Ecosyste.ms: Issues

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GitHub / nipreps/fmriprep issues and pull requests

#2960 - What does the 'sloppy' flag do?

Issue - State: closed - Opened by NickESouter over 1 year ago - 4 comments
Labels: documentation

#2959 - ENH: Resample morphometrics to fsLR dscalar CIFTI-2 files if `--cifti-output` is used

Pull Request - State: closed - Opened by effigies over 1 year ago - 2 comments

#2958 - codespell: config, action + some typo fixups

Pull Request - State: closed - Opened by yarikoptic over 1 year ago

#2958 - codespell: config, action + some typo fixups

Pull Request - State: closed - Opened by yarikoptic over 1 year ago

#2957 - CI: Minor updates to CircleCI config to improve resilience

Pull Request - State: closed - Opened by effigies over 1 year ago

#2957 - CI: Minor updates to CircleCI config to improve resilience

Pull Request - State: closed - Opened by effigies over 1 year ago

#2956 - ENH: Add option to exclude projecting high variance voxels to surface (update of #2855)

Pull Request - State: closed - Opened by madisoth over 1 year ago - 6 comments

#2955 - Surface Morphometrics in fsLR 32k space

Issue - State: closed - Opened by hough129 over 1 year ago

#2954 - TEST: Verify nipreps/niworkflows#780 on fMRIPrep

Pull Request - State: closed - Opened by effigies over 1 year ago

#2953 - ENH: Add option to exclude projecting high variance voxels to surface

Pull Request - State: closed - Opened by effigies over 1 year ago

#2953 - ENH: Add option to exclude projecting high variance voxels to surface

Pull Request - State: closed - Opened by effigies over 1 year ago

#2952 - Using inversion recovery image when T1w is not available

Issue - State: closed - Opened by manzouri over 1 year ago - 2 comments

#2952 - Using inversion recovery image when T1w is not available

Issue - State: closed - Opened by manzouri over 1 year ago - 2 comments

#2950 - DOC: update the description of the carpetplot in the sample report

Pull Request - State: closed - Opened by celprov over 1 year ago - 2 comments

#2950 - DOC: update the description of the carpetplot in the sample report

Pull Request - State: closed - Opened by celprov over 1 year ago - 2 comments

#2949 - NetworkX version issue

Issue - State: closed - Opened by sanosenx86 over 1 year ago - 1 comment
Labels: bug

#2949 - NetworkX version issue

Issue - State: closed - Opened by sanosenx86 over 1 year ago - 1 comment
Labels: bug

#2948 - Odd ghosting in coreg, dark sdc images, bad roi & carpet plots

Issue - State: closed - Opened by athenahowell over 1 year ago - 5 comments
Labels: bug

#2947 - Fieldmaps causing fMRIprep to get crash

Issue - State: open - Opened by NickESouter over 1 year ago - 18 comments
Labels: bug

#2947 - Fieldmaps causing fMRIprep to get crash

Issue - State: closed - Opened by NickESouter over 1 year ago - 20 comments
Labels: bug

#2946 - fMRIPrep roadmap (m8,16)

Issue - State: open - Opened by esavary over 1 year ago

#2945 - FIX: Pass reference image to unwarp_wf, use reference fieldwarp for single shot

Pull Request - State: closed - Opened by effigies over 1 year ago - 3 comments

#2944 - DOC: Altered CLI option grouping

Pull Request - State: closed - Opened by Lestropie over 1 year ago - 2 comments

#2944 - DOC: Altered CLI option grouping

Pull Request - State: closed - Opened by Lestropie over 1 year ago - 2 comments

#2943 - DOC: Update lesion ROI documentation, warn in docs and app about upcoming changes

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

#2941 - ENH: Merge T2w images and coregister to T1w template

Pull Request - State: closed - Opened by effigies over 1 year ago - 3 comments

#2941 - ENH: Merge T2w images and coregister to T1w template

Pull Request - State: closed - Opened by effigies over 1 year ago - 3 comments

#2940 - MNT: Warn that AROMA support will be removed in a future version

Pull Request - State: closed - Opened by effigies over 1 year ago

#2939 - FIX: Build leftovers

Pull Request - State: closed - Opened by effigies over 1 year ago

#2938 - CI: Weekly docker build from scratch

Pull Request - State: closed - Opened by effigies over 1 year ago - 2 comments

#2937 - RF: Use DataFrame.rename instead of ad hoc process

Pull Request - State: closed - Opened by effigies over 1 year ago

#2937 - RF: Use DataFrame.rename instead of ad hoc process

Pull Request - State: closed - Opened by effigies over 1 year ago

#2936 - Remove ICA-AROMA

Issue - State: closed - Opened by effigies over 1 year ago - 13 comments
Labels: feature

