Ecosyste.ms: Issues

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GitHub / nipreps/smriprep issues and pull requests

#465 - Build(deps): Bump jinja2 from 3.1.4 to 3.1.5

Pull Request - State: open - Opened by dependabot[bot] about 2 months ago
Labels: dependencies, python

#464 - Build(deps): Bump astral-sh/setup-uv from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] about 2 months ago
Labels: dependencies, github_actions

#463 - REL: 0.17.0

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

#463 - REL: 0.17.0

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

#462 - fix: Restore init_resample_midthickness_wf for backwards compatibility

Pull Request - State: closed - Opened by effigies 2 months ago - 5 comments

#461 - chore(ci): Update build step, enable pre-release tests

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

#460 - feat: Output fsLR meshes on subject surfaces

Pull Request - State: closed - Opened by effigies 2 months ago - 3 comments

#459 - ENH: Support spatial normalization to alternative modalities

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

#458 - chore: Adopt src/ layout and tox

Pull Request - State: closed - Opened by effigies 2 months ago - 3 comments

#457 - ENH: Add `t2w_file` output to `TemplateFlowSelect`

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

#455 - Build(deps): Bump codecov/codecov-action from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies, github_actions

#453 - FIX: Stop excluding FS minc_modify_header used during fallback registration

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

#452 - ENH: Add T2w as an additional channel in spatial normalization

Pull Request - State: open - Opened by laviniawuensch 5 months ago - 1 comment

#451 - ENH: Calculate T1/T2 ratio

Pull Request - State: open - Opened by effigies 6 months ago

#450 - FIX: Select function in segmentation resampling workflow

Pull Request - State: open - Opened by mgxd 6 months ago - 1 comment

#450 - FIX: Select function in segmentation resampling workflow

Pull Request - State: closed - Opened by mgxd 6 months ago - 3 comments

#449 - REL: 0.16.0

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

#448 - RF: Load package data with acres

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

#448 - RF: Load package data with acres

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

#447 - Write out fsnative surface files registered to fsLR space

Issue - State: open - Opened by tsalo 7 months ago - 12 comments
Labels: enhancement

#447 - Write out fsnative surface files registered to fsLR space

Issue - State: closed - Opened by tsalo 7 months ago - 12 comments
Labels: enhancement

#446 - Add `space-fsaverage` to `sphere_reg` output files

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

#445 - MNT: Unpin libitk 5.3 (ANTs 2.5.3 is built with 5.4)

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

#444 - chore: Clean up doc builds, environment, style checks

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

#443 - RF: Use genericised "anat" input/output for TemplateDimensions

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

#442 - Build(deps): Bump scikit-learn from 1.4.1.post1 to 1.5.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies, python

#441 - Build(deps): Bump urllib3 from 2.2.1 to 2.2.2

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies, python

#440 - FIX: Avoid datasink connection, which will always invalidate cache

Pull Request - State: closed - Opened by mgxd 9 months ago - 3 comments

#439 - Build(deps): Bump requests from 2.31.0 to 2.32.0

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies, python

#438 - Error in documentation on nipreps.org/smriprep/usage.html

Issue - State: open - Opened by crossmanith 9 months ago - 1 comment
Labels: good first issue, documentation

#437 - Build(deps): Bump jinja2 from 3.1.3 to 3.1.4

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies, python

#436 - STY: Apply ruff/flake8-implicit-str-concat rule ISC001

Pull Request - State: closed - Opened by DimitriPapadopoulos 10 months ago

#436 - STY: Apply ruff/flake8-implicit-str-concat rule ISC001

Pull Request - State: closed - Opened by DimitriPapadopoulos 10 months ago

#435 - MNT: complete transition from flake8/black to ruff

Pull Request - State: open - Opened by DimitriPapadopoulos 10 months ago - 1 comment

#435 - MNT: complete transition from flake8/black to ruff

Pull Request - State: closed - Opened by DimitriPapadopoulos 10 months ago - 1 comment

#434 - Build(deps): Bump tqdm from 4.66.2 to 4.66.3

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies, python

#433 - RF: Remove much of the hardcoded `T1w` fields in favor of `anat`

Pull Request - State: closed - Opened by mgxd 10 months ago - 2 comments

#432 - Myelin maps (T1w/T2w)

