Ecosyste.ms: Issues

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GitHub / nipreps/fmriprep issues and pull requests

#3146 - ENH: Pass FLAIR images to anatomical workflow builder to include in boilerplate

Pull Request - State: closed - Opened by effigies 8 months ago - 1 comment

#3145 - MNT: optimise size of PNG files

Pull Request - State: closed - Opened by DimitriPapadopoulos 8 months ago - 1 comment

#3144 - MNT: update vendored docs script `github_link.py`

Pull Request - State: closed - Opened by DimitriPapadopoulos 8 months ago - 1 comment

#3141 - MNT: Update tedana pin, test on Python 3.12

Pull Request - State: closed - Opened by effigies 8 months ago - 1 comment

#3140 - Tag resampling nodes with memory estimates

Issue - State: closed - Opened by effigies 8 months ago

#3138 - chore: update to latest migas api

Pull Request - State: closed - Opened by mgxd 8 months ago - 1 comment

#3137 - DOC: Improve report captions and update expected outputs in docs

Pull Request - State: closed - Opened by effigies 8 months ago - 1 comment
Labels: next

#3137 - DOC: Improve report captions and update expected outputs in docs

Pull Request - State: closed - Opened by effigies 8 months ago - 1 comment
Labels: next

#3136 - RF: Write out anatomical template derivatives

Pull Request - State: closed - Opened by effigies 8 months ago - 1 comment
Labels: next

#3135 - CI: Test on Python 3.12

Pull Request - State: closed - Opened by DimitriPapadopoulos 8 months ago - 4 comments

#3134 - Final revisions for next branch

Pull Request - State: closed - Opened by effigies 8 months ago - 1 comment
Labels: next

#3133 - Enable longitudinal structural analysis

Issue - State: open - Opened by ChristianNSchmitz 8 months ago - 1 comment

#3132 - MNT: Bump environment

Pull Request - State: closed - Opened by effigies 8 months ago - 1 comment

#3131 - ENH: Restore carpetplot and other final adjustments

Pull Request - State: closed - Opened by effigies 8 months ago - 4 comments

#3129 - ENH: Restore CIFTI-2 generation

Pull Request - State: closed - Opened by effigies 8 months ago - 3 comments
Labels: next

#3126 - ENH: Restore resampling to surface GIFTIs

Pull Request - State: closed - Opened by effigies 8 months ago - 2 comments

#3125 - t2smap OOM

Issue - State: open - Opened by bpinsard 8 months ago - 4 comments
Labels: bug

#3123 - --use-syn-sdc not doing sdc with fmriprep v 23.1.4

Issue - State: closed - Opened by julfou81 9 months ago - 4 comments
Labels: bug

#3122 - OSError: Duplicate node name "func_preproc_*_wf" found.

Issue - State: closed - Opened by lsempf 9 months ago - 1 comment
Labels: bug

#3121 - ENH: Restore resampling BOLD to volumetric templates

Pull Request - State: closed - Opened by effigies 9 months ago - 3 comments
Labels: next

#3120 - ENH: Restore confound generation

Pull Request - State: closed - Opened by effigies 9 months ago - 3 comments
Labels: next

#3119 - CIFTI resampling weights

Issue - State: closed - Opened by effigies 9 months ago - 11 comments
Labels: CIFTI / Grayordinates, next

#3118 - Change `scanner` to `boldref` in non-HMC transform filenames

Pull Request - State: closed - Opened by tsalo 9 months ago - 5 comments

#3117 - BOLD reference to T1w transforms are mislabeled

Issue - State: closed - Opened by tsalo 9 months ago - 1 comment
Labels: bug, impact: low, effort: low

#3116 - ENH: Restore resampling to T1w target

Pull Request - State: closed - Opened by effigies 9 months ago - 4 comments
Labels: next

#3115 - Bump urllib3 from 2.0.4 to 2.0.7

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 2 comments
Labels: dependencies, python

#3114 - RF: Update primary bold workflow to incorporate single shot resampling

Pull Request - State: closed - Opened by effigies 9 months ago - 4 comments

#3113 - Bump pillow from 10.0.0 to 10.0.1

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies, python

#3112 - Bump codespell-project/actions-codespell from 1 to 2

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#3111 - Bump actions/checkout from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#3110 - Update GitHub actions

Pull Request - State: closed - Opened by DimitriPapadopoulos 9 months ago - 4 comments

#3109 - MNT: http:// → https://

Pull Request - State: closed - Opened by DimitriPapadopoulos 9 months ago - 1 comment

#3108 - fMRIPrep 23.2.0alpha

Pull Request - State: closed - Opened by effigies 9 months ago - 20 comments

#3107 - MNT: Bump version requirements

Pull Request - State: closed - Opened by effigies 9 months ago - 1 comment

#3106 - FIX: Swap direction of fmap-EPI transform

Pull Request - State: closed - Opened by effigies 9 months ago - 1 comment
Labels: next

#3104 - ERROR: a valid license file is required for FreeSurfer to run.

