SPiN-Lab/connPFM issues and pull requests

#102 - calculate all histograms in parallel so we don't have to keep the surrogates ets matrices in `even_detection`

Pull Request - State: closed - Opened by vinferrer over 2 years ago - 1 comment
Labels: refactoring

#101 - Use Dask for qsub and parallell jobs

Pull Request - State: closed - Opened by vinferrer over 2 years ago - 3 comments
Labels: enhancement, refactoring

#100 - Add python 3.10 and eliminate python 3.6 from testing

Pull Request - State: closed - Opened by vinferrer over 2 years ago - 1 comment
Labels: testing

#99 - Save sparse matrices as sparse

Pull Request - State: closed - Opened by vinferrer over 2 years ago - 1 comment
Labels: enhancement

#98 - python 3.10 and don't use pickles for reproducible problems

Issue - State: closed - Opened by vinferrer over 2 years ago
Labels: testing

#97 - Save ETS matrix as sparse matrix format

Issue - State: closed - Opened by vinferrer over 2 years ago
Labels: enhancement, effort: low

#96 - Compressed Sparse Row matrix implementation for ETS matrix computations

Pull Request - State: closed - Opened by vinferrer over 2 years ago - 9 comments
Labels: enhancement, refactoring

#95 - Eliminate calculation of ETS on the original BOLD signal

Pull Request - State: closed - Opened by vinferrer over 2 years ago - 1 comment
Labels: refactoring

#94 - Bold ets part is not neccesary anymore

Issue - State: closed - Opened by vinferrer over 2 years ago - 3 comments

#93 - Reduce ETS memory comsup

Issue - State: closed - Opened by vinferrer over 2 years ago
Labels: enhancement

#92 - Change readme and figure to last version

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

#91 - Correct betas shape for multiecho data

Pull Request - State: closed - Opened by vinferrer over 2 years ago - 1 comment
Labels: bug

#90 - Ohbm poster changes

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

#89 - Jobs variable is a list when used in the console

Pull Request - State: closed - Opened by vinferrer over 2 years ago - 1 comment
Labels: bug

#88 - Control number of parallel processes in ev_workflow

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

#87 - Update Readme

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

#86 - Change readme so it has a little description of what the software does

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

#85 - Avoid that surrogate_generator loads the data again

Pull Request - State: closed - Opened by vinferrer over 2 years ago - 1 comment
Labels: refactoring

#84 - Refractor load_data and generate_surrogates functions

Pull Request - State: closed - Opened by vinferrer over 2 years ago
Labels: refactoring

#83 - Add docstrings to main functions

Pull Request - State: open - Opened by vinferrer over 2 years ago - 2 comments
Labels: documentation, priority: low

#82 - Use --prefix option to establish the full path for the debiasing output

Pull Request - State: closed - Opened by vinferrer over 2 years ago - 1 comment
Labels: enhancement, refactoring

#81 - Use --prefix option to establish the full path for the debiasing files

Issue - State: closed - Opened by vinferrer over 2 years ago
Labels: enhancement, refactoring

#80 - Correct HRF shape in debias and output names for multiecho

Pull Request - State: closed - Opened by vinferrer over 2 years ago - 1 comment
Labels: bug

#79 - Add multiecho testing for PFM

Pull Request - State: closed - Opened by vinferrer over 2 years ago - 3 comments
Labels: testing

#78 - Make the conversion to integrer before multipying by the nTE

Pull Request - State: closed - Opened by vinferrer over 2 years ago - 1 comment
Labels: bug

#77 - HRF is defined as `nscans` divided by number of echos

Pull Request - State: closed - Opened by vinferrer over 2 years ago - 1 comment
Labels: bug

#76 - PFM related code needs refactoring

Issue - State: open - Opened by eurunuela over 2 years ago - 1 comment
Labels: refactoring

#75 - Multi-echo pipeline does not work

Issue - State: closed - Opened by eurunuela over 2 years ago
Labels: bug

#74 - Doc string missing in functions

Issue - State: open - Opened by vinferrer over 2 years ago
Labels: documentation, effort: medium, priority: medium

#73 - Eliminate docker image and tests

Pull Request - State: closed - Opened by vinferrer over 2 years ago - 2 comments
Labels: impact: low, testing

#72 - Move connPFM_slim container to OSF

Pull Request - State: closed - Opened by vinferrer over 2 years ago
Labels: refactoring

#71 - Singularity hub doesn't exist anymore

Issue - State: closed - Opened by vinferrer over 2 years ago - 1 comment

#70 - subsample_idx has a larger size due to multiple echoes

Pull Request - State: closed - Opened by vinferrer over 2 years ago - 5 comments
Labels: bug

