Ecosyste.ms: Issues

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GitHub / aramis-lab/clinica issues and pull requests

#1059 - [CI] Increase timeout of t1-Freesurfer test workflows from 12h to 24h...

Pull Request - State: closed - Opened by NicolasGensollen 10 months ago
Labels: CI

#1058 - Bump pillow from 10.0.1 to 10.2.0

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago
Labels: dependencies, python

#1057 - [ENH] Allow the clinica file reader to read dwi dti images

Pull Request - State: closed - Opened by NicolasGensollen 10 months ago - 1 comment
Labels: enhancement

#1056 - Allow the Clinica file reader to get DWI DTI output images

Issue - State: closed - Opened by NicolasGensollen 10 months ago
Labels: enhancement

#1055 - [FIX] Fix calls to `get_subject_session_list`

Pull Request - State: closed - Opened by NicolasGensollen 10 months ago
Labels: fix

#1054 - Bump actions/setup-python from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago
Labels: dependencies, github_actions

#1053 - Add BIDS Conversion for Blood Recording Data into ADNI-to-BIDS

Issue - State: closed - Opened by Ianyliu 10 months ago - 2 comments
Labels: enhancement, inactive

#1052 - Fix `get_subject_session_list` return value

Pull Request - State: closed - Opened by NicolasGensollen 10 months ago

#1051 - Wrong return value documented in `get_subject_session_list`

Issue - State: closed - Opened by NicolasGensollen 10 months ago
Labels: bug

#1050 - Improve BIDS compliance for preprocessed DWI files

Pull Request - State: closed - Opened by NicolasGensollen 10 months ago
Labels: pipeline

#1049 - Support for DKT atlas in pet-surface

Issue - State: closed - Opened by PavanChaggar 11 months ago - 6 comments
Labels: enhancement, pipeline, inactive

#1048 - Bump jinja2 from 3.1.2 to 3.1.3

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago
Labels: dependencies, python

#1047 - [DOC] Some documentation fixes

Pull Request - State: closed - Opened by NicolasGensollen 11 months ago
Labels: doc

#1046 - Bump fonttools from 4.38.0 to 4.43.0

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago
Labels: dependencies, python

#1045 - [REF TEST] Refactor data handling

Pull Request - State: closed - Opened by NicolasGensollen 11 months ago
Labels: enhancement

#1044 - Does the Clinica ADNI-to-BIDS pipeline build field maps?

Issue - State: closed - Opened by likeajumprope 11 months ago - 6 comments
Labels: enhancement, converter

#1043 - Get rid of Niflow and unpin Nibabel

Pull Request - State: closed - Opened by NicolasGensollen 11 months ago
Labels: dependencies

#1042 - [DOC] Add entry in documentation for NOW 2023

Pull Request - State: closed - Opened by NicolasGensollen 12 months ago
Labels: doc

#1041 - [ADNI] Allow convert fmri multiband

Pull Request - State: closed - Opened by NicolasGensollen 12 months ago
Labels: enhancement, converter

#1040 - [CI] Run SPM based non regression tests in the same process

Pull Request - State: closed - Opened by NicolasGensollen 12 months ago
Labels: CI

#1039 - [Converters] Make sure the PhaseEncodingDirection is BIDS compliant

Issue - State: open - Opened by MatthieuJoulot 12 months ago - 2 comments
Labels: bug, converter

#1038 - Fix dwi positive direction in dwi-preprocessing

Pull Request - State: closed - Opened by MatthieuJoulot 12 months ago - 1 comment
Labels: fix

#1037 - Bump actions/setup-python from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago
Labels: dependencies, github_actions

#1036 - Bump actions/stale from 8 to 9

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago
Labels: dependencies, github_actions

#1035 - Fix dwi positive direction in dwi-preprocessing

Pull Request - State: closed - Opened by MatthieuJoulot 12 months ago

#1034 - Issue with FSL PhaseEncodingDirection in DWI-Preprocessing Pipeline

Issue - State: closed - Opened by souravraha 12 months ago - 7 comments
Labels: bug

#1033 - Fix fast non regression tests on CI

Issue - State: closed - Opened by NicolasGensollen 12 months ago
Labels: CI

#1032 - MAINT: Use ruff for linting and formatting

Pull Request - State: closed - Opened by ghisvail 12 months ago
Labels: enhancement

