smoia/phys2cvr issues and pull requests

#125 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: open - Opened by pre-commit-ci[bot] about 1 month ago

#124 - adding asymmetric vascular range

Pull Request - State: open - Opened by ccomellalue 3 months ago
Labels: Minormod

#123 - Updated versioneer to v0.29

Pull Request - State: closed - Opened by kristinazvolanek 11 months ago - 1 comment
Labels: Internal

#122 - Update versioneer for newer Python versions

Issue - State: closed - Opened by kristinazvolanek 11 months ago

#121 - [Snyk] Security upgrade setuptools from 40.5.0 to 70.0.0

Pull Request - State: closed - Opened by smoia about 1 year ago
Labels: Invalid

#120 - Update installation to add python 3.12 compatibility and update a few settings

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago
Labels: Minormod

#119 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#118 - [Snyk] Security upgrade pillow from 9.5.0 to 10.3.0

Pull Request - State: closed - Opened by smoia over 1 year ago
Labels: Internal

#117 - [Snyk] Security upgrade pillow from 9.5.0 to 10.2.0

Pull Request - State: closed - Opened by smoia over 1 year ago
Labels: Internal, Duplicate

#116 - [Snyk] Security upgrade pillow from 9.5.0 to 10.2.0

Pull Request - State: closed - Opened by smoia over 1 year ago
Labels: Internal, Duplicate

#115 - [Snyk] Security upgrade fonttools from 4.38.0 to 4.43.0

Pull Request - State: closed - Opened by smoia over 1 year ago
Labels: Internal

#114 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago
Labels: Internal

#113 - Implement signal dispersion

Issue - State: open - Opened by smoia over 1 year ago
Labels: Enhancement

#112 - Implement masking based on R2 or lags

Issue - State: open - Opened by smoia over 1 year ago
Labels: Enhancement

#111 - Implement CVR regressor refinement based on voxels showing largest CVR response (correlation with initial PetCO2 timecouse > threshold)

Issue - State: open - Opened by CesarCaballeroGaudes over 1 year ago
Labels: Enhancement

#110 - Implement wavelet denoising

Issue - State: open - Opened by smoia over 1 year ago
Labels: Enhancement

#109 - Add option to remove voxels with large standard deviation (large vessels)

Issue - State: open - Opened by CesarCaballeroGaudes over 1 year ago
Labels: Enhancement

#108 - Implement manual x-corr slider

Issue - State: closed - Opened by smoia over 1 year ago
Labels: Enhancement

#107 - Manual shift for alignment of petco2 signal and ROI average timecourses

Issue - State: open - Opened by CesarCaballeroGaudes over 1 year ago
Labels: Enhancement

#106 - Implement optional mapping for second (absolute) peak in PetCO2 vs GM cross correlation

Issue - State: open - Opened by smoia over 1 year ago
Labels: Enhancement

#105 - logos (1 official, 2 simple one, 3 complete)

Pull Request - State: closed - Opened by RazkinMalen over 1 year ago - 1 comment
Labels: Documentation, Outreach

#104 - Documentation folder and content added

Pull Request - State: closed - Opened by merelvdthiel over 1 year ago
Labels: Documentation

#103 - test functions for io module

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

#102 - Check english and clarify docstrings

Pull Request - State: closed - Opened by merelvdthiel over 1 year ago
Labels: Documentation

#101 - Bh23 second pull

Pull Request - State: closed - Opened by RazkinMalen over 1 year ago
Labels: Duplicate, Invalid

#100 - Changes in english on the dockstrings of the functions init.py , _version.py , io.py , phys2cvr.py

Pull Request - State: closed - Opened by RazkinMalen over 1 year ago
Labels: Documentation

#99 - Check English and clarify docstrings

Pull Request - State: closed - Opened by merelvdthiel over 1 year ago
Labels: Documentation

#98 - Check English in the CLI

Pull Request - State: closed - Opened by AniqueSchuller over 1 year ago
Labels: Documentation

#97 - Allow multiple regressors of interest

Pull Request - State: open - Opened by beccaclements99 over 1 year ago
Labels: Minormod-breaking

#96 - [Snyk] Security upgrade pillow from 9.5.0 to 10.0.0

Pull Request - State: closed - Opened by smoia over 1 year ago
Labels: Duplicate, Invalid

#95 - Implement Loguru for better logging

Issue - State: open - Opened by smoia over 1 year ago
Labels: Enhancement

#94 - Add option to return additional timecourses, e.g. the PetCO2 fitted signal and the denoised signal

Issue - State: open - Opened by CesarCaballeroGaudes almost 2 years ago - 2 comments
Labels: Enhancement

#93 - [Snyk] Security upgrade pillow from 9.5.0 to 10.0.1

Pull Request - State: closed - Opened by smoia almost 2 years ago
Labels: Internal

#92 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago
Labels: Invalid

#91 - Denoise average ROI signal before computing cross-correlation with signal of interest

Issue - State: open - Opened by smoia almost 2 years ago
Labels: Enhancement

#90 - Fix bandpass Butterworth filter order to get a better filter, add option to change order in CLI

Pull Request - State: closed - Opened by smoia almost 2 years ago - 1 comment
Labels: BugFIX, Released

