tedana.readthedocs.io/en/latest/?badge=latest)
@@ -19,16 +15,35 @@ multi-echo functional magnetic resonance imaging (fMRI) data.
 [![All Contributors](https://img.shields.io/badge/all_contributors-20-orange.svg?style=flat-square)](#contributors)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-
-## About
-
-``tedana`` originally came about as a part of the [ME-ICA](https://github.com/me-ica/me-ica) pipeline.
-The ME-ICA pipeline originally performed both pre-processing and TE-dependent analysis of multi-echo fMRI data; however, ``tedana`` now assumes that you're working with data which has been previously preprocessed.
+``TE``-``de``pendent ``ana``lysis (``tedana``) is a Python library for denoising multi-echo functional magnetic resonance imaging (fMRI) data.
+``tedana`` originally came about as a part of the [ME-ICA](https://github.com/me-ica/me-ica) pipeline, although it has since diverged.
+An important distinction is that while the ME-ICA pipeline originally performed both pre-processing and TE-dependent analysis of multi-echo fMRI data,
+``tedana`` now assumes that you're working with data which has been previously preprocessed.
 
 ![http://tedana.readthedocs.io/](https://user-images.githubusercontent.com/7406227/40031156-57b7cbb8-57bc-11e8-8c51-5b29f2e86a48.png)
 
 More information and documentation can be found at https://tedana.readthedocs.io.
 
+## Citing `tedana`
+
+If you use `tedana`, please cite the following papers, as well as our [most recent Zenodo release](https://zenodo.org/badge/latestdoi/110845855):
+
+- DuPre, E. M., Salo, T., Ahmed, Z., Bandettini, P. A., Bottenhorn, K. L.,
+  Caballero-Gaudes, C., Dowdle, L. T., Gonzalez-Castillo, J., Heunis, S.,
+  Kundu, P., Laird, A. R., Markello, R., Markiewicz, C. J., Moia, S.,
+  Staden, I., Teves, J. B., Uruñuela, E., Vaziri-Pashkam, M.,
+  Whitaker, K., & Handwerker, D. A. (2021).
+  [TE-dependent analysis of multi-echo fMRI with tedana.](https://doi.org/10.21105/joss.03669)
+  _Journal of Open Source Software_, _6(66)_, 3669.
+  doi:10.21105/joss.03669.
+- Kundu, P., Inati, S. J., Evans, J. W., Luh, W. M., & Bandettini, P. A. (2011).
+  [Differentiating BOLD and non-BOLD signals in fMRI time series using multi-echo EPI.](https://doi.org/10.1016/j.neuroimage.2011.12.028)
+  _NeuroImage_, _60_, 1759-1770.
+- Kundu, P., Brenowitz, N. D., Voon, V., Worbe, Y., Vértes, P. E., Inati, S. J.,
+  Saad, Z. S., Bandettini, P. A., & Bullmore, E. T. (2013).
+  [Integrated strategy for improving functional connectivity mapping using multiecho fMRI.](https://doi.org/10.1073/pnas.1301725110)
+  _Proceedings of the National Academy of Sciences_, _110_, 16187-16192.
+
 ## Installation
 
 ### Use `tedana` with your local Python environment
@@ -75,6 +90,20 @@ conda deactivate
 NOTE: Conda < 4.6 users will need to use the soon-to-be-deprecated option `source` rather than `conda` for the activation and deactivation steps.
 You can read more about managing conda environments and this discrepancy [here](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html).
 
