Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / PennLINC/qsiprep issues and pull requests
#818 - write out a json sidecar for the merged, preprocessed dwi file
Issue -
State: open - Opened by mattcieslak 27 days ago
Labels: enhancement
#817 - [CI] Swap synthstrip for bet when sloppy mode is chosen
Pull Request -
State: closed - Opened by mattcieslak about 1 month ago
- 1 comment
#816 - [CI] add back pypi
Pull Request -
State: closed - Opened by mattcieslak about 1 month ago
- 1 comment
#815 - Preprocessing multi-session anat data
Issue -
State: open - Opened by jhauneuro about 1 month ago
- 4 comments
Labels: bug
#814 - [CI] Update CI to be more efficient
Pull Request -
State: closed - Opened by mattcieslak about 1 month ago
- 1 comment
#813 - [CI] Check into circleci performance
Issue -
State: closed - Opened by mattcieslak about 1 month ago
- 1 comment
Labels: enhancement
#812 - Replace hyperlinks with BibTeX references
Issue -
State: open - Opened by tsalo about 1 month ago
Labels: documentation
#811 - Track immediate `Sources` when possible
Issue -
State: open - Opened by tsalo about 1 month ago
Labels: enhancement
#810 - Use file lock to avoid concurrent edits to dataset_description.json
Issue -
State: open - Opened by tsalo about 1 month ago
Labels: enhancement
#809 - Collect templates from TemplateFlow instead of package data
Pull Request -
State: closed - Opened by tsalo about 1 month ago
- 2 comments
Labels: refactor
#808 - Use nireports for HTML reports
Pull Request -
State: closed - Opened by tsalo about 2 months ago
- 5 comments
Labels: refactor
#807 - Drop mentions of the qsiprep-docker wrapper
Pull Request -
State: closed - Opened by tsalo about 2 months ago
- 2 comments
Labels: breaking-change
#806 - qsiprep pennbbl/qsiprep:0.21.4 is linked to the development version v0.21.5.dev0+g36b93fe.d20240504
Issue -
State: closed - Opened by johnaeanderson about 2 months ago
- 2 comments
Labels: bug
#805 - Use nireports for report generation
Issue -
State: closed - Opened by tsalo about 2 months ago
Labels: enhancement
#804 - dsi_studio_autotrack not running
Issue -
State: open - Opened by aazor about 2 months ago
- 6 comments
Labels: bug
#803 - Drop internal copies of templates in favor of re-orienting TemplateFlow templates
Issue -
State: closed - Opened by tsalo about 2 months ago
Labels: enhancement
#802 - [RF] Remove the recon workflows from QSIPrep
Pull Request -
State: closed - Opened by mattcieslak about 2 months ago
- 5 comments
Labels: breaking-change
#801 - [DOCS] Update reconstruction.rst to use dashes in flags instead of underscores
Pull Request -
State: closed - Opened by arokem about 2 months ago
- 2 comments
#800 - Bad preprocessing results for dwi with PSR+ image orientation
Issue -
State: open - Opened by jhauneuro about 2 months ago
Labels: bug
#799 - 2 phases SDC outputs partial fieldmap
Issue -
State: open - Opened by jhauneuro about 2 months ago
Labels: bug
#798 - top of brain cut after preprocessing using version 0.22.0
Issue -
State: open - Opened by jhauneuro about 2 months ago
- 5 comments
Labels: bug
#797 - error when using option --distortion-group-merge
Issue -
State: open - Opened by jhauneuro about 2 months ago
Labels: bug
#796 - Add logging message when qc metrics on raw data are low
Issue -
State: open - Opened by mattcieslak 2 months ago
Labels: enhancement
#795 - [FIX] Update bundle list for hbcd_scalar_maps
Pull Request -
State: closed - Opened by mattcieslak 2 months ago
- 1 comment
#794 - [BUG] List of bundles not fixed in hbcd recon workflow
Issue -
State: closed - Opened by mattcieslak 2 months ago
Labels: bug
#793 - TOPUP distortion correction field is flipped for my LPS oriented dwi data
Issue -
State: open - Opened by jhauneuro 2 months ago
- 3 comments
Labels: bug
#792 - error encountered at eddy step when no T1w data are available
Issue -
State: open - Opened by jhauneuro 2 months ago
- 4 comments
Labels: bug
#790 - EDDY_CUDA Failure: GPU can only use 1 CPU thread
Issue -
State: closed - Opened by amirhusseinab 2 months ago
- 4 comments
Labels: bug
#789 - FUGUE error (no attribute 'FUGUEvsm2ANTSwarp')
Issue -
State: closed - Opened by jhauneuro 2 months ago
- 3 comments
Labels: bug
#788 - [FIX]: CUDA threads for Eddy
Pull Request -
State: closed - Opened by araikes 2 months ago
- 2 comments
#787 - [ENH] Compress recon derivatives
Pull Request -
State: closed - Opened by mattcieslak 3 months ago
- 1 comment
#786 - [ENH] Compress nifti files written by the tortoise workflows
Issue -
State: closed - Opened by mattcieslak 3 months ago
Labels: enhancement
#785 - [ENH] Compress tck files from Autotrack workflow
Issue -
State: closed - Opened by mattcieslak 3 months ago
Labels: enhancement
#784 - [FIX] Make hsvs workflow work
Pull Request -
State: closed - Opened by mattcieslak 3 months ago
- 1 comment
#783 - [FIX] Use new bundle names
Pull Request -
State: closed - Opened by mattcieslak 3 months ago
- 1 comment
#782 - [ENH] Update DSI Studio to Hao
Pull Request -
State: closed - Opened by mattcieslak 3 months ago
- 1 comment
#781 - Fix bad phase connection when using `--denoise-after-combining`
Pull Request -
State: closed - Opened by tsalo 3 months ago
- 4 comments
Labels: bug
#780 - WIP [ENH] Add singleshell benchmarking recon workflow
Pull Request -
State: open - Opened by mattcieslak 3 months ago
#779 - [ENH] QSIPrep and SDCFlows
Issue -
State: open - Opened by mattcieslak 3 months ago
#778 - [FIX] Fix the mif2fib workflow
Pull Request -
State: closed - Opened by mattcieslak 3 months ago
- 1 comment
#777 - mrtrix_multishell_msmt_ACT-hsvs crashing
Issue -
State: closed - Opened by DVSneuro 3 months ago
- 2 comments
Labels: bug
#776 - network connection required for mrtrix_multishell_msmt_pyafq_tractometry?
