nipreps/fmriprep issues and pull requests

#2207 - Transforms-only and apply-transforms modes

Issue - State: open - Opened by effigies about 4 years ago - 4 comments
Labels: feature, derivatives, impact: medium, effort: high, next

#2188 - Register structural and func to a standard template

Issue - State: closed - Opened by StephDocTUM about 4 years ago - 4 comments
Labels: question

#2143 - Check for excess resampling

Issue - State: closed - Opened by mgxd about 4 years ago - 1 comment
Labels: impact: low, effort: low

#2113 - ENH: Enable ``--bold2t1w-init header`` for FreeSurfer-based runs

Pull Request - State: closed - Opened by effigies about 4 years ago - 23 comments

#2113 - ENH: Enable ``--bold2t1w-init header`` for FreeSurfer-based runs

Pull Request - State: closed - Opened by effigies about 4 years ago - 23 comments

#2108 - PIN: nipreps/niworkflows#485

Pull Request - State: closed - Opened by effigies about 4 years ago - 16 comments

#2108 - PIN: nipreps/niworkflows#485

Pull Request - State: closed - Opened by effigies about 4 years ago - 16 comments

#2094 - Filtered framewise displacement

Issue - State: open - Opened by rciric about 4 years ago - 6 comments
Labels: confounds, impact: medium, effort: medium

#2046 - fmriprep trying to create folder that ends with a dot in its name in Windows?

Issue - State: open - Opened by sangillee over 4 years ago - 7 comments
Labels: bug

#2046 - fmriprep trying to create folder that ends with a dot in its name in Windows?

Issue - State: open - Opened by sangillee over 4 years ago - 7 comments
Labels: bug

#2044 - FAQ: Can fMRIPrep resume execution after encountering an error?

Pull Request - State: closed - Opened by effigies over 4 years ago - 3 comments

#2044 - FAQ: Can fMRIPrep resume execution after encountering an error?

Pull Request - State: closed - Opened by effigies over 4 years ago - 3 comments

#2042 - Group reports

Issue - State: open - Opened by oesteban over 4 years ago - 8 comments
Labels: group-level

#2028 - DOC: BIDS filter input example

Pull Request - State: closed - Opened by utooley over 4 years ago - 11 comments

#1998 - [NOMRG] UX: Display errors as summary/details elements

Pull Request - State: closed - Opened by effigies over 4 years ago - 6 comments

#1998 - [NOMRG] UX: Display errors as summary/details elements

Pull Request - State: closed - Opened by effigies over 4 years ago - 6 comments

#1939 - ENH: Add fmriprep.main to allow python -m fmriprep

Pull Request - State: closed - Opened by effigies over 4 years ago - 1 comment

#1939 - ENH: Add fmriprep.main to allow python -m fmriprep

Pull Request - State: closed - Opened by effigies over 4 years ago - 1 comment

#1938 - How to use session labels?

Issue - State: closed - Opened by jbruegge over 4 years ago - 2 comments

#1905 - Unfold AROMA variants of confounds with ``--ica-aroma`` flag

Issue - State: closed - Opened by oesteban over 4 years ago - 1 comment
Labels: confounds

#1905 - Unfold AROMA variants of confounds with ``--ica-aroma`` flag

Issue - State: closed - Opened by oesteban over 4 years ago - 1 comment
Labels: confounds

#1902 - MNT: Ensure data is packaged in sdist

Pull Request - State: closed - Opened by effigies over 4 years ago - 1 comment

#1875 - Outdated cache, while nothing changed

Issue - State: closed - Opened by bpinsard over 4 years ago - 5 comments
Labels: nipype issue, templateflow, impact: medium, effort: medium

#1850 - UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9

Issue - State: closed - Opened by JMb63 over 4 years ago - 3 comments

#1845 - Unexpected lack of images in html report and incomplete output

Issue - State: closed - Opened by dittothat over 4 years ago - 7 comments

#1845 - Unexpected lack of images in html report and incomplete output

Issue - State: closed - Opened by dittothat over 4 years ago - 7 comments

#1841 - OSError: [Errno 16] Device or resource busy: '.nfs0000001807639d980000059d'

