ME-ICA/tedana issues and pull requests

#962 - Reference logger is no longer used

Issue - State: closed - Opened by tsalo over 1 year ago
Labels: bug

#961 - RTD build is failing

Issue - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: bug, documentation

#960 - Fix style issues

Pull Request - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: refactoring

#959 - Document decision tree steps in report

Pull Request - State: closed - Opened by tsalo over 1 year ago - 21 comments
Labels: refactoring

#958 - Bahman tahayori patch 1

Pull Request - State: closed - Opened by BahmanTahayori over 1 year ago - 1 comment

#957 - August 2023 Developers Call

Issue - State: closed - Opened by handwerkerd over 1 year ago
Labels: discussion, community

#956 - -tedpca command-line interface

Issue - State: closed - Opened by Lestropie over 1 year ago - 3 comments

#955 - need multiple reports when using Auto_tedana with multiple runs

Issue - State: closed - Opened by oricon over 1 year ago - 3 comments

#954 - docs: add handwerkerd as a contributor for code

Pull Request - State: closed - Opened by allcontributors[bot] over 1 year ago

#953 - June 2023 developers call

Issue - State: closed - Opened by handwerkerd over 1 year ago
Labels: discussion, community

#952 - Align with old meica

Pull Request - State: closed - Opened by handwerkerd over 1 year ago - 11 comments
Labels: TE-dependence

#951 - logging MAPCA subsampling

Pull Request - State: closed - Opened by handwerkerd over 1 year ago - 3 comments
Labels: enhancement, decomposition

#950 - tedpca CLI fix

Pull Request - State: closed - Opened by handwerkerd over 1 year ago - 2 comments
Labels: bug

#949 - Problem with tedpca

Issue - State: closed - Opened by BahmanTahayori over 1 year ago - 6 comments
Labels: bug

#948 - Multiple documentation updates

Pull Request - State: closed - Opened by handwerkerd over 1 year ago - 4 comments

#947 - May 2023 developers call

Issue - State: closed - Opened by handwerkerd over 1 year ago
Labels: discussion, community

#945 - Update python-publish.yml

Pull Request - State: closed - Opened by tsalo almost 2 years ago
Labels: bug

#942 - Re-do interactive reports demo in documentation

Issue - State: closed - Opened by handwerkerd almost 2 years ago
Labels: documentation, priority: medium, effort: low, impact: medium

#941 - Improving integration tests

Issue - State: open - Opened by handwerkerd almost 2 years ago
Labels: enhancement, testing, priority: medium, effort: high, impact: medium

#940 - ica_reclassify registry fixes

Pull Request - State: closed - Opened by handwerkerd almost 2 years ago

#939 - Drop Python 3.6 and 3.7 support in DTM branch

Issue - State: closed - Opened by tsalo almost 2 years ago

#938 - add pandas version check >= 1.5.2 and mod behavior

Pull Request - State: closed - Opened by pmolfese almost 2 years ago - 2 comments
Labels: bug

#937 - April 2023 developers call

Issue - State: closed - Opened by handwerkerd almost 2 years ago
Labels: discussion, community

#936 - Updating contributor information

Issue - State: closed - Opened by handwerkerd almost 2 years ago - 2 comments
Labels: documentation, community, priority: high, effort: low

#935 - Pandas 1.5.2 and 2.0.0 change to_csv() parameters

Issue - State: closed - Opened by pmolfese almost 2 years ago
Labels: maintenance

#934 - Minimal dependency installation

Issue - State: open - Opened by effigies almost 2 years ago - 1 comment
Labels: maintenance

#933 - NO-MRG Fix coverage

Pull Request - State: closed - Opened by tsalo almost 2 years ago - 1 comment

#932 - March 2023 developers call

Issue - State: closed - Opened by handwerkerd almost 2 years ago
Labels: discussion, community