+You can confirm that ``tedana`` has successfully installed by launching a Python instance and running:
+
+```python
+import tedana
+```
+
+You can check that it is available through the command line interface (CLI) with:
+
+```bash
+tedana --help
+```
+
+If no error occurs, ``tedana`` has correctly installed in your environment!
+
 ### Use and contribute to `tedana` as a developer
 
 If you aim to contribute to the `tedana` code base and/or documentation, please first read the developer installation instructions in [our contributing section](https://github.com/ME-ICA/tedana/blob/main/CONTRIBUTING.md). You can then continue to set up your preferred development environment.
@@ -133,6 +162,9 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     <td align="center"><a href="https://github.com/smoia"><img src="https://avatars3.githubusercontent.com/u/35300580?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Stefano Moia</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=smoia" title="Code">💻</a> <a href="https://github.com/ME-ICA/tedana/pulls?q=is%3Apr+reviewed-by%3Asmoia" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/ME-ICA/tedana/commits?author=smoia" title="Documentation">📖</a></td>
     <td align="center"><a href="https://www.notzaki.com/"><img src="https://avatars1.githubusercontent.com/u/9019681?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Zaki A.</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/issues?q=author%3AnotZaki" title="Bug reports">🐛</a> <a href="https://github.com/ME-ICA/tedana/commits?author=notZaki" title="Code">💻</a> <a href="https://github.com/ME-ICA/tedana/commits?author=notZaki" title="Documentation">📖</a></td>
   </tr>
+  <tr>
+    <td align="center"><a href="https://github.com/manfredg"><img src="https://avatars.githubusercontent.com/u/1173430?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Manfred G Kitzbichler</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=manfredg" title="Code">💻</a></td>
+  </tr>
 </table>
 
 <!-- markdownlint-restore -->

diff --git a/docs/approach.rst b/docs/approach.rst
@@ -19,6 +19,8 @@ This is performed in a series of steps, including:
 .. image:: /_static/tedana-workflow.png
   :align: center
 
+We provide more detail on each step below.
+The figures shown in this walkthrough are generated in the `provided notebooks <https://github.com/ME-ICA/tedana/tree/joss/docs/notebooks>`_.
 
 ***************
 Multi-echo data

diff --git a/docs/index.rst b/docs/index.rst
@@ -4,11 +4,6 @@
 tedana: TE Dependent ANAlysis
 #############################
 
-The ``tedana`` package is part of the ME-ICA pipeline, performing TE-dependent
-analysis of multi-echo functional magnetic resonance imaging (fMRI) data.
-``TE``-``de``\pendent ``ana``\lysis (``tedana``) is a Python module for denoising
-multi-echo functional magnetic resonance imaging (fMRI) data.
-
 .. image:: https://img.shields.io/pypi/v/tedana.svg
    :target: https://pypi.python.org/pypi/tedana/
    :alt: Latest Version
@@ -17,9 +12,13 @@ multi-echo functional magnetic resonance imaging (fMRI) data.
    :target: https://pypi.python.org/pypi/tedana/
    :alt: PyPI - Python Version
 
+.. image:: https://joss.theoj.org/papers/10.21105/joss.03669/status.svg
+   :target: https://doi.org/10.21105/joss.03669
+   :alt: JOSS DOI
+
 .. image:: https://zenodo.org/badge/110845855.svg
    :target: https://zenodo.org/badge/latestdoi/110845855
-   :alt: DOI
+   :alt: Zenodo DOI
 
 .. image:: https://circleci.com/gh/ME-ICA/tedana.svg?style=shield
    :target: https://circleci.com/gh/ME-ICA/tedana
@@ -62,14 +61,15 @@ multi-echo functional magnetic resonance imaging (fMRI) data.
 About
 *****
 
+``TE``-``de``pendent ``ana``lysis (``tedana``) is a Python library for denoising multi-echo functional magnetic resonance imaging (fMRI) data.
+``tedana`` originally came about as a part of the `ME-ICA`_ pipeline, although it has since diverged.
+An important distinction is that while the ME-ICA pipeline originally performed both pre-processing and TE-dependent analysis of multi-echo fMRI data,
+``tedana`` now assumes that you're working with data which has been previously preprocessed.
+
+
 .. image:: https://user-images.githubusercontent.com/7406227/40031156-57b7cbb8-57bc-11e8-8c51-5b29f2e86a48.png
   :target: http://tedana.readthedocs.io/
 
-``tedana`` originally came about as a part of the `ME-ICA`_ pipeline.
-The ME-ICA pipeline originally performed both pre-processing and TE-dependent
-analysis of multi-echo fMRI data; however, ``tedana`` now assumes that you're
-working with data which has been previously preprocessed.
-
 For a summary of multi-echo fMRI, which is the imaging technique ``tedana`` builds on,
 visit `Multi-echo fMRI`_.
 