#69 - Missing tests for multi-echo data

Issue - State: closed - Opened by eurunuela over 2 years ago - 2 comments
Labels: effort: medium, impact: high, priority: high, testing

#68 - Get data directory with absolute path

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

#67 - Add io file for reading a saving files, and support multi-echo

Pull Request - State: closed - Opened by eurunuela over 2 years ago - 2 comments
Labels: refactoring

#66 - Documentation is missing

Issue - State: open - Opened by eurunuela almost 3 years ago
Labels: documentation, effort: high, impact: high, priority: low

#65 - Removed release drafter

Pull Request - State: closed - Opened by eurunuela almost 3 years ago

#64 - Fix time-locked ETS thresholding bug

Pull Request - State: closed - Opened by eurunuela almost 3 years ago

#63 - Change how surrogate histograms are calculated

Pull Request - State: closed - Opened by eurunuela almost 3 years ago

#62 - change OSF input file to SPC

Pull Request - State: closed - Opened by vinferrer almost 3 years ago - 2 comments
Labels: testing

#61 - Change OSF input data to spc

Issue - State: closed - Opened by vinferrer almost 3 years ago
Labels: testing

#60 - Remove standardizing to psc from all maskers.

Pull Request - State: closed - Opened by eurunuela almost 3 years ago - 2 comments

#59 - Assume input data is on signal percentage change

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

#58 - Modify inverse_transform so it works properly

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

#57 - Add group and distance options to CLI

Pull Request - State: closed - Opened by eurunuela almost 3 years ago
Labels: enhancement

#56 - Change the download of the container to singularity library

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

#55 - Debiasing with "groups" option is not available through the CLI

Issue - State: closed - Opened by eurunuela almost 3 years ago
Labels: enhancement, effort: low, impact: high, priority: medium

#54 - Add option to calculate threshold on each surrogate independently

Pull Request - State: closed - Opened by eurunuela almost 3 years ago - 1 comment
Labels: enhancement

#53 - Calculate thresholds independently for each surrogate

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

#52 - don't delete cache docker image

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

#51 - add last changes for OHBM2022

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

#50 - add zenodo badge

Pull Request - State: closed - Opened by vinferrer almost 3 years ago

#49 - add figure one for OHBM

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

#48 - Extend testing to different versions of Python with matrix configuration

Pull Request - State: closed - Opened by vinferrer almost 3 years ago - 2 comments
Labels: testing

#47 - Output rss and peak timepoints as txt

Pull Request - State: closed - Opened by vinferrer almost 3 years ago - 1 comment
Labels: enhancement

#46 - Update debiasing call for stability selection PFM

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

#45 - correct the path to compute_slars.py inside the image

Pull Request - State: closed - Opened by vinferrer almost 3 years ago - 1 comment
Labels: bug

#44 - Add matrix argument as an output string for ev_workflow

Pull Request - State: closed - Opened by vinferrer almost 3 years ago - 1 comment
Labels: enhancement

#43 - Build docker with current brach for both PRs and main branches

Pull Request - State: closed - Opened by vinferrer almost 3 years ago - 1 comment
Labels: testing

#42 - [Option] Compute correlation between the stability selection paths in one timepoint

Issue - State: open - Opened by CesarCaballeroGaudes about 3 years ago
Labels: enhancement

#41 - [ENH] Add different thresholding options to connectivity analysis

Pull Request - State: closed - Opened by eurunuela about 3 years ago - 5 comments
Labels: enhancement, impact: high, priority: high

#40 - The connectivity analysis should have different thresholding options

Issue - State: closed - Opened by eurunuela about 3 years ago
Labels: enhancement, effort: medium, impact: high, priority: medium, refactoring

#39 - Deb output

Pull Request - State: closed - Opened by vinferrer about 3 years ago - 1 comment
Labels: enhancement, effort: low

#38 - add Integration tests to the toolbox

Pull Request - State: closed - Opened by vinferrer about 3 years ago - 2 comments
Labels: impact: high, testing

#37 - implement integration tests in the toolbox

Issue - State: closed - Opened by vinferrer about 3 years ago - 2 comments
Labels: effort: medium, impact: high, priority: medium, testing

#36 - Add testing to slars_stability.py

Pull Request - State: closed - Opened by vinferrer about 3 years ago - 1 comment
Labels: testing

#35 - Start using connpfm official docker repository

Pull Request - State: closed - Opened by vinferrer about 3 years ago - 1 comment
Labels: testing

#34 - solve connpfm_slim_trial problem

Issue - State: closed - Opened by vinferrer about 3 years ago

#33 - Change docker repo to official connpfm

Issue - State: closed - Opened by vinferrer about 3 years ago

#32 - Run `compute_slars.py` in a container

Issue - State: closed - Opened by vinferrer about 3 years ago
Labels: enhancement, effort: medium, impact: medium, priority: high

