Releases: UNFmontreal/Dcm2Bids
3.2.0
Dear dcm2bids Community,
We are excited to announce the release of dcm2bids version 3.2.0 🎉 🥳
It comes with a couple of new features such as:
- Our new container allows you to enjoy the full dcm2bids experience with defacing and bids validation more easily.
- dcm2bids is now compatible with BIDS 1.9.0
- Updated documentation
Thank you
Arnaud and Sam
We would like to thank @smeisler and the users from neurostars for their feedback.
What's Changed
- Bump urllib3 from 2.0.6 to 2.0.7 by @dependabot in #281
- Fixed Nick's name by @jcohenadad in #285
- Fetch all descriptions: id list by @arnaudbore in #283
- Bump jinja2 from 3.1.2 to 3.1.3 by @dependabot in #287
- Bump gitpython from 3.1.37 to 3.1.41 by @dependabot in #286
- Bump idna from 3.4 to 3.7 by @dependabot in #291
- [BF] Replace macos-latest with macos-13 by @arnaudbore in #299
- Bump requests from 2.31.0 to 2.32.0 by @dependabot in #297
- Bump jinja2 from 3.1.3 to 3.1.4 by @dependabot in #296
- Changed 'there' to 'their' by @joey-scanga in #292
- Bump urllib3 from 2.0.7 to 2.2.2 by @dependabot in #302
- Update to BIDS 1.9 by @arnaudbore in #301
- Bump certifi from 2023.7.22 to 2024.7.4 by @dependabot in #305
- [ENH] Allow disable automatic reorder entities by @arnaudbore in #303
- Update dev to match master' state by @SamGuay in #306
- [ENH] Allow user to use relative path for bids uri by @arnaudbore in #304
- Update GHA to use setup-python@v5 instead of v1 by @SamGuay in #309
- [BF] Fix output log and output folder with dcm2bids_helper by @arnaudbore in #312
- [BF] Fix check folder by @arnaudbore in #313
- Document new features + docker by @SamGuay in #311
- Update master to 3.2.0 by @arnaudbore in #314
New Contributors
- @jcohenadad made their first contribution in #285
- @joey-scanga made their first contribution in #292
Full Changelog: 3.1.1...3.2.0
3.1.1
Here is the newest release of dcm2bids ! 🎉 🥳
No new feature but two useful fixes !
Hope you like this new feature less buggy ⛔ 🐛
Arnaud and Sam
What's Changed
- Bump gitpython from 3.1.35 to 3.1.37 by @dependabot in #277
- [BF] Auto extractors and merge regex expressions by @arnaudbore in #275
- [ENH] fix binary by @arnaudbore in #278
Full Changelog: 3.1.0...3.1.1
3.1.0
We are excited to announce the newest release of dcm2bids ! 🎉 🥳
This update introduces some new features, improvements, and bug fixes to enhance your DICOM to BIDS conversion experience.
Everything embedded into this version comes from the community ❤️. Here are few examples.
- During OHBM we've been asked to support archives as a dicom input, it's part of Dcm2bids 3.1.0. Check
dcm2bids --help
output. link - While helping people on Neurostars, @smeisler indicates that he needed to run pydeface after dcm2bids conversion since he needed both versions before and after defacing, it's now part of Dcm2bids 3.1.0. Check custom_entities in post-op section. link
- If you want to speed up dcm2bids conversion @SamGuay wrote a really nice tutorial to convert your data faster than ever.
Your questions and concerns remain our top priority and continue to shape the future of Dcm2bids!
Thank you
Arnaud and Sam
We would like to thank @smeisler, @Remi-Gau, @raniaezzo, @arokem and the users from neurostars for their feedbacks.
What's Changed
- [MAINT] validate citation.cff by @Remi-Gau in #257
- Bump gitpython from 3.1.32 to 3.1.34 by @dependabot in #259
- Bump gitpython from 3.1.34 to 3.1.35 by @dependabot in #261
- Fix typos in scaffold files by @SamGuay in #263
- [ENH] Add possibility to input dicom tar or zip archives by @arnaudbore in #262
- Fix post op - pydeface by @arnaudbore in #260
- Fix release tags in GHA by @SamGuay in #266
- Release 3.0.3 by @arnaudbore in #265
- [ENH] - Automate help message in doc by @SamGuay in #267
- [DOC] - Tutorial on parallel x dcm2bids by @SamGuay in #268
Full Changelog: 3.0.2...3.1.0
3.0.2
First of all thank you to everybody who came see our poster during OHBM 2023 in Montreal !
