Ecosyste.ms: Issues

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GitHub / nipy/nipype issues and pull requests

#3595 - Error in Mrtrix3's DWIPreproc

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

#3594 - dcm2niix - Do consider exit 1 to be an error

Pull Request - State: open - Opened by yarikoptic over 1 year ago - 4 comments

#3593 - FSL FAST output PATH problems

Issue - State: open - Opened by Ede1994 over 1 year ago

#3592 - dcm2niix node does not error out whenever dcm2niix exits with 1

Issue - State: open - Opened by yarikoptic over 1 year ago - 6 comments

#3591 - ANTSRegistration() error formatting command line argument 'transforms'

Issue - State: closed - Opened by ramroomh over 1 year ago - 3 comments

#3590 - MNT: Replace deprecated locale.getdefaultlocale

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

#3589 - CI: Test on Python 3.11

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

#3588 - MNT: Require Python 3.8+, auto-upgrade syntax

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

#3587 - FIX: Test failures

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

#3586 - DataSink: Add possibility to replace regex match with another regex match in

Issue - State: open - Opened by JohannesWiesner over 1 year ago - 1 comment
Labels: enhancement

#3583 - Fix bugs with `fsl_out=True` and `lta_out=True`

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

#3582 - fsl_out=True does not work for freesurfer.TKregister2

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

#3581 - Error using fsl.EDDY

Issue - State: open - Opened by DavidBarriere over 1 year ago - 2 comments

#3580 - Error when running mri_convert from pycham

Issue - State: open - Opened by MattP1994 over 1 year ago - 1 comment
Labels: faq

#3579 - dcm2niix converted_files duplicate entry

Issue - State: closed - Opened by mauriliogenovese over 1 year ago - 1 comment

#3578 - Issue running nipype.interfaces.spm

Issue - State: closed - Opened by nmossazg12 over 1 year ago - 5 comments

#3577 - add contrast outputs for EstimatedModel

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

#3576 - Missing contrast outputs for SPM EstimateModel

Issue - State: closed - Opened by manuegrx over 1 year ago - 1 comment

#3575 - [REF] io.open() → open()

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

#3574 - Can't use in Jypeter notebook

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

#3573 - Mideface integration

Issue - State: open - Opened by vferat over 1 year ago - 1 comment

#3572 - MapNode and Workflow.connect show unexpected interaction behavior

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

#3571 - FIX: update self.inputs.optimization in outputs for GTMPVC

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

#3570 - optmization_schema error in GTMPVC - petsurfer interface

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

#3569 - Normalize and Normalize12 use "estimate" and not "est" as the jobtype

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

#3568 - STY: Remove duplicated trait in EddyOutputSpec

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

#3567 - repeated output_spec in `fsl.epi.eddy`

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

#3566 - McFlirt incorrect output filename expected

Issue - State: open - Opened by stebo85 over 1 year ago - 3 comments

#3565 - Reconsider CI management

Issue - State: open - Opened by effigies over 1 year ago - 5 comments

#3563 - `locale.getdefaultlocale()` is deprecated

Issue - State: closed - Opened by jwodder over 1 year ago - 1 comment

#3562 - Can not specify own_atlas in CAT12Segment

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

#3561 - [REF] Stop using deprecated import internally

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

#3560 - REL: 1.8.6

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

#3559 - CI: Drop nipy tests until a fixed nipy is released

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

#3558 - [ENH] Enable SPM voxel-based FDR

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

#3555 - Error when importing dipy interfaces

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

#3554 - Issue 3553 add mvecs to dcm2niix

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

#3553 - Dcm2niix interface: Add `mvecs` output

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

#3552 - Getting AFNI version in a simpler way

Issue - State: open - Opened by mrneont over 1 year ago - 3 comments

#3551 - Support for PET-BIDS

Issue - State: open - Opened by jrdalenberg over 1 year ago - 1 comment

#3550 - Add github action to shellcheck master on push and PRs

Pull Request - State: open - Opened by yarikoptic over 1 year ago - 2 comments

#3549 - codespell: config, workflow, typos fixed

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

#3548 - [FIX] update merge_imgs input type of dcm2niix Node

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

#3547 - Allow use of glob patterns in in_files for fsl.Merge

Issue - State: open - Opened by somso2e over 1 year ago - 1 comment

#3543 - AttributeError: module 'networkx' has no attribute 'to_scipy_sparse_matrix'

Issue - State: closed - Opened by mikiminachx almost 2 years ago - 2 comments

#3542 - Workflow's nodes' output directories point to TMPDIR instead of base_dir

Issue - State: open - Opened by tsalo almost 2 years ago - 7 comments

#3541 - BF: Update dcmstack interface for Py3 / newer pydicom

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

#3540 - One test fails in network sandbox on patched `=nipype-1.8.4`

Issue - State: closed - Opened by TheChymera almost 2 years ago - 2 comments

#3539 - 18 test failures (`IndexError` and `AssertionError`) on `1.8.4`

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

#3538 - FIX: NiBabel 5, and NetworkX 3 and DIPY 1.6 compatibility

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

#3537 - Build failure with nibabel 5.0

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

#3536 - Running into TraitError on JSON load.

