Ecosyste.ms: Issues

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GitHub / aramis-lab/clinica issues and pull requests

#1377 - Questions about the clinica data

Issue - State: open - Opened by fyb99 8 days ago

#1376 - [FIX] Fix type mismatch in `clinica.iotools.bids_utils`

Pull Request - State: open - Opened by NicolasGensollen 9 days ago - 2 comments

#1375 - PosixPath vs. string type error in `bids_utils.py`

Issue - State: open - Opened by NicolasGensollen 9 days ago
Labels: bug

#1374 - Issues when running AIBL converter

Issue - State: open - Opened by fyb99 9 days ago - 8 comments

#1372 - Circular import bug with `DTIBasedMeasure`

Issue - State: closed - Opened by NicolasGensollen 9 days ago - 1 comment
Labels: bug

#1371 - [FIX] Fix usage of group labels in non-regression tests

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

#1370 - Release `0.9.3`

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

#1368 - Clinica run t1-volumn Cannot find files

Issue - State: open - Opened by Ouzaixin 11 days ago - 1 comment
Labels: bug

#1366 - [ENH] Improve handling of group labels and IDs

Pull Request - State: closed - Opened by NicolasGensollen 14 days ago

#1365 - Improve handling of group labels and IDs

Issue - State: closed - Opened by NicolasGensollen 14 days ago

#1364 - [CI] Build and deploy documentation on master

Pull Request - State: closed - Opened by NicolasGensollen 15 days ago

#1363 - docs are not up to date online or something up with rendering?

Issue - State: closed - Opened by yarikoptic 15 days ago - 3 comments
Labels: CI

#1362 - Progress codespell forward, fixup typos it detects

Pull Request - State: closed - Opened by yarikoptic 15 days ago - 1 comment

#1361 - Problems when using t1-linear

Issue - State: closed - Opened by fyb99 24 days ago - 1 comment

#1360 - Problems when performing t1-volume processing

Issue - State: open - Opened by fyb99 25 days ago - 3 comments

#1359 - [REF] AIBL-to-BIDS : code refactoring for sessions file creation

Pull Request - State: closed - Opened by AliceJoubert 25 days ago - 1 comment
Labels: enhancement, converter

#1358 - Question abot ADNI converter

Issue - State: closed - Opened by fyb99 27 days ago - 7 comments

#1356 - Release `0.9.2`

Pull Request - State: closed - Opened by NicolasGensollen 29 days ago - 2 comments

#1355 - [ENH] Add new possibilities to pet-linear

Pull Request - State: open - Opened by ravih18 30 days ago

#1354 - [REF] AIBL-to-BIDS : refactor code for creating participants.tsv

Issue - State: open - Opened by AliceJoubert 30 days ago
Labels: converter

#1353 - [REF] AIBL-to-BIDS : refactor code for creating scans.tsv

Issue - State: open - Opened by AliceJoubert 30 days ago
Labels: converter

#1352 - [REF][TEST] AIBL-to-BIDS : add tests for creating scans.tsv functions

Issue - State: open - Opened by AliceJoubert 30 days ago
Labels: converter

#1350 - [REF] AIBL-to-BIDS : refactor code for creating sessions files

Issue - State: closed - Opened by AliceJoubert 30 days ago
Labels: enhancement, converter

#1349 - [TEST] AIBL-to-BIDS utils are lacking unit tests for `sessions.tsv` creation

Issue - State: closed - Opened by AliceJoubert about 1 month ago
Labels: converter

#1348 - [FIX] Correct the `pet-linear` pipeline

Pull Request - State: closed - Opened by ravih18 about 1 month ago
Labels: fix

#1347 - [TEST] AIBL-to-BIDS : add unit tests to functions related to creating sessions.tsv files

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

#1346 - Enhancement of `pet-linear` pipeline

Issue - State: open - Opened by ravih18 about 1 month ago - 1 comment
Labels: enhancement

#1345 - Correct `pet-linear`

Issue - State: closed - Opened by ravih18 about 1 month ago
Labels: bug

#1344 - update ADNI clinical data

Issue - State: closed - Opened by AyaRabea about 1 month ago - 3 comments
Labels: bug

#1343 - [FIX] ADNI utils `load_clinical_csv` should avoid hidden files

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

#1342 - [FIX] ADNI-to-BIDS : incorporate the fix for KeyError "APGEN"

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

#1340 - [FIX] Fix logging in OASIS and AIBL converters

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

#1339 - [CI] Replace `macos-12` GitHub runner image

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

#1338 - [CI] Replace the macOS 12 runner image from GitHub

Issue - State: closed - Opened by NicolasGensollen about 1 month ago
Labels: CI

#1337 - [REF] Modify AIBL-to-BIDS PET json keys to fit BIDS specifications

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

#1336 - [REF] OASIS-to-BIDS writing sessions tsv files now use simpler code with data frames

