aramis-lab/clinica issues and pull requests

#1284 - [DOC] Refactor UKB-To-BIDS documentation page

Pull Request - State: open - Opened by AliceJoubert 27 days ago
Labels: doc

#1283 - [TEST] Put `ixi-to-bids` test back

Pull Request - State: closed - Opened by NicolasGensollen 27 days ago

#1282 - [TEST] Temporarily skip non regression test for `ixi-to-bids`

Pull Request - State: closed - Opened by NicolasGensollen 27 days ago

#1281 - [TEST] Skip statistic-surface test

Pull Request - State: closed - Opened by NicolasGensollen 28 days ago

#1280 - [FIX] Fix some issues around the usage of `Tracer` and `SUVRReferenceRegion` in some pipeline

Pull Request - State: closed - Opened by NicolasGensollen 28 days ago

#1279 - [FIX] Fix `get_spm_version`

Pull Request - State: closed - Opened by NicolasGensollen 28 days ago

#1278 - [FIX] Handle string and integer logging levels in `cprint`

Pull Request - State: closed - Opened by NicolasGensollen 28 days ago
Labels: fix

#1277 - [FIX] Skip question when testing `T1Freesurfer` pipeline

Pull Request - State: closed - Opened by NicolasGensollen 28 days ago

#1276 - [DOC] Add documentation page for converter IXI-to-BIDS

Pull Request - State: closed - Opened by AliceJoubert about 1 month ago
Labels: converter, doc

#1275 - [ENH] Add dependencies to CAPS `dataset_description.json`

Pull Request - State: open - Opened by NicolasGensollen about 1 month ago
Labels: enhancement

#1274 - Add documentation for `Ixi-to-BIDS` converter

Issue - State: closed - Opened by NicolasGensollen about 1 month ago
Labels: converter, doc

#1273 - Add non-regression tests for Ixi-to-BIDS

Issue - State: open - Opened by NicolasGensollen about 1 month ago
Labels: converter

#1272 - [DOC] Modify `habs-to-bids` name in documentation title

Pull Request - State: closed - Opened by NicolasGensollen about 1 month ago
Labels: doc

#1271 - [FIX] Fix bugs in data handling utilities

Pull Request - State: closed - Opened by NicolasGensollen about 1 month ago
Labels: fix

#1270 - [FIX] Fix `InfoType` in output file names

Pull Request - State: closed - Opened by NicolasGensollen about 1 month ago
Labels: fix

#1269 - Replacing unmaintained `BrainStat`

Issue - State: open - Opened by NicolasGensollen about 1 month ago
Labels: dependencies

#1268 - [FIX] Fix numpy deprecation

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

#1267 - [ENH] Implement `LoggingLevel` as an `IntEnum`

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

#1266 - [ENH] Add third-party software version getters

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

#1265 - [DOC] Restructuration proposition

Pull Request - State: open - Opened by AliceJoubert about 1 month ago
Labels: doc

#1264 - [MAINT] Replace broken badge in README

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

#1263 - [MAINT] Bump dependencies

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

#1262 - Release `0.8.4`

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

#1261 - [FIX] Specify path to SPM when using Matlab and SPM12

Pull Request - State: closed - Opened by NicolasGensollen about 1 month ago
Labels: fix

#1260 - [DOC] Clarify the documentation for converters (1) : ADNI-TO-BIDS

Issue - State: open - Opened by AliceJoubert about 1 month ago
Labels: enhancement, doc

#1259 - [CONV] ADNI-TO-BIDS/IXI-TO-BIDS : Standardization of the -sl option to -tsv

Issue - State: open - Opened by AliceJoubert about 1 month ago
Labels: enhancement, converter

#1258 - [ENH] Replace spm index tissue map mapping with enum

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

#1257 - [MAINT] Update license copyright date

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

#1255 - Running T1-linear raises an error related to CAPS

Issue - State: closed - Opened by AliceJoubert about 1 month ago - 2 comments
Labels: bug

#1254 - [ENH] Add the possibility to use ANTsPy instead of ANTs for `PETLinear`

Pull Request - State: open - Opened by NicolasGensollen about 2 months ago

#1253 - [TEST] Skip question when testing `PETVolume` pipeline

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

#1252 - Support latest version of the BIDS specifications

Issue - State: open - Opened by NicolasGensollen about 2 months ago
Labels: enhancement