#31 - execute compute_slars.py in a container so the jobs don't change the execution enviroment

Pull Request - State: closed - Opened by vinferrer about 3 years ago - 2 comments
Labels: bug, enhancement, testing

#30 - Surrogate_auc gets NaNs

Issue - State: closed - Opened by vinferrer about 3 years ago
Labels: bug, effort: high, impact: high, priority: high

#29 - Avoid creating the nilearn_cache folder when using nilearn maskers

Pull Request - State: closed - Opened by vinferrer about 3 years ago - 2 comments
Labels: impact: low, refactoring

#28 - Do not assume debiasing outfile name

Issue - State: closed - Opened by vinferrer about 3 years ago - 1 comment
Labels: enhancement, refactoring

#27 - Debiasing function should have a prefix option

Issue - State: closed - Opened by eurunuela about 3 years ago
Labels: enhancement, effort: low, impact: high, priority: medium, refactoring

#26 - Add script to debias with no information about connectivty or co-fluctuation, i.e., PFM-only

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

#25 - Change ETS plots max and min values

Pull Request - State: closed - Opened by vinferrer about 3 years ago - 4 comments

#24 - Add debiasing testing

Pull Request - State: closed - Opened by vinferrer about 3 years ago - 5 comments
Labels: effort: low, testing

#23 - [ENH] Do not apply inverse transform if not necessary

Pull Request - State: closed - Opened by vinferrer about 3 years ago - 1 comment
Labels: enhancement, priority: low

#22 - `Utils` testing

Pull Request - State: closed - Opened by vinferrer about 3 years ago - 3 comments
Labels: testing

#21 - Add CAPs workflow

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

#20 - Allow non parallel workflow for integration testing

Pull Request - State: closed - Opened by vinferrer about 3 years ago - 1 comment
Labels: enhancement, testing

#19 - Change unit test docker image to an image with afni installed

Pull Request - State: closed - Opened by vinferrer about 3 years ago
Labels: testing

#18 - Change testing image to afni

Issue - State: closed - Opened by vinferrer about 3 years ago
Labels: impact: medium, testing

#17 - Add unit tests for `ev.py`

Pull Request - State: closed - Opened by vinferrer about 3 years ago - 1 comment
Labels: testing

#16 - Fix `debiasing` imports in `connPFM.py`

Pull Request - State: closed - Opened by vinferrer about 3 years ago
Labels: bug

#15 - Add nsurrogates option to `ev_workflow`and `event_detection` functions

Pull Request - State: closed - Opened by vinferrer about 3 years ago
Labels: bug

#14 - `even_detection` assumes 100 surrogates always

Issue - State: closed - Opened by vinferrer about 3 years ago
Labels: bug

#13 - Allow non parallelized pipeline for testing

Issue - State: closed - Opened by vinferrer about 3 years ago
Labels: testing

#12 - Move all code into main structure

Pull Request - State: closed - Opened by eurunuela about 3 years ago
Labels: refactoring

#11 - Implement unit tests

Issue - State: closed - Opened by vinferrer about 3 years ago - 1 comment
Labels: effort: high, impact: high, priority: medium, testing

#10 - Add logger to the toolbox

Pull Request - State: closed - Opened by vinferrer about 3 years ago
Labels: enhancement, hacktoberfest-accepted

#9 - Configure lint test and ensure it passes.

Pull Request - State: closed - Opened by vinferrer about 3 years ago - 2 comments
Labels: hacktoberfest-accepted, testing

#8 - Setup connPFM installation with pip

Pull Request - State: closed - Opened by vinferrer about 3 years ago
Labels: refactoring, hacktoberfest-accepted

#7 - Replace prints with logger

Issue - State: closed - Opened by eurunuela about 3 years ago
Labels: enhancement, good first issue, effort: low, impact: medium, priority: low

#5 - Add linting test

Issue - State: closed - Opened by eurunuela about 3 years ago
Labels: effort: low, impact: low, priority: low

#4 - Merge all workflows

Issue - State: closed - Opened by eurunuela about 3 years ago
Labels: effort: high, impact: high, priority: high, refactoring

#3 - Make pip install work

Issue - State: closed - Opened by eurunuela about 3 years ago
Labels: good first issue, effort: low, impact: medium, priority: medium

#2 - Add qsub templates

Issue - State: open - Opened by eurunuela about 3 years ago - 1 comment
Labels: enhancement, effort: medium, impact: high, priority: low

GitHub / SPiN-Lab/connPFM issues and pull requests