nipy/nipype

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Workflows and interfaces for neuroimaging packages

Stars: 835
Forks: 538
Open beginner issues: 1
Indexed issues: 409
Avg merge: 1h 7m
Merged PRs (30d): 3

Dominant language: Python
License: No license data
Last GitHub push: Sep 3, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: help wanted good first issue

Beginner friendly Everything

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409 open issues indexed

FSL Eddy interface does not take a list of FWHM Open

Difficulty 2/5 1-3 hours Newbie friendliness 76/100

nipy/nipype#3767 · Opened Sep 4, 2026
Depth-first execution of nodes with an iterable as input (question) Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

nipy/nipype#3757 · 1 comment · Opened Jul 16, 2026
Improve type hints of interface classes that inherit from BaseInterface Open

Difficulty 5/5 Over a week Newbie friendliness 28/100

nipy/nipype#3741 · 1 comment · Opened Feb 9, 2026
[ENH] SPM NewSegment with SPM25 Open

Difficulty 3/5 1-2 days Newbie friendliness 64/100

nipy/nipype#3736 · 1 comment · Opened Sep 15, 2025
Error while checking node hash, forcing re-run Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nipy/nipype#3730 · Opened Jul 16, 2025
nipype.interfaces.fsl.model.Cluster: Howto get stdout results table? Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nipy/nipype#3727 · 1 comment · Opened Jun 11, 2025
Guidelines needed for gpu running interfaces Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nipy/nipype#3726 · Opened May 6, 2025
Performing an exact antsRegistrationSyN.sh command Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nipy/nipype#3711 · Opened Jan 30, 2025
Setting up PATH for nipype.interfaces.ants Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nipy/nipype#3710 · 2 comments · Opened Jan 29, 2025
No pe volumes generated by FSL Estimate Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nipy/nipype#3706 · Opened Dec 19, 2024
Normalize runtime threads in gantt chart Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

nipy/nipype#3700 · 1 reaction · Opened Nov 18, 2024
traits.trait_errors.TraitError: Each element of the 'in_files' trait of a SmoothInputSpec instance must be a pathlike object or string representing an existing file, but a value of 'xxx’ <class 'str'> was specified. Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nipy/nipype#3693 · 8 comments · Opened Oct 17, 2024
MCFLIRT naming error with FSL 6.0.7.13 Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nipy/nipype#3684 · 3 comments · Opened Sep 28, 2024
nipype.interfaces.spm.model use_vox_fdr_correction attribute error Open

question

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nipy/nipype#3669 · 2 comments · Opened Sep 10, 2024
freesurfer reconall outputs missing Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nipy/nipype#3667 · 1 comment · Opened Aug 28, 2024
[ENH] Interface for tcksift2 Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nipy/nipype#3666 · Opened Aug 12, 2024
[ENH] Interface for MRTrix's tcksift Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nipy/nipype#3665 · Opened Aug 12, 2024
Must Obtain Valid Freesurfer License Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nipy/nipype#3664 · 1 comment · Opened Aug 2, 2024
Broken link to "self-assessment" on Quickstart wiki page Open

Difficulty 1/5 Under an hour Newbie friendliness 45/100

nipy/nipype#3660 · Opened Jul 23, 2024
nipype.interfaces.cat12.preprocess.CAT12Segment FileNotFoundError: No such file or directory '/[....]/catROIs_T1w.xml' for output 'label_rois' of a CAT12Segment interface Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nipy/nipype#3654 · 5 comments · Opened Jun 6, 2024
nipype.interfaces.cat12.preprocess.CAT12Segment does not accept compressed `.nii.gz` files Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nipy/nipype#3653 · 9 comments · Opened Jun 6, 2024
AttributeError: 'PythonQtStdOutRedirect' object has no attribute 'fileno' Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

nipy/nipype#3649 · 1 comment · Opened May 23, 2024
[ENH] String Interpolation Open

