Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

documentation and resource updates #1114

Merged
merged 3 commits into from
Aug 8, 2024
Merged

documentation and resource updates #1114

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
96e8109
documentation and resource updates
handwerkerd Jul 24, 2024
79581c6
Merge branch 'main' into documentation-and-resource-updates
handwerkerd Aug 7, 2024
e817205
Fixed citation numbering and updated posters
n-reddy Aug 7, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Binary file added docs/_static/tedana-ohbm2023-poster.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/_static/tedana-ohbm2024-poster.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
8 changes: 4 additions & 4 deletions docs/index.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -112,8 +112,8 @@ When using tedana, please include the following citations:
}
</script>
<p>
<span id="tedana_citation">tedana</span>
This link is for the most recent version of the code and that page has links to DOIs
<span id="tedana_citation"></span>
1. This link is for the most recent version of the code and that page has links to DOIs
for older versions. To support reproducibility, please cite the version you used:
<a id="tedana_doi_url" href="https://doi.org/10.5281/zenodo.1250561">https://doi.org/10.5281/zenodo.1250561</a>
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This isn't an issue for this PR, but it looks like there aren't zenodo DOIs for tedana versions past 23.0.1. @tsalo Do you know who/how to add version to zenodo and where in our new release workflow that should be happening?

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

It looks like the Zenodo setting was somehow disabled. I just re-enabled it, so it should work the next time we make a release.

<img src onerror='fillCitation()' alt=""/>
Expand Down Expand Up @@ -156,9 +156,9 @@ You can also learn more about `why citing software is important`_.
Posters
*******

.. image:: /_static/tedana-ohbm2019-poster.png
.. image:: /_static/tedana-ohbm2024-poster.png

.. image:: /_static/tedana-ohbm2018-poster.png
.. image:: /_static/tedana-ohbm2023-poster.png


*******************
Expand Down
21 changes: 12 additions & 9 deletions docs/multi-echo.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -424,6 +424,9 @@ individual echo level (see above).
Instead, we recommend that researchers apply the same transforms to all echoes in an ME-EPI series.
That is, that they calculate head motion correction parameters from one echo
and apply the resulting transformation to all echoes.
Based on `Mao et. al. Imaging Neuroscience 2024`_, we recommend using the earliest echo.

.. _Mao et. al. Imaging Neuroscience 2024: https://doi.org/10.1162/imag_a_00151


2. Perform slice timing correction and motion correction **before** multi-echo denoising
Expand Down Expand Up @@ -514,19 +517,19 @@ Journal articles describing multi-echo methods
Videos
======

* An `educational session from OHBM 2017`_ by Dr. Prantik Kundu about multi-echo denoising
* A `series of lectures from the OHBM 2017 multi-echo session`_ on multiple facets of multi-echo data analysis
* | Multi-echo fMRI lecture from the `2018 NIH FMRI Summer Course`_ by Javier Gonzalez-Castillo
| `Slides from 2018 NIH FMRI Summer Course`_
* NIMH Center for Multimodal Neuroimaging `Advantages of multi-echo fMRI`_ (2019) by Dan Handwerker, Javier Gonzalez-Castillo, and Vinai Roopchansingh
* | Multi-echo fMRI lecture from the `2024 NIH FMRI Summer Course`_ by Dan Handwerker
| `Slides from 2024 NIH FMRI Summer Course`_
* | MRI Together 2022 Conference Presentations by Eneko Uruñuela
| Tedana: Analysis of echo-time dependent fMRI data (`recording <https://youtu.be/4wsEodepyI8?t=96>`_, `slides <https://eurunuela.github.io/tedana_MRITogether_2022>`_)
| A tour of tedana (`tour recording <https://youtu.be/P4cV-sGeltk?t=10>`_, `tour slides <https://eurunuela.github.io/tedana_tutorial_MRITogether_2022/>`_)
* | NIMH Center for Multimodal Neuroimaging `Advantages of multi-echo fMRI`_ (2019) by Dan Handwerker, Javier Gonzalez-Castillo, and Vinai Roopchansingh
* | Multi-echo fMRI lecture from the `2018 NIH FMRI Summer Course`_ by Javier Gonzalez-Castillo
| `Slides from 2018 NIH FMRI Summer Course`_

.. _educational session from OHBM 2017: https://www.pathlms.com/ohbm/courses/5158/sections/7788/video_presentations/75977
.. _series of lectures from the OHBM 2017 multi-echo session: https://www.pathlms.com/ohbm/courses/5158/sections/7822
.. _2018 NIH FMRI Summer Course: https://fmrif.nimh.nih.gov/course/fmrif_course/2018/14_Javier_20180713
.. _Slides from 2018 NIH FMRI Summer Course: https://fmrif.nimh.nih.gov/COURSE/fmrif_course/2018/content/14_Javier_20180713.pdf
.. _2024 NIH FMRI Summer Course: https://youtu.be/Uc-1DcgNQzk?feature=shared
.. _Slides from 2024 NIH FMRI Summer Course: https://fmrif.nimh.nih.gov/images/3/3a/12_MultiEcho_Summer_Handwerker2024.pdf
.. _2018 NIH FMRI Summer Course: https://www.youtube.com/watch?v=83bavs4rlUg
.. _Slides from 2018 NIH FMRI Summer Course: https://fmrif.nimh.nih.gov/images/1/12/14_Javier_20180713.pdf
.. _Advantages of multi-echo fMRI: https://youtu.be/G1Ftd2IwF14


Expand Down