#931 - Switch to CalVer after decision tree modularization

Issue - State: closed - Opened by tsalo almost 2 years ago
Labels: maintenance

#930 - February 2023 developers call

Issue - State: closed - Opened by handwerkerd almost 2 years ago
Labels: discussion, community

#929 - Divergence between older MEICA component selection and tedana

Issue - State: closed - Opened by handwerkerd about 2 years ago
Labels: priority: medium, effort: medium, impact: medium, breaking change

#928 - [DOC] Remove Josh as maintainer

Pull Request - State: closed - Opened by jbteves about 2 years ago - 3 comments

#927 - Add MRI Together conference presentations to documentation

Issue - State: closed - Opened by handwerkerd about 2 years ago
Labels: documentation, effort: low

#926 - January 2023 developers call

Issue - State: closed - Opened by handwerkerd about 2 years ago
Labels: discussion, community

#924 - Sorting varex for decision tree criterion I011

Pull Request - State: closed - Opened by handwerkerd about 2 years ago - 3 comments
Labels: bug, breaking change

#923 - Decision tree step incorrectly assumes a sorted component table

Issue - State: closed - Opened by handwerkerd about 2 years ago - 2 comments
Labels: bug, priority: medium, effort: low, impact: medium

#922 - Add check of a component metric is used that includes n/a values

Issue - State: open - Opened by handwerkerd about 2 years ago
Labels: bug, priority: medium, effort: medium, impact: medium

#921 - Check metrics exist before running tree. Possibly calculate metrics from tree

Issue - State: closed - Opened by handwerkerd about 2 years ago - 1 comment
Labels: enhancement, priority: low, effort: medium, impact: medium

#920 - Refactor the tedana.py workflow to better use modularized code

Issue - State: open - Opened by handwerkerd about 2 years ago
Labels: enhancement, priority: low, refactoring, effort: high, impact: medium

#919 - harmonize terminology across codebase

Issue - State: open - Opened by handwerkerd about 2 years ago
Labels: priority: low, refactoring, effort: medium, impact: low

#918 - Add more tests for the html report

Issue - State: open - Opened by handwerkerd about 2 years ago - 1 comment
Labels: good first issue, testing, priority: low, effort: medium, impact: low, impact: medium

#917 - Fix example code in denoising documentation

Pull Request - State: closed - Opened by tsalo about 2 years ago - 1 comment
Labels: documentation

#916 - docs: add giadaan as a contributor for doc

Pull Request - State: closed - Opened by allcontributors[bot] about 2 years ago - 2 comments

#915 - Listing standards on inspecting components and reclassification

Issue - State: open - Opened by handwerkerd about 2 years ago - 4 comments
Labels: documentation, effort: medium, impact: medium

#914 - December 2022 developers call

Issue - State: closed - Opened by handwerkerd about 2 years ago
Labels: discussion, community

#913 - Code snippets in the new denoising page don't work

Issue - State: closed - Opened by eurunuela about 2 years ago
Labels: good first issue, documentation, priority: medium, effort: low, impact: low

#912 - Add Nashiro dataset to documentation

Pull Request - State: closed - Opened by Kasambx about 2 years ago - 3 comments
Labels: documentation

#911 - RICA documentation

Pull Request - State: closed - Opened by giadaan about 2 years ago - 4 comments

#910 - custom sections for napoleon output files

Pull Request - State: closed - Opened by giadaan about 2 years ago - 4 comments
Labels: documentation

#909 - Exp/3 pca seq

Pull Request - State: open - Opened by pablosmig about 2 years ago - 4 comments

#908 - Issue892

Pull Request - State: closed - Opened by eurunuela about 2 years ago - 1 comment

#907 - add_na_to_rationale: Add n/a to accepted components rationale

Pull Request - State: closed - Opened by karimox about 2 years ago - 5 comments

#906 - [FIX] Use capital names in desc-ICAOrth_mixing.tsv columns

Pull Request - State: closed - Opened by pablosmig about 2 years ago - 3 comments

#905 - Module is named after Python Built-In Module

Issue - State: closed - Opened by awstanton about 2 years ago - 6 comments
Labels: priority: medium, effort: low, impact: medium

#904 - Column names in orthogonalized mixing matrix do not match ones in metrics file

Issue - State: closed - Opened by tsalo about 2 years ago
Labels: bug, good first issue

#903 - Add discussion template for tedana "consultations"?

