nipreps/nirodents issues and pull requests

#65 - fix: typo in setup.cfg

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

#64 - problems with Nirodents installation in Docker - Apple Silicon

Issue - State: closed - Opened by Pomierny 5 months ago - 3 comments
Labels: bug

#63 - MouseIn template issue

Issue - State: open - Opened by AnriiGegliuk 8 months ago - 1 comment
Labels: bug

#62 - problem with 3d mouse brain extraction

Issue - State: closed - Opened by esther1262 over 1 year ago - 4 comments
Labels: bug

#61 - Move deployment to GH actions

Issue - State: open - Opened by oesteban almost 2 years ago
Labels: enhancement

#60 - MAINT: Replace versioneer with setuptools-scm & adapt packaging to PEP517

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

#59 - MAINT: Flexibilize dependency pinnings

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

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

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

#57 - main: update docker

Pull Request - State: closed - Opened by eilidhmacnicol over 2 years ago

#56 - CI: docker deployment

Pull Request - State: closed - Opened by eilidhmacnicol over 2 years ago - 6 comments

#55 - pin: bump niworkflows to 1.5.x

Pull Request - State: closed - Opened by eilidhmacnicol over 2 years ago

#54 - fix/n4

Pull Request - State: closed - Opened by eilidhmacnicol over 2 years ago

#53 - FIX: input image absolute path

Pull Request - State: closed - Opened by eilidhmacnicol about 3 years ago - 1 comment

#52 - FIX: final n4 on clipped image

Pull Request - State: closed - Opened by eilidhmacnicol about 3 years ago

#51 - FIX: update brain extraction notebook

Pull Request - State: closed - Opened by eilidhmacnicol about 3 years ago

#50 - running nirodents on ubuntu

Issue - State: open - Opened by eriktaylor about 3 years ago - 2 comments
Labels: bug, documentation

#49 - FIX: reorder pre-brainextraction massaging

Pull Request - State: closed - Opened by eilidhmacnicol about 3 years ago

#48 - PIN: niworkflows 1.4.x

Pull Request - State: closed - Opened by eilidhmacnicol about 3 years ago

#47 - DOC: update changes.rst

Pull Request - State: closed - Opened by eilidhmacnicol about 3 years ago - 1 comment

#46 - specify input_image requires absolute path

Issue - State: closed - Opened by grandjeanlab over 3 years ago
Labels: bug, documentation, good first issue

#45 - ENH: improved clip function

Pull Request - State: closed - Opened by eilidhmacnicol over 3 years ago - 3 comments

#44 - ENH: improved brain extraction parameters

Pull Request - State: closed - Opened by eilidhmacnicol almost 4 years ago - 4 comments

#43 - Masking mouse brains

Issue - State: open - Opened by araikes almost 4 years ago - 14 comments

#42 - FIX: cli updated so antsai no longer default

Pull Request - State: closed - Opened by eilidhmacnicol about 4 years ago - 2 comments

#41 - Enh/improve aniso bspline

Pull Request - State: closed - Opened by eilidhmacnicol about 4 years ago - 3 comments

#40 - ENH: scale Laplacian smoothing with voxel size

Pull Request - State: closed - Opened by eilidhmacnicol about 4 years ago - 2 comments

#39 - unused gaussian_filter function?

Issue - State: open - Opened by eilidhmacnicol about 4 years ago

#38 - ENH: Continue refactoring the workflow

Pull Request - State: closed - Opened by oesteban over 4 years ago - 4 comments

#37 - REL: Preparing a 1.0 release

Pull Request - State: closed - Opened by oesteban over 4 years ago - 1 comment

#36 - ENH: adapt antsai paramaters from cli

Pull Request - State: closed - Opened by eilidhmacnicol over 4 years ago - 4 comments

#35 - ENH: Deep revision of the workflow

Pull Request - State: closed - Opened by oesteban over 4 years ago - 9 comments

#34 - ENH: Add RATS (commented out) and PCNN to dockerfile

Pull Request - State: closed - Opened by oesteban over 4 years ago - 2 comments

#33 - ENH: Second refactor of workflow - make ``antsAI`` optional

Pull Request - State: closed - Opened by oesteban over 4 years ago - 1 comment

#32 - ENH: Add an entrypoint in container images

Pull Request - State: closed - Opened by oesteban over 4 years ago - 1 comment

#31 - ENH: Several improvements over the overhaul

Pull Request - State: closed - Opened by oesteban over 4 years ago - 2 comments

#30 - ENH: Workflow overhaul

Pull Request - State: closed - Opened by oesteban over 4 years ago - 3 comments

#29 - FIX: update wf

Pull Request - State: closed - Opened by eilidhmacnicol over 4 years ago - 3 comments