We listened to you and we added an option to reorganize your NIFTIs into a BIDS structure. Check this link.
We also extended the possibilities provided by the item sidecar_changes.
Congrats 🥳
What's Changed
- codespell: add config and action to codespell the code to avoid known typos by @yarikoptic in #245
- Bump certifi from 2023.5.7 to 2023.7.22 by @dependabot in #247
- Bring all 3 Arnauds into 1 by @yarikoptic in #246
- Add option to skip_dcm2niix and reorganize NIFTI and JSON files by @arnaudbore in #248
- Allowing Numericals in JSON custom fields by @smeisler in #250
- Bump gitpython from 3.1.31 to 3.1.32 by @dependabot in #251
New Contributors
- @yarikoptic made their first contribution in #245
- @dependabot made their first contribution in #247
Full Changelog: 3.0.1...3.0.2
3.0.1
We could not be more proud of the 3.0.1 dcm2bids release 😊 . We put everything we've learned from our past experiences and listen to all our users' ideas into this version.
Advanced searching criterias such as extractors combined with custom entities, the ability to compare floats or the auto_extract_entities option directly accessible from dcm2bids command will make the conversion to BIDS smoother than ever and significantly reduce the complexity and the length of your configuration file especially for multi-site acquisitions.
We highly encourage you to dive into the documentation since we added quite a lot of new features.
Please don't hesitate to give us your feedback using this #240.
Thank you again for all our users who contributed in some ways to this release. Thank you @SamGuay for the long discussions and late debug sessions. 🎉
Arnaud
What's Changed
- [DOC] fix typo and add detail about entity reordering by @Remi-Gau in #183
- update version to match release by @SamGuay in #185
- [ENH] Refactorisation - Major API upgrade by @arnaudbore in #200
- Get README from bids toolkit by @arnaudbore in #201
- Add bids-validator option by @arnaudbore in #206
- Upgrade feature Intended for by @arnaudbore in #207
- [ENH] Upgrade custom entities by @arnaudbore in #208
- [FIX] Broken scaffold no more by @SamGuay in #209
- [FIX,ENH] - Improve dcm2bids_helper mod by @SamGuay in #210
- Generalization of sidecarchanges using ids by @arnaudbore in #213
- [ENH] dataType -> datatype and modalityLabel -> suffix by @arnaudbore in #214
- Fix log n version by @SamGuay in #219
- [BF] valid participant by @arnaudbore in #215
- Allow a criteria item to be a dict with a key - any (or) or all (and) by @arnaudbore in #217
- Add an option to use duplicates instead of runs as suggested in heudiconv project. by @arnaudbore in #218
- [BF] Valid session by @arnaudbore in #222
- add test helper by @arnaudbore in #220
- [BF] dcm2bids_scaffold by @arnaudbore in #224
- prevent doc deployment by pushing to master by @SamGuay in #226
- [ENH] Add major OS executables on new release by @SamGuay in #221
- [ENH] Generalization of defaceTpl to post_op by @arnaudbore in #225
- [ENH] Rename all cap var by @arnaudbore in #227
- Revert doc to 2.1.9 by @arnaudbore in #228
- Automated version-control documentation for 2.1.9 and up by @SamGuay in #231
- Fix GHA for docs + layouts by @SamGuay in #234
- [ENH] Add float comparison by @arnaudbore in #229
- [Quick Fix] Add specific message when no acquisition was found by @arnaudbore in #235
- Fix typo src_file dst_file by @arnaudbore in #236
- Improve doc for v3.0.0 by @arnaudbore in #223
- [FIX] - update the alias for dev and latest by @SamGuay in #237
- Quick fix version by @arnaudbore in #238
- Update docs by @smeisler in #239
- [BF] fix sidecars suggested by Sam by @arnaudbore in #243
New Contributors
Full Changelog: 2.1.9...3.0.1
3.0.0rc1
Ok let's be clear after working very hard on this we are definitively biased so we decided to ask ChatGPT to write for us a short fun description for our brand new version.
Introducing the latest version of dcm2bids: the superhero of medical imaging data conversion! With simplified configuration, enhanced DICOM handling, comprehensive data validation, advanced options, and amazing new features, dcm2bids will transform your data into BIDS format like magic. Join the fun and unleash your scientific superpowers today!