Issue - State: closed - Opened by dmd over 4 years ago - 2 comments

#1841 - OSError: [Errno 16] Device or resource busy: '.nfs0000001807639d980000059d'

Issue - State: closed - Opened by dmd over 4 years ago - 2 comments

#1837 - UNC infant atlas

Issue - State: closed - Opened by ajdneuro12 over 4 years ago - 4 comments
Labels: templateflow

#1804 - improve ICA-AROMA documentation

Issue - State: closed - Opened by jdkent almost 5 years ago - 4 comments
Labels: documentation

#1792 - MAINT: Purge Cython and depend on SDCflows

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

#1792 - MAINT: Purge Cython and depend on SDCflows

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

#1788 - FIX: Ignore sourcedata and derivatives when fetching data

Pull Request - State: closed - Opened by effigies almost 5 years ago - 7 comments

#1788 - FIX: Ignore sourcedata and derivatives when fetching data

Pull Request - State: closed - Opened by effigies almost 5 years ago - 7 comments

#1784 - Remove ICA-AROMA dependency

Issue - State: closed - Opened by rciric almost 5 years ago - 12 comments
Labels: impact: low, effort: high

#1774 - fmriprep - ‘NiftiException’ what(): Error: cant open file

Issue - State: open - Opened by sameera2004 almost 5 years ago - 11 comments
Labels: me-epi

#1774 - fmriprep - ‘NiftiException’ what(): Error: cant open file

Issue - State: open - Opened by sameera2004 almost 5 years ago - 11 comments
Labels: me-epi

#1743 - DIAGNOSTIC: Print traceback when atexit calls are registered

Pull Request - State: closed - Opened by effigies almost 5 years ago - 1 comment

#1743 - DIAGNOSTIC: Print traceback when atexit calls are registered

Pull Request - State: closed - Opened by effigies almost 5 years ago - 1 comment

#1732 - [DOC] Update .zenodo.json

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

#1732 - [DOC] Update .zenodo.json

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

#1701 - FIX: Correct BOLD-T1w registration description if DoF != 9

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

#1701 - FIX: Correct BOLD-T1w registration description if DoF != 9

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

#1698 - Reports: "get zip file" button

Issue - State: open - Opened by oesteban almost 5 years ago - 2 comments
Labels: reports, impact: high, effort: medium

#1650 - Permission issue running with podman

Issue - State: closed - Opened by crcox about 5 years ago - 8 comments

#1650 - Permission issue running with podman

Issue - State: closed - Opened by crcox about 5 years ago - 8 comments

#1621 - CI: Check all versions with better diagnostic messages

Pull Request - State: closed - Opened by effigies about 5 years ago - 17 comments

#1621 - CI: Check all versions with better diagnostic messages

Pull Request - State: closed - Opened by effigies about 5 years ago - 17 comments

#1614 - CI: Reduce pointless expenditures

Pull Request - State: closed - Opened by effigies about 5 years ago

#1614 - CI: Reduce pointless expenditures

Pull Request - State: closed - Opened by effigies about 5 years ago

#1572 - Lesion masks in the input directory result in a crash triggered by bids-validator.