#1031 - Add ressources estimations for pipelines

Issue - State: open - Opened by NicolasGensollen 12 months ago - 3 comments
Labels: doc

#1030 - Fix bad warning

Pull Request - State: closed - Opened by camillebrianceau 12 months ago

#1029 - [FIX] Ignore real and imaginary scans in ADNI

Pull Request - State: closed - Opened by NicolasGensollen 12 months ago

#1028 - Add flair to processing check

Pull Request - State: closed - Opened by MatthieuJoulot 12 months ago

#1027 - [FEAT] Add Pydra tasks for BIDS and CAPS I/O

Pull Request - State: closed - Opened by ghisvail 12 months ago - 2 comments

#1026 - MAINT: Use flake8 pre-commit hook over pep8speaks

Pull Request - State: closed - Opened by ghisvail 12 months ago - 1 comment

#1025 - MAINT: Add hook to ensure consistency of Poetry files

Pull Request - State: closed - Opened by ghisvail 12 months ago

#1024 - CI: Use pre-commit for linting

Pull Request - State: closed - Opened by ghisvail 12 months ago - 1 comment

#1023 - Release `0.7.7`

Pull Request - State: closed - Opened by NicolasGensollen 12 months ago

#1022 - Fix RuntimeWarning in CLI due to empty option groups

Pull Request - State: closed - Opened by NicolasGensollen 12 months ago

#1021 - [ADNI] Expose multiband fMRI conversion

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago - 1 comment

#1020 - Change maintainers email address

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago

#1019 - [FIX] Fix `_create_merge_file_from_bids`

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago

#1018 - [INFRA] Update `isort` version in `pre-commit` config

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago

#1017 - [DOC] Fix some broken links in docs

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago - 1 comment

#1016 - [ADNI] Handle reading new format of clinical csv

Pull Request - State: closed - Opened by MatthieuJoulot about 1 year ago - 1 comment

#1015 - [FIX] Hardcode link and description for `Genfi2BIDS`

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago

#1013 - [FIX] Fix `merge-tsv` iotools

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago - 1 comment

#1012 - [IOTOOLS] Regression on clinica iotools merge-tsv

Issue - State: closed - Opened by MatthieuJoulot about 1 year ago
Labels: bug

#1011 - Request for Technical Support on Memory Issues with Clinica Software

Issue - State: closed - Opened by mtmmu88 about 1 year ago - 1 comment
Labels: inactive

#1010 - ADNI converter not able to convert T1 images

Issue - State: closed - Opened by RR979 about 1 year ago - 12 comments
Labels: bug, converter, inactive

#1009 - [ENH] Expose `n_procs` option to `Adni2BIDS` `Oasis2BIDS` and `Aibl2BIDS`

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago - 2 comments

#1007 - Enable user control over the number of jobs for converters

Issue - State: closed - Opened by NicolasGensollen about 1 year ago - 1 comment
Labels: enhancement, converter

#1006 - Use pathlib in pipelines

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago - 3 comments
Labels: enhancement

#1005 - [GENFI] Enable use of tsv to extract more clinical data

Pull Request - State: closed - Opened by MatthieuJoulot about 1 year ago - 1 comment

#1004 - [FIX] fix `reconstruction_method` CLI option

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago - 1 comment

#1003 - CLI of pipeline `PETLinear` broken in `0.7.6` release

Issue - State: closed - Opened by NicolasGensollen about 1 year ago
Labels: bug, pipeline

#1002 - ADNI converter unable to handle new csv name

Issue - State: closed - Opened by MatthieuJoulot about 1 year ago
Labels: bug, converter, doc

#1001 - [GENFI] Enable use of tsv to extract more clinical data

Pull Request - State: closed - Opened by MatthieuJoulot about 1 year ago - 1 comment

#1000 - [FIX] Fix bad session labels in `T1Linear` pipeline

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago

#999 - Bump urllib3 from 1.26.17 to 1.26.18

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies, python

#998 - Clinica Run T1-Linear Fails Due to FileNotFoundError in N4BiasFieldCorrection Node

