Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nipreps/smriprep issues and pull requests

#293 - modified gifti_surface_wf to remove the fsnative transform and replace using to_scanner

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

#293 - modified gifti_surface_wf to remove the fsnative transform and replace using to_scanner

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

#292 - modified gifti_surface_wf to remove the fsnative transform and replace using to_scanner

Pull Request - State: closed - Opened by ericfeczko about 2 years ago - 6 comments

#292 - modified gifti_surface_wf to remove the fsnative transform and replace using to_scanner

Pull Request - State: closed - Opened by ericfeczko about 2 years ago - 6 comments

#291 - FIX: Disable -T2pial and -FLAIRpial at -autorecon1 stage

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

#291 - FIX: Disable -T2pial and -FLAIRpial at -autorecon1 stage

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

#290 - FIX: Re-add missing getfullpath FreeSurfer binary

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

#290 - FIX: Re-add missing getfullpath FreeSurfer binary

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

#287 - FIX: Re-add fsr-checkxopts to Docker image

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

#287 - FIX: Re-add fsr-checkxopts to Docker image

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

#286 - Autorecon1 Crashing

Issue - State: closed - Opened by smeisler over 2 years ago - 48 comments
Labels: bug, freesurfer

#286 - Autorecon1 Crashing

Issue - State: closed - Opened by smeisler over 2 years ago - 48 comments
Labels: bug, freesurfer

#285 - REL: 0.9.0

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

#285 - REL: 0.9.0

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

#284 - RFC: Do we want versioned docs? And do we want to maintain them ourselves?

Issue - State: open - Opened by effigies over 2 years ago - 3 comments
Labels: documentation

#284 - RFC: Do we want versioned docs? And do we want to maintain them ourselves?

Issue - State: open - Opened by effigies over 2 years ago - 3 comments
Labels: documentation

#283 - DOC: Fix build

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

#283 - DOC: Fix build

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

#282 - FIX: Override nipype handling of recon-all hemi input

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

#282 - FIX: Override nipype handling of recon-all hemi input

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

#281 - DOCKER: Bundle FreeSurfer 7.2

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

#281 - DOCKER: Bundle FreeSurfer 7.2

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

#280 - ENH: Add initial FastSurfer interface (WIP)

Pull Request - State: open - Opened by pcamach2 over 2 years ago - 22 comments

#278 - Incorporating FastSurfer to sMRIPrep as surface reconstruction option

Issue - State: open - Opened by pcamach2 over 2 years ago - 8 comments
Labels: enhancement

#278 - Incorporating FastSurfer to sMRIPrep as surface reconstruction option

Issue - State: open - Opened by pcamach2 over 2 years ago - 8 comments
Labels: enhancement

#277 - MAINT: Allow compatibility with new niworkflows minor

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

#277 - MAINT: Allow compatibility with new niworkflows minor

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

#276 - DOC: update scipy url

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

#276 - DOC: update scipy url

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

#275 - FIX: Lingering boilerplate fixes

Pull Request - State: closed - Opened by mgxd almost 3 years ago

#275 - FIX: Lingering boilerplate fixes

Pull Request - State: closed - Opened by mgxd almost 3 years ago

#274 - DOCKER: Update Dockerfile to match fMRIPrep, using FSL 6 for testing

Pull Request - State: closed - Opened by effigies almost 3 years ago

#274 - DOCKER: Update Dockerfile to match fMRIPrep, using FSL 6 for testing

Pull Request - State: closed - Opened by effigies almost 3 years ago

#273 - ENH: Register T1w template to FreeSurfer nu.mgz instead of T1.mgz

Pull Request - State: closed - Opened by effigies almost 3 years ago - 5 comments

#272 - [WIP] FIX: Anatomic fast track (except freesurfer/surface rec.)

Pull Request - State: closed - Opened by nuKs almost 3 years ago - 3 comments

#272 - [WIP] FIX: Anatomic fast track (except freesurfer/surface rec.)

