nipreps/smriprep issues and pull requests

#361 - MNT: Update installation environment

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

#360 - RF: Break up surface workflows for easier mix-and-match in fMRIPrep

Pull Request - State: closed - Opened by effigies about 1 year ago - 3 comments
Labels: next

#360 - RF: Break up surface workflows for easier mix-and-match in fMRIPrep

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

#359 - ENH: Separate surfaces and morphometrics into standalone outputs

Pull Request - State: open - Opened by mgxd about 1 year ago - 2 comments

#359 - ENH: Separate surfaces and morphometrics into standalone outputs

Pull Request - State: closed - Opened by mgxd about 1 year ago - 4 comments

#358 - ENH: Add Multimodal Surface Matching

Pull Request - State: open - Opened by mgxd about 1 year ago - 3 comments

#358 - ENH: Add Multimodal Surface Matching

Pull Request - State: closed - Opened by mgxd about 1 year ago - 4 comments

#357 - DOCKER: Include 3T18yoSchwartzReactN32 FreeSurfer atlas in image

Pull Request - State: closed - Opened by psadil about 1 year ago - 6 comments

#356 - Include 3T18yoSchwartzReactN32 in Docker

Issue - State: closed - Opened by psadil about 1 year ago - 2 comments
Labels: bug

#356 - Include 3T18yoSchwartzReactN32 in Docker

Issue - State: closed - Opened by psadil about 1 year ago - 2 comments
Labels: bug

#355 - ENH: insert the gradunwarp workflow in anat template workflow

Pull Request - State: open - Opened by bpinsard about 1 year ago - 11 comments

#355 - ENH: insert the gradunwarp workflow in anat template workflow

Pull Request - State: open - Opened by bpinsard about 1 year ago - 14 comments

#354 - Build(deps): Bump certifi from 2023.5.7 to 2023.7.22

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

#354 - Build(deps): Bump certifi from 2023.5.7 to 2023.7.22

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

#353 - Add MSMSulc

Issue - State: open - Opened by edickie about 1 year ago - 3 comments

#353 - Add MSMSulc

Issue - State: closed - Opened by edickie about 1 year ago - 6 comments

#352 - Built-in Local Gyrification Index (LGI) Flag

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

#352 - Built-in Local Gyrification Index (LGI) Flag

Issue - State: closed - Opened by margokersey about 1 year ago - 1 comment
Labels: enhancement

#351 - MNT: Infrastructure updates

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

#350 - FIX: Pass sphere_reg_fsLR to ds_reg_fsLR

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

#350 - FIX: Pass sphere_reg_fsLR to ds_reg_fsLR

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

#349 - MNT: fix flake8 warning

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

#349 - MNT: fix flake8 warning

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

#348 - MNT: apply pyupgrade suggestions

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

#348 - MNT: apply pyupgrade suggestions

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

#347 - MNT: Python 3.11 should be supported

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

#347 - MNT: Python 3.11 should be supported

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

#346 - MNT: fix typos found by codespell

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

#346 - MNT: fix typos found by codespell

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

#345 - REL: 0.12.0

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

#344 - MNT: Add `sloppy` argument to workflows, distinguish from `debug`

Pull Request - State: closed - Opened by mgxd over 1 year ago - 4 comments

#344 - MNT: Add `sloppy` argument to workflows, distinguish from `debug`

Pull Request - State: closed - Opened by mgxd over 1 year ago - 4 comments

#343 - Add option to use SynthSeg as alternative to recon-all

Issue - State: open - Opened by tsalo over 1 year ago - 5 comments
Labels: enhancement

#343 - Add option to use SynthSeg as alternative to recon-all

Issue - State: open - Opened by tsalo over 1 year ago - 4 comments
Labels: enhancement

#342 - WRAPPER: docker unable to find image of version 0.11.0

Issue - State: closed - Opened by Kellsens over 1 year ago - 2 comments

#341 - FLAIR surface refinement not mentioned in boilerplate text

Issue - State: closed - Opened by effigies over 1 year ago
Labels: bug, reports

#340 - Output FreeSurfer surface area in fsLR space

Issue - State: closed - Opened by tsalo over 1 year ago - 2 comments
Labels: enhancement

#339 - ENH: Project fsLR mesh onto native sphere to enable single-shot resampling into fsLR

Pull Request - State: closed - Opened by effigies over 1 year ago - 3 comments

#338 - Add white FreeSurfer surface to derivatives; replace smoothwm?

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

#337 - ENH: Use ANTs DenoiseImage before conforming anatomical images

Pull Request - State: closed - Opened by effigies over 1 year ago - 4 comments

#336 - FIX: Query templateflow files to see if resolution is available

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

#335 - DEP: Loosen niworkflow restriction

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

#334 - smriprep unable to allocate job

Issue - State: closed - Opened by girishmm over 1 year ago - 4 comments
Labels: bug

#333 - CI: Fix codecov in CircleCI, remove Travis config

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

#332 - PATCH: Add security fix to vendored jquery

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

#331 - CI: Prioritize tags on release

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

#330 - Docker pushes fail on tags

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

#329 - DOC: Update boilerplate generation with TemplateFlow reference

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

#328 - RF: Reflect function name on nipype workflow

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

#327 - Add Connectome Workbench to listed external dependencies

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

#326 - smriprep errors out during autorecon2-vol due to missing lta file

Issue - State: closed - Opened by girishmm over 1 year ago - 3 comments

#325 - ENH: Enable resampling morphometrics to fsLR CIFTI-2 files

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

#324 - Can smriprep be used to create a custom template?