Issue - State: open - Opened by effigies 10 months ago - 2 comments
Labels: enhancement

#431 - Brain tissue segmentation fmriprep wrong labelling for few subjects

Issue - State: open - Opened by emvdmeijden 10 months ago
Labels: bug

#431 - Brain tissue segmentation fmriprep wrong labelling for few subjects

Issue - State: open - Opened by emvdmeijden 10 months ago
Labels: bug

#430 - Build(deps): Bump idna from 3.6 to 3.7

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies, python

#429 - Enable longitudinal structural analysis

Issue - State: open - Opened by ChristianNSchmitz over 1 year ago - 13 comments
Labels: freesurfer, effort:medium, impact:high

#428 - Build(deps): Bump pillow from 10.2.0 to 10.3.0

Pull Request - State: open - Opened by dependabot[bot] 11 months ago
Labels: dependencies, python

#428 - Build(deps): Bump pillow from 10.2.0 to 10.3.0

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies, python

#427 - REL: 0.15.0

Pull Request - State: closed - Opened by effigies 11 months ago - 1 comment

#426 - MNT: set copyright owner in LICENSE file

Pull Request - State: closed - Opened by DimitriPapadopoulos 11 months ago - 1 comment

#425 - Build(deps): Bump the actions-infrastructure group with 2 updates

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago
Labels: dependencies

#425 - Build(deps): Bump the actions-infrastructure group with 2 updates

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago
Labels: dependencies

#424 - FIX: Patch version for smriprep-docker

Pull Request - State: closed - Opened by effigies 11 months ago - 1 comment

#423 - CI: Small cleanups to GHA

Pull Request - State: closed - Opened by effigies 11 months ago - 1 comment

#422 - MNT: Apply Repo-Review suggestions

Pull Request - State: closed - Opened by DimitriPapadopoulos 11 months ago - 1 comment

#422 - MNT: Apply Repo-Review suggestions

Pull Request - State: closed - Opened by DimitriPapadopoulos 11 months ago - 1 comment

#421 - backport fix copy of dseg.tsv following templateflow update for LTS

Pull Request - State: open - Opened by bpinsard 11 months ago - 2 comments

#420 - [FIX] Require recent templateflow, select correct aparc dseg.tsv

Pull Request - State: closed - Opened by bpinsard 11 months ago - 2 comments

#418 - FIX: Fetch templates during workflow construction

Pull Request - State: open - Opened by mgxd 12 months ago - 1 comment

#417 - REL: 0.14.0

Pull Request - State: closed - Opened by effigies 12 months ago - 2 comments

#416 - FIX: Re-add cohort identifier to template name

Pull Request - State: closed - Opened by mgxd 12 months ago - 9 comments

#415 - fmriprep error "ValueError: 'MNIPediatricAsym:cohort-3' is not in list"

Issue - State: closed - Opened by emvdmeijden 12 months ago - 1 comment
Labels: bug

#414 - Any smriprep fix for Freesurfer 7.3.2 FLAIR Pial Surface placement bug?

Issue - State: open - Opened by nordicpioneer about 1 year ago - 3 comments
Labels: freesurfer

#413 - Support newMSM

Issue - State: open - Opened by effigies about 1 year ago
Labels: enhancement

#412 - Build(deps): Bump codecov/codecov-action from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies, github_actions

#411 - Build(deps): Bump pillow from 10.0.1 to 10.2.0

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 3 comments
Labels: dependencies, python

#410 - Build(deps): Bump jinja2 from 3.1.2 to 3.1.3

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 4 comments
Labels: dependencies, python

#409 - Build(deps): Bump actions/upload-artifact from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 2 comments
Labels: dependencies, github_actions

#408 - Build(deps): Bump actions/download-artifact from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 2 comments
Labels: dependencies, github_actions

#407 - 23.2.0a3: `template_iterator_wf.select_xfm` failing with `MNIPediatricAsym` when cohort specified

Issue - State: open - Opened by smeisler about 1 year ago - 15 comments
Labels: bug

#406 - Build(deps): Bump actions/setup-python from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies, github_actions

#405 - ENH: Add 59k atlases

Pull Request - State: closed - Opened by effigies about 1 year ago - 1 comment

#404 - FIX: Repair FreeSurfer Dependency in Dockerfile (tcsh)