Pull Request - State: open - Opened by nuKs almost 3 years ago - 2 comments

#271 - CI: Use latest pip to ensure better dependency resolution

Pull Request - State: closed - Opened by effigies almost 3 years ago - 1 comment

#271 - CI: Use latest pip to ensure better dependency resolution

Pull Request - State: closed - Opened by effigies almost 3 years ago - 1 comment

#270 - CI: Drop test for direct invocation of setup.py

Pull Request - State: closed - Opened by effigies almost 3 years ago - 1 comment

#270 - CI: Drop test for direct invocation of setup.py

Pull Request - State: closed - Opened by effigies almost 3 years ago - 1 comment

#269 - tutorial for smri

Issue - State: closed - Opened by skgtohn almost 3 years ago
Labels: documentation

#268 - FIX: Resample aseg with nearest-neighbor interpolation

Pull Request - State: closed - Opened by effigies almost 3 years ago - 1 comment

#268 - FIX: Resample aseg with nearest-neighbor interpolation

Pull Request - State: closed - Opened by effigies almost 3 years ago - 1 comment

#267 - Issue about segmentation result with data including lesion-mask

Issue - State: open - Opened by shz8012 about 3 years ago - 2 comments

#267 - Issue about segmentation result with data including lesion-mask

Issue - State: open - Opened by shz8012 about 3 years ago - 2 comments

#266 - Rel/0.8.0

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

#266 - Rel/0.8.0

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

#265 - indexed_gzip.indexed_gzip.CrcError: CRC/size validation failed - the GZIP data might be corrupt

Issue - State: closed - Opened by oesteban about 3 years ago - 3 comments
Labels: bug

#265 - indexed_gzip.indexed_gzip.CrcError: CRC/size validation failed - the GZIP data might be corrupt

Issue - State: closed - Opened by oesteban about 3 years ago - 3 comments
Labels: bug

#264 - FIX: Revert to FAST for tissue probability maps

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

#264 - FIX: Revert to FAST for tissue probability maps

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

#263 - FIX: Revert to FAST

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

#263 - FIX: Revert to FAST

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

#262 - CI: Run pytest on GitHub Actions

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

#262 - CI: Run pytest on GitHub Actions

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

#261 - TemplateFlow interface doctests fail

Issue - State: closed - Opened by effigies about 3 years ago - 1 comment
Labels: bug

#261 - TemplateFlow interface doctests fail

Issue - State: open - Opened by effigies about 3 years ago - 1 comment
Labels: bug

#260 - [WIP] ENH: Extract probabilities from FreeSurfer segmentations

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

#260 - [WIP] ENH: Extract probabilities from FreeSurfer segmentations

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

#259 - MAINT: Use PAT for docker login

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

#259 - MAINT: Use PAT for docker login

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

#258 - MAINT: CircleCI housekeeping

Pull Request - State: closed - Opened by mgxd about 3 years ago - 5 comments

#258 - MAINT: CircleCI housekeeping

Pull Request - State: closed - Opened by mgxd about 3 years ago - 5 comments

#257 - FIX: Account for label entity when querying brain mask

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

#257 - FIX: Account for label entity when querying brain mask

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

#256 - MAINT: Ease packaging tests, pin niworkflows to dev branch

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

#256 - MAINT: Ease packaging tests, pin niworkflows to dev branch

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

#255 - Incorrect interpolation of discrete labels in the FreeSurfer anatomical segmentation

Issue - State: closed - Opened by jalmar over 3 years ago - 8 comments
Labels: bug, freesurfer, effort:low, impact:high

#255 - Incorrect interpolation of discrete labels in the FreeSurfer anatomical segmentation

Issue - State: open - Opened by jalmar over 3 years ago - 8 comments
Labels: bug, freesurfer, effort:low, impact:high

#254 - Wrong probseg fmriprep output from freesurfer pipeline

Issue - State: closed - Opened by julfou81 over 3 years ago - 15 comments
Labels: help wanted, freesurfer, effort:medium, impact:high

#254 - Wrong probseg fmriprep output from freesurfer pipeline

Issue - State: closed - Opened by julfou81 over 3 years ago - 15 comments
Labels: help wanted, freesurfer, effort:medium, impact:high