#2936 - Remove ICA-AROMA

Issue - State: open - Opened by effigies over 1 year ago - 10 comments
Labels: feature

#2934 - Error in nodes _midthickness0 and _midthickness1

Issue - State: closed - Opened by heffjos over 1 year ago - 2 comments
Labels: bug

#2931 - MNT: Update Ubuntu, FreeSurfer, AFNI and Convert3D

Pull Request - State: closed - Opened by effigies over 1 year ago - 4 comments

#2931 - MNT: Update Ubuntu, FreeSurfer, AFNI and Convert3D

Pull Request - State: closed - Opened by effigies over 1 year ago - 4 comments

#2930 - DOC: Update docs following read-through

Pull Request - State: closed - Opened by effigies over 1 year ago - 1 comment
Labels: documentation

#2929 - Errors in bold_std_trans_wf + bold_confounds_wf

Issue - State: closed - Opened by LuRoe7 over 1 year ago - 1 comment
Labels: bug

#2918 - --ignore fieldmaps --use-syn-sdc not working with fmriprep v 22.1.0

Issue - State: closed - Opened by julfou81 almost 2 years ago
Labels: bug

#2917 - Exception raised while executing Node get_dummy

Issue - State: closed - Opened by Heechberri almost 2 years ago - 3 comments
Labels: bug

#2917 - Exception raised while executing Node get_dummy

Issue - State: closed - Opened by Heechberri almost 2 years ago - 3 comments
Labels: bug

#2916 - CI action to build the Docker image with no layer caching

Issue - State: closed - Opened by effigies almost 2 years ago

#2916 - CI action to build the Docker image with no layer caching

Issue - State: closed - Opened by effigies almost 2 years ago

#2915 - Transition more packages to conda

Issue - State: closed - Opened by effigies almost 2 years ago - 1 comment

#2913 - RF: Split fMRIPrep into fit and derivatives workflows

Pull Request - State: closed - Opened by effigies almost 2 years ago - 5 comments

#2913 - RF: Split fMRIPrep into fit and derivatives workflows

Pull Request - State: closed - Opened by effigies almost 2 years ago - 5 comments
Labels: next

#2904 - Remove Pandas Index.ravel()

Issue - State: closed - Opened by effigies almost 2 years ago
Labels: maintenance

#2898 - ENH: Tag memory based on data shape, annotate T2SMap

Pull Request - State: closed - Opened by effigies almost 2 years ago - 2 comments
Labels: memory, impact: high, effort: low, backport candidate

#2898 - ENH: Tag memory based on data shape, annotate T2SMap

Pull Request - State: closed - Opened by effigies almost 2 years ago - 2 comments
Labels: memory, impact: high, effort: low, backport candidate

#2896 - CifTi files created with --cifti-output are the same regardless of the --use-aroma flag

Issue - State: closed - Opened by narunpat almost 2 years ago - 1 comment
Labels: question

#2893 - Duplicated boilerplate in CITATION.md

Issue - State: open - Opened by mateuszpawlik almost 2 years ago - 1 comment
Labels: bug, reports, impact: low, effort: low

#2892 - lesion mask: inconsistent documentation ?

Issue - State: closed - Opened by Remi-Gau almost 2 years ago - 3 comments
Labels: documentation

#2892 - lesion mask: inconsistent documentation ?

Issue - State: closed - Opened by Remi-Gau almost 2 years ago - 3 comments
Labels: documentation

#2891 - SDC report svg on SBRef pepolar scheme alternates between SBRef and BOLD.

Issue - State: open - Opened by bpinsard almost 2 years ago - 4 comments
Labels: bug

#2890 - Naming of html reports and aroma regressors

Issue - State: open - Opened by burdinskid13 almost 2 years ago - 3 comments
Labels: feature, reports

#2890 - Naming of html reports and aroma regressors

Issue - State: open - Opened by burdinskid13 almost 2 years ago - 3 comments
Labels: feature, reports

#2889 - pepolar scheme using SBRef considered as sophisticated.

Issue - State: closed - Opened by bpinsard almost 2 years ago - 5 comments
Labels: bug

#2888 - Rename .func.gii to .time.gii?

