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spm_2_bids

convert SPM output to BIDS derivatives

https://github.com/cpp-lln-lab/spm_2_bids

Science Score: 67.0%

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    CITATION.cff file
    Found CITATION.cff file
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    Found codemeta.json file
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    Found .zenodo.json file
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    DOI references
    Found 3 DOI reference(s) in README
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    Links to: zenodo.org
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    Scientific vocabulary similarity
    Low similarity (7.0%) to scientific vocabulary

Keywords

bids converter matlab spm
Last synced: 6 months ago · JSON representation ·

Repository

convert SPM output to BIDS derivatives

Basic Info
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 1
  • Open Issues: 7
  • Releases: 3
Topics
bids converter matlab spm
Created over 4 years ago · Last pushed 12 months ago
Metadata Files
Readme License Citation

README.md

tests and coverage with matlab codecov DOI View spm_2_bids on File Exchange

spm2bids

Small code base to help convert the MRI spm output to a valid bids derivatives.

This code only generates the plausible BIDS derivatives filename for given file that has been preprocessed with SPM.

Most of the renaming is based on the SPM prefixes combinations.

It is configurable to adapt to new set of prefixes.

Dependencies

Can be installed with :

For MATLAB

bash make install_dev

For Octave

bash make install_dev_octave

Usage

```matlab file = 'wmsub-01desc-skullstrippedT1w.nii';

[newfilename, pth, json] = spm2_bids(file);

new_filename =

'sub-01space-IXI549Spacedesc-preproc_T1w.nii'); ```

For more see the documentation.

Owner

  • Name: Crossmodal Perception and Plasticity laboratory
  • Login: cpp-lln-lab
  • Kind: organization
  • Location: Louvain la Neuve, Belgium

Citation (CITATION.cff) 

cff-version: 1.2.0

title: "spm_2_bids"

version: 0.3.0

abstract: Toolbox to convert SPM output files to valid BIDS derivatives.

message: "If you use this software, please cite it as below."

repository-code: "https://github.com/cpp-lln-lab/spm_2_bids.git"

contact:
  - affiliation: "Université catholique de Louvain"
    email: remi.gau@uclouvain.be
    family-names: Gau
    given-names: Rémi

authors:
- family-names: "Gau"
  given-names: "Rémi"
  orcid: "https://orcid.org/0000-0002-1535-9767"
  affiliation: "Université catholique de Louvain"

license: GPL-3.0

keywords:
  - BIDS
  - brain imaging data structure
  - neuroimaging
  - converter
  - MRI
  - MATLAB
  - Octave
  - SPM

GitHub Events

Total
  • Delete event: 3
  • Issue comment event: 13
  • Push event: 7
  • Pull request event: 10
  • Pull request review event: 4
  • Create event: 7
Last Year
  • Delete event: 3
  • Issue comment event: 13
  • Push event: 7
  • Pull request event: 10
  • Pull request review event: 4
  • Create event: 7

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: 11 days
  • Total issue authors: 0
  • Total pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 1.33
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 6
Past Year
  • Issues: 0
  • Pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: 11 days
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 1.33
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 6
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Top Authors
Issue Authors
Pull Request Authors
  • dependabot[bot] (13)
  • pre-commit-ci[bot] (5)
  • Remi-Gau (5)
  • FeHoff (1)
Top Labels
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dependencies (13) github_actions (13)

Dependencies

docs/requirements.txt pypi
  • Sphinx *
  • myst-parser *
  • rstcheck *
  • sphinx-copybutton *
  • sphinx_rtd_theme *
  • sphinxcontrib-matlabdomain *
requirements.txt pypi
  • jinja2 *
  • jupyterlab *
  • miss_hit ==0.9.33
  • octave_kernel *
  • pre-commit *
.github/workflows/run_tests_matlab.yml actions
  • actions/checkout v3 composite
  • codecov/codecov-action v3 composite
  • matlab-actions/run-command v1.1.2 composite
  • matlab-actions/setup-matlab v1.2.3 composite
.github/workflows/run_tests_octave.yml actions
  • actions/checkout v3 composite
  • joergbrech/moxunit-action v1.2.0 composite
.github/workflows/validate_cff.yml actions
  • actions/checkout v3 composite
  • citation-file-format/cffconvert-github-action 2.0.0 composite
binder/environment.yml conda
  • octave_kernel