Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / aramis-lab/clinica issues and pull requests

#955 - ADNI-to-BIDS problem with MRI

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

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

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

#953 - dti-preprocessing not generating .bvec files

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

#952 - ADNI-to-BIDS problem with PET

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

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

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

#949 - Bump scipy from 1.9.3 to 1.10.0

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

#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

#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

#889 - [REF TEST] Refactor and test `generate_index_file`

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

#888 - [FIX] Refactor and test `generate_acq_file`

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

#887 - Wrong phase mapping in `generate_acq_file`

Issue - State: closed - Opened by NicolasGensollen over 1 year ago - 3 comments
Labels: bug

#886 - [TEST] Add non regression test for B0 flirt pipeline

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

#885 - Pydra implementation of statistics-volume

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

#884 - CI: Improve publish workflow

Pull Request - State: closed - Opened by ghisvail almost 2 years ago - 1 comment

#883 - [REF TEST] Refactor B0 computation related DWI utilities

Pull Request - State: closed - Opened by NicolasGensollen almost 2 years ago

#882 - [REF] Refactor `rename_into_caps` DWI utilities

Pull Request - State: closed - Opened by NicolasGensollen almost 2 years ago

#881 - Remove unused `ApplyXFM` node from EPI pipeline

Pull Request - State: closed - Opened by NicolasGensollen almost 2 years ago

#880 - Unused node `ApplyXFM` in EPI pipeline

Issue - State: closed - Opened by NicolasGensollen almost 2 years ago
Labels: bug

#879 - [REF TEST] Refactor `converter_utils`

Pull Request - State: closed - Opened by NicolasGensollen almost 2 years ago

#878 - [REF TEST] Refactor and add unit tests for `check_dependency`

Pull Request - State: closed - Opened by NicolasGensollen almost 2 years ago - 1 comment

#877 - MNT: Bump lxml to version 4.9.2

Pull Request - State: closed - Opened by ghisvail almost 2 years ago

#876 - DOC: Improve getting started section of the readme

Pull Request - State: closed - Opened by ghisvail almost 2 years ago

#875 - MNT: Restrict networkx to version 2

Pull Request - State: closed - Opened by ghisvail almost 2 years ago - 1 comment

#874 - Bump future from 0.18.2 to 0.18.3

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, python

#873 - [CI] Fix documentation build

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

#872 - [FIX] Handle 4D images with dummy fourth dimension

Pull Request - State: closed - Opened by NicolasGensollen almost 2 years ago - 1 comment

#871 - [PET] Improve how to 4D images with 1 volume are handled

Issue - State: closed - Opened by alexandreroutier almost 2 years ago - 4 comments

#869 - [REF, TEST] Refactor and test pipeline handling

Pull Request - State: closed - Opened by NicolasGensollen almost 2 years ago - 1 comment

#867 - [CI, TEST] Run SPM instantiation tests in same process

Pull Request - State: closed - Opened by NicolasGensollen almost 2 years ago

#866 - [CI] Fix typos in pipeline

Pull Request - State: closed - Opened by NicolasGensollen almost 2 years ago

#865 - GENFI to BIDS converter

Pull Request - State: closed - Opened by MatthieuJoulot almost 2 years ago - 1 comment

#864 - MNT: Bump pydra to version 0.21

Pull Request - State: closed - Opened by ghisvail almost 2 years ago

#863 - MNT: Bump pydra-bids to version 0.0.6

Pull Request - State: closed - Opened by ghisvail almost 2 years ago - 1 comment

#862 - [CI] Remove catch error and DWI non regression fast

Pull Request - State: closed - Opened by NicolasGensollen almost 2 years ago

#861 - MNT: Enable install and testing for Python 3.11

Pull Request - State: closed - Opened by ghisvail almost 2 years ago

#860 - DOC: Add badge for monthly downloads

Pull Request - State: closed - Opened by ghisvail almost 2 years ago

#859 - [CI] Reduce n_jobs for tests

Pull Request - State: closed - Opened by NicolasGensollen almost 2 years ago

#858 - [FIX] Fix `statistics-volume-correction` call to `_check_information()`

Pull Request - State: closed - Opened by AudreyDuran almost 2 years ago - 4 comments

#857 - Bump actions/stale from 6 to 7

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, github_actions

#856 - [FIX] Fix non regression tests DWI

Pull Request - State: closed - Opened by NicolasGensollen almost 2 years ago

#855 - [TEST] Fix test pet surface

Pull Request - State: closed - Opened by NicolasGensollen almost 2 years ago

#854 - CI: Apply formatting rules to Jenkins files

Pull Request - State: closed - Opened by ghisvail almost 2 years ago - 1 comment

#853 - [CI] Clean typos in Jenkins files

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