#28 - rodent_brain_extraction_wf is not a directed acyclic graph (DAG)

Issue - State: closed - Opened by oesteban over 4 years ago - 1 comment
Labels: bug

#27 - MAINT: Run black on the full repo, address pep8 errors

Pull Request - State: closed - Opened by oesteban over 4 years ago - 3 comments

#26 - ENH: Setup a smoke test on CircleCI + minor improvements to CLI

Pull Request - State: closed - Opened by oesteban over 4 years ago - 1 comment

#25 - FIX: Correctly pin niworkflows branch and use new interface

Pull Request - State: closed - Opened by oesteban over 4 years ago - 1 comment

#24 - Wrong mask being called from template flow

Issue - State: closed - Opened by eilidhmacnicol over 4 years ago - 1 comment

#23 - MAIN: tidy workflow

Pull Request - State: closed - Opened by eilidhmacnicol over 4 years ago - 2 comments

#22 - FIX: resampling bug

Pull Request - State: closed - Opened by eilidhmacnicol over 4 years ago - 2 comments

#21 - ResampleImageBySpacing unintended outputs

Issue - State: closed - Opened by eilidhmacnicol over 4 years ago

#20 - MAINT: Update version pinning of nipype and niworkflows to dev versions

Pull Request - State: closed - Opened by oesteban over 4 years ago - 1 comment

#19 - ENH: Add AFNI to docker image

Pull Request - State: closed - Opened by oesteban over 4 years ago - 1 comment

#18 - FIX: Data init file

Pull Request - State: closed - Opened by eilidhmacnicol over 4 years ago - 2 comments

#17 - FIX: Set correct binary path for ANTS

Pull Request - State: closed - Opened by oesteban over 4 years ago - 1 comment

#16 - ENH: add mosaic plots and wrapper

Pull Request - State: closed - Opened by eilidhmacnicol over 4 years ago - 6 comments

#15 - Add a smoke test on CircleCI

Issue - State: closed - Opened by oesteban over 4 years ago - 1 comment

#14 - Pacify flake8

Issue - State: closed - Opened by oesteban over 4 years ago - 1 comment

#13 - ENH: Add continuous deployment (to Pypi) and Dockerfile via CircleCI

Pull Request - State: closed - Opened by oesteban over 4 years ago - 1 comment

#12 - Containers

Issue - State: closed - Opened by eilidhmacnicol over 4 years ago

#11 - Script to run ``artsBrainExtraction`` on all our rats

Issue - State: closed - Opened by oesteban over 4 years ago - 1 comment

#10 - Write down evaluation protocol into draft

Issue - State: open - Opened by oesteban over 4 years ago - 1 comment

#9 - Generate a mosaic view, given the target image and the mask

Issue - State: closed - Opened by oesteban over 4 years ago - 2 comments

#8 - Scripts to run comparison on Sherlock

Issue - State: closed - Opened by oesteban over 4 years ago - 1 comment

#7 - Cut a new release to test CI/CD

Issue - State: open - Opened by oesteban over 4 years ago

#6 - Basic CI configuration

Issue - State: closed - Opened by oesteban over 4 years ago

#5 - ENH: Add an executable and install it with pip

Pull Request - State: closed - Opened by oesteban over 4 years ago - 1 comment

#4 - ENH: Base infrastructure

Pull Request - State: closed - Opened by oesteban over 4 years ago - 1 comment

#3 - Rodent T2w preprocessing: brain tissue segmentation

Issue - State: open - Opened by oesteban over 5 years ago

#2 - Rodent T2w preprocessing: brain extraction

Issue - State: closed - Opened by oesteban over 5 years ago

#1 - Rodent T2w preprocessing: calculate T2w template and validate headers

Issue - State: closed - Opened by oesteban over 5 years ago - 1 comment

GitHub / nipreps/nirodents issues and pull requests