Difficulty 5/5 Over a week Newbie friendliness 45/100

nipy/nipype#3646 · Opened Apr 15, 2024
Set number of threads in MRTrix3's interfaces Open

nipy/nipype#3645 · 2 comments · 1 assignee · Opened Apr 11, 2024
Request: flag to glob.glob to search recursively for template in Selectfiles() Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nipy/nipype#3644 · Opened Apr 9, 2024
Prov dependency Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nipy/nipype#3643 · 2 comments · Opened Apr 3, 2024
AFNI Zeropad out_file undefined Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nipy/nipype#3640 · 1 comment · Opened Mar 20, 2024
dcm2niix interface default output file orientation error Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

nipy/nipype#3625 · Opened Dec 29, 2023
Request for Flexible Factorial Support in nipype.interfaces.spm Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nipy/nipype#3619 · Opened Dec 10, 2023
"TraitError: Each element of the 'in_files' trait of a SmoothInputSpec instance must be a pathlike object or string representing an existing file Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nipy/nipype#3616 · 2 comments · Opened Nov 29, 2023
FSL FAST output PATH problems Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nipy/nipype#3593 · Opened Jul 25, 2023
dcm2niix node does not error out whenever dcm2niix exits with 1 Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nipy/nipype#3592 · 6 comments · Opened Jul 21, 2023
DataSink: Add possibility to replace regex match with another regex match in Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 42/100

nipy/nipype#3586 · 1 comment · Opened Jul 5, 2023
nipype/nipype/interfaces/fsl /preprocess.py - FAST other_priors Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

nipy/nipype#3585 · Opened Jul 3, 2023
nipype.algorithms.modelgen.SpecifySPMModel: unclear input format for realignment_parameters Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

nipy/nipype#3584 · 1 comment · Opened Jun 30, 2023
Error using fsl.EDDY Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nipy/nipype#3581 · 2 comments · Opened Jun 21, 2023
Error when running mri_convert from pycham Open

faq

Difficulty 4/5 3-5 days Newbie friendliness 20/100

nipy/nipype#3580 · 1 comment · Opened Jun 15, 2023
Mideface integration Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nipy/nipype#3573 · 1 comment · Opened May 19, 2023
McFlirt incorrect output filename expected Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

nipy/nipype#3566 · 3 comments · Opened Apr 26, 2023
Reconsider CI management Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nipy/nipype#3565 · 5 comments · Opened Apr 18, 2023
nipype.algorithms.modelgen.SpecifySPMModel can't handle relative filepaths when being inside a node Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nipy/nipype#3564 · 4 comments · Opened Apr 14, 2023
Can not specify own_atlas in CAT12Segment Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

nipy/nipype#3562 · Opened Apr 7, 2023
dcm2niix interface doesn't list cropped files in output Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nipy/nipype#3557 · Opened Apr 2, 2023
Getting AFNI version in a simpler way Open

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

nipy/nipype#3552 · 3 comments · 1 reaction · Opened Mar 23, 2023
Support for PET-BIDS Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nipy/nipype#3551 · 1 comment · Opened Mar 14, 2023
Allow use of glob patterns in in_files for fsl.Merge Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nipy/nipype#3547 · 1 comment · Opened Mar 3, 2023
Setting an input on a MapNode within a Workflow has no effect Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nipy/nipype#3546 · Opened Mar 3, 2023
FSL MultipleRegressDesign sorts regressors, causing unexpected ordering of regressors/contrasts. Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nipy/nipype#3544 · Opened Feb 8, 2023
Workflow's nodes' output directories point to TMPDIR instead of base_dir Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nipy/nipype#3542 · 7 comments · Opened Feb 1, 2023
ProbTrackXBaseInputSpec random_seed type error Open

Difficulty 2/5 1-3 hours Newbie friendliness 62/100

nipy/nipype#3534 · Opened Jan 19, 2023

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