Ecosyste.ms: Issues

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GitHub / PennLINC/qsiprep issues and pull requests

#883 - Pin nireports version and allow GIFs

Pull Request - State: closed - Opened by tsalo 7 days ago - 1 comment
Labels: bug

#882 - FOR HBCD: publish on Zenodo to obtain DOI specifically linked to the current version of software

Issue - State: closed - Opened by LuciMoore 8 days ago - 2 comments
Labels: enhancement

#881 - [FIX] synthstrip extra arg

Pull Request - State: closed - Opened by mattcieslak 8 days ago - 1 comment
Labels: bug

#880 - Hardcode extensions for GIF figures

Pull Request - State: closed - Opened by tsalo 8 days ago - 4 comments
Labels: bug, ignore-for-release

#879 - Restructure documentation and document how to run tests locally

Pull Request - State: closed - Opened by tsalo 8 days ago - 2 comments
Labels: documentation

#878 - Prepare for 1.0.0rc1 release

Pull Request - State: closed - Opened by tsalo 11 days ago - 3 comments
Labels: maintenance, documentation

#877 - Switch to ruff

Pull Request - State: open - Opened by tsalo 11 days ago - 1 comment
Labels: maintenance

#876 - Replace paths in JSONs with BIDS-URIs

Issue - State: open - Opened by tsalo 12 days ago
Labels: enhancement

#875 - Move common metadata to top of JSON

Pull Request - State: closed - Opened by tsalo 12 days ago - 1 comment
Labels: enhancement, breaking-change

#874 - Rename confounds file to `desc-confounds_timeseries`

Pull Request - State: closed - Opened by tsalo 12 days ago
Labels: breaking-change

#873 - Add QSIPrep paper to boilerplate

Pull Request - State: closed - Opened by tsalo 13 days ago - 1 comment
Labels: documentation

#872 - Remove `aggr_ses_reports` field

Pull Request - State: closed - Opened by tsalo 13 days ago - 1 comment
Labels: maintenance

#871 - HTML report in 0.23.0 missing sections?

Issue - State: open - Opened by michellewang 13 days ago - 5 comments
Labels: bug

#870 - Add warning for pennbbl Docker image

Pull Request - State: closed - Opened by tsalo 13 days ago - 2 comments
Labels: maintenance

#869 - Replace pennbbl with pennlinc in package

Pull Request - State: closed - Opened by tsalo 13 days ago - 3 comments
Labels: maintenance, breaking-change, documentation

#868 - Write out thermal noise map

Issue - State: open - Opened by tsalo 13 days ago - 1 comment
Labels: enhancement

#867 - Change _cnr to stat-cnr_dwimap

Pull Request - State: closed - Opened by tsalo 13 days ago - 1 comment
Labels: breaking-change

#866 - Document the transforms produced by QSIPrep

Pull Request - State: closed - Opened by tsalo 14 days ago - 1 comment
Labels: documentation

#865 - Write out coregistration transform

Issue - State: open - Opened by tsalo 14 days ago - 2 comments
Labels: enhancement

#864 - [ENH] Replace the `cnr` suffix with `stat-CNR_dwimap`.

Issue - State: closed - Opened by mattcieslak 14 days ago - 2 comments
Labels: breaking-change

#863 - Use correct base name with `--distortion-group-merge average`

Pull Request - State: closed - Opened by tsalo 15 days ago - 1 comment
Labels: bug

#862 - Make grouping account for acquisition entity

Pull Request - State: closed - Opened by tsalo 15 days ago - 1 comment
Labels: enhancement

#861 - Remove underscore versions of all parameters

Pull Request - State: closed - Opened by tsalo 15 days ago - 4 comments
Labels: maintenance, breaking-change

#860 - Limit distortion groups to a single `acq` entity value

Issue - State: closed - Opened by tsalo 15 days ago
Labels: enhancement

#859 - Change T1wACPC to ACPC and T1wNative to anat

Pull Request - State: closed - Opened by tsalo 15 days ago - 5 comments
Labels: breaking-change

#858 - Duplicate node name error

Issue - State: open - Opened by jhauneuro 18 days ago - 2 comments
Labels: bug

#857 - Is --subject-anatomical-reference available to test?