Issue - State: open - Opened by tsalo about 2 years ago - 1 comment
Labels: documentation, discussion, community

#902 - Add information about Nashiro dataset to documentation

Issue - State: closed - Opened by tsalo about 2 years ago - 2 comments
Labels: good first issue, documentation, priority: low, impact: low

#901 - Include prefix in report, log, and figures

Issue - State: closed - Opened by tsalo about 2 years ago - 2 comments
Labels: enhancement, priority: medium, effort: medium, breaking change

#900 - Mention dropping non-steady-state volumes in documentation

Issue - State: closed - Opened by tsalo about 2 years ago - 2 comments
Labels: documentation

#898 - Improve documentation on masking options

Issue - State: closed - Opened by handwerkerd about 2 years ago
Labels: documentation, priority: medium, effort: low, impact: medium

#897 - November 2022 developers call

Issue - State: closed - Opened by handwerkerd about 2 years ago
Labels: discussion, community

#896 - Add recommendations for distortion correction

Pull Request - State: closed - Opened by tsalo over 2 years ago - 6 comments
Labels: documentation

#895 - Add links to several multi-echo datasets

Pull Request - State: closed - Opened by tsalo over 2 years ago - 1 comment
Labels: documentation

#894 - Add info on distortion across echoes to documentation

Issue - State: closed - Opened by tsalo over 2 years ago
Labels: documentation

#893 - Add F-T2 and F-S0 maps to verbose outputs

Pull Request - State: closed - Opened by tsalo over 2 years ago - 2 comments
Labels: enhancement

#892 - Add "n/a" to accepted components rationale

Issue - State: closed - Opened by eurunuela over 2 years ago - 4 comments
Labels: good first issue, priority: low, effort: low, impact: low

#891 - Save F_T2* and F_S0 maps

Issue - State: closed - Opened by handwerkerd over 2 years ago - 7 comments
Labels: priority: medium, effort: medium, impact: low

#890 - October 2022 developers call

Issue - State: closed - Opened by handwerkerd over 2 years ago - 3 comments
Labels: discussion, community

#889 - Additional fields in dataset_description.json identifying source files

Issue - State: closed - Opened by andreifoldes over 2 years ago - 5 comments

#888 - Improve summaries and visualizations of results with modularized decision tree

Issue - State: open - Opened by handwerkerd over 2 years ago
Labels: enhancement, help wanted, good first issue, reports, priority: medium, impact: medium

#887 - inconsistent version numbers

Issue - State: closed - Opened by handwerkerd over 2 years ago - 3 comments
Labels: bug, priority: low, effort: low, impact: low, maintenance

#886 - September 2022 developers call

Issue - State: closed - Opened by handwerkerd over 2 years ago
Labels: discussion, community

#885 - Update CONTRIBUTING.md

Pull Request - State: closed - Opened by jbteves over 2 years ago - 2 comments

#884 - August 2022 developers call

Issue - State: closed - Opened by handwerkerd over 2 years ago - 2 comments
Labels: community

#883 - Add Rica documentation

Issue - State: closed - Opened by n-reddy over 2 years ago - 1 comment
Labels: good first issue, priority: low, effort: low, impact: medium

