Ecosyste.ms: Issues

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GitHub / aramis-lab/clinica issues and pull requests

#1183 - Enable debugging for converters using multiprocessing

Issue - State: closed - Opened by NicolasGensollen 5 months ago
Labels: enhancement

#1182 - Deprecated `get_cmap` function was removed in Matplotlib 3.9.0

Issue - State: closed - Opened by NicolasGensollen 5 months ago
Labels: bug

#1181 - [FIX] Fix logging in adni to bids

Pull Request - State: closed - Opened by NicolasGensollen 5 months ago

#1178 - Fix logic in adni_utils by restoring loops in create_file

Pull Request - State: closed - Opened by AliceJoubert 5 months ago - 2 comments
Labels: bug, converter

#1177 - add "real" and "imaginary" file endings to return fmap in adni_utils.py

Pull Request - State: closed - Opened by likeajumprope 5 months ago - 1 comment

#1176 - [MAINT] Delete `SurfStat` vendored toolbox

Pull Request - State: closed - Opened by NicolasGensollen 5 months ago

#1175 - [ENH] Proposition for adni_fmap renaming function

Pull Request - State: closed - Opened by AliceJoubert 5 months ago
Labels: enhancement, converter

#1174 - Refactor and test `adni_fmap.py`

Issue - State: open - Opened by NicolasGensollen 5 months ago - 1 comment
Labels: converter

#1173 - Bump jinja2 from 3.1.3 to 3.1.4

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, python

#1171 - [CI] Change unorganized folder for adni to bids tests

Pull Request - State: closed - Opened by NicolasGensollen 5 months ago

#1170 - Bump tqdm from 4.66.1 to 4.66.3

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, python

#1169 - [FIX] Fixes DWI preprocessing using T1 when images are 3D

Pull Request - State: closed - Opened by NicolasGensollen 5 months ago
Labels: fix

#1167 - pet-files not found

Issue - State: closed - Opened by espentrydal 5 months ago - 8 comments
Labels: bug, converter

#1166 - nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node 0-InitNode.

Issue - State: closed - Opened by espentrydal 5 months ago - 18 comments
Labels: bug, pipeline

#1165 - Move documentation build and deploy to GitHub Actions

Issue - State: closed - Opened by NicolasGensollen 5 months ago - 3 comments
Labels: enhancement, CI

#1164 - Remove clinica surfstat toolbox

Issue - State: closed - Opened by NicolasGensollen 5 months ago
Labels: dependencies

#1163 - Ignore hidden CSV files in `load_clinical_csv`

Issue - State: open - Opened by NicolasGensollen 5 months ago - 1 comment
Labels: bug, converter

#1162 - [ENH] Unify DatasetType class

Pull Request - State: closed - Opened by AliceJoubert 5 months ago - 3 comments
Labels: enhancement

#1161 - [CI] Fix MacOS GitHub runner target

Pull Request - State: closed - Opened by NicolasGensollen 5 months ago
Labels: CI

#1160 - [ENH] Add crop_nifti to public API

Pull Request - State: closed - Opened by AliceJoubert 5 months ago
Labels: enhancement

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

Pull Request - State: closed - Opened by NicolasGensollen 5 months ago - 2 comments
Labels: enhancement

#1157 - ADNI_to_BIDS : PET : Wrong preprocessing sequence

Issue - State: closed - Opened by HuguesRoy 5 months ago
Labels: bug

#1156 - [ENH] Move crop_nifti function

Pull Request - State: closed - Opened by AliceJoubert 5 months ago
Labels: enhancement

#1155 - [MAINT] Update OASIS website URL

Pull Request - State: closed - Opened by NicolasGensollen 5 months ago
Labels: converter

#1154 - Update OASIS URL in documentation and code

Issue - State: closed - Opened by NicolasGensollen 5 months ago
Labels: converter

#1151 - Unify the two `DatasetType` enumerations

Issue - State: closed - Opened by NicolasGensollen 5 months ago
Labels: good first issue

#1150 - Release `0.8.1`

Pull Request - State: closed - Opened by NicolasGensollen 5 months ago

#1149 - [CI] Run CI on maintenance branches

Pull Request - State: closed - Opened by NicolasGensollen 5 months ago
Labels: CI

#1148 - Remove code duplication for function `crop_nifti`

Issue - State: closed - Opened by NicolasGensollen 5 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 5 months ago - 2 comments

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

Pull Request - State: closed - Opened by NicolasGensollen 5 months ago
Labels: pipeline, fix

#1145 - [CI] Run CI on maintenance branches

Pull Request - State: closed - Opened by NicolasGensollen 5 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 5 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 5 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 6 months ago - 8 comments
Labels: bug, pipeline

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

Pull Request - State: closed - Opened by ghisvail 6 months ago

#1140 - [REF] Refactor converters

Pull Request - State: closed - Opened by NicolasGensollen 6 months ago - 2 comments