Please check the documentation 🎉
What's Changed
- [DOC] fix typo and add detail about entity reordering by @Remi-Gau in #183
- update version to match release by @SamGuay in #185
- [ENH] Refactorisation - Major API upgrade by @arnaudbore in #200
- Get README from bids toolkit by @arnaudbore in #201
- Add bids-validator option by @arnaudbore in #206
- Upgrade feature Intended for by @arnaudbore in #207
- [ENH] Upgrade custom entities by @arnaudbore in #208
- [FIX] Broken scaffold no more by @SamGuay in #209
- [FIX,ENH] - Improve dcm2bids_helper mod by @SamGuay in #210
- Generalization of sidecarchanges using ids by @arnaudbore in #213
- [ENH] dataType -> datatype and modalityLabel -> suffix by @arnaudbore in #214
- Fix log n version by @SamGuay in #219
- [BF] valid participant by @arnaudbore in #215
- Allow a criteria item to be a dict with a key - any (or) or all (and) by @arnaudbore in #217
- Add an option to use duplicates instead of runs as suggested in heudiconv project. by @arnaudbore in #218
- [BF] Valid session by @arnaudbore in #222
- add test helper by @arnaudbore in #220
- [BF] dcm2bids_scaffold by @arnaudbore in #224
- prevent doc deployment by pushing to master by @SamGuay in #226
- [ENH] Add major OS executables on new release by @SamGuay in #221
- [ENH] Generalization of defaceTpl to post_op by @arnaudbore in #225
- [ENH] Rename all cap var by @arnaudbore in #227
- Revert doc to 2.1.9 by @arnaudbore in #228
- Automated version-control documentation for 2.1.9 and up by @SamGuay in #231
- Fix GHA for docs + layouts by @SamGuay in #234
- [ENH] Add float comparison by @arnaudbore in #229
- [Quick Fix] Add specific message when no acquisition was found by @arnaudbore in #235
- Fix typo src_file dst_file by @arnaudbore in #236
- Improve doc for v3.0.0 by @arnaudbore in #223
New Contributors
Full Changelog: 2.1.8...3.0.0rc1
2.1.9
I had some issues with pypi. Sorry for this.
What's Changed
- Fix if dot in dcm files names by @arnaudbore in #169
- Support output_dir override #170 by @GMerakis in #171
- BF - forgot bval bvec by @arnaudbore in #172
New Contributors
Full Changelog: 2.1.7...2.1.9
2.1.8
This will be our last PR before moving to a new API.
What's Changed
- Fix if dot in dcm files names by @arnaudbore in #169
- Support output_dir override #170 by @GMerakis in #171
- BF - forgot bval bvec by @arnaudbore in #172
New Contributors
Full Changelog: 2.1.7...2.1.8
2.1.7
Thank you to everyone who was involved in this release.
Last time I said "more to come soon" this time I won't commit to anything.
BUT we already have plan to make a major break release jumping directly to 3.0.0 and add more flexibility to the searchMethod.
See you soon with a new release 😆
What's Changed
- [BUG, ENH] - fix erroneous install command by @SamGuay in #128
- Fix #130 by @SamGuay in #131
- Minor doc updates by @jstaph in #148
- [DOC] fix a few typos in config docs by @keithcallenberg in #150
- reformat tables in oneliners by @SamGuay in #155
- [WIP] Remove python3.6 by @arnaudbore in #156
- [BF] fix intendedFor by @arnaudbore in #107
- [WIP] Fix Entity Table Order by @arnaudbore in #157
- [BUG, ENH] Update tutorial and documentation by @SamGuay in #162
- [WIP][BF] dcm2bids_helper by @arnaudbore in #161
- Fix windows paths patch by @SamGuay in #163
- [DOC][ENH] - Add instructions with Anaconda Navigator + Warning about spaces in paths by @SamGuay in #165
- Fix windows paths by @arnaudbore in #158
- [FIX] freeze doc packages by @SamGuay in #166
- [FIX] Add a timeout when trying to retrieve dcm2bids version by @po09i in #154
- fix re option by @arnaudbore in #167
- update_to_2.1.7 by @arnaudbore in #168
New Contributors
- @jstaph made their first contribution in #148
- @keithcallenberg made their first contribution in #150
- @po09i made their first contribution in #154
Full Changelog: 2.1.6...2.1.7