Issue - State: closed - Opened by effigies almost 2 years ago - 4 comments
Labels: discussion

#2888 - Rename .func.gii to .time.gii?

Issue - State: closed - Opened by effigies almost 2 years ago - 4 comments
Labels: discussion

#2880 - fieldmaps not being filtered by session using bids-filter-file

Issue - State: closed - Opened by dcmonroe almost 2 years ago - 5 comments
Labels: bug

#2874 - mkdir failures in nipype nodes

Issue - State: closed - Opened by effigies almost 2 years ago - 3 comments
Labels: bug

#2868 - RF: Split derivatives into primary and secondary workflows.

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

#2864 - Resource monitor files being emitted to output directory

Issue - State: open - Opened by effigies about 2 years ago - 1 comment
Labels: bug

#2863 - MNT: Pin environment

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

#2863 - MNT: Pin environment

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

#2861 - auto-recon error

Issue - State: closed - Opened by juansanchezpena about 2 years ago - 8 comments
Labels: bug

#2856 - NodeExecutionError & FileNotFoundError while performing fmriPrep steps using docker

Issue - State: closed - Opened by kartikeysaran about 2 years ago - 3 comments
Labels: bug

#2856 - NodeExecutionError & FileNotFoundError while performing fmriPrep steps using docker

Issue - State: closed - Opened by kartikeysaran about 2 years ago - 3 comments
Labels: bug

#2855 - ENH: Add option to exclude projecting high variance voxels to surface

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

#2855 - ENH: Add option to exclude projecting high variance voxels to surface

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

#2842 - Allow dummy-scans to be specified per-task

Issue - State: open - Opened by effigies about 2 years ago
Labels: fmripost

#2835 - TOPUP issues in functionals, even though the topup field looks reasonable

Issue - State: closed - Opened by cmpetty about 2 years ago - 8 comments

#2835 - TOPUP issues in functionals, even though the topup field looks reasonable

Issue - State: closed - Opened by cmpetty about 2 years ago - 8 comments

#2830 - FSL's topup implementation (fmriprep >=21) significantly worse than AFNI's Qwarp (fmriprep <20)

Issue - State: closed - Opened by Gilles86 about 2 years ago - 19 comments
Labels: bug, sdc

#2827 - T2SMap error

Issue - State: closed - Opened by quach-al about 2 years ago - 5 comments
Labels: bug, me-epi, multiecho

#2812 - --skip-confounds flag (or similar)

Issue - State: closed - Opened by effigies about 2 years ago - 9 comments

#2811 - error in generating confounds

Issue - State: closed - Opened by IFaillenot over 2 years ago - 6 comments
Labels: bug

#2810 - MNI rigid-body output space

Issue - State: closed - Opened by Lestropie over 2 years ago - 6 comments
Labels: feature, derivatives

#2808 - Unusual fieldmap data

Issue - State: closed - Opened by MasonTWells over 2 years ago - 5 comments

#2808 - Unusual fieldmap data

Issue - State: closed - Opened by MasonTWells over 2 years ago - 5 comments

#2807 - [WIP] First steps towards minimal flag

Pull Request - State: open - Opened by 36000 over 2 years ago - 1 comment

#2807 - [WIP] First steps towards minimal flag

Pull Request - State: closed - Opened by 36000 over 2 years ago - 2 comments

#2806 - fmriprep --minimal mode

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

#2806 - fmriprep --minimal mode

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

#2805 - fmriprep-apply CLI tool

Issue - State: closed - Opened by effigies over 2 years ago - 3 comments

#2796 - Image Artefacts after SDC correction

Issue - State: closed - Opened by xuyangwen over 2 years ago - 2 comments
Labels: bug, sdc

#2793 - unsmoothed first volume in smoothAROMAnonaggr*.nii.gz

Issue - State: closed - Opened by ka251 over 2 years ago - 3 comments

#2790 - Fieldmaps for multiple techniques

Issue - State: closed - Opened by xuyangwen over 2 years ago - 5 comments
Labels: documentation

#2790 - Fieldmaps for multiple techniques

Issue - State: closed - Opened by xuyangwen over 2 years ago - 5 comments
Labels: documentation

#2777 - Incorrect/dark functional images after SDC with SyN

Issue - State: closed - Opened by alexsayal over 2 years ago - 16 comments
Labels: bug, SyN-SDC, sdc

#2777 - Incorrect/dark functional images after SDC with SyN

Issue - State: closed - Opened by alexsayal over 2 years ago - 16 comments
Labels: bug, SyN-SDC, sdc