February 09, 2021 tedana newsletter

[tedana-newsletter]

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tedana February 2021

Update Since our late December newsletter, we have created a new stable release available on PyPI! You can upgrade your local installation to the latest 0.0.9 version by running pip install -U tedana We encourage everyone to go and check it out, as it includes many new bug fixes, improvements, and breaking changes.

New Contributors

We are excited to welcome three new contributors since our last newsletter: M. Versluis, Z. Ahmed, and A. Khojandi! Thanks to all of our contributors for their continued input and help in creating tedana. The community has now grown to 20 contributors, and we always look forward to seeing more new faces! If you’re not sure where to start, please feel free to open an issue or join our next monthly developer's call.

Governance Updates

We have recently overhauled our governance structure, moving from a Benevolent-Dictator-for-Life (BDFL) model to a steering committee structure. We have also implemented specific maintainer roles to better track project leadership, and we encourage contributors to self-describe their work on tedana in the new contributions description file. You can learn more about our new governance structure and current project leadership in our documentation. We encourage any community members who are interested in taking a more active role in tedana to open an issue and add themselves as maintainers!

Code Enhancements

• New interactive reports! Check them out! User-facing documentation is available here. You can also see two example reports here.
• If no BOLD-like ICA components are found, tedana will now re-run the ICA step with a new seed.
• Documentation has been improved both on readthedocs and inside of docstrings.
• Added new documentation for multi-echo acquisition on Philips scanners here.
• T2* values now have a nonzero floor to prevent divide-by-zero errors during optimal combination.
• When opening an issue, there is now a NeuroStars link for more general questions.
• Added variance-explained method for PCA.

Breaking Changes

• The main branch is now "main" instead of "master."
• "T1c" is now "mir" for minimum image regression.
• For the "--manacc" option, you should supply a list of integers instead of a comma-separated string.

Bug Fixes

• Windows path support added for our testing suite.