@@ -114,14 +114,27 @@ When using tedana, please include the following citations:
       <p>
       <span id="tedana_citation">tedana</span> Available from: <a id="tedana_doi_url" href="https://doi.org/10.5281/zenodo.1250561">https://doi.org/10.5281/zenodo.1250561</a>
       <img src onerror='fillCitation()' alt=""/>
+      </p>
 
       <p>
-      2. Kundu, P., Inati, S. J., Evans, J. W., Luh, W. M. & Bandettini, P. A. (2011).
+      2. DuPre, E. M., Salo, T., Ahmed, Z., Bandettini, P. A., Bottenhorn, K. L.,
+      Caballero-Gaudes, C., Dowdle, L. T., Gonzalez-Castillo, J., Heunis, S.,
+      Kundu, P., Laird, A. R., Markello, R., Markiewicz, C. J., Moia, S.,
+      Staden, I., Teves, J. B., Uruñuela, E., Vaziri-Pashkam, M.,
+      Whitaker, K., & Handwerker, D. A. (2021).
+      <a href=https://doi.org/10.21105/joss.03669>TE-dependent analysis of multi-echo fMRI with tedana.</a>
+      <i>Journal of Open Source Software</i>, <i>6(66)</i>, 3669.
+      doi:10.21105/joss.03669.
+      </p>
+
+      <p>
+      3. Kundu, P., Inati, S. J., Evans, J. W., Luh, W. M., & Bandettini, P. A. (2011).
       <a href=https://doi.org/10.1016/j.neuroimage.2011.12.028>Differentiating BOLD and non-BOLD signals in fMRI time series using multi-echo EPI.</a>
       <i>NeuroImage</i>, <i>60</i>, 1759-1770.
       </p>
+
       <p>
-      3. Kundu, P., Brenowitz, N. D., Voon, V., Worbe, Y., Vértes, P. E., Inati, S. J.,
+      4. Kundu, P., Brenowitz, N. D., Voon, V., Worbe, Y., Vértes, P. E., Inati, S. J.,
       Saad, Z. S., Bandettini, P. A., & Bullmore, E. T. (2013).
       <a href=https://doi.org/10.1073/pnas.1301725110>Integrated strategy for improving functional connectivity mapping using multiecho fMRI.</a>
       <i>Proceedings of the National Academy of Sciences</i>, <i>110</i>, 16187-16192.

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -13,11 +13,27 @@ packages will need to be installed:
 - scipy
 - mapca
 
-You can then install ``tedana`` with:
+You can also install several optional dependencies, notably ``duecredit``.
+Please see the :doc:`FAQ <faq>` for more information on how tedana uses ``duecredit``.
+
+After installing relevant dependencies, you can then install ``tedana`` with:
 
 .. code-block:: bash
 
   pip install tedana
 
 In addition to the Python package, installing ``tedana`` will add the ``tedana``
 and ``t2smap`` workflow CLIs to your path.
+You can confirm that ``tedana`` has successfully installed by launching a Python instance and running:
+
+.. code-block:: python
+
+  import tedana
+
+You can check that it is available through the command line interface (CLI) with:
+
+.. code-block:: bash
+
+  tedana --help
+
+If no error occurs, ``tedana`` has correctly installed in your environment!
diff --git a/examples/plot_approach_figures.ipynb → docs/notebooks/plot_approach_figures.ipynb b/examples/plot_approach_figures.ipynb → docs/notebooks/plot_approach_figures.ipynb
diff --git a/examples/plot_metric_simulations.ipynb → docs/notebooks/plot_metric_simulations.ipynb b/examples/plot_metric_simulations.ipynb → docs/notebooks/plot_metric_simulations.ipynb
diff --git a/paper/figure_01.png b/paper/figure_01.png