Issue - State: closed - Opened by dkp over 1 year ago - 2 comments
Labels: documentation

#323 - CI: Update build to match fMRIPrep

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

#322 - ENH: Add cortical ribbon workflow

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

#321 - ENH: make cortical ribbon volume based on signed distance of white/pial surfaces

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

#320 - Replace hardcoded `t1w` with `anat` for multi-modality workflows / nodes

Issue - State: open - Opened by mgxd over 1 year ago - 1 comment
Labels: effort:medium, impact:low, maintenance

#319 - ENH: Merge T2w images and coregister to T1w template

Pull Request - State: closed - Opened by effigies over 1 year ago - 3 comments

#318 - --output-layout bids as default for 0.10.x series

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

#317 - FIX: Ensure `FSSurfaceReport` uses nii images

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

#316 - `FSSurfaceReport` MGHImage incompatibility

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

#315 - MAINT: Rotate CircleCI secrets and setup up org-level context

Pull Request - State: closed - Opened by oesteban over 1 year ago
Labels: backport-candidate

#314 - the volume and surface in T1w sapce didn't align precisely

Issue - State: closed - Opened by precity about 2 years ago - 1 comment
Labels: bug, lts

#313 - REL: 0.10.0

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

#313 - REL: 0.10.0

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

#312 - FIX: Expand surfaces pattern to allow morphometrics

Pull Request - State: closed - Opened by mgxd almost 2 years ago

#311 - ENH: Bind FreeSurfer subjects directory

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

#311 - ENH: Bind FreeSurfer subjects directory

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

#310 - CI: Fix expected ds054 outputs

Pull Request - State: closed - Opened by effigies almost 2 years ago

#310 - CI: Fix expected ds054 outputs

Pull Request - State: closed - Opened by effigies almost 2 years ago

#309 - WRAPPER: Update patch location, use --patch syntax

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

#309 - WRAPPER: Update patch location, use --patch syntax

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

#308 - CI: Set max Python version to 3.10

Pull Request - State: closed - Opened by effigies almost 2 years ago

#308 - CI: Set max Python version to 3.10

Pull Request - State: closed - Opened by effigies almost 2 years ago

#307 - autorecon3 always rerun

Issue - State: closed - Opened by effigies almost 2 years ago - 2 comments
Labels: bug

#307 - autorecon3 always rerun

Issue - State: open - Opened by effigies almost 2 years ago - 1 comment
Labels: bug

#306 - Improve documentation on longitudinal option.

Issue - State: open - Opened by bpinsard almost 2 years ago - 1 comment
Labels: documentation

#306 - Improve documentation on longitudinal option.

Issue - State: open - Opened by bpinsard almost 2 years ago - 1 comment
Labels: documentation

#305 - ENH: Output thickness, curvature, and sulcal depth files

Pull Request - State: closed - Opened by mgxd almost 2 years ago - 7 comments

#305 - ENH: Output thickness, curvature, and sulcal depth files

Pull Request - State: closed - Opened by mgxd almost 2 years ago - 7 comments

#304 - CI: Simplify actions to build once, test many

Pull Request - State: closed - Opened by effigies almost 2 years ago - 2 comments

#304 - CI: Simplify actions to build once, test many

Pull Request - State: closed - Opened by effigies almost 2 years ago - 2 comments

#303 - RF: Split anatomical workflow into fit and derivatives workflows

Pull Request - State: closed - Opened by effigies about 2 years ago - 3 comments
Labels: next

#302 - CI: Update CircleCI docker orb

Pull Request - State: closed - Opened by effigies about 2 years ago

#302 - CI: Update CircleCI docker orb

Pull Request - State: closed - Opened by effigies about 2 years ago

#301 - WRAPPER: Fix help merge in smriprep-docker

Pull Request - State: closed - Opened by effigies about 2 years ago

#301 - WRAPPER: Fix help merge in smriprep-docker

Pull Request - State: closed - Opened by effigies about 2 years ago

#300 - Fit/apply breakdown

Issue - State: open - Opened by effigies about 2 years ago
Labels: enhancement

#300 - Fit/apply breakdown

Issue - State: closed - Opened by effigies about 2 years ago
Labels: enhancement

#299 - Integrate SynthStrip?

Issue - State: open - Opened by oesteban about 2 years ago - 5 comments
Labels: enhancement

#299 - Integrate SynthStrip?

Issue - State: open - Opened by oesteban about 2 years ago - 8 comments
Labels: enhancement

#298 - FIX: Update removed `-autorecon-hemi` flag

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

#298 - FIX: Update removed `-autorecon-hemi` flag

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

#297 - FreeSurfer execution when both T2w and FLAIR present

Issue - State: open - Opened by Lestropie about 2 years ago - 4 comments

#297 - FreeSurfer execution when both T2w and FLAIR present

Issue - State: open - Opened by Lestropie about 2 years ago - 4 comments

#296 - ENH: Output thickness, curvature, and sulcal depth files

Pull Request - State: closed - Opened by ericfeczko about 2 years ago - 5 comments

#296 - ENH: Output thickness, curvature, and sulcal depth files

Pull Request - State: closed - Opened by ericfeczko about 2 years ago - 5 comments

#295 - FIX: Use `mris_convert --to-scanner`, and update normalization step

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

#295 - FIX: Use `mris_convert --to-scanner`, and update normalization step

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

#294 - midthickness node Crashing

Issue - State: closed - Opened by Mahdieh-dst about 2 years ago - 10 comments
Labels: bug

GitHub / nipreps/smriprep issues and pull requests