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

Pull Request - State: closed - Opened by AliceJoubert 6 months ago
Labels: python

#1138 - Bump idna from 3.6 to 3.7

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

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

Issue - State: closed - Opened by NicolasGensollen 6 months ago
Labels: enhancement

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

Issue - State: closed - Opened by tharpm95 6 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 6 months ago
Labels: python

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

Pull Request - State: closed - Opened by NicolasGensollen 6 months ago
Labels: converter

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

Pull Request - State: closed - Opened by AliceJoubert 6 months ago
Labels: python

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

Pull Request - State: closed - Opened by AliceJoubert 6 months ago
Labels: python

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

Pull Request - State: closed - Opened by AliceJoubert 6 months ago
Labels: python

#1130 - Use regex in `_convert_subject_to_rid()`

Issue - State: closed - Opened by NicolasGensollen 6 months ago
Labels: good first issue

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

Issue - State: closed - Opened by NicolasGensollen 6 months ago
Labels: good first issue

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

Issue - State: closed - Opened by NicolasGensollen 6 months ago
Labels: enhancement, good first issue

#1126 - [DOC] Add PVC definition to glossary

Pull Request - State: closed - Opened by AliceJoubert 6 months ago
Labels: doc

#1125 - [DOC] Add PSF definition to glossary

Pull Request - State: closed - Opened by AliceJoubert 6 months ago
Labels: doc

#1124 - [DOC] Add SUVR definition in glossary

Pull Request - State: closed - Opened by AliceJoubert 6 months ago
Labels: doc

#1123 - [DOC] Add FWHM definition to glossary

Pull Request - State: closed - Opened by AliceJoubert 6 months ago
Labels: doc

#1122 - [ENH] Refactor pet pipelines architecture

Pull Request - State: closed - Opened by NicolasGensollen 6 months ago
Labels: Stale

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

Pull Request - State: closed - Opened by NicolasGensollen 6 months ago
Labels: doc

#1120 - [ENH] Refactor Freesurfer pipelines architecture

Pull Request - State: closed - Opened by NicolasGensollen 6 months ago
Labels: pipeline

#1119 - Add FMAP conversion capability for ADNI

Pull Request - State: closed - Opened by tharpm95 6 months ago - 12 comments

#1118 - Bump pillow from 10.2.0 to 10.3.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

#1117 - Update the "Installation" documentation page

Issue - State: closed - Opened by AliceJoubert 6 months ago - 1 comment
Labels: doc, inactive

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

Pull Request - State: closed - Opened by NicolasGensollen 6 months ago
Labels: doc

#1114 - Add glossary entry for PSF

Issue - State: closed - Opened by NicolasGensollen 6 months ago
Labels: good first issue, doc

#1113 - Add glossary entry for SUVR

Issue - State: closed - Opened by NicolasGensollen 6 months ago
Labels: good first issue, doc

#1112 - Add glossary entry for FWHM

Issue - State: closed - Opened by NicolasGensollen 6 months ago
Labels: good first issue, doc

#1111 - Add glossary entry for PVC

Issue - State: closed - Opened by NicolasGensollen 6 months ago
Labels: good first issue, doc

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

Pull Request - State: closed - Opened by NicolasGensollen 6 months ago
Labels: doc

#1109 - Release `0.8.0`

Pull Request - State: closed - Opened by NicolasGensollen 6 months ago

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

Pull Request - State: closed - Opened by NicolasGensollen 6 months ago
Labels: doc

#1107 - Add a glossary to the documentation

Issue - State: closed - Opened by NicolasGensollen 6 months ago
Labels: doc

#1106 - [MAINT] Bump pydra to 0.23

Pull Request - State: closed - Opened by ghisvail 6 months ago
Labels: Stale

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

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

#1103 - FileNotFoundError:lh.white_exp-007'

Issue - State: closed - Opened by Luoyu-Wang 7 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 7 months ago

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

Issue - State: closed - Opened by NicolasGensollen 7 months ago - 3 comments
Labels: enhancement

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

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

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

Pull Request - State: closed - Opened by NicolasGensollen 7 months ago - 3 comments
Labels: doc

#1098 - TotalReadoutTime and PhaseEncodingDirection

Issue - State: open - Opened by ta4218 7 months ago - 1 comment

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

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

#1096 - Hippocampus mask unavailable/incompatible

Issue - State: closed - Opened by naji-s 7 months ago - 1 comment
Labels: bug, inactive

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

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

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

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

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

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

#1092 - [FIX] Fix linter on dev

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

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

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

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

Pull Request - State: closed - Opened by ghisvail 7 months ago - 1 comment

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

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

#1088 - [ENH] Refactor DWI pipelines architecture

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

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

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

#1086 - BUG: Use appropriate numpy dtype for objects

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

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

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

#1084 - [MAINT] Bump pre-commit hooks

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