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Remi-GauRemi-Gau
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Merge pull request #36 from cpp-lln-lab/add_child_protection
[ENH] Add input checks to several functions
2 parents ba39937 + 0e24e40 commit 15e21bf

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‎.github/workflows/run_tests_matlab.yml

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branches:
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- dev
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- main
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- master
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pull_request:
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branches: ['*']
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schedule:
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git clone https://github.com/MOcov/MOcov.git --depth 1
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- name: Add bids-matlab
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run: |
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git clone https://github.com/bids-standard/bids-matlab.git --depth 1
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run: make install_dev
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- name: Run commands
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uses: matlab-actions/[email protected]

‎.gitignore

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.DS_Store
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*.nii
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*.json
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*.xml
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*.log
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*.asv
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*.m~
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*.mat
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*.html
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# files in the demo folder related to running the demo analysis
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# demos/roi
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atlas/visual_topography_probability_atlas/
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# test folder and dummy data
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# ignore content of the build folder of the doc
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docs/build/*
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# visual studio code stuff
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.vscode
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demos/*/*.json
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demos/*/*/*.json
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atlas/visual_topography_probability_atlas/
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demos/*/derivatives
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atlas/*.json
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#for testing
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coveragage_html
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lib/bids-matlab
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## MATLAB / OCTAVE gitignore template
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# From : https://github.com/github/gitignore/blob/master/Global/MATLAB.gitignore
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# Windows default autosave extension
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*.asv
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# OSX / *nix default autosave extension
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*.m~
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# Compiled MEX binaries (all platforms)
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*.mex*
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# Packaged app and toolbox files
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*.mlappinstall
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*.mltbx
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# Generated helpsearch folders
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helpsearch*/
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# Simulink code generation folders
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slprj/
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sccprj/
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# Matlab code generation folders
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codegen/
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# Simulink autosave extension
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*.autosave
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# Simulink cache files
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*.slxc
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# Octave session info
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octave-workspace

‎.readthedocs copy.yml

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# .readthedocs.yml
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# Read the Docs configuration file
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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# Required
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version: 2
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration: docs/source/conf.py
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builder: html
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fail_on_warning: true
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# Build documentation with MkDocs
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#mkdocs:
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# configuration: mkdocs.yml
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# Optionally build your docs in additional formats such as PDF
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formats:
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- pdf
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# Optionally set the version of Python and requirements required to build your docs
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python:
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version: 3.7
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install:
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- requirements: requirements.txt

‎CITATION.cff

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cff-version: 1.2.0
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title: "CPP ROI"
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version: v0.2.0dev
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abstract: Set of Octave and Matlab functions, demos and scripts to help manage ROIs and to play nice with BIDS datasets.
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message: "If you use this software, please cite it as below."
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repository-code: "https://github.com/cpp-lln-lab/CPP_ROI"
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contact:
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- affiliation: "Université catholique de Louvain"
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email: [email protected]
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family-names: Gau
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given-names: Rémi
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authors:
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- family-names: "Gau"
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given-names: "Rémi"
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orcid: "https://orcid.org/0000-0002-1535-9767"
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affiliation: "Université catholique de Louvain"
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- family-names: "Barilari"
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given-names: "Marco"
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orcid: "https://orcid.org/0000-0002-3313-3120"
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affiliation: "Université catholique de Louvain"
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- family-names: "Battal"
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given-names: "Ceren"
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orcid: "https://orcid.org/0000-0002-9844-7630"
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affiliation: "Université catholique de Louvain"
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- family-names: "Falagiarda"
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given-names: "Federica"
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orcid: "https://orcid.org/0000-0001-7844-1605"
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affiliation: "Université catholique de Louvain"
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license: GPL-3.0
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keywords:
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- BIDS
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- brain imaging data structure
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- neuroimaging
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- MRI
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- MATLAB
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- Octave
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- SPM
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- ROI
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- region of interest

‎Makefile

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.PHONY: clean install_dev
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clean:
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rm -rf coverage*
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rm version.txt
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install_dev:
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git clone https://github.com/bids-standard/bids-matlab.git --branch dev --depth 1 lib/bids-matlab
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version.txt: CITATION.cff
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grep -w "^version" CITATION.cff | sed "s/version: /v/g" > version.txt
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validate_cff: CITATION.cff
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cffconvert --validate