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

#1335 - [FIX][TEST] Fix usage of method `BIDSubjectID.to_study_id()` in unit tests

Pull Request - State: closed - Opened by AliceJoubert about 1 month ago
Labels: iotools, fix

#1334 - [MAINT] Add python version classifiers to `pyproject.toml`

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

#1333 - [MAINT] Support Python `3.13`

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

#1332 - [MAINT] Support Python 3.13

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

#1330 - [REF] OASIS-to-BIDS create_scans_dict

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

#1329 - [FIX] Add import for `ClinicaMissingDependencyError` in `anat_linear_utils.py`

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

#1328 - [BUG] ADNI-to-BIDS --xml_path option results in a KeyError

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

#1327 - [REF] OASIS-to-BIDS : writing sessions.tsv can use another data format

Issue - State: closed - Opened by AliceJoubert about 1 month ago
Labels: converter

#1325 - [REF] OASIS-to-BIDS : improve code quality for function `create_sessions_dict`

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

#1324 - [DOC] Modify download instructions for OASIS-to-BIDS data

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

#1323 - [CI] OASIS-to-BIDS data to update

Issue - State: closed - Opened by AliceJoubert about 1 month ago - 1 comment
Labels: bug, CI

#1322 - [BUG] OASIS-to-BIDS informative logs are not relevant

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

#1321 - [FIX] OASIS-to-BIDS is not up to date with online data

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

#1320 - [REF] OASIS1-to-BIDS `create_sessions_dict` function can be simplified

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

#1319 - [DOC] OASIS-to-BIDS converter download instructions

Issue - State: closed - Opened by AliceJoubert about 1 month ago
Labels: doc, dependencies

#1318 - [FIX] IXI-to-BIDS function `define_participants` should output sorted participants list

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

#1317 - [BUG] The function `define_participants` return value is not deterministic

Issue - State: closed - Opened by NicolasGensollen about 1 month ago - 1 comment
Labels: bug

#1316 - [DOC] Update contributing guidelines

Pull Request - State: closed - Opened by NicolasGensollen about 1 month ago - 2 comments
Labels: doc

#1315 - [DOC] Improve contributing guidelines

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

#1314 - [BUG] OASIS-to-BIDS converter is not up-to-date with online clinical data

Issue - State: closed - Opened by AliceJoubert about 2 months ago
Labels: bug, converter

#1313 - [TEST][REF] Move functions specific to OASIS1 converter in a dedicated utils file and add unit tests

Pull Request - State: closed - Opened by AliceJoubert about 2 months ago - 1 comment
Labels: converter

#1312 - [FIX] Fixing OASIS1 BIDSSubjectID Method

Pull Request - State: closed - Opened by AliceJoubert about 2 months ago
Labels: converter

#1311 - [REF] Refactor and clean `utils.input_files` module

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

#1310 - [CONV] IXI-to-BIDS modifications to fit BIDS specifications 1.10

Pull Request - State: closed - Opened by AliceJoubert about 2 months ago - 2 comments
Labels: converter

#1308 - Improvements to module `input_files`

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

#1307 - [DOC] Add warning message about ADNI new download interface

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

#1306 - GENFI2BIDS fails for downloads that omit DWI modality images

Issue - State: open - Opened by MauricePasternak about 2 months ago - 1 comment
Labels: bug

#1305 - Release `0.9.1`

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

#1304 - [FIX] Bump `scipy` and make `brainstat` optional

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

#1299 - Issues when converting T1 MRI of the ADNI database.

Issue - State: open - Opened by fyb99 2 months ago - 23 comments
Labels: converter

#1298 - KIRBY21 BIDS converter

Pull Request - State: open - Opened by MatthieuJoulot 2 months ago

#1294 - Key Error : APGEN1

Issue - State: closed - Opened by Ryurin 2 months ago - 13 comments
Labels: bug

#1290 - MIRIAD converter to BIDS

Pull Request - State: open - Opened by MatthieuJoulot 2 months ago - 2 comments

#1285 - [ENH] Allow the T1-Linear pipeline to go over (subject, session) couples that do not have data

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

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

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

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

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

#1281 - [TEST] Skip statistic-surface test

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

#1279 - [FIX] Fix `get_spm_version`

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

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

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

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

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

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

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

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

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

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

Issue - State: closed - Opened by NicolasGensollen 3 months ago
Labels: converter, doc

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

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

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

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

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

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

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

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

#1269 - Replacing unmaintained `BrainStat`

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

#1268 - [FIX] Fix numpy deprecation

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

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

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

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

Pull Request - State: closed - Opened by NicolasGensollen 3 months ago - 1 comment
Labels: enhancement

#1265 - [DOC] Restructuration proposition

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

#1264 - [MAINT] Replace broken badge in README

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

#1263 - [MAINT] Bump dependencies

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