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Release 2.1.0 - #64

Merged

AGrigis merged 83 commits into

mainfrom

dev

Sep 17, 2026

Merged

Release 2.1.0#64
AGrigis merged 83 commits into
mainfrom
dev

Commits on Apr 1, 2026
- brainprep/_version: set version to 2.1.0.dev.
  AGrigis
  committed
  093309f
- brainprep/workflow: start adding morphologist.
  AGrigis
  committed
  573528b
- Merge branch 'dev' of https://github.com/brainprepdesk/brainprep into dev
  AGrigis
  committed
  560dcbf
- README: fix badge.
  AGrigis
  committed
  fc54e6f
Commits on Apr 8, 2026
- containers/Dockerfile.quasiraw: rm freesurfer & add SynthStrip
  nasironeeb
  committed
  12ecd39
Commits on Apr 10, 2026
- Replace "worflow" by "workflow"
  AymericGaudin
  committed
  eee472e
- brainprep/tools/scaling: brainprep command line corrections
  AymericGaudin
  committed
  456aef4
- brainprep/wrappers: print subprocess stdout live.
  AGrigis
  committed
  c14f40d
- brainprep/workflow/sulcire: add morphologists workflows.
  AGrigis
  committed
  357a7cf
- brainprep/decorators: add and apply signature hook.
  AGrigis
  committed
  6495372
- brainprep: fix CI.
  AGrigis
  committed
  56491f6
- brainprep/tools/scaling: replace relative path by absolute in pre-parsed bids table
  AymericGaudin
  committed
  06dafed
- brainprep/tools: ruff check
  AymericGaudin
  committed
  34930a3
- CHANGELOG: update.
  AGrigis
  committed
  7b8c4a1
Commits on Apr 14, 2026
- brainprep/interfaces/utils: Correct error when calling sed
  AymericGaudin
  committed
  f930455
Commits on Apr 15, 2026
Commits on Apr 16, 2026
- doc/user_guide/vbm: fix QC documentation.
  AGrigis
  committed
  9c53282
- brainprep/decorators: add module name in signature hook.
  AGrigis
  committed
  ffc115d
- tools/scaling/scaling_cli: add timepoint filter for longitudinal analysis.
  AGrigis
  committed
  1fda11e
- containers/Dockerfile: fix FreeSurfer SynthStrip install.
  AGrigis
  committed
  9f460f7
- fix: handle None timepoints in collect_config
  nasironeeb
  committed
  1480b6d
Commits on Apr 17, 2026
- Merge pull request #53 from nasironeeb/dev
  AGrigis
  authored
  4e46caa
- tools/scaling/scaling_cli: remove subject from the selection.
  AGrigis
  committed
  d59ba11
Commits on Apr 21, 2026
- brainprep/interfaces/cat12: create session folders in longitudinal vbm
  AymericGaudin
  committed
  0be3660
- brainprep/interfaces/cat12: Look for the right output files in the longitudinal pipeline
  AymericGaudin
  committed
  18cf5d2
Commits on Apr 22, 2026
- Merge pull request #54 from AymericGaudin/vbm_long
  AGrigis
  authored
  9a44366
- Merge branch 'dev' of https://github.com/brainprepdesk/brainprep into dev
  AGrigis
  committed
  3bbb5d0
Commits on Apr 27, 2026
- brainprep/interfaces/freesurfer: replace np.in1d with np.isin for Numpy 2.0 compatibility
  nasironeeb
  committed
  72c1ed8
Commits on Apr 30, 2026
- brainprep/wrappers: redirect stderr to stdout.
  AGrigis
  committed
  aba2b65
- brainprep/decorators: move print command location.
  AGrigis
  committed
  5459112
- brainprep/interfaces/cat12: code refactoring.
  AGrigis
  committed
  b97dc24
- brainprep/decorators: log all executed commands.
  AGrigis
  committed
  9c53119
- brainprep/workflow: fix workspace name conflicts.
  AGrigis
  committed
  a1f32bd
Commits on May 7, 2026
- brainprep/cli: add interface CLI.
  AGrigis
  committed
  8f0e5eb
- brainprep/workflow/dmriprep: add dMRI preprocessing workflow.
  AGrigis
  committed
  2820b3f
- examples/workflows: add clear working directory.
  AGrigis
  committed
  6d7380b
- brainprep/config: add dMRI preprocessing config options.
  AGrigis
  committed
  5a47a3b
- pyproject: check for unused imports.
  AGrigis
  committed
  b8938fe
Commits on May 12, 2026
- brainprep/cli: adapt the code so that any interface can be called from the CLI.
  AGrigis
  committed
  4d7c4a8
- containers/Dockerfile.dmriprep: add container creation draft.
  AGrigis
  committed
  1bb1e55
- brainprep: fix CI.
  AGrigis
  committed
  2bdc3a1
- Merge pull request #55 from nasironeeb/dev
  AGrigis
  authored
  9f5a24d
Commits on Jul 10, 2026
- brainprep/interfaces/fmriprep: fix fmriprep parameters + output names.
  AGrigis
  committed
  e9f7f43
Commits on Jul 22, 2026
- faster quasiraw pipeline + mask interpolation fixed
  Duplums
  committed
  f43ae9a
Commits on Aug 3, 2026
Commits on Aug 4, 2026
Commits on Aug 5, 2026
Commits on Aug 7, 2026
- brainprep/workflow/defacing: add T2w and FLAIR support in defacing workflow.
  AGrigis
  committed
  5e78d5a
- brainprep/tests: clear rst report before each test.
  AGrigis
  committed
  74b368c
- brainprep/workflow/defacing: fix enum.
  AGrigis
  committed
  7c8d76d
- Merge pull request #60 from Duplums/fast-quasiraw
  AGrigis
  authored
  988a688
Commits on Aug 21, 2026
- brainprep/workflow/quasiraw: fix parameters.
  AGrigis
  committed
  9d38683
- brainprep/workflow/reporting: add reproting workflow.
  AGrigis
  committed
  1dc7f5c
Commits on Aug 24, 2026
- brainprep/interfaces: reorganize interfaces.
  AGrigis
  committed
  92eadd8
Commits on Aug 25, 2026
- brainprep/interfaces/fmriprep: deal with sbref.
  AGrigis
  committed
  cdf1e03
- doc: update documentation.
  AGrigis
  committed
  e078adb
Commits on Aug 27, 2026
- containers: Update morphologist version
  AymericGaudin
  committed
  6582902
- tools/scaling/scaling_cli: fix bugs + add longitudinal option.
  AGrigis
  committed
  564a7a4
- tools/build: run 'examples' tests localy using apptainer.
  AGrigis
  committed
  a4c4e37
- tools/build: fix execution commands.
  AGrigis
  committed
  957cc01
- Merge pull request #62 from AymericGaudin/update-morphologist
  AGrigis
  authored
  230522e
Commits on Sep 17, 2026
- brainprep/workflow/dmriprep: add synb0 support.
  AGrigis
  committed
  98ebe7e
- tools/build/build_images: use apptainer command.
  AGrigis
  committed
  2e371bf
- brainprep/interfaces/synb0disco: add synb0 interface.
  AGrigis
  committed
  9f9e9c3
- brainprep/_version: update version.
  AGrigis
  committed
  9842672
- github/workflows: bump actions.
  AGrigis
  committed
  4ae4b72

Commits

Commits on Apr 1, 2026

Commits on Apr 8, 2026

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Commits on Sep 17, 2026