Pull Request - State: closed - Opened by psadil about 1 year ago - 9 comments

#403 - `recon-all` not detected (v0.13.1) during run with singularity

Issue - State: closed - Opened by psadil about 1 year ago - 9 comments
Labels: bug

#402 - FIX: invert result of skull-strip check in auto mode

Pull Request - State: closed - Opened by psadil about 1 year ago - 1 comment

#401 - T1w images incorrectly detected as skull-stripped (difference between 0.12.2 -> 0.13.1)

Issue - State: closed - Opened by psadil about 1 year ago - 1 comment
Labels: bug

#400 - Denoise and INU correct anatomical images post-merge

Issue - State: open - Opened by effigies about 1 year ago - 1 comment
Labels: enhancement

#399 - FIX: T1w_preproc -> t1w_preproc

Pull Request - State: closed - Opened by effigies about 1 year ago - 1 comment

#398 - 23.2.0a1: `DynamicTraitedSpec` object has no attribute `T1w_preproc`

Issue - State: closed - Opened by smeisler about 1 year ago - 1 comment
Labels: bug

#397 - STY: Adopt ruff for linting and formatting

Pull Request - State: closed - Opened by effigies about 1 year ago - 1 comment

#396 - MNT: Use a generator instead of a list where possible

Pull Request - State: closed - Opened by DimitriPapadopoulos about 1 year ago - 2 comments

#395 - Move to ruff?

Issue - State: closed - Opened by DimitriPapadopoulos about 1 year ago - 3 comments
Labels: enhancement

#394 - MNT: update target Python version for black

Pull Request - State: closed - Opened by DimitriPapadopoulos about 1 year ago - 1 comment

#392 - ENH: Add T2w/FLAIR usage to boilerplate

Pull Request - State: closed - Opened by effigies about 1 year ago - 1 comment

#391 - Build(deps): Bump actions/checkout from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies, github_actions

#390 - TEST: Add smoke tests for main anatomical workflows

Pull Request - State: closed - Opened by effigies about 1 year ago - 2 comments

#389 - REL: 0.13.0

Pull Request - State: closed - Opened by effigies about 1 year ago - 5 comments

#388 - RF: Split template and fsLR resampling and sinking into isolated workflows

Pull Request - State: closed - Opened by effigies about 1 year ago - 1 comment
Labels: next

#387 - MNT: Remove AFNI from smriprep docker container

Pull Request - State: closed - Opened by effigies over 1 year ago - 1 comment
Labels: next

#386 - ENH: Annotate mris_expand with thread usage

Pull Request - State: closed - Opened by effigies over 1 year ago - 2 comments
Labels: next

#385 - Morphometry conventions

Issue - State: closed - Opened by effigies over 1 year ago - 1 comment

#384 - FIX: Update surfaces with fsnative2t1w_xfm

Pull Request - State: closed - Opened by effigies over 1 year ago - 1 comment

#383 - FIX: Invert sulcal depth metric before passing to MSM, use HCP atlas files

Pull Request - State: closed - Opened by effigies over 1 year ago - 1 comment

#382 - add missing fsLR reg sphere to io_spec

Pull Request - State: closed - Opened by bpinsard over 1 year ago - 1 comment

#381 - anat-fast-track crashing, io_spec missing fields?

Issue - State: closed - Opened by bpinsard over 1 year ago
Labels: bug

#380 - Build(deps): Bump urllib3 from 2.0.4 to 2.0.7

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 4 comments
Labels: dependencies

#379 - MNT: Use a set literal, not a list literal

Pull Request - State: closed - Opened by DimitriPapadopoulos over 1 year ago - 1 comment

#378 - DOC: Fix misspelling found by codespell

Pull Request - State: closed - Opened by DimitriPapadopoulos over 1 year ago - 1 comment

#377 - DOC: http:// → htttps://

Pull Request - State: closed - Opened by DimitriPapadopoulos over 1 year ago - 1 comment

#376 - sMRIPrep 0.13

Pull Request - State: closed - Opened by effigies over 1 year ago - 1 comment

#375 - FIX: Add surface-modify-sphere call to catch potential sphere elongation

Pull Request - State: closed - Opened by mgxd over 1 year ago - 1 comment