Issue -
State: open - Opened by DVSneuro 3 months ago
- 1 comment
Labels: bug
#775 - Module merge_dwis has no output called out_dwi_phase
Issue -
State: closed - Opened by GHarmata 3 months ago
Labels: bug
#774 - Save SIFT2 mu parameter
Pull Request -
State: closed - Opened by araikes 3 months ago
- 3 comments
#773 - [BUG] output-resolution shouldn't be mandatory if --recon-input is used
Issue -
State: open - Opened by mattcieslak 3 months ago
Labels: bug
#772 - SIFT2 mu
Issue -
State: closed - Opened by araikes 3 months ago
- 1 comment
Labels: bug
#771 - [CI] add optional bundles
Pull Request -
State: closed - Opened by mattcieslak 3 months ago
#770 - Error when using mif_to_fib in recon workflow
Issue -
State: closed - Opened by ameliecr 3 months ago
- 1 comment
Labels: bug
#769 - Fix FUGUE bug
Pull Request -
State: closed - Opened by tsalo 3 months ago
- 3 comments
Labels: bug, testing
#768 - [ENH] Update dependencies in docker image
Pull Request -
State: closed - Opened by mattcieslak 3 months ago
- 1 comment
#767 - [ENH] Add BabyAFQ
Issue -
State: open - Opened by mattcieslak 3 months ago
- 11 comments
Labels: enhancement
#766 - [FIX] Update autotrack workflow to get all dsi studio bundles
Pull Request -
State: closed - Opened by mattcieslak 3 months ago
- 1 comment
#765 - SIFT2 parameters
Issue -
State: closed - Opened by araikes 3 months ago
- 1 comment
Labels: bug
#764 - MAINT: Upgrade pyAFQ to 1.3.2
Pull Request -
State: closed - Opened by arokem 4 months ago
- 2 comments
#763 - Run integration tests with pytest
Pull Request -
State: closed - Opened by tsalo 4 months ago
- 5 comments
Labels: refactor
#762 - AtlasPack atlas integration
Issue -
State: open - Opened by araikes 4 months ago
Labels: enhancement
#761 - Write out QSIRecon pipeline-wise reports
Pull Request -
State: closed - Opened by tsalo 4 months ago
- 5 comments
Labels: bug
#760 - Drop functions to read sidecar JSONs
Pull Request -
State: closed - Opened by tsalo 4 months ago
- 6 comments
Labels: refactor
#759 - Remove `ReadSidecarJSON` and `get_metadata_for_nifti`
Issue -
State: closed - Opened by tsalo 4 months ago
Labels: refactor
#758 - Recon reports are broken
Issue -
State: open - Opened by araikes 4 months ago
Labels: bug
#757 - Request for option to include ses-<label> entity in all files when a session is present
Issue -
State: open - Opened by psadil 4 months ago
- 8 comments
Labels: enhancement
#756 - [FIX]: changed typo and removed native_reference
Pull Request -
State: open - Opened by chiuhoward 4 months ago
#755 - Parts of documentation not rendering for latest
Issue -
State: closed - Opened by cookpa 4 months ago
Labels: bug, documentation
#754 - preprocessed T1w data as input to QSIPrep
Issue -
State: open - Opened by PandaFaye 4 months ago
Labels: enhancement
#753 - qsirecon workflow connection error: Trying to connect anat_ingress_wf.register_fs_to_qsiprep_wf:outputnode.brain to anat_ingress_wf.outputnode:brain but input 'brain' of node 'anat_ingress_wf.outputnode' is already connected
Issue -
State: closed - Opened by PandaFaye 4 months ago
- 1 comment
Labels: bug
#752 - Error when using FUGUE for fieldmap (after removing niworkflows)
Issue -
State: closed - Opened by kjamison 5 months ago
- 3 comments
Labels: bug
#751 - synthseg error when using GPU
Issue -
State: closed - Opened by jhauneuro 5 months ago
- 10 comments
Labels: bug
#750 - b0 harmonization error if there is only one b0 image in a series
Issue -
State: open - Opened by bermanj100 5 months ago
- 1 comment
Labels: bug
#749 - dsistudio autotrack recon not saving out all bundles
Issue -
State: closed - Opened by hamsiradhakrishnan 5 months ago
- 6 comments
Labels: bug
#748 - Fix API documentation
Pull Request -