Issue - State: closed - Opened by jhauneuro 18 days ago - 1 comment
Labels: question

#856 - Infer the appropriate MNIInfant cohort based on the participant's age

Pull Request - State: closed - Opened by tsalo 18 days ago - 1 comment
Labels: enhancement

#855 - Rename `--anat-space-definition` to `--subject-anatomical-reference`

Pull Request - State: closed - Opened by tsalo 18 days ago - 1 comment
Labels: bug, breaking-change

#854 - Consistently label spaces in filenames

Issue - State: closed - Opened by tsalo 18 days ago - 3 comments
Labels: enhancement, breaking-change

#853 - Rename ACPC-aligned T1w/T2w space to something that is modality-independent

Issue - State: closed - Opened by tsalo 18 days ago - 6 comments
Labels: enhancement, breaking-change

#851 - Remove unused identity transform from anatomical derivatives

Issue - State: open - Opened by tsalo 18 days ago - 2 comments
Labels: bug

#849 - Add ability to ignore phase data

Pull Request - State: closed - Opened by tsalo 19 days ago - 2 comments
Labels: bug

#848 - Add `--report-output-level` parameter

Issue - State: open - Opened by tsalo 19 days ago - 7 comments
Labels: enhancement

#847 - Rename `--anat-space-definition` to `--subject-anatomical-reference`

Issue - State: closed - Opened by tsalo 19 days ago
Labels: enhancement, breaking-change

#846 - Use "Apptainer" instead of "Singularity"

Pull Request - State: closed - Opened by arokem 20 days ago - 4 comments
Labels: documentation

#845 - Denoising patch radius clarifications

Issue - State: open - Opened by araikes 21 days ago
Labels: enhancement

#844 - [ENH] Add derivatives metadata

Pull Request - State: closed - Opened by mattcieslak 21 days ago

#842 - [CI] DSDTI_nofmap test data _has_ a fieldmap in it

Issue - State: open - Opened by mattcieslak 25 days ago
Labels: bug

#841 - [FIX] Add denoising reportlets back to html

Pull Request - State: closed - Opened by mattcieslak 25 days ago - 1 comment

#840 - Switch to ruff for formatting

Issue - State: open - Opened by tsalo 25 days ago
Labels: maintenance

#839 - [FIX] Include linear interpolation (#829)

Pull Request - State: closed - Opened by araikes 26 days ago - 2 comments
Labels: bug

#838 - error when using `--distortion-group-merge average`

Issue - State: closed - Opened by chiarammatti 26 days ago
Labels: bug

#837 - Compare to other modalities' pipelines

Pull Request - State: open - Opened by tsalo 29 days ago - 1 comment
Labels: documentation

#836 - anat output orientation and dim in html report are incorrect

Issue - State: open - Opened by jhauneuro about 1 month ago - 2 comments
Labels: bug

#835 - Add acq-<label> to filename of html report

Issue - State: open - Opened by jhauneuro about 1 month ago - 8 comments
Labels: enhancement

#833 - [BUG] Missing unringing report for RPG method

Issue - State: closed - Opened by mattcieslak about 1 month ago
Labels: bug

#832 - [ENH] Enable session selection

Pull Request - State: closed - Opened by mattcieslak about 1 month ago - 1 comment

#831 - [FIX] use correct arguments for merging distortion groups

Pull Request - State: closed - Opened by mattcieslak about 1 month ago

#830 - Document major differences between QSIPrep and sMRIPrep/fMRIPrep

Issue - State: open - Opened by tsalo about 1 month ago
Labels: documentation

#828 - rf(py314): Replace deprecated pkgutil.find_loader

Pull Request - State: closed - Opened by effigies about 1 month ago - 3 comments

#827 - Patch2Self error

Issue - State: open - Opened by araikes about 1 month ago - 4 comments
Labels: bug

#826 - Infer appropriate MNIInfant cohort based on participant age

Issue - State: closed - Opened by tsalo about 2 months ago - 1 comment
Labels: enhancement

#825 - [FIX] Constrain threading for intramodal template

Pull Request - State: closed - Opened by mattcieslak about 2 months ago - 1 comment

#824 - Add MNIInfant to template enum

Pull Request - State: closed - Opened by tsalo about 2 months ago - 1 comment
Labels: bug

#819 - Upsampling is introducing artifact

Issue - State: closed - Opened by mattcieslak 2 months ago
Labels: bug

#818 - write out a json sidecar for the merged, preprocessed dwi file

Issue - State: closed - Opened by mattcieslak 3 months ago
Labels: enhancement

#817 - [CI] Swap synthstrip for bet when sloppy mode is chosen

Pull Request - State: closed - Opened by mattcieslak 3 months ago - 1 comment

#816 - [CI] add back pypi

Pull Request - State: closed - Opened by mattcieslak 3 months ago - 1 comment

#815 - Preprocessing multi-session anat data

Issue - State: closed - Opened by jhauneuro 3 months ago - 4 comments
Labels: bug

