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‎.codespellrc

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[codespell]
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skip = .git,*.pdf,*.svg,external
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# nd,nam - import module short
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# fith - oddness coming from AFNI
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# whos - smth used in matlab things
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# SMAL - Stanford CNI MRS Library
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# Suh - name
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# noo,crasher - field/var name used
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# Reson - short journal name
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# ALS, FWE - neuroimaging specific abbrevs
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# Comision - foreign word used
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ignore-words-list = te,inport,objekt,jist,nd,hel,inout,fith,whos,fot,ue,shs,smal,nam,filetest,suh,noo,reson,als,fwe,crasher,comision

‎.git-blame-ignore-revs

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# Commits with messages like "STY: black" or "run black"
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# Wed Apr 5 14:01:05 2023 -0400 - effigies@gmail.com - STY: black [ignore-rev]
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# Wed Sep 14 14:12:07 2022 -0400 - mathiasg@stanford.edu - STY: Black
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# Tue Apr 19 14:09:31 2022 -0400 - markiewicz@stanford.edu - STY: black [ignore-rev]
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# Fri Apr 15 06:59:48 2022 -0700 - markiewicz@stanford.edu - STY: black [ignore-rev]
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# Fri Apr 8 21:34:43 2022 -0400 - markiewicz@stanford.edu - STY: black [ignore-rev]
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# Sun Apr 3 10:27:07 2022 -0400 - markiewicz@stanford.edu - STY: black [ignore-rev]
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# Sat Apr 2 21:32:56 2022 -0400 - markiewicz@stanford.edu - STY: black [ignore-rev]
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# Sat Apr 2 12:49:15 2022 -0400 - markiewicz@stanford.edu - STY/TEST: Make specs and run black [ignore-rev]
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# Sun Mar 20 21:19:39 2022 -0400 - markiewicz@stanford.edu - STY: black [ignore-rev]
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87cc1b54981113024ec3fd594881f72cf67513fb
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# Wed Dec 8 17:02:09 2021 -0500 - markiewicz@stanford.edu - STY: black [ignore-rev]
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5ac2f18ac116832d81a13f0c83e0a6aeda1457cf
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# Thu Dec 2 09:30:42 2021 -0500 - markiewicz@stanford.edu - STY: black
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ee50279ebf061a70ff502e7d2e51385b285cfda4
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# Tue Oct 26 11:18:02 2021 +0200 - code@oscaresteban.es - sty: run black
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5d9adbbb77b7047b9b47cd2fa079dee0094cfc91
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# Wed Oct 20 12:07:15 2021 +0200 - fabio.bernardoni@uniklinikum-dresden.de - run black on the preprocess.py file to improve formatting
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674e9b0eeca082efb5322b61fea57ee89a3e4a24
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# Wed Oct 13 16:08:23 2021 -0400 - markiewicz@stanford.edu - ENH: Add expected steps for FreeSurfer 7 recon-all (#3389)
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# Wed Oct 13 14:26:48 2021 -0400 - markiewicz@stanford.edu - STY: black
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# Wed Sep 29 16:53:54 2021 +0200 - code@oscaresteban.es - sty: run black on affected files
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# Thu Jun 24 17:43:22 2021 +0200 - code@oscaresteban.es - sty: run black
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# Thu Sep 23 08:56:28 2021 -0400 - markiewicz@stanford.edu - STY: black
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# Fri Apr 30 17:19:55 2021 -0400 - markiewicz@stanford.edu - STY: black
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# Fri Apr 30 16:50:00 2021 -0400 - markiewicz@stanford.edu - STY: black
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# Thu Apr 1 12:26:08 2021 -0400 - markiewicz@stanford.edu - STY: black
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# Thu Dec 3 09:24:05 2020 +1100 - tom.g.close@gmail.com - run black over touched files
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# Fri Aug 14 17:15:15 2020 -0400 - markiewicz@stanford.edu - STY: Black
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# Sat Mar 14 12:44:20 2020 -0400 - markiewicz@stanford.edu - STY: black
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# Sun Mar 8 15:05:28 2020 +0100 - 3453485+daniel-ge@users.noreply.github.com - FIX: get length of generator + STY: Black
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# Wed Mar 4 16:30:39 2020 -0500 - markiewicz@stanford.edu - STY: black
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# Thu Feb 27 15:08:42 2020 -0800 - code@oscaresteban.es - sty: black
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# Thu Jan 2 11:29:05 2020 -0800 - code@oscaresteban.es - sty: black
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# Sun Dec 29 17:47:51 2019 -0800 - code@oscaresteban.es - sty: black
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# Thu Jan 2 11:29:05 2020 -0800 - code@oscaresteban.es - sty: black
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# Sun Dec 29 17:47:51 2019 -0800 - code@oscaresteban.es - sty: black
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# Thu Dec 19 09:22:22 2019 -0500 - markiewicz@stanford.edu - STY: Black
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# Thu Dec 19 15:51:11 2019 -0500 - markiewicz@stanford.edu - STY: Black
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# Fri Nov 15 14:38:10 2019 -0500 - steve@steventilley.com - run black
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# Fri Nov 15 14:34:03 2019 -0500 - steve@steventilley.com - run black
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# Thu Nov 14 11:14:51 2019 -0500 - markiewicz@stanford.edu - Merge pull request #3096 from effigies/sty/black
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# Thu Nov 14 09:15:20 2019 -0500 - markiewicz@stanford.edu - STY: Black setup.py
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# Thu Nov 14 09:14:38 2019 -0500 - markiewicz@stanford.edu - STY: Black for tools/
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# Wed Nov 13 23:41:15 2019 -0500 - markiewicz@stanford.edu - STY: Black
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# Tue Nov 12 09:43:34 2019 -0500 - markiewicz@stanford.edu - STY: Black files pre-merge
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‎.github/workflows/codespell.yml