#253 - What is the default template used by antsBrainExtraction.sh？

Issue - State: closed - Opened by luckyxiaoqi about 3 years ago - 1 comment
Labels: question

#253 - What is the default template used by antsBrainExtraction.sh？

Issue - State: closed - Opened by luckyxiaoqi about 3 years ago - 1 comment
Labels: question

#252 - Crash because of unset `SUBJECTS_DIR`

Issue - State: closed - Opened by oesteban about 3 years ago - 1 comment
Labels: bug

#252 - Crash because of unset `SUBJECTS_DIR`

Issue - State: closed - Opened by oesteban about 3 years ago - 1 comment
Labels: bug

#251 - Resample morphometry into surface template spaces

Issue - State: open - Opened by effigies over 3 years ago - 1 comment
Labels: enhancement

#251 - Resample morphometry into surface template spaces

Issue - State: open - Opened by effigies over 3 years ago - 1 comment
Labels: enhancement

#249 - PIN: nipreps/niworkflows bugfix branch

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

#249 - PIN: nipreps/niworkflows bugfix branch

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

#233 - ENH: Use 4+ empty edge planes to detect skull-stripped images

Pull Request - State: closed - Opened by effigies almost 4 years ago - 2 comments

#233 - ENH: Use 4+ empty edge planes to detect skull-stripped images

Pull Request - State: closed - Opened by effigies almost 4 years ago - 2 comments

#229 - Skull-stripping failure on Quickshear-defaced images?

Issue - State: open - Opened by effigies about 4 years ago - 5 comments
Labels: bug, skull-stripping, effort:medium, impact:medium

#226 - More forgiving FreeSurfer check

Issue - State: open - Opened by effigies about 4 years ago - 1 comment
Labels: enhancement, effort:medium, impact:low

#226 - More forgiving FreeSurfer check

Issue - State: open - Opened by effigies about 4 years ago - 1 comment
Labels: enhancement, effort:medium, impact:low

#224 - Check continuity of fast-track, esp. multi-session datasets and w/cohort normalization

Issue - State: open - Opened by oesteban about 4 years ago - 8 comments
Labels: bug

#211 - Fast-track not finding all expectations with ``--cifti-output``

Issue - State: closed - Opened by oesteban over 4 years ago - 3 comments
Labels: bug, effort:medium, impact:high

#200 - Brainmask incorrectly applied to externally-initiated FreeSurfer

Issue - State: open - Opened by effigies over 4 years ago
Labels: bug, freesurfer

#184 - FreeSurfer 7

Issue - State: closed - Opened by effigies over 4 years ago - 1 comment
Labels: freesurfer

#184 - FreeSurfer 7

Issue - State: closed - Opened by effigies over 4 years ago - 1 comment
Labels: freesurfer

#167 - ENH: Add option to skip brain extraction

Pull Request - State: closed - Opened by mgxd over 4 years ago - 7 comments

#167 - ENH: Add option to skip brain extraction

Pull Request - State: closed - Opened by mgxd over 4 years ago - 7 comments

#153 - On the feasibility of replacing N4BiasFieldCorrection with SPM Segment

Issue - State: open - Opened by dangom almost 5 years ago - 2 comments

#153 - On the feasibility of replacing N4BiasFieldCorrection with SPM Segment

Issue - State: open - Opened by dangom almost 5 years ago - 2 comments

#123 - segmentation fault in mri_convert

Issue - State: closed - Opened by eds-slim almost 5 years ago - 11 comments

#123 - segmentation fault in mri_convert

Issue - State: open - Opened by eds-slim almost 5 years ago - 10 comments

#109 - Replace FSL FAST with ANTs-Atropos for brain tissue segmentation

Issue - State: open - Opened by effigies about 5 years ago - 4 comments
Labels: bug, effort:low, impact:medium

#69 - Register the FLAIR or T2 to the T1w space

Issue - State: closed - Opened by wanjiag over 5 years ago - 5 comments
Labels: enhancement, effort:medium, impact:medium