Ecosyste.ms: Issues

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GitHub / aramis-lab/clinica issues and pull requests

#1161 - [CI] Fix MacOS GitHub runner target

Pull Request - State: closed - Opened by NicolasGensollen 7 months ago
Labels: CI

#1160 - [ENH] Add crop_nifti to public API

Pull Request - State: closed - Opened by AliceJoubert 7 months ago
Labels: enhancement

#1158 - [ENH] Implement dataset description for CAPS datasets

Pull Request - State: closed - Opened by NicolasGensollen 7 months ago - 2 comments
Labels: enhancement

#1157 - ADNI_to_BIDS : PET : Wrong preprocessing sequence

Issue - State: closed - Opened by HuguesRoy 7 months ago
Labels: bug

#1156 - [ENH] Move crop_nifti function

Pull Request - State: closed - Opened by AliceJoubert 7 months ago
Labels: enhancement

#1155 - [MAINT] Update OASIS website URL

Pull Request - State: closed - Opened by NicolasGensollen 7 months ago
Labels: converter

#1154 - Update OASIS URL in documentation and code

Issue - State: closed - Opened by NicolasGensollen 7 months ago
Labels: converter

#1151 - Unify the two `DatasetType` enumerations

Issue - State: closed - Opened by NicolasGensollen 7 months ago
Labels: good first issue

#1150 - Release `0.8.1`

Pull Request - State: closed - Opened by NicolasGensollen 7 months ago

#1149 - [CI] Run CI on maintenance branches

Pull Request - State: closed - Opened by NicolasGensollen 7 months ago
Labels: CI

#1148 - Remove code duplication for function `crop_nifti`

Issue - State: closed - Opened by NicolasGensollen 7 months ago - 1 comment
Labels: enhancement

#1147 - [MAINT] Move `merge_nifti_images_in_time_dimension_task` in dwi tasks module

Pull Request - State: closed - Opened by NicolasGensollen 7 months ago - 2 comments

#1146 - [FIX] Fix DWI preprocessing using T1 rename to caps node

Pull Request - State: closed - Opened by NicolasGensollen 7 months ago
Labels: pipeline, fix

#1145 - [CI] Run CI on maintenance branches

Pull Request - State: closed - Opened by NicolasGensollen 7 months ago
Labels: CI

#1144 - [FIX] Fix `DXSUM_PDXCONV_ADNIALL` unknown clinical file for adni-to-bids converter

Pull Request - State: closed - Opened by NicolasGensollen 7 months ago
Labels: converter, fix

#1143 - The clinical `DXSUM_PDXCONV_ADNIALL` file from ADNI has been renamed to `DXSUM_PDXCONV`

Issue - State: closed - Opened by NicolasGensollen 7 months ago - 2 comments
Labels: bug, converter

#1142 - dwi-preprocessing-using-t1 fail with RuntimeError: Mismatch in number of expected outputs

Issue - State: closed - Opened by espentrydal 7 months ago - 8 comments
Labels: bug, pipeline

#1141 - [ENH] Add tasks for reading BIDS files and dataset

Pull Request - State: closed - Opened by ghisvail 7 months ago

#1140 - [REF] Refactor converters

Pull Request - State: closed - Opened by NicolasGensollen 7 months ago - 2 comments

#1139 - [MAINT] Delete clinica.utils.mri_registration module

Pull Request - State: closed - Opened by AliceJoubert 7 months ago
Labels: python

#1138 - Bump idna from 3.6 to 3.7

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, python

#1137 - Delete `clinica.utils.mri_registration` module

Issue - State: closed - Opened by NicolasGensollen 8 months ago
Labels: enhancement

#1136 - Some clinical CSV files downloaded by users contain double quotes

Issue - State: closed - Opened by tharpm95 8 months ago - 3 comments
Labels: bug, converter, inactive

#1135 - [MAINT] Move read_participant_tsv function and make it private

Pull Request - State: closed - Opened by AliceJoubert 8 months ago
Labels: python

#1134 - [REF] Encode names of dataset as an enum

Pull Request - State: closed - Opened by NicolasGensollen 8 months ago
Labels: converter

#1133 - [MAINT] Change to regex for subject conversation to RID + tests

Pull Request - State: closed - Opened by AliceJoubert 8 months ago
Labels: python

#1132 - [MAINT] Use of regex for subject conversion to RID + unit tests

Pull Request - State: closed - Opened by AliceJoubert 8 months ago
Labels: python

#1131 - [MAINT] Change to use str.removesuffix

Pull Request - State: closed - Opened by AliceJoubert 8 months ago
Labels: python