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---
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name: Codespell
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on:
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push:
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branches: [master]
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pull_request:
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branches: [master]
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jobs:
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codespell:
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name: Check for spelling errors
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Codespell
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uses: codespell-project/actions-codespell@v1

‎.github/workflows/tests.yml

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depends: REQUIREMENTS
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deb-depends: true
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nipype-extras: doc,tests,profiler,duecredit,ssh
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- os: ubuntu-20.04
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python-version: 3.8
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check: test
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pip-flags: ''
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depends: NUMPY123
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deb-depends: true
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nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
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# - os: ubuntu-20.04
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# python-version: 3.8
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# check: test
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# pip-flags: ''
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# depends: NUMPY123
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# deb-depends: true
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# nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
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env:
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DEPENDS: ${{ matrix.depends }}
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‎.gitignore

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venv/
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venv/

‎.pre-commit-config.yaml

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# See https://pre-commit.com/hooks.html for more hooks
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v3.4.0
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rev: v4.4.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files
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- repo: https://github.com/psf/black
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rev: 23.3.0
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‎.zenodo.json

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{
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"name": "Yvernault, Benjamin"
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},
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{
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"name": "Hamalainen, Carlo",
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"orcid": "0000-0001-7655-3830"
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},
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{
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"affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
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"name": "Christian, Horea",
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"orcid": "0000-0001-7037-2449"
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},
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{
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"name": "Hamalainen, Carlo",
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"orcid": "0000-0001-7655-3830"
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},
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{
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"affiliation": "Stanford University",
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"name": "Ćirić , Rastko",
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"name": "Dias, Maria de Fatima",
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"orcid": "0000-0001-8878-1750"
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},
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{
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"name": "Moloney, Brendan"
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},
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{
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"affiliation": "Otto-von-Guericke-University Magdeburg, Germany",
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"affiliation": "Child Mind Institute",
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"name": "Giavasis, Steven"
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{
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},
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"affiliation": "SRI International",
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},
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{
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"affiliation": "CEA",
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"name": "Papadopoulos Orfanos, Dimitri",
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"orcid": "0000-0002-1242-8990"
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},
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{
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"name": "Bannert, Michael M.",
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‎Makefile

