aramis-lab/clinica issues and pull requests

#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

#969 - ADNI2BIDS: Log when dataframes extracted from clinical data are empty

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

#968 - Release `0.7.6`

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

#967 - [FIX] DWI preprocessing using T1 pipeline not generating bvec file

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 about 1 year ago

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

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

#957 - [FIX] No failure when creation date is not null and other improvements to `_check_derived_image_xml`

Pull Request - State: closed - Opened by NicolasGensollen about 1 year ago - 5 comments

#956 - [REF] Refactor AIBL utils

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

#955 - ADNI-to-BIDS problem with MRI

Issue - State: closed - Opened by danielliu99 about 1 year ago - 9 comments
Labels: bug, converter

#954 - [MAINT] Bump `certifi` to `2023.7.22`

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

#953 - dti-preprocessing not generating .bvec files

Issue - State: closed - Opened by ta4218 about 1 year ago - 1 comment

#952 - ADNI-to-BIDS problem with PET

Issue - State: closed - Opened by Ryurin about 1 year ago - 11 comments
Labels: bug, converter

#951 - WIP: Use pydra-ants for ANTs tasks

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

#950 - MNT: Bump scikit-image to 0.21 and lxml to 4.9.3

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

#949 - Bump scipy from 1.9.3 to 1.10.0

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

#948 - [CI] try running anat daily non regression tests sequentially on Linux

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

#947 - [REF TEST] Refactor `compute_default_filename`

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

#946 - [MAINT] remove `get_sessions_map_AIBL`

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

#945 - [MAINT] Remove `create_phase_in_radsec` and `resample_fmap_to_b0`

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

#944 - [TEST] Add unit test for longitudinal utils

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

#943 - [ENH] Enable the `clinica_file_reader` to work with run numbers

Pull Request - State: closed - Opened by NicolasGensollen over 1 year ago - 3 comments

#942 - Add CITATION.cff

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

#941 - OASIS3 to BIDS not working well with me

Issue - State: closed - Opened by YasmineMH1997 over 1 year ago - 14 comments
Labels: converter, inactive

#940 - [ENH] Improve BIDS compatibility of `T1Linear` and `FLAIRLinear` CAPS outputs

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

#939 - T1-linear: error running t1-linear with --random_seed

Issue - State: closed - Opened by camillebrianceau over 1 year ago - 1 comment
Labels: bug, wontfix

#938 - [CI] Fix the destination folder to deploy the documentation

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

#937 - [TEST] Add unit tests for groups utils

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

#936 - Release `0.7.5`

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

#935 - [ENH] Improve BIDS compatibility of `PetLinear` CAPS output

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

#934 - [GENFI] add try/except to get EchoTime and RepetitionTime

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

#933 - [TEST] Add unit tests for function `container_from_filename`

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

#932 - FIX: Convert NIFD collections with new visit format

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

#931 - REF: Use PETPVC task from pydra-petpvc

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

#930 - [GENFI] Handle T1 converted as T2

Pull Request - State: closed - Opened by MatthieuJoulot over 1 year ago - 2 comments

#929 - Probably Bugs with the NIFD converter

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

#928 - [REF, TEST] Add tests and refactor adni utility `get_closest_visit`

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

#927 - [GENFI] TSV improvements

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

#926 - [REF, TEST] Add tests and refactor ADNI `get_preferred_visit_name`

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

#925 - Bump requests from 2.28.1 to 2.31.0

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

#924 - [REF] Refactor `get_visit_id` ADNI utility function

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

#923 - [GENFI] Patch conversion issue

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

#922 - Genfi patch

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

#921 - [TEST] Add missing tests

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

#920 - [ADNI] Fix uns1 issue

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

#919 - [PYDRA] Machine learning spatial svm pydra pipeline

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

#918 - [ENH TEST] Improve `compare_folders` error message

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

#917 - Bump pymdown-extensions from 9.7 to 10.0

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

#916 - Add random seed for ANTs

Pull Request - State: closed - Opened by 14thibea over 1 year ago - 7 comments
Labels: enhancement

#915 - [ENH] Improve function `viscode_to_session`

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

#914 - [ADNI] Fix viscode error

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

#913 - ValueError: invalid literal for int() with base 10: 'ns1'

Issue - State: closed - Opened by mselimata over 1 year ago - 12 comments
Labels: bug, converter

#912 - [GENFI] Update genfi patch

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

#911 - Oasis3 improvements

Pull Request - State: closed - Opened by MatthieuJoulot over 1 year ago - 5 comments

#910 - Fix variables for spatial svm

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

#909 - [GENFI] Converter improvements

Pull Request - State: closed - Opened by MatthieuJoulot over 1 year ago - 2 comments

#908 - [INFRA] add `pytest-mock` and `pytest-random-order` to dependencies

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

#907 - [TEST] Add unit tests for StatisticsVolume utility functions

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

#906 - [CI] Fix daily non regression tests Jenkinsfile

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

#905 - [TEST] run MATLAB based tests in same group

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

#903 - [REF TEST] refactor and add unit tests to DWI EPI pipeline utility functions

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

#902 - [REF TEST] Rework DWI EPI pipeline

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

#900 - [TEST] Test workflow `prepare_phasediff_fmap`

Pull Request - State: closed - Opened by NicolasGensollen over 1 year ago - 3 comments

#899 - Release `0.7.4`

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

#898 - Bump actions/stale from 7 to 8

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

#897 - [REF] Extract Step 2 of `DWIPreprocessingUsingPhasediff` into its own workflow

Pull Request - State: closed - Opened by NicolasGensollen over 1 year ago - 3 comments

#896 - Issue: Error running !clinica run t1-linear

Issue - State: closed - Opened by ridaqp over 1 year ago - 4 comments
Labels: bug, duplicate

#895 - Do not need shutils.move() in mris_expand(in_surface)

Pull Request - State: closed - Opened by sungoku over 1 year ago
Labels: Stale

#894 - [PYDRA] Statistics Volume Correction

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

#893 - [REF] Use `eddy_fsl_pipeline` in `DWIPreprocessingUsingPhasediff`

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

#892 - [TEST] Add non regression test for Eddy FSL pipeline

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

#891 - MNT: Bump pydra to version 0.22

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

#890 - pet-surafce pipeline Error: FileNotFoundError: [Errno 2] No such file or directory: '/some/path/to/surf/lh.white_exp-007'

Issue - State: closed - Opened by sungoku over 1 year ago - 4 comments
Labels: bug, inactive

GitHub / aramis-lab/clinica issues and pull requests