#89 - Possible problem in bandpass filtering

Issue - State: closed - Opened by farnazdelavari almost 2 years ago - 1 comment

#88 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 2 years ago

#87 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 2 years ago
Labels: Internal

#86 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 2 years ago

#85 - All the changes contained in this version are listed in the PR specification

Pull Request - State: open - Opened by smoia over 2 years ago
Labels: Majormod, Minormod-breaking, Refactoring

#84 - Add option to add orthogonalised regressors in phys2cvr

Pull Request - State: closed - Opened by smoia over 2 years ago
Labels: Minormod-breaking, Refactoring

#83 - Improve the modularization of the phys2cvr.py code

Issue - State: open - Opened by CesarCaballeroGaudes over 2 years ago

#82 - Implement statistical thresholding and find "smarter" ways than Sidak corrections

Issue - State: open - Opened by smoia over 2 years ago
Labels: Enhancement

#81 - Finish implementing orthogonalisation methods

Issue - State: closed - Opened by smoia over 2 years ago
Labels: Enhancement

#80 - Create figures using nilearn plotting

Issue - State: open - Opened by smoia over 2 years ago
Labels: Enhancement

#79 - Improve CLI help and docstrings

Issue - State: open - Opened by smoia over 2 years ago
Labels: Documentation, Urgent

#78 - Implement sentry

Issue - State: open - Opened by smoia over 2 years ago
Labels: Enhancement, Urgent

#77 - Improve logging, boilerplate, citaitons, and duecredit

Issue - State: open - Opened by smoia over 2 years ago
Labels: Documentation, Enhancement

#76 - Integrate phys2denoise belt-related models

Issue - State: open - Opened by smoia over 2 years ago
Labels: Enhancement

#75 - Add possiblity to flip regressor of interest (important for belts)

Issue - State: open - Opened by smoia over 2 years ago
Labels: Enhancement

#74 - Implement different response function convolutions, as well as skipping the step, for regressors of interest

Issue - State: open - Opened by smoia over 2 years ago
Labels: Enhancement

#73 - Change name related to current "convolution" step to the more precise PetCO2hrf modelling

Issue - State: open - Opened by smoia over 2 years ago
Labels: Refactoring

#72 - Improve `auto` settings to include all labels and plugins

Pull Request - State: closed - Opened by smoia over 2 years ago - 1 comment
Labels: Released

#71 - Implement multiple regressors _independendent_ lags

Issue - State: open - Opened by smoia over 2 years ago
Labels: Enhancement

#70 - Implement multiple regressor dependent lags

Issue - State: open - Opened by smoia over 2 years ago
Labels: Enhancement

#69 - Refactor declaring forced types code

Issue - State: open - Opened by smoia over 2 years ago
Labels: Refactoring

#68 - Check optimal shift delta lags

Issue - State: open - Opened by smoia over 2 years ago
Labels: Refactoring

#67 - Improve selection/exclusion of timepoints for Xcorr on the CLI

Issue - State: open - Opened by smoia over 2 years ago
Labels: Enhancement

#66 - Generate figure of cross correlation with "cleaned" average GM (using regressors)

Issue - State: open - Opened by smoia over 2 years ago
Labels: Enhancement

#65 - [Snyk] Security upgrade numpy from 1.21.3 to 1.22.2

Pull Request - State: closed - Opened by snyk-bot over 2 years ago

#64 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 2 years ago

#63 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 2 years ago

#62 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 2 years ago

#61 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 2 years ago

#60 - [Snyk] Security upgrade setuptools from 39.0.1 to 65.5.1

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

#59 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 2 years ago

#58 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 2 years ago

#57 - Pre-commit autoupdate [skip ci]

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 2 years ago

#56 - Add colormaps to plot lag maps (and sneak in contributors updates)

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

#55 - [Snyk] Security upgrade setuptools from 39.0.1 to 65.5.1

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

#54 - Add pre-commit and format all code

Pull Request - State: closed - Opened by smoia almost 3 years ago - 1 comment

#53 - Update README.md

Pull Request - State: closed - Opened by kristinazvolanek almost 3 years ago - 1 comment

#52 - Fix dimensionality check for functional images

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

#51 - Nifti not a 4D volume

Issue - State: closed - Opened by srithetree about 3 years ago - 2 comments

#50 - Add the possibility to skip the cross correlation step when creating lagged regressors

Pull Request - State: closed - Opened by smoia over 3 years ago - 1 comment

#49 - Allow confounding matrix and mask to be optional in `stats.regression`

Pull Request - State: closed - Opened by smoia over 3 years ago - 1 comment

#48 - Enhance cross correlation to allow both regressor and reference to be shifted and consider max abs corr

Pull Request - State: closed - Opened by smoia over 3 years ago - 1 comment

#47 - Let signal be resampled over any axis of the input timeseries (default to first dimension)

Pull Request - State: closed - Opened by smoia over 3 years ago - 1 comment

#46 - Change behaviour to create petco2hrf fmri proxy due to the SPC of average signal being more robust than average of SPC

Pull Request - State: closed - Opened by smoia over 3 years ago - 1 comment

#26 - Allow to provide a mask to exclude voxels from the computations, and a separate ROI to use for Xcorr average signal (and lag correction)

Pull Request - State: closed - Opened by smoia almost 4 years ago - 1 comment

GitHub / smoia/phys2cvr issues and pull requests