‎README.md

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# CPP ROI
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---
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## :warning:
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[![miss_hit_style](https://github.com/cpp-lln-lab/CPP_ROI/actions/workflows/miss_hit_style.yml/badge.svg)](https://github.com/cpp-lln-lab/CPP_ROI/actions/workflows/miss_hit_style.yml)
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[![miss_hit_quality](https://github.com/cpp-lln-lab/CPP_ROI/actions/workflows/miss_hit_quality.yml/badge.svg)](https://github.com/cpp-lln-lab/CPP_ROI/actions/workflows/miss_hit_quality.yml)
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[![tests and coverage with matlab](https://github.com/cpp-lln-lab/CPP_ROI/actions/workflows/run_tests_matlab.yml/badge.svg)](https://github.com/cpp-lln-lab/CPP_ROI/actions/workflows/run_tests_matlab.yml)
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[![codecov](https://codecov.io/gh/cpp-lln-lab/CPP_ROI/branch/main/graph/badge.svg?token=8IoRQtbFUV)](https://codecov.io/gh/cpp-lln-lab/CPP_ROI)
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**This code is fairly unstable and might still change.**
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So make sure you "pin" which version or commit you are using for a given
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project, if you don't want your code to break in the future.
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---
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# CPP ROI
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Set of Octave and Matlab functions, demos and scripts to help manage ROIs and to
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Fire up Octave or Matlab and type
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```matlab
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cd CPP_ROI
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% Th following adds the relevant folders to your path.
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% This needs to be done once per session (your path will not be saved)
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initCppRoi
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```
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If you are using CPP_SPM, you got nothing to do as CPP_ROI is already installed
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as a submodule, and intitialized when running `initCppSpm`.
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### Dependencies
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======= TODO
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| Dependencies | Used version |
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| ---------------------------------------------------------- | ------------ |
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| [Matlab](https://www.mathworks.com/products/matlab.html) | 20??? |
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| or [octave](https://www.gnu.org/software/octave/) | 4.? |
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| [SPM12](https://www.fil.ion.ucl.ac.uk/spm/software/spm12/) | v7487 |
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- bids-matlab (INSERT URL)
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- currently still needs some CPP_SPM function but ultimately should be
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standalone: this will most likely happen when some functions are passed to
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bids-matlab
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| Dependencies | Used version |
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| --------------------------------------------------------------- | ------------ |
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| [Matlab](https://www.mathworks.com/products/matlab.html) | 20??? |
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| or [octave](https://www.gnu.org/software/octave/) | 4.? |
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| [SPM12](https://www.fil.ion.ucl.ac.uk/spm/software/spm12/) | v7487 |
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| [bids-matlab](https://github.com/bids-standard/bids-matlab.git) | >=0.1.0 |
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- Other dependencies (MarsBar) are shipped with CPP_ROI in the `lib` folder.
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## Features
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- create ROI from probability maps
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- create ROI filenames that "BIDS-ish"
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- create ROI from atlas (see below)
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- create ROI filenames that are "BIDS-ish"
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- extract ROI with a given numerical label
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- extract ROI from one hemisphere
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<!-- add REF and URL -->
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<!-- add REF and URL -->

‎demos/roi/roi_script.m

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sphere.radius = 1; % starting radius
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specification = struct( ...
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'mask1', roiName, ...
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specification = struct('mask1', roiName, ...
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roiName = removeSpmPrefix(roiName, spm_get_defaults('realign.write.prefix'));
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roiName = removePrefix(roiName, spm_get_defaults('realign.write.prefix'));
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end

‎docs/README.md

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# Setting up sphinx to create a matlab doc
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## Set up virtual environment
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```bash
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virtualenv -p python3 cpp_spm
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source cpp_spm/bin/activate
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```
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## Quick start on the doc
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See the [sphinx doc](https://www.sphinx-doc.org/en/master/usage/quickstart.html)
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for more.
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This
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[blog post](https://medium.com/@richdayandnight/a-simple-tutorial-on-how-to-document-your-python-project-using-sphinx-and-rinohtype-177c22a15b5b)
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is also useful.
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```bash
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```
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## Setting up conf.py for matlab doc
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[matlabdomain for sphinx](https://github.com/sphinx-contrib/matlabdomain).
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extensions = [
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'sphinx.ext.autodoc']
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```
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`conf.py`) to the folder containing your matlab code:
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```
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## reStructured text markup
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reStructured text mark up primers:
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- on the [sphinx site](https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html)
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- more
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[python oriented](https://pythonhosted.org/an_example_pypi_project/sphinx.html)
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- typical doc strings templates
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- [google way](https://www.sphinx-doc.org/en/master/usage/extensions/example_google.html)
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- [numpy](https://www.sphinx-doc.org/en/master/usage/extensions/example_numpy.html#example-numpy)
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## "Templates"
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```rst
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```
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```
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## Build the documentation locally
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```
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## Build the documentation with Read the Docs
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Add a [`.readthedocs.yml`](../.readthedocs.yml) file in the root of your repo.
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details.
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You can then trigger the build of the doc by going to the
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[read the docs website](https://readthedocs.org).
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You might need to be added as a maintainer of the doc.
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The doc can be built from any branch of a repo.
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Information on how to write and build the documentation can be found in our
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[CONTRIBUTING guidelines](https://github.com/cpp-lln-lab/.github/blob/main/CONTRIBUTING.md).

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