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 2 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