#1130 - Use regex in `_convert_subject_to_rid()`

Issue - State: closed - Opened by NicolasGensollen 8 months ago
Labels: good first issue

#1129 - Move `read_participant_tsv` function and make it private

Issue - State: closed - Opened by NicolasGensollen 8 months ago
Labels: good first issue

#1128 - Use `str.removesuffix` in t1 linear utility function

Issue - State: closed - Opened by NicolasGensollen 8 months ago
Labels: enhancement, good first issue

#1126 - [DOC] Add PVC definition to glossary

Pull Request - State: closed - Opened by AliceJoubert 8 months ago
Labels: doc

#1125 - [DOC] Add PSF definition to glossary

Pull Request - State: closed - Opened by AliceJoubert 8 months ago
Labels: doc

#1124 - [DOC] Add SUVR definition in glossary

Pull Request - State: closed - Opened by AliceJoubert 8 months ago
Labels: doc

#1123 - [DOC] Add FWHM definition to glossary

Pull Request - State: closed - Opened by AliceJoubert 8 months ago
Labels: doc

#1122 - [ENH] Refactor pet pipelines architecture

Pull Request - State: closed - Opened by NicolasGensollen 8 months ago
Labels: Stale

#1121 - [DOC] Remove unused documentation page `ICMClusterInstallation`

Pull Request - State: closed - Opened by NicolasGensollen 8 months ago
Labels: doc

#1120 - [ENH] Refactor Freesurfer pipelines architecture

Pull Request - State: closed - Opened by NicolasGensollen 8 months ago
Labels: pipeline

#1119 - Add FMAP conversion capability for ADNI

Pull Request - State: closed - Opened by tharpm95 8 months ago - 12 comments

#1118 - Bump pillow from 10.2.0 to 10.3.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, python

#1117 - Update the "Installation" documentation page

Issue - State: closed - Opened by AliceJoubert 8 months ago - 1 comment
Labels: doc, inactive

#1115 - [DOC] Remove unused documentation page `BeforeYouInstall`

Pull Request - State: closed - Opened by NicolasGensollen 8 months ago
Labels: doc

#1114 - Add glossary entry for PSF

Issue - State: closed - Opened by NicolasGensollen 8 months ago
Labels: good first issue, doc

#1113 - Add glossary entry for SUVR

Issue - State: closed - Opened by NicolasGensollen 8 months ago
Labels: good first issue, doc

#1112 - Add glossary entry for FWHM

Issue - State: closed - Opened by NicolasGensollen 8 months ago
Labels: good first issue, doc

#1111 - Add glossary entry for PVC

Issue - State: closed - Opened by NicolasGensollen 8 months ago
Labels: good first issue, doc

#1110 - [DOC] Add glossary page to the documentation

Pull Request - State: closed - Opened by NicolasGensollen 8 months ago
Labels: doc

#1109 - Release `0.8.0`

Pull Request - State: closed - Opened by NicolasGensollen 8 months ago

#1108 - [DOC] Some updates to the CAPS documentation

Pull Request - State: closed - Opened by NicolasGensollen 8 months ago
Labels: doc

#1107 - Add a glossary to the documentation

Issue - State: closed - Opened by NicolasGensollen 8 months ago
Labels: doc

#1106 - [MAINT] Bump pydra to 0.23

Pull Request - State: closed - Opened by ghisvail 8 months ago
Labels: Stale

#1105 - [REF] Refactor dependency checking logic for third party softwares

Pull Request - State: closed - Opened by NicolasGensollen 8 months ago
Labels: enhancement

#1103 - FileNotFoundError:lh.white_exp-007'

Issue - State: closed - Opened by Luoyu-Wang 8 months ago - 4 comments
Labels: bug, pipeline, inactive

#1102 - Seeking assistance with creating a PVC_PSF_TSV file

Issue - State: closed - Opened by Luoyu-Wang 8 months ago

#1101 - Add version and possibly other metadata to CAPS datasets

Issue - State: closed - Opened by NicolasGensollen 8 months ago - 3 comments
Labels: enhancement

#1100 - [DOC] Update documentation for statistics surface pipeline

Pull Request - State: closed - Opened by NicolasGensollen 8 months ago
Labels: doc

#1099 - [DOC] Improve third-party software documentation page

Pull Request - State: closed - Opened by NicolasGensollen 8 months ago - 3 comments
Labels: doc

#1098 - TotalReadoutTime and PhaseEncodingDirection

Issue - State: open - Opened by ta4218 9 months ago - 1 comment

#1097 - [CI] Load module Matlab 2019b on MacOS CI machines

Pull Request - State: closed - Opened by NicolasGensollen 9 months ago
Labels: CI