State: closed - Opened by tsalo 5 months ago
- 2 comments
Labels: documentation
#747 - Eddy error when using GPU
Issue -
State: closed - Opened by araikes 5 months ago
- 2 comments
Labels: bug
#746 - [DOC] Update reconstruction.rst
Pull Request -
State: closed - Opened by chiuhoward 5 months ago
- 2 comments
#745 - [ENH] Update to NiPreps-style config file
Pull Request -
State: closed - Opened by mattcieslak 5 months ago
#744 - [FIX] stop bizarre argsort behavior in best b=0
Pull Request -
State: closed - Opened by mattcieslak 5 months ago
#743 - [ENH] Allow multithreading in eddy
Pull Request -
State: closed - Opened by mattcieslak 5 months ago
#742 - [MAINT] remove pypi
Pull Request -
State: closed - Opened by mattcieslak 5 months ago
#741 - [ENH] add parallel argument for topup
Pull Request -
State: closed - Opened by mattcieslak 5 months ago
#740 - [BUG] coregistration issues
Issue -
State: closed - Opened by mattcieslak 5 months ago
- 5 comments
Labels: bug
#739 - [FIX] use b0 ref from eddy-processed data
Pull Request -
State: closed - Opened by mattcieslak 5 months ago
#738 - [FIX] PyAFQ was not being written to derivatives
Pull Request -
State: closed - Opened by mattcieslak 5 months ago
#737 - [ENH] Allow topup to use multiple threads
Pull Request -
State: closed - Opened by psadil 5 months ago
- 1 comment
#736 - [FIX] revert citeproc for old pandoc
Pull Request -
State: closed - Opened by mattcieslak 5 months ago
#735 - [ENH] Add recon workflow for hbcd beta
Pull Request -
State: closed - Opened by mattcieslak 5 months ago
#734 - [FIX] recon workflows when --anat-modality T2w was used
Pull Request -
State: closed - Opened by mattcieslak 5 months ago
#733 - [FIX] remove old nodes from csdsi_3dshore.json
Pull Request -
State: closed - Opened by kjamison 5 months ago
- 1 comment
#731 - bug in mrtrix_multishell_msmt_ACT-hsvs recon? TypeError: expected str, bytes or os.PathLike object, not NoneType
Issue -
State: closed - Opened by DVSneuro 5 months ago
- 3 comments
Labels: bug
#730 - [ENH] Update TORTOISE for lower cuda memory use
Pull Request -
State: closed - Opened by mattcieslak 5 months ago
#729 - MAINT: Pin current version of pyAFQ (1.3.1)
Pull Request -
State: closed - Opened by arokem 5 months ago
- 3 comments
#728 - [FIX] Switch back to 18.04
Pull Request -
State: closed - Opened by mattcieslak 5 months ago
#727 - [ENH] update base image for cuda
Pull Request -
State: closed - Opened by mattcieslak 6 months ago
#726 - [ENH] Add --prefer-gpus
Pull Request -
State: closed - Opened by mattcieslak 6 months ago
#725 - [ENH] add --prefer-gpu
Issue -
State: open - Opened by mattcieslak 6 months ago
- 2 comments
Labels: enhancement
#724 - [FIX] Update Everything
Pull Request -
State: closed - Opened by mattcieslak 6 months ago
#723 - QSIPrep should fail when missing critical files
Issue -
State: open - Opened by araikes 6 months ago
- 3 comments
Labels: bug
#722 - [ENH] Update DSI Studio, FSL
Pull Request -
State: closed - Opened by mattcieslak 6 months ago
#721 - Reconstruction dwi outputs not included in derivatives when using a custom atlas
Issue -
State: open - Opened by pcamach2 6 months ago
Labels: bug
#720 - omp_nthreads not passed to merge_and_denoise_wf on one branch
Issue -
State: open - Opened by psadil 6 months ago
- 1 comment
Labels: bug
#718 - Error in connecting qsirecon nodes (0.20.1dev)
Issue -
State: closed - Opened by smeisler 6 months ago
- 24 comments
Labels: bug
#717 - Referencing a non-existing variable when using QSIRecon with mrtrix_multishell_msmt_ACT-hsvs specs.
Issue -
State: closed - Opened by GalKepler 6 months ago
- 1 comment
Labels: bug
#716 - Two desc-<value> pairs in qsirecon output
Issue -
State: closed - Opened by chiuhoward 6 months ago
- 8 comments
Labels: bug