Issue - State: closed - Opened by AnnJingLyu 9 months ago - 4 comments
Labels: bug

#3103 - `mritotal` subcommands not found

Issue - State: closed - Opened by tsalo 9 months ago - 3 comments
Labels: bug

#3102 - Bump pillow from 10.0.0 to 10.0.1

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 2 comments
Labels: dependencies

#3101 - FIX: Use Py2-compatible version file template for fmriprep-docker

Pull Request - State: closed - Opened by effigies 9 months ago - 1 comment

#3100 - Bump urllib3 from 2.0.4 to 2.0.6

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 2 comments
Labels: dependencies

#3099 - FIX: Connect EPI-to-fieldmap transform

Pull Request - State: closed - Opened by effigies 9 months ago
Labels: next

#3098 - FIX: Minor fixes to work with MSMSulc-enabled smriprep-next

Pull Request - State: closed - Opened by effigies 9 months ago - 1 comment

#3097 - MNT: http:// → https://

Pull Request - State: closed - Opened by DimitriPapadopoulos 9 months ago - 1 comment

#3096 - Fix typo found by codespell

Pull Request - State: closed - Opened by DimitriPapadopoulos 9 months ago

#3095 - Report clearly bids filters

Issue - State: open - Opened by celprov 10 months ago - 3 comments
Labels: documentation, good first issue, impact: medium, effort: low

#3094 - FIX: Eliminate distortions in phasediff images caused by unmasked fieldmap estimates

Pull Request - State: closed - Opened by effigies 10 months ago - 3 comments

#3093 - Strange pattern on distortion corrected images

Issue - State: closed - Opened by jameswyngaarden 10 months ago - 1 comment
Labels: bug

#3092 - msmsulc error

Issue - State: closed - Opened by zugmana 10 months ago - 3 comments
Labels: bug

#3091 - Build(deps): Bump cryptography from 41.0.3 to 41.0.4

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 2 comments
Labels: dependencies

#3090 - DOCKER: Remove mritotal and dependencies from FreeSurfer ignore file

Pull Request - State: closed - Opened by E-Loba 10 months ago - 3 comments

#3089 - fieldmap-less distortion correction not working

Issue - State: closed - Opened by DVSneuro 10 months ago - 5 comments
Labels: bug

#3088 - mritotal: Command not found.

Issue - State: closed - Opened by E-Loba 10 months ago - 4 comments
Labels: bug, impact: low, effort: low

#3087 - MSM - mismatch

Issue - State: closed - Opened by juansanchezpena 10 months ago - 3 comments
Labels: bug, CIFTI / Grayordinates

#3085 - ENH: Add MSMSulc

Pull Request - State: closed - Opened by mgxd 10 months ago - 1 comment

#3085 - ENH: Add MSMSulc

Pull Request - State: open - Opened by mgxd 10 months ago - 1 comment

#3084 - ENH: Add MSMSulc

Pull Request - State: closed - Opened by mgxd 10 months ago - 2 comments

#3084 - ENH: Add MSMSulc

Pull Request - State: closed - Opened by mgxd 10 months ago - 2 comments

#3083 - FileNotFoundError: 'aparc_a2009s_stats' of a ReconAll interface

Issue - State: closed - Opened by celprov 10 months ago - 1 comment
Labels: bug

#3083 - FileNotFoundError: 'aparc_a2009s_stats' of a ReconAll interface

Issue - State: closed - Opened by celprov 10 months ago - 1 comment
Labels: bug

#3082 - ENH: Add reporting workflow for BOLD fit

Pull Request - State: closed - Opened by effigies 10 months ago - 8 comments
Labels: next

#3082 - ENH: Add reporting workflow for BOLD fit

Pull Request - State: open - Opened by effigies 10 months ago - 2 comments
Labels: next

