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* Limit adaptive mask calculation to brain mask. Limit adaptive mask calculation to brain mask. Expand on logic of first adaptive mask method. Update tedana/utils.py Improve docstring. Update test. Add decreasing-signal-based adaptive mask. Keep removing. Co-Authored-By: Dan Handwerker <[email protected]> * Use `compute_epi_mask` in t2smap workflow. * Try fixing the tests. * Fix make_adaptive_mask. * Update test_utils.py * Update test_utils.py * Improve docstring. * Update utils.py * Update test_utils.py * Revert "Update test_utils.py" This reverts commit 259b002. * Don't take absolute value of echo means. * Log echo-wise thresholds in adaptive mask. * Add comment about non-zero voxels. * Update utils.py * Update test_utils.py * Update test_utils.py * Update test_utils.py * Log the thresholds again. * Address review. * Fix test. --------- Co-authored-by: Dan Handwerker <[email protected]>
Updates the requirements on [scikit-learn](https://github.com/scikit-learn/scikit-learn) to permit the latest version. - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](scikit-learn/scikit-learn@0.21.0...1.4.2) --- updated-dependencies: - dependency-name: scikit-learn dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…#1076) Updates the requirements on [pandas](https://github.com/pandas-dev/pandas) to permit the latest version. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Commits](pandas-dev/pandas@v2.0.0...v2.2.2) --- updated-dependencies: - dependency-name: pandas dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…ICA#1078) Updates the requirements on [bokeh](https://github.com/bokeh/bokeh) to permit the latest version. - [Changelog](https://github.com/bokeh/bokeh/blob/branch-3.5/docs/CHANGELOG) - [Commits](bokeh/bokeh@1.0.0...3.4.1) --- updated-dependencies: - dependency-name: bokeh dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* docs: update README.md * docs: update .all-contributorsrc --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com>
…choes (ME-ICA#1061) * Limit adaptive mask calculation to brain mask. Limit adaptive mask calculation to brain mask. Expand on logic of first adaptive mask method. Update tedana/utils.py Improve docstring. Update test. Add decreasing-signal-based adaptive mask. Keep removing. Co-Authored-By: Dan Handwerker <[email protected]> * Use `compute_epi_mask` in t2smap workflow. * Try fixing the tests. * Fix make_adaptive_mask. * Update test_utils.py * Update test_utils.py * Improve docstring. * Identify the last good echo instead of sum. Improve docstring. Update test_utils.py Update test_utils.py Fix make_adaptive_mask. Try fixing the tests. Use `compute_epi_mask` in t2smap workflow. Limit adaptive mask calculation to brain mask. Limit adaptive mask calculation to brain mask. Expand on logic of first adaptive mask method. Update tedana/utils.py Improve docstring. Update test. Add decreasing-signal-based adaptive mask. Keep removing. Co-Authored-By: Dan Handwerker <[email protected]> * Fix. * Update utils.py * Update utils.py * Try fixing. * Update utils.py * Update utils.py * add checks * Just loop over voxels. * Update utils.py * Update utils.py * Update test_utils.py * Revert "Update test_utils.py" This reverts commit 259b002. * Update test_utils.py * Update test_utils.py * Remove checks. * Don't take absolute value of echo means. * Log echo-wise thresholds in adaptive mask. * Add comment about non-zero voxels. * Update utils.py * Update utils.py * Update test_utils.py * Update test_utils.py * Update test_utils.py * Log the thresholds again. * Update test_utils.py * Update test_utils.py * Update test_utils.py * Add simulated data to adaptive mask test. * Clean up the tests. * Add value that tests the base mask. * Remove print in test. * Update tedana/utils.py Co-authored-by: Dan Handwerker <[email protected]> * Update tedana/utils.py Co-authored-by: Dan Handwerker <[email protected]> --------- Co-authored-by: Dan Handwerker <[email protected]>
* Draft function to calculate decay model fit. * Calculate root mean squared error instead. * Incorporate metrics. * Output RMSE results. * Output results in tedana. * Hopefully fix things. * Update decay.py * Try improving performance. * Update decay.py * Fix again. * Use tqdm. * Update decay.py * Update decay.py * Update decay.py * Update expected outputs. * Add figures. * Update outputs. * Include global signal in confounds file. * Update fiu_four_echo_outputs.txt * Rename function. * Rename function. * Update tedana.py * Update tedana/decay.py Co-authored-by: Dan Handwerker <[email protected]> * Update decay.py * Update decay.py * Whoops. * Apply suggestions from code review Co-authored-by: Dan Handwerker <[email protected]> * Fix things maybe. * Fix things. * Update decay.py * Remove any files that are built through appending. * Update outputs. * Add section on plots to docs. * Fix the description. * Update docs/outputs.rst Co-authored-by: Dan Handwerker <[email protected]> * Update docs/outputs.rst * Fix docstring. --------- Co-authored-by: Dan Handwerker <[email protected]>
* Use nearest-neighbors interpolation in plot_stat_map. * Only use NN interp for component maps.