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zipdoc: html
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zip documentation.zip doc/_build/html
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.git-blame-ignore-revs: .git/HEAD
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git log --grep "\[ignore-rev\]\|STY: black\|run black" -i --pretty=format:"# %ad - %ae - %s%n%H" > .git-blame-ignore-revs
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echo >> .git-blame-ignore-revs
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‎doc/changelog/0.X.X-changelog.rst

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* ENH: Generate Dockerfiles with neurodocker (https://github.com/nipy/nipype/pull/2202)
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* ENH: FLAIR options for recon-all (https://github.com/nipy/nipype/pull/2279)
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* ENH: Config option for setting maxtasksperchild when multiprocessing (https://github.com/nipy/nipype/pull/2284)
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* FIX: Testing maintainance and improvements (https://github.com/nipy/nipype/pull/2252)
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* FIX: Testing maintenance and improvements (https://github.com/nipy/nipype/pull/2252)
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* ENH: Add elapsed_time and final metric_value to ants.Registration (https://github.com/nipy/nipype/pull/1985)
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* ENH: Improve terminal_output feature (https://github.com/nipy/nipype/pull/2209)
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* ENH: Simple interface to FSL std2imgcoords (https://github.com/nipy/nipype/pull/2209, prev #1398)
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* ENH: Add cosine-basis high-pass-filter to CompCor, allow skip of initial volumes (https://github.com/nipy/nipype/pull/2107, https://github.com/nipy/nipype/pull/#2122)
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* FIX: Catch more dcm2niix DTI conversions (https://github.com/nipy/nipype/pull/2110)
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* FIX: Retrieve aseg + wmparc stats properly (https://github.com/nipy/nipype/pull/2117)
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* ENH: ANTs MeasureImageSimilarity Inteface (https://github.com/nipy/nipype/pull/2128)
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* ENH: ANTs MeasureImageSimilarity Interface (https://github.com/nipy/nipype/pull/2128)
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* FIX: CompCor filter_basis of correct size, pre-filter column headers (https://github.com/nipy/nipype/pull/2136, https://github.com/nipy/nipype/pull/2138)
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* ENH: FreeSurfer lta_convert and mri_coreg interfaces (https://github.com/nipy/nipype/pull/2140, https://github.com/nipy/nipype/pull/2172)
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* ENH: Speed up S3DataGrabber (https://github.com/nipy/nipype/pull/2143)
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Release 0.10.0 (October 10, 2014)
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=================================
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* ENH: New miscelaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
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* ENH: New miscellaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
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to enable parallel processing of very large images.
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* ENH: Updated FSL interfaces: BEDPOSTX and XFibres, former interfaces are still
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versions of BEDPOSTX: BEDPOSTXGPU, BEDPOSTX5GPU, and BEDPOSTX4GPU
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* ENH: Added experimental support for MIPAV algorithms thorugh JIST plugins
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* ENH: Added experimental support for MIPAV algorithms through JIST plugins
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* ENH: New dipy interfaces: Denoise, Resample
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* ENH: New Freesurfer interfaces: Tkregister2 (for conversion of fsl style matrices to freesurfer format), MRIPretess
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* ENH: New FSL interfaces: WarpPoints, WarpPointsToStd, EpiReg, ProbTrackX2, WarpUtils, ConvertWarp
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* ENH: New miscelaneous interfaces: AddCSVRow, NormalizeProbabilityMapSet, AddNoise
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* ENH: New miscellaneous interfaces: AddCSVRow, NormalizeProbabilityMapSet, AddNoise
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* ENH: New AFNI interfaces: Eval, Means, SVMTest, SVMTrain
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* ENH: FUGUE interface has been refactored to use the name_template system, 3 examples
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* API: Added max_jobs parameter to plugin_args. limits the number of jobs
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‎doc/changelog/1.X.X-changelog.rst