#1096 - Hippocampus mask unavailable/incompatible

Issue - State: closed - Opened by naji-s 9 months ago - 1 comment
Labels: bug, inactive

#1095 - Number of DWIs, b-vals and b-vecs mismatch

Issue - State: open - Opened by ta4218 9 months ago - 7 comments

#1094 - [INFRA] Remove Jenkinsfile for slow non regression tests

Pull Request - State: closed - Opened by NicolasGensollen 9 months ago
Labels: CI

#1093 - [INFRA] Remove Jenkinsfile for fast non regression tests

Pull Request - State: closed - Opened by NicolasGensollen 9 months ago
Labels: CI

#1092 - [FIX] Fix linter on dev

Pull Request - State: closed - Opened by NicolasGensollen 9 months ago

#1091 - [MAINT] Bump nipype from `1.8.3` to `1.8.6`

Pull Request - State: closed - Opened by NicolasGensollen 9 months ago
Labels: dependencies

#1090 - [BUG] Fix regression with max_features in sklearn

Pull Request - State: closed - Opened by ghisvail 9 months ago - 1 comment

#1089 - [FIX] Some fixes to T1Freesurfer longitudinal pipelines

Pull Request - State: closed - Opened by NicolasGensollen 9 months ago
Labels: pipeline, fix

#1088 - [ENH] Refactor DWI pipelines architecture

Pull Request - State: closed - Opened by NicolasGensollen 9 months ago
Labels: enhancement, pipeline

#1087 - [BUG] Fix regression with max_features in sklearn

Pull Request - State: closed - Opened by ghisvail 9 months ago

#1086 - BUG: Use appropriate numpy dtype for objects

Pull Request - State: closed - Opened by ghisvail 9 months ago

#1085 - [BUG] Fix deprecation warning with SSL protocol

Pull Request - State: closed - Opened by ghisvail 9 months ago

#1084 - [MAINT] Bump pre-commit hooks

Pull Request - State: closed - Opened by ghisvail 9 months ago

#1083 - [FIX] Fixes to `DWIDTI` and `DWIConnectome` pipelines

Pull Request - State: closed - Opened by NicolasGensollen 9 months ago
Labels: pipeline, fix

#1082 - PET-tau does not found by adni-to-bids

Issue - State: closed - Opened by shaharEd 9 months ago - 3 comments
Labels: bug, converter, inactive

#1080 - Bump pre-commit/action from 3.0.0 to 3.0.1

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies, github_actions

#1079 - Pet Pipeline: Non-Selective Reprocessing of Eligible Bids Entries

Issue - State: open - Opened by souravraha 10 months ago - 7 comments
Labels: bug, pipeline, inactive

#1078 - [FIX] Use `compute_average_b0_task` in workflows

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

#1077 - [FIX] Fix forgotten argument in non regression tests

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

#1076 - [FIX] Fix bad names in DWI preprocessing using phasediff pipeline

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

#1075 - Cannot conduct "dwi-preprocessing-using-t1" without using cuda

Issue - State: closed - Opened by felicityshaw 10 months ago - 9 comments
Labels: bug, pipeline, inactive

#1074 - [ENH] Improvements to DWI preprocessing pipelines

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

#1073 - [FIX] Fix broken Nipype interfaces

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

#1072 - [ENH] Simplify imports for DWI pipelines

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

#1071 - [ENH] Set the random seed in DWI pipeline using ANTs

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

#1070 - [FIX] Update regexp dwi connectome utility function

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

#1069 - Clinica Pipeline Compatibility Issue with Ants Package Versions

Issue - State: closed - Opened by souravraha 10 months ago - 11 comments
Labels: doc

#1067 - [CI] Run DWI non regression tests on GitHub actions

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

#1066 - [TST] Refactor DWI non regression tests

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

#1065 - [MAINT] Add compatibility with Python 3.12

Pull Request - State: closed - Opened by ghisvail 10 months ago - 2 comments
Labels: dependencies

#1064 - [CI] Split `t1-linear` and `t1-volume` non regression tests

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

#1063 - [CI] Run fast non regression tests on main

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

#1062 - [CI] Run unit tests on new GitHub M1 runners

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

#1061 - [FIX] Fix bug with DWI ADC images which aren't removed by the ADNI to BIDS converter

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

#1060 - Improve Modality Detection in Clinica's ADNI to BIDS Converter

Issue - State: closed - Opened by souravraha 10 months ago - 2 comments
Labels: bug, converter