#3081 - ENH: Generate anatomical derivatives useful for resampling

Pull Request - State: open - Opened by effigies 11 months ago - 1 comment
Labels: next

#3081 - ENH: Generate anatomical derivatives useful for resampling

Pull Request - State: closed - Opened by effigies 11 months ago - 4 comments
Labels: next

#3080 - One visual report per session for dataset with many sessions for a single subject

Issue - State: closed - Opened by celprov 11 months ago - 1 comment
Labels: feature, reports, impact: medium, effort: medium

#3079 - CI: Stop testing legacy layout

Pull Request - State: closed - Opened by effigies 11 months ago - 1 comment

#3079 - CI: Stop testing legacy layout

Pull Request - State: closed - Opened by effigies 11 months ago - 1 comment
Labels: next

#3078 - RF: Update derivative cache spec, calculate per-BOLD, reuse boldref2fmap

Pull Request - State: closed - Opened by effigies 11 months ago - 1 comment
Labels: next

#3077 - FIX: Update connections to unwarp_wf, convert ITK transforms to text

Pull Request - State: closed - Opened by effigies 11 months ago
Labels: next

#3076 - MNT: Pin sdcflows 2.5.x

Pull Request - State: closed - Opened by effigies 11 months ago - 2 comments

#3076 - MNT: Pin sdcflows 2.5.x

Pull Request - State: open - Opened by effigies 11 months ago - 1 comment

#3075 - RF: Update workflow to use sdcflows@master unwarp_wf

Pull Request - State: closed - Opened by effigies 11 months ago - 1 comment

#3073 - MNT: Update environment

Pull Request - State: closed - Opened by effigies 11 months ago - 3 comments

#3072 - Build(deps): Bump tornado from 6.3.2 to 6.3.3

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 3 comments
Labels: dependencies

#3071 - `--cifti-output` + `--fs-no-reconall` produces confusing error messages

Issue - State: open - Opened by effigies 11 months ago
Labels: bug, impact: low, effort: low

#3070 - Changes needed to satisfy current derivatives validator

Issue - State: open - Opened by effigies 11 months ago
Labels: bug

#3070 - Changes needed to satisfy current derivatives validator

Issue - State: open - Opened by effigies 11 months ago
Labels: bug

#3069 - Segmentation fault error

Issue - State: closed - Opened by caaperezag 11 months ago - 1 comment
Labels: bug

#3068 - Running fmriprep on M2 chip Mac using Docker

Issue - State: closed - Opened by MtKana 11 months ago - 4 comments
Labels: bug

#3067 - MNT: Depend on newer sphinx

Pull Request - State: closed - Opened by effigies 11 months ago - 1 comment

#3066 - CI: Improve tag detection for docker builds

Pull Request - State: closed - Opened by effigies 11 months ago - 1 comment

#3066 - CI: Improve tag detection for docker builds

Pull Request - State: closed - Opened by effigies 11 months ago - 1 comment

#3065 - fMRIPrep on TBI data

Issue - State: closed - Opened by shilpitju1 11 months ago - 8 comments

#3064 - ENH: insert gradunwarp in bold workflow

Pull Request - State: open - Opened by bpinsard 11 months ago - 1 comment

#3064 - ENH: insert gradunwarp in bold workflow

Pull Request - State: open - Opened by bpinsard 11 months ago - 1 comment

#3063 - Bump certifi from 2023.5.7 to 2023.7.22

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 3 comments
Labels: dependencies

#3063 - Bump certifi from 2023.5.7 to 2023.7.22

Pull Request - State: open - Opened by dependabot[bot] 12 months ago - 1 comment
Labels: dependencies

#3062 - PATCH: Use mutualinfo cost function for MCFLIRT

Pull Request - State: closed - Opened by effigies 12 months ago - 5 comments

#3061 - MNT: Install ANTs from conda-forge

Pull Request - State: closed - Opened by effigies 12 months ago - 8 comments

#3061 - MNT: Install ANTs from conda-forge

Pull Request - State: closed - Opened by effigies 12 months ago - 8 comments

#3060 - FIX: Pass sbref files to SyN workflow

Pull Request - State: closed - Opened by effigies 12 months ago - 3 comments

#3060 - FIX: Pass sbref files to SyN workflow

Pull Request - State: closed - Opened by effigies 12 months ago - 3 comments

#3059 - Low process ulimits can result in missing output failures (here in fsl2itk)

Issue - State: closed - Opened by Shotgunosine 12 months ago - 26 comments
Labels: faq