Issue - State: closed - Opened by mtmmu88 about 1 year ago - 18 comments
Labels: bug, pipeline

#997 - [Pydra] Port `b0_flirt_pipeline` to Pydra

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago
Labels: Stale

#996 - [INFRA] Split the anat pipelines between freesurfer-based and others

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago
Labels: CI

#995 - WIP: Add Pydra-based pipeline for pet-surface

Pull Request - State: closed - Opened by ghisvail about 1 year ago - 4 comments
Labels: Stale

#994 - Add support for Python 3.12

Issue - State: closed - Opened by NicolasGensollen about 1 year ago
Labels: enhancement

#993 - [INFRA] Run pet non regression tests with GitHub actions

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago

#991 - [INFRA] Fix bad names in non regression workflow

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago

#989 - [INFRA] Run DWI non regression tests with GitHub actions

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago - 1 comment
Labels: CI

#988 - CI: Enable cache for Poetry

Pull Request - State: closed - Opened by ghisvail about 1 year ago

#987 - [INFRA] Run anat non regression tests with GitHub actions

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago

#986 - Bump pillow from 9.3.0 to 10.0.1

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies, python

#985 - Non regression tests for converters are slower on Linux CI machines than MacOS machines

Issue - State: open - Opened by NicolasGensollen about 1 year ago - 4 comments
Labels: converter, CI

#984 - Bump urllib3 from 1.26.12 to 1.26.17

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies, python

#983 - Potentially remove documentation relative to ICM cluster

Issue - State: closed - Opened by NicolasGensollen about 1 year ago - 2 comments
Labels: doc

#982 - [DOC] Fix some typos in the general documentation

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago

#981 - [INFRA] Fix outdated documentation

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago

#980 - Update documentation for pipeline `StatisticsSurface`

Issue - State: closed - Opened by NicolasGensollen about 1 year ago - 1 comment
Labels: doc

#979 - [TEST] Make unit test deterministic

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago

#978 - [DOC] Fix some typos in the pipelines docs

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago

#977 - Issue: error clinica convert oasis3-to-bids Oasis3test Oasis3test/ClinicalData Oasis3BidsRun

Issue - State: closed - Opened by SimonChenS about 1 year ago - 9 comments
Labels: bug, converter, inactive

#976 - Contrast Manager Failing During Statistics-Volume Pipeline

Issue - State: closed - Opened by J-V1 about 1 year ago - 9 comments
Labels: bug, pipeline, inactive

#975 - Running into an issue with running statistics-volume

Issue - State: closed - Opened by J-V1 about 1 year ago

#974 - [REF] Refactor converters

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago - 1 comment
Labels: enhancement

#973 - Do not check for `ANTSPATH` anymore

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago - 1 comment

#972 - [TEST] Make IOtools non regression tests "fast" tests

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago

#971 - [INFRA] Add workflow for non regression test for converters

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago - 6 comments

#970 - Bump actions/checkout from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies, github_actions

#968 - Release `0.7.6`

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago

#966 - ADNI to BIDS "Clinical data cannot be extracted"

Issue - State: closed - Opened by mondrus96 about 1 year ago - 9 comments
Labels: bug, converter

#965 - MNT: Fix lock file checking

Pull Request - State: closed - Opened by ghisvail about 1 year ago

#964 - [INFRA] Add `MRtrix3` to conda environnement

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago

#963 - Bump pygments from 2.13.0 to 2.15.0

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies, python

#962 - MNT: Bump pybids version to 0.16

Pull Request - State: closed - Opened by ghisvail about 1 year ago

#961 - Cannot install Clinica with MLflow

Issue - State: closed - Opened by ghisvail about 1 year ago - 2 comments
Labels: bug, dependencies

#960 - [Pydra] Port DWI `eddy_fsl_pipeline` to Pydra

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago - 1 comment

#959 - [FIX] Fix BIDS violations in adni to bids converter

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

#958 - BIDS Validator errors in scans.tsv files for ADNI2BIDS converter

Issue - State: closed - Opened by NicolasGensollen over 1 year ago
Labels: bug, converter

#956 - [REF] Refactor AIBL utils

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