…E-ICA#1100) Updates the requirements on [scipy](https://github.com/scipy/scipy) to permit the latest version. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](scipy/scipy@v1.2.0...v1.13.1) --- updated-dependencies: - dependency-name: scipy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…ME-ICA#1101) Updates the requirements on [scikit-learn](https://github.com/scikit-learn/scikit-learn) to permit the latest version. - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](scikit-learn/scikit-learn@0.21.0...1.5.0) --- updated-dependencies: - dependency-name: scikit-learn dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…CA#1104) * Update numpy requirement from <=1.26.4,>=1.16 to >=1.16,<=2.0.0 Updates the requirements on [numpy](https://github.com/numpy/numpy) to permit the latest version. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](numpy/numpy@v1.16.0...v2.0.0) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Use np.nan instead of np.NaN --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Taylor Salo <[email protected]>
* Filter out non-diagonal affine warning. * Fix warning capture. * Update tedana/reporting/static_figures.py Co-authored-by: Dan Handwerker <[email protected]> * Update static_figures.py --------- Co-authored-by: Dan Handwerker <[email protected]>
…ICA#1109) * Update bokeh requirement from <=3.4.1,>=1.0.0 to <=3.5.0,>=3.5.0 Updates the requirements on [bokeh](https://github.com/bokeh/bokeh) to permit the latest version. - [Changelog](https://github.com/bokeh/bokeh/blob/branch-3.6/docs/CHANGELOG) - [Commits](bokeh/bokeh@1.0.0...3.5.0) --- updated-dependencies: - dependency-name: bokeh dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Update pyproject.toml --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Taylor Salo <[email protected]>
ME-ICA#1108) * Update scikit-learn requirement from <=1.5.0,>=0.21 to <=1.5.1,>=1.5.1 Updates the requirements on [scikit-learn](https://github.com/scikit-learn/scikit-learn) to permit the latest version. - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](scikit-learn/scikit-learn@0.21.0...1.5.1) --- updated-dependencies: - dependency-name: scikit-learn dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Update pyproject.toml to restore minimum version of scikit-learn --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Dan Handwerker <[email protected]>
…E-ICA#1106) * Update scipy requirement from <=1.13.1,>=1.2.0 to <=1.14.0,>=1.14.0 Updates the requirements on [scipy](https://github.com/scipy/scipy) to permit the latest version. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](scipy/scipy@v1.2.0...v1.14.0) --- updated-dependencies: - dependency-name: scipy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Update pyproject.toml to retain minimum version of scipy --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Dan Handwerker <[email protected]> Co-authored-by: Eneko Uruñuela <[email protected]>
…A#1112) Updates the requirements on [numpy](https://github.com/numpy/numpy) to permit the latest version. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](numpy/numpy@v1.16.0...v2.0.1) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* install instructions * Update docs/installation.rst Co-authored-by: Taylor Salo <[email protected]> * Update docs/installation.rst Co-authored-by: Eneko Uruñuela <[email protected]> --------- Co-authored-by: Taylor Salo <[email protected]> Co-authored-by: Eneko Uruñuela <[email protected]>
…ICA#1116) Updates the requirements on [bokeh](https://github.com/bokeh/bokeh) to permit the latest version. - [Changelog](https://github.com/bokeh/bokeh/blob/3.5.1/docs/CHANGELOG) - [Commits](bokeh/bokeh@1.0.0...3.5.1) --- updated-dependencies: - dependency-name: bokeh dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Get required metrics from decision tree. * Continue changes. * More updates. * Store necessary_metrics as a list. * Update selection_nodes.py * Update selection_utils.py * Update across the package. * Keep updating. * Update tedana.py * Add extra metrics to list. * Update ica_reclassify.py * Draft metric-based regressor correlations. * Fix typo. * Work on trees. * Expand regular expressions in trees. * Fix up the expansion. * Really fix it though. * Fix style issue. * Added external regress integration test * Got intregration test with external regressors working * Added F tests and options * added corr_no_detrend.json * updated names and reporting * Run black. * Address style issues. * Try fixing test bugs. * Update test_component_selector.py * Update component_selector.py * Use component table directly in selectcomps2use. * Fix. * Include generated metrics in necessary metrics. * Update component_selector.py * responding to feedback from tsalo * Update component_selector.py * Update test_component_selector.py * fixed some testing failures * fixed test_check_null_succeeds * fixed ica_reclassify bug and selector_properties test * ComponentSelector initialized before loading data * fixed docstrings * updated building decision tree docs * using external regressors and most tests passing * removed corr added tasks * fit_model moved to stats * removed and cleaned up external_regressors_config option * Added task regressors and some tests. Now alll in decision tree * cleaning up decision tree json files * removed mot12_csf.json changed task to signal * fixed tests with task_keep signal * Update tedana/metrics/external.py Co-authored-by: Taylor Salo <[email protected]> * Update tedana/metrics/_utils.py Co-authored-by: Taylor Salo <[email protected]> * Update tedana/metrics/collect.py Co-authored-by: Taylor Salo <[email protected]> * Update tedana/metrics/external.py Co-authored-by: Taylor Salo <[email protected]> * Update tedana/metrics/external.py Co-authored-by: Taylor Salo <[email protected]> * Responding to review comments * reworded docstring * Added type hints to external.py * fixed external.py type hints * type hints to _utils collect and component_selector * type hints and doc improvements in selection_utils * no expand_node recursion * removed expand_nodes expand_node expand_dict * docstring lines break on punctuation * updating external tests and docs * moved test data downloading to tests.utils.py and started test for fit_regressors * fixed bug where task regressors retained in partial models * matched testing external regressors to included mixing and fixed bugs * Made single function for detrending regressors * added tests for external fit_regressors and fix_mixing_to_regressors * Full tests in test_external_metrics.py * adding tests * fixed extern regress validation warnings and added tests * sorting set values for test outputs * added to test_metrics * Added docs to building_decision_trees.rst * Added motion task decision tree flow chart * made recommended change to external_regressor_config * Finished documentation and renamed demo decision trees * added link to example external regressors tsv file * Apply suggestions from code review Fixed nuissance typos Co-authored-by: Taylor Salo <[email protected]> * Minor documentation edits --------- Co-authored-by: Taylor Salo <[email protected]> Co-authored-by: Taylor Salo <[email protected]> Co-authored-by: Neha Reddy <[email protected]>
* Update multi-echo.rst * Update multi-echo.rst
* Add type hints to metric functions. * Use keyword arguments. * Update tests. * Update dependence.py * Update collect.py * Fix other stuff.
* documentation and resource updates * Fixed citation numbering and updated posters --------- Co-authored-by: Neha Reddy <[email protected]>
* Refactor the gscontrol function. * Update docstring. * Fix things. * Update ica_reclassify.py * Update fiu_four_echo_outputs.txt * Update. * Incorporate classification tags into MIR. * Update gscontrol.py * Clean up gscontrol_raw. * Fix. * Update reclassify_debug_out.txt * Update gscontrol.py
…A#1120) Updates the requirements on [numpy](https://github.com/numpy/numpy) to permit the latest version. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](numpy/numpy@v1.16.0...v2.1.0) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…E-ICA#1121) Updates the requirements on [scipy](https://github.com/scipy/scipy) to permit the latest version. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](scipy/scipy@v1.2.0...v1.14.1) --- updated-dependencies: - dependency-name: scipy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…ICA#1122) Updates the requirements on [bokeh](https://github.com/bokeh/bokeh) to permit the latest version. - [Changelog](https://github.com/bokeh/bokeh/blob/3.5.2/docs/CHANGELOG) - [Commits](bokeh/bokeh@1.0.0...3.5.2) --- updated-dependencies: - dependency-name: bokeh dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Robert Smith <[email protected]>
Co-authored-by: Robert Smith <[email protected]>
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