#1251 - [ENH] Add function `log_and_warn`

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

#1250 - [MAINT] Remove upper bound constraint on `cattrs` version

Pull Request - State: closed - Opened by NicolasGensollen about 2 months ago - 2 comments
Labels: dependencies

#1249 - Incorrect assumption in `cattrs` version constraint

Issue - State: closed - Opened by NicolasGensollen about 2 months ago
Labels: dependencies

#1248 - [DOC] Add documentation to retrieve the labels of connectivity matrices

Pull Request - State: closed - Opened by NicolasGensollen 2 months ago
Labels: doc

#1247 - [DOC] Add FreeSurfer dependency to dwi-connectome documentation

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

#1246 - Missing third-party dependency in documentation of `DWIConnectome`

Issue - State: closed - Opened by NicolasGensollen 2 months ago
Labels: doc

#1245 - Urgent Assistance Required for Runtime Error in Clinica Version 07.6 with MATLAB 2024a and SPM12

Issue - State: open - Opened by mtmmu88 2 months ago - 8 comments

#1244 - [ENH] Add the possibility to use `ANTsPy` instead of `ANTs` for `T1Linear` and `FlairLinear`

Pull Request - State: closed - Opened by NicolasGensollen 2 months ago - 1 comment
Labels: pipeline, dependencies

#1243 - [ENH] Cleaning of Iotools

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

#1242 - [FIX] Fix broken import

Pull Request - State: closed - Opened by NicolasGensollen 2 months ago
Labels: fix

#1241 - Release `0.8.3`

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

#1240 - [FIX] Fix t1-freesurfer pipeline handler

Pull Request - State: closed - Opened by NicolasGensollen 2 months ago
Labels: fix

#1239 - [CONV] Implementing new converter for IXI dataset

Pull Request - State: closed - Opened by AliceJoubert 3 months ago - 8 comments
Labels: converter

#1238 - [ENH] Add function `log_and_raise`

Pull Request - State: closed - Opened by NicolasGensollen 3 months ago

#1237 - [REF] Move `PETSurface` pipeline to new `clinica.pipelines.pet` module

Pull Request - State: open - Opened by NicolasGensollen 3 months ago

#1236 - [ENH] Add enumeration for hemispheres

Pull Request - State: closed - Opened by NicolasGensollen 3 months ago

#1235 - [FIX] Fix cross sectional to longitudinal conversion logic

Pull Request - State: closed - Opened by NicolasGensollen 3 months ago
Labels: fix

#1234 - [BUG] Type issue when trying to make a cross-sectional BIDS dataset longitudinal

Issue - State: closed - Opened by AliceJoubert 3 months ago
Labels: bug

#1233 - Release `0.8.2`

Pull Request - State: closed - Opened by NicolasGensollen 3 months ago

#1232 - [CI] Remove poetry install step from documentation pipeline

Pull Request - State: closed - Opened by NicolasGensollen 3 months ago

#1231 - [MAINT] Backport to maint-0.8

Pull Request - State: closed - Opened by NicolasGensollen 3 months ago

#1230 - [FIX] Change check on type in converter NIFD

Pull Request - State: closed - Opened by AliceJoubert 3 months ago
Labels: fix

#1229 - [FIX] Change check on type in converter NIFD

Pull Request - State: closed - Opened by AliceJoubert 3 months ago

#1228 - Investigate removal of weird break statement in `compute_atlas_statistics`

Issue - State: open - Opened by NicolasGensollen 3 months ago

#1227 - [FIX] Change check on type in converter NIFD

Pull Request - State: closed - Opened by AliceJoubert 3 months ago - 1 comment
Labels: converter, fix

#1226 - [REF] Move `PETVolume` pipeline to new `clinica.pipelines.pet` module

Pull Request - State: closed - Opened by NicolasGensollen 3 months ago

#1225 - Bump zipp from 3.17.0 to 3.19.1

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago
Labels: dependencies, python