Full Commit History Since 0.0.9a1 

54f65eb Update acquisition.rst to include information for Philips scanners (#579) by mjversluis on Thu Jul 9 20:16:37 2020 +0200
03694bd docs: add mjversluis as a contributor (#580) by allcontributors[bot] on Thu Jul 9 14:48:10 2020 -0400
ddaa4d5 [DOC] multi-echo reports (#457) by Elizabeth DuPre on Sun Jul 12 21:17:18 2020 -0400
5ccc4f2 [DOC] Include [all] in developer setup install guidelines (#572) by Taylor Salo on Fri Jul 17 18:16:16 2020 -0400
06de703 docs: add mvaziri as a contributor (#587) by allcontributors[bot] on Sun Jul 19 13:34:52 2020 -0400
d933592 [FIX] Add non-zero floor to T2* values (#585) by Taylor Salo on Sun Aug 2 13:56:31 2020 -0400
387db31 [TST] Show logging output during integration tests (#588) by Taylor Salo on Fri Aug 7 13:26:06 2020 -0400
75bdda8 [MAINT] Add workflow to autodeploy to PyPi (#568) by Taylor Salo on Fri Aug 21 10:59:04 2020 -0400
150b5c0 [DOC] Use README as long_desc (#595) by Elizabeth DuPre on Wed Aug 26 11:25:53 2020 -0400
3374356 [ENH] Use list of ints for manacc instead of comma-separated string (#598) by Taylor Salo on Fri Sep 18 16:18:55 2020 -0400
b0b81bc [DOC] Miscellaneous improvements to documentation (#575) by Taylor Salo on Mon Sep 21 22:58:52 2020 -0400
e4e3e26 [DOC] Added link for tedana NeuroStars tag. (#608) by aykhojandi on Mon Sep 28 12:00:44 2020 -0400
5f64cbc docs: add aykhojandi as a contributor (#610) by allcontributors[bot] on Mon Oct 5 10:36:31 2020 -0400
65dda07 [DOC] Rewrite new PCA section (#613) by Eneko Uruñuela on Mon Oct 19 19:13:37 2020 +0200
0eaa3ba [DOC] Reporting documentation (#465) by Javier Gonzalez-Castillo on Mon Oct 19 18:18:21 2020 -0400
005e9d9 [REF] Rename T1c to "minimum image regression" (#609) by Taylor Salo on Mon Oct 19 18:34:25 2020 -0400
91b0379 docs: add smoia as a contributor (#616) by allcontributors[bot] on Tue Oct 20 13:50:51 2020 -0400
61af3f1 [MAINT] Add all contributors to Zenodo file (#614) by Taylor Salo on Mon Nov 2 21:13:44 2020 -0500
c121195 Add diagonal reference line to kappa/rho plot (#625) by Zaki A on Mon Dec 7 14:18:38 2020 -0600
b4a58c8 Allow CI for all-contributors (#627) by Joshua Teves on Mon Dec 7 16:54:08 2020 -0500
23d58f4 [DOC] add notZaki as a contributor (#630) by allcontributors[bot] on Mon Dec 7 17:41:46 2020 -0500
45e5ad7 [DOC] Governance update (#615) by Dan Handwerker on Tue Dec 8 09:49:00 2020 -0500
5369e1d [FIX] Show logs in re-runs (#637) by Zaki A on Mon Jan 4 08:55:56 2021 -0600
4ecdf4b [DOC] Add docstring to fit_loglinear (#646) by Taylor Salo on Fri Jan 15 11:53:00 2021 -0500
63070e2 [FIX] Eliminate duplicate lines in logs (#645) by Taylor Salo on Fri Jan 15 11:53:41 2021 -0500
dae9f20 [DOC] Add NeuroStars question link (#651) by Taylor Salo on Sat Jan 16 10:13:52 2021 -0500
6bfb6fa [DOC] Log count of floored voxels in T2* estimation (#656) by Taylor Salo on Fri Jan 22 17:26:27 2021 -0500
82bda7c [ENH] Implement variance explained threshold-based PCA option (#658) by Taylor Salo on Fri Jan 22 17:26:50 2021 -0500
1e7d42f [DOC] Clarify role of components in output (#660) by Zaki A on Tue Jan 26 09:04:46 2021 -0600
dd513ae docs: add notZaki as a contributor (#661) by allcontributors[bot] on Tue Jan 26 10:05:12 2021 -0500
f422a2f [REF] Replace deprecated get_data() with get_fdata() (#664) by Zaki A on Wed Jan 27 09:05:47 2021 -0600
74b922d [ENH] Add threshold argument to make_adaptive_mask (#635) by Taylor Salo on Wed Jan 27 17:28:53 2021 -0500
cd59211 [ENH] Add ability to re-run ICA when no BOLD components are found (#663) by Taylor Salo on Thu Jan 28 10:11:52 2021 -0500
ca7e145 [ENH] Allow tedpca argument to be a float inside a string (#665) by Zaki A on Thu Jan 28 13:33:24 2021 -0600
65a285d [REF] Replaces master with main where possible (#667) by Joshua Teves on Mon Feb 1 18:57:35 2021 -0500
197513d [DOC] Starts contribution page (#624) by Joshua Teves on Tue Feb 2 09:36:40 2021 -0500
9516608 [MAINT] Add new contributors to Zenodo file (#671) by Taylor Salo on Wed Feb 3 13:32:54 2021 -0500
14be852 [MAINT] Move long description logic from info.py to setup.py (#670) by Zaki A on Wed Feb 3 13:41:41 2021 -0600
f8802df [FIX] Normalize data to zero mean and unit variance before dimension estimation (#636) by Zaki A on Fri Feb 5 09:22:26 2021 -0600
08f6a87 [MAINT] Support Windows' paths; Update zenodo & contributor count (#672) by Zaki A on Fri Feb 5 12:26:35 2021 -0600