#882 - July 2022 Developers' call. 7/21

Issue - State: closed - Opened by handwerkerd over 2 years ago
Labels: community

#881 - CFF

Issue - State: open - Opened by CPernet over 2 years ago - 5 comments

#880 - [FIX] Fix beta calculation in OLS functions

Pull Request - State: closed - Opened by tsalo over 2 years ago - 1 comment

#875 - [REF] Replace duecredit with BibTeX

Pull Request - State: closed - Opened by tsalo almost 3 years ago - 12 comments

#873 - Enhance reports with BibTeX citations

Issue - State: closed - Opened by tsalo almost 3 years ago - 1 comment
Labels: enhancement, reports

#866 - Add information about Spreng dataset to documentation

Issue - State: closed - Opened by tsalo almost 3 years ago
Labels: good first issue, documentation, priority: low, impact: low

#865 - Add minimally-processed Spreng dataset to datasets module

Issue - State: closed - Opened by tsalo almost 3 years ago - 1 comment
Labels: priority: low, effort: medium, impact: medium, datasets

#861 - Revisiting #230 - incorporate decay curve fit information into workflow

Issue - State: closed - Opened by madisoth almost 3 years ago - 1 comment
Labels: enhancement, T2*/S0 estimation

#856 - Memory issue reported with nonlinear T2* estimation in fMRIPrep

Issue - State: open - Opened by tsalo almost 3 years ago - 5 comments
Labels: bug, T2*/S0 estimation

#851 - It is not clear how to use Rica's component table to rerun tedana

Issue - State: closed - Opened by eurunuela almost 3 years ago - 2 comments
Labels: documentation, priority: medium, effort: low, impact: medium

#850 - [FIX] Address SameFileErrors when running manual classification on an existing output directory

Pull Request - State: closed - Opened by tsalo almost 3 years ago
Labels: bug

#845 - Update Contributing.md file

Issue - State: closed - Opened by aryangupta701 almost 3 years ago - 2 comments
Labels: documentation

#837 - [NO-MRG] Changes from Power replication

Pull Request - State: closed - Opened by tsalo about 3 years ago - 1 comment

#832 - DOC: Use RST link for ME-ICA

Pull Request - State: closed - Opened by effigies about 3 years ago - 1 comment

#831 - [ENH] Use JSON for mapping files to groups

Pull Request - State: closed - Opened by tsalo about 3 years ago - 3 comments
Labels: datasets

#830 - Remove panel width restriction from docs

Issue - State: closed - Opened by tsalo about 3 years ago - 1 comment
Labels: good first issue, documentation, discussion, impact: low

#828 - Use custom docstring section for generated files

Issue - State: closed - Opened by tsalo about 3 years ago - 1 comment
Labels: good first issue, documentation, discussion, impact: low

#827 - Less aggressive masking for first echo

Issue - State: open - Opened by handwerkerd about 3 years ago - 5 comments
Labels: enhancement, priority: low, effort: high, impact: medium, breaking change

#825 - [DOC] Add manfredg as a contributor for code

Pull Request - State: closed - Opened by allcontributors[bot] over 3 years ago - 1 comment

#823 - [DOC] Add documentation page on denoising approaches

Pull Request - State: closed - Opened by tsalo over 3 years ago - 24 comments
Labels: documentation

#822 - [ENH] Remove accepted and rejected outputs

Pull Request - State: closed - Opened by tsalo over 3 years ago - 3 comments

#820 - Replace Zenodo JSON with CITATION.cff

Issue - State: closed - Opened by tsalo over 3 years ago - 2 comments
Labels: discussion, community

#819 - Remove accepted and rejected time series from the standard file outputs

Issue - State: closed - Opened by handwerkerd over 3 years ago - 7 comments
Labels: good first issue, discussion, priority: low, impact: medium, breaking change

#818 - [MAINT] Add 3.10 unit test, compatibilities in setup.cfg

Pull Request - State: closed - Opened by jbteves over 3 years ago - 8 comments

#817 - Add Python 3.10 Support

Issue - State: closed - Opened by jbteves over 3 years ago - 2 comments
Labels: maintenance

GitHub / ME-ICA/tedana issues and pull requests