#1224 - [REF] Move `PETLinear` pipeline to new `clinica.pipelines.pet` module

Pull Request - State: closed - Opened by NicolasGensollen 3 months ago

#1223 - [REF] Move class `PETPipeline` to new `clinica.pipelines.pet` module

Pull Request - State: closed - Opened by NicolasGensollen 3 months ago

#1222 - Bump certifi from 2024.2.2 to 2024.7.4

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago
Labels: dependencies, python

#1221 - [DOC] Clarify TSV file origin for PET Surface pipeline

Pull Request - State: closed - Opened by AliceJoubert 3 months ago
Labels: doc

#1220 - [ENH] Proposition of a function to translate study ids to bids ids

Pull Request - State: closed - Opened by AliceJoubert 3 months ago - 2 comments
Labels: enhancement, converter

#1219 - [ENH] Improve tests for bids_utils

Pull Request - State: closed - Opened by AliceJoubert 3 months ago
Labels: converter

#1218 - [FIX] ADNI-to-BIDS now takes into account existing scans.tsv

Pull Request - State: open - Opened by AliceJoubert 3 months ago
Labels: converter, fix

#1217 - [FIX] Fix issue with enumeration as default value in CLI

Pull Request - State: closed - Opened by NicolasGensollen 3 months ago

#1216 - [MAINT] Bump `requests` from `2.32.0` to `2.32.3`

Pull Request - State: closed - Opened by NicolasGensollen 3 months ago

#1215 - [FIX] Fix function `crop_nifti` to perform cropping instead of resampling

Pull Request - State: closed - Opened by NicolasGensollen 3 months ago

#1214 - Function `crop_nifti` performs resampling instead of cropping

Issue - State: closed - Opened by NicolasGensollen 3 months ago
Labels: bug

#1213 - [TEST] Mock remote atlases in unit tests

Pull Request - State: closed - Opened by NicolasGensollen 4 months ago - 1 comment

#1212 - Remote atlas unit tests are failing

Issue - State: closed - Opened by NicolasGensollen 4 months ago
Labels: bug

#1211 - Bump scikit-learn from 1.4.0 to 1.5.0

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies, python

#1210 - Bump urllib3 from 2.2.0 to 2.2.2

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies, python

#1209 - [DOC] Online documentation not accessible until early July

Issue - State: closed - Opened by NicolasGensollen 4 months ago - 1 comment
Labels: doc

#1208 - [REF] BIDS : proposition for function create_participants_df from bids_utils

Pull Request - State: open - Opened by AliceJoubert 4 months ago
Labels: converter

#1207 - [ENH] Use enumeration for SUVR reference regions

Pull Request - State: closed - Opened by NicolasGensollen 4 months ago

#1206 - [MAINT] Missing unit tests for bids_utils

Pull Request - State: closed - Opened by AliceJoubert 4 months ago - 1 comment
Labels: converter

#1205 - [TEST] Update test for nifd-to-bids converter

Pull Request - State: closed - Opened by NicolasGensollen 4 months ago

#1204 - [MAINT] Remove function BidsGuess

Pull Request - State: closed - Opened by AliceJoubert 4 months ago
Labels: converter

#1203 - [TEST] Update test for aibl-to-bids converter

Pull Request - State: closed - Opened by NicolasGensollen 4 months ago

#1202 - [TEST] Update test for habs-to-bids converter

Pull Request - State: closed - Opened by NicolasGensollen 4 months ago

#1201 - [CI] Fix deploy step in documentation pipeline

Pull Request - State: closed - Opened by NicolasGensollen 4 months ago
Labels: CI

#1200 - [REF] BIDS : refactor function `create_participants_df` from `bids_utils`

Pull Request - State: closed - Opened by AliceJoubert 4 months ago
Labels: converter

#1199 - [DOC] ADNI-to-BIDS : add Field Mapping (FMAP) specificities

Pull Request - State: closed - Opened by AliceJoubert 4 months ago - 1 comment
Labels: converter, doc

#1198 - [FIX] ADNI-to-BIDS fmap conversion : delete real/imaginary files properly, enable converting to the same folder for fmap

Pull Request - State: closed - Opened by AliceJoubert 4 months ago - 2 comments
Labels: converter, fix

GitHub / aramis-lab/clinica issues and pull requests