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1.8.6 (April 05, 2023)
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======================
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Bug-fix release in the 1.8.x series.
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* FIX: Update dcmstack interface for Py3 / newer pydicom (https://github.com/nipy/nipype/pull/3541)
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* FIX: NiBabel 5, and NetworkX 3 and DIPY 1.6 compatibility (https://github.com/nipy/nipype/pull/3538)
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* FIX: Check for non-mandatory output in DWIBiasCorrect (https://github.com/nipy/nipype/pull/3523)
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* FIX: Removed leftover debug print statement in FEAT class (https://github.com/nipy/nipype/pull/3521)
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* DOC: Fix a few more typos (https://github.com/nipy/nipype/pull/3516)
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* DOC: Fix typos found by codespell (https://github.com/nipy/nipype/pull/3512)
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* CI: Drop nipy tests until a fixed nipy is released (https://github.com/nipy/nipype/pull/3559)
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* CI: Disable nipy tests generally, re-add with max numpy (https://github.com/nipy/nipype/pull/3532)
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* CI: GitHub Workflows security hardening (https://github.com/nipy/nipype/pull/3519)
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* CI: Allow tutorial test cancellation (https://github.com/nipy/nipype/pull/3514)
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==========================
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* FIX: ANTS LaplacianThickness cmdline opts fixed up (https://github.com/nipy/nipype/pull/2846)
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* FIX: Resolve LinAlgError during SVD (https://github.com/nipy/nipype/pull/2838)
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* ENH: Add interfaces wrapping DIPY worflows (https://github.com/nipy/nipype/pull/2830)
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* ENH: Add interfaces wrapping DIPY workflows (https://github.com/nipy/nipype/pull/2830)
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* ENH: Update BIDSDataGrabber for pybids 0.7 (https://github.com/nipy/nipype/pull/2737)
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* ENH: Add FSL `eddy_quad` interface (https://github.com/nipy/nipype/pull/2825)
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* ENH: Support tckgen -select in MRtrix3 v3+ (https://github.com/nipy/nipype/pull/2823)

‎doc/interfaces.rst

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:Release: |version|
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Previous versions: `1.8.6 <http://nipype.readthedocs.io/en/1.8.6/>`_ `1.8.5 <http://nipype.readthedocs.io/en/1.8.5/>`_
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---------

‎nipype/__init__.py

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‎nipype/algorithms/icc.py

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# ICC(3,1) = (mean square subject - mean square error) /
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‎nipype/info.py

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# nipype version information
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# Remove .dev0 for release
8-
__version__ = "1.8.6.dev0"
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__version__ = "1.8.7.dev0"
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def get_nipype_gitversion():

‎nipype/interfaces/afni/base.py

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,9 @@
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from sys import platform
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import shutil
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9-
from ... import logging, LooseVersion
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from looseversion import LooseVersion
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from ... import logging
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from ...utils.filemanip import split_filename, fname_presuffix
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from ..base import (
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CommandLine,

‎nipype/interfaces/ants/registration.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -865,7 +865,7 @@ class Registration(ANTSCommand):
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--write-composite-transform 0'
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One can use multiple similarity metrics in a single registration stage.The Node below first
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performs a linear registation using only the Mutual Information ('Mattes')-metric.
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performs a linear registration using only the Mutual Information ('Mattes')-metric.
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In a second stage, it performs a non-linear registration ('Syn') using both a
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Mutual Information and a local cross-correlation ('CC')-metric. Both metrics are weighted
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equally ('metric_weight' is .5 for both). The Mutual Information- metric uses 32 bins.

‎nipype/interfaces/ants/segmentation.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1009,10 +1009,10 @@ def _run_interface(self, runtime, correct_return_codes=(0,)):
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runtime = super(BrainExtraction, self)._run_interface(runtime)
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# Still, double-check if it didn't found N4
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if "we cant find" in runtime.stdout:
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if "we can't find" in runtime.stdout:
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for line in runtime.stdout.split("\n"):
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if line.strip().startswith("we cant find"):
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tool = line.strip().replace("we cant find the", "").split(" ")[0]
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if line.strip().startswith("we can't find"):
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tool = line.strip().replace("we can't find the", "").split(" ")[0]
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break
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errmsg = (

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