#814 - [CI] Update CI to be more efficient

Pull Request - State: closed - Opened by mattcieslak 3 months ago - 1 comment

#813 - [CI] Check into circleci performance

Issue - State: closed - Opened by mattcieslak 3 months ago - 1 comment
Labels: enhancement

#812 - Replace hyperlinks with BibTeX references

Issue - State: open - Opened by tsalo 3 months ago
Labels: documentation

#811 - Track immediate `Sources` when possible

Issue - State: open - Opened by tsalo 3 months ago
Labels: enhancement

#810 - Use file lock to avoid concurrent edits to dataset_description.json

Issue - State: open - Opened by tsalo 3 months ago
Labels: enhancement

#809 - Collect templates from TemplateFlow instead of package data

Pull Request - State: closed - Opened by tsalo 3 months ago - 2 comments
Labels: refactor

#808 - Use nireports for HTML reports

Pull Request - State: closed - Opened by tsalo 3 months ago - 5 comments
Labels: refactor

#807 - Drop mentions of the qsiprep-docker wrapper

Pull Request - State: closed - Opened by tsalo 3 months ago - 2 comments
Labels: breaking-change

#805 - Use nireports for report generation

Issue - State: closed - Opened by tsalo 3 months ago
Labels: enhancement

#804 - dsi_studio_autotrack not running

Issue - State: open - Opened by aazor 4 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 4 months ago
Labels: enhancement

#802 - [RF] Remove the recon workflows from QSIPrep

Pull Request - State: closed - Opened by mattcieslak 4 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 4 months ago - 2 comments

#800 - Bad preprocessing results for dwi with PSR+ image orientation

Issue - State: open - Opened by jhauneuro 4 months ago - 2 comments
Labels: bug

#799 - 2 phases SDC outputs partial fieldmap

Issue - State: open - Opened by jhauneuro 4 months ago
Labels: bug

#798 - top of brain cut after preprocessing using version 0.22.0

Issue - State: open - Opened by jhauneuro 4 months ago - 5 comments
Labels: bug

#797 - error when using option --distortion-group-merge

Issue - State: closed - Opened by jhauneuro 4 months ago - 12 comments
Labels: bug

#796 - Add logging message when qc metrics on raw data are low

Issue - State: open - Opened by mattcieslak 4 months ago
Labels: enhancement

#795 - [FIX] Update bundle list for hbcd_scalar_maps

Pull Request - State: closed - Opened by mattcieslak 4 months ago - 1 comment

#794 - [BUG] List of bundles not fixed in hbcd recon workflow

Issue - State: closed - Opened by mattcieslak 4 months ago
Labels: bug

#793 - TOPUP distortion correction field is flipped for my LPS oriented dwi data

Issue - State: open - Opened by jhauneuro 4 months ago - 3 comments
Labels: bug

#792 - error encountered at eddy step when no T1w data are available

Issue - State: open - Opened by jhauneuro 4 months ago - 4 comments
Labels: bug

#790 - EDDY_CUDA Failure: GPU can only use 1 CPU thread

Issue - State: closed - Opened by amirhusseinab 4 months ago - 10 comments
Labels: bug

#789 - FUGUE error (no attribute 'FUGUEvsm2ANTSwarp')

Issue - State: closed - Opened by jhauneuro 4 months ago - 3 comments
Labels: bug

#788 - [FIX]: CUDA threads for Eddy

Pull Request - State: closed - Opened by araikes 4 months ago - 2 comments

#787 - [ENH] Compress recon derivatives

Pull Request - State: closed - Opened by mattcieslak 4 months ago - 1 comment

#786 - [ENH] Compress nifti files written by the tortoise workflows

Issue - State: closed - Opened by mattcieslak 4 months ago
Labels: enhancement

#785 - [ENH] Compress tck files from Autotrack workflow

Issue - State: closed - Opened by mattcieslak 4 months ago
Labels: enhancement

#784 - [FIX] Make hsvs workflow work

Pull Request - State: closed - Opened by mattcieslak 4 months ago - 1 comment

#783 - [FIX] Use new bundle names

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

#782 - [ENH] Update DSI Studio to Hao

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

#781 - Fix bad phase connection when using `--denoise-after-combining`

Pull Request - State: closed - Opened by tsalo 5 months ago - 4 comments
Labels: bug

#780 - WIP [ENH] Add singleshell benchmarking recon workflow

Pull Request - State: open - Opened by mattcieslak 5 months ago - 1 comment

#779 - [ENH] QSIPrep and SDCFlows

Issue - State: open - Opened by mattcieslak 5 months ago