Issue - State: closed - Opened by TheChymera almost 2 years ago - 4 comments

#3535 - Tentative `=>networkx-3.0` support

Pull Request - State: closed - Opened by TheChymera almost 2 years ago - 4 comments

#3534 - ProbTrackXBaseInputSpec random_seed type error

Issue - State: open - Opened by lamaresh almost 2 years ago

#3533 - dcm2niix -m default

Issue - State: open - Opened by lamaresh almost 2 years ago - 2 comments

#3532 - CI: Disable nipy tests generally, re-add with max numpy

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

#3531 - ModuleNotFoundError: No module named 'nipype.workflows.fmri' & 5 failed tests

Issue - State: open - Opened by dvartak over 4 years ago - 2 comments

#3530 - networkx >= 3.0 unsupported

Issue - State: closed - Opened by thomas-vincent almost 2 years ago - 3 comments

#3529 - [ENH] Issue 3345: Adding FreeSurfer longitudinal interfaces

Pull Request - State: closed - Opened by l-espana almost 2 years ago - 16 comments

#3528 - BUG: Reading serialized event requires conversion of dates

Pull Request - State: closed - Opened by hjmjohnson about 2 years ago - 4 comments
Labels: bug

#3527 - generate_gantt_chart fails to convert strings to datetime objects

Issue - State: closed - Opened by hjmjohnson about 2 years ago - 4 comments
Labels: bug, help-wanted

#3526 - Remove `dot` dependency

Issue - State: open - Opened by mgxd about 2 years ago - 1 comment

#3525 - N4BiasFieldCorrection issues

Issue - State: open - Opened by Yueup about 2 years ago

#3524 - Numpy Dependency Issue When Running `make tests`

Issue - State: closed - Opened by awstanton about 2 years ago - 3 comments

#3523 - FIX: Check for non-mandatory output in DWIBiasCorrect

Pull Request - State: closed - Opened by MatthieuJoulot about 2 years ago - 6 comments

#3522 - [CI] python-version should be a string, not a float

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

#3521 - Removed leftover debug print statement in FEAT class

Pull Request - State: closed - Opened by somso2e about 2 years ago - 2 comments

#3520 - Unnecessary print used in the FEAT class

Issue - State: closed - Opened by somso2e about 2 years ago - 1 comment

#3519 - GitHub Workflows security hardening

Pull Request - State: closed - Opened by sashashura about 2 years ago - 5 comments

#3518 - spm.Normalize12() issue. Mutually exclusive fields, aren't ?

Issue - State: open - Opened by Brainarea about 2 years ago - 1 comment

#3517 - DockerHub pushes are failing on tags

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

#3516 - DOC: Fix a few more typos

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

#3515 - DOC: Main figure is small in recent builds

Issue - State: open - Opened by effigies about 2 years ago
Labels: doc, help-wanted

#3514 - CI: Allow tutorial test cancellation

Pull Request - State: closed - Opened by mgxd about 2 years ago - 1 comment

#3513 - CI: Set up build-test-deploy workflow on GHA

Pull Request - State: closed - Opened by effigies about 2 years ago - 1 comment

#3512 - DOC: Fix typos found by codespell

Pull Request - State: closed - Opened by DimitriPapadopoulos about 2 years ago - 1 comment

#3511 - REL: 1.8.5

Pull Request - State: closed - Opened by effigies about 2 years ago - 1 comment

#3509 - FIX: Deployed Matlab applications must not call addpath()

Pull Request - State: closed - Opened by DimitriPapadopoulos about 2 years ago - 1 comment

#3508 - ENH: Explicitly specify write_text encoding format

Pull Request - State: closed - Opened by hjmjohnson about 2 years ago - 2 comments
Labels: bug, maintenance

#3506 - FIX: Use interpolation/method in numpy.percentile as available

Pull Request - State: closed - Opened by effigies about 2 years ago - 3 comments

#3504 - MAINT: Add github action to trigger tutorials for release branches

Pull Request - State: closed - Opened by mgxd about 2 years ago - 6 comments

#3499 - reconall node error

Issue - State: open - Opened by lamaresh over 2 years ago - 1 comment

#3498 - DataSink substition does not remove substituted directory

Issue - State: open - Opened by fladd over 2 years ago - 1 comment
Labels: bug

#3497 - ModuleNotFoundError: No module named 'nipype.workflows.misc'

Issue - State: open - Opened by roya2022 over 2 years ago - 1 comment

#3496 - RFC: Change parameterize_dirs to default to False?

Issue - State: open - Opened by effigies over 2 years ago - 1 comment
Labels: discussion

#3491 - Error when running nipype-tutorial container in VScode

Issue - State: closed - Opened by yufang1039 over 2 years ago - 5 comments

#3474 - [ENH] Added some options to mrconvert's interface

Pull Request - State: closed - Opened by GalKepler over 2 years ago - 1 comment

#3467 - Missing registration options for `mri_surf2surf`

Issue - State: open - Opened by ghisvail over 2 years ago - 5 comments

#3460 - spm.Coregister() error

Issue - State: open - Opened by AnnaZhuravleva over 2 years ago - 1 comment