Issue - State: closed - Opened by danlurie over 5 years ago - 2 comments
Labels: documentation, impact: high, effort: low

#1535 - Replace `mcflirt` with `3dVolreg`

Issue - State: open - Opened by chrisgorgo over 5 years ago - 3 comments
Labels: feature, impact: high, effort: medium, blocked

#1524 - Add a page describing how to interpret visual reports

Issue - State: closed - Opened by chrisgorgo over 5 years ago - 1 comment
Labels: documentation, help wanted

#1443 - [MRG] FIX: Output NaN columns for CompCor on failure

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

#1443 - [MRG] FIX: Output NaN columns for CompCor on failure

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

#1343 - ENH: Conform confound regressor names to Derivatives RC2

Pull Request - State: closed - Opened by effigies over 5 years ago - 6 comments

#1343 - ENH: Conform confound regressor names to Derivatives RC2

Pull Request - State: closed - Opened by effigies over 5 years ago - 6 comments

#1310 - Brief boilerplate

Issue - State: open - Opened by oesteban almost 6 years ago
Labels: feature, reports, impact: low, help wanted, effort: medium

#1300 - Crash on AROMA if all ICs are classified as motion

Issue - State: closed - Opened by andersonwinkler almost 6 years ago - 27 comments
Labels: bug, confounds

#1288 - DOC: Note GIFTI surface alignment

Pull Request - State: closed - Opened by effigies almost 6 years ago - 1 comment

#1288 - DOC: Note GIFTI surface alignment

Pull Request - State: closed - Opened by effigies almost 6 years ago - 1 comment

#1222 - Running fmriprep docker image from XNAT with --fs-no-reconall option

Issue - State: closed - Opened by stefanpsz almost 6 years ago - 7 comments
Labels: question, freesurfer

#1205 - Allow choosing --aroma-melodic-dimensionality for each functional scan

Issue - State: closed - Opened by czarrar almost 6 years ago - 2 comments
Labels: confounds

#1195 - [DOC] Additions to include before responding to reviews of the pre-print

Pull Request - State: closed - Opened by oesteban about 6 years ago - 4 comments

#1179 - PIN: pybids 0.6.3

Pull Request - State: closed - Opened by effigies about 6 years ago - 3 comments

#1179 - PIN: pybids 0.6.3

Pull Request - State: closed - Opened by effigies about 6 years ago - 3 comments

#1142 - Mislabeled confounds in reports

Issue - State: closed - Opened by chrisgorgo about 6 years ago
Labels: bug, reports, confounds

#1119 - Generate carpetplots even if MNI is not one of the output spaces

Issue - State: closed - Opened by oesteban about 6 years ago - 7 comments
Labels: confounds, impact: high, effort: high

#1115 - RF: Create T1-MNI normalization workflow

Pull Request - State: closed - Opened by effigies about 6 years ago - 6 comments

#1115 - RF: Create T1-MNI normalization workflow

Pull Request - State: closed - Opened by effigies about 6 years ago - 6 comments

#1010 - Multi-echo: replace CompCor with ME-ICA

Issue - State: closed - Opened by oesteban over 6 years ago - 20 comments
Labels: potential hackathon project, help wanted, confounds, me-epi, multiecho

#842 - [WIP] ENH: Conform offsets, relative to center-of-mass

Pull Request - State: closed - Opened by effigies over 6 years ago - 5 comments

#842 - [WIP] ENH: Conform offsets, relative to center-of-mass

Pull Request - State: closed - Opened by effigies over 6 years ago - 5 comments

#790 - FreeSurfer reconall failures processing Talairach

Issue - State: closed - Opened by oesteban over 6 years ago - 5 comments
Labels: bug

#790 - FreeSurfer reconall failures processing Talairach

Issue - State: closed - Opened by oesteban over 6 years ago - 5 comments
Labels: bug

#755 - Running only functionals

Issue - State: open - Opened by oesteban over 6 years ago - 50 comments
Labels: feature, impact: high, effort: high

#593 - [WIP] FIX: aCompCor volume

Pull Request - State: closed - Opened by effigies almost 7 years ago

#593 - [WIP] FIX: aCompCor volume

Pull Request - State: closed - Opened by effigies almost 7 years ago

#326 - Add preprocessing of cardiac and respiratory data

Issue - State: open - Opened by chrisgorgo over 7 years ago - 3 comments
Labels: feature, potential hackathon project, confounds

GitHub / nipreps/fmriprep issues and pull requests