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Remi-GauRemi-Gau
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Merge pull request #16 from Remi-Gau/metadata
[ENH] Add metadata information and posibilty to print Mapping
2 parents 140b0e1 + 3f1ce76 commit 1c42276

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‎.gitignore‎

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*DS_Store
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*.m~
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*octave-workspace
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.vscode
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*.json
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env/
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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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‎CITATION.cff‎

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title: "spm_2_bids"
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version: v0.1.0dev
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version: 0.1.0dev
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abstract: Toolbox to convert SPM output files to valid BIDS derivatives.
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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/spm_2_bids.git"
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contact:
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- BIDS
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- brain imaging data structure
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- neuroimaging
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- converter
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- MRI
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- MATLAB
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- Octave

‎Makefile‎

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install_dev: lib/bids-matlab lib/JSONio
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lib/bids-matlab:
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git clone https://github.com/bids-standard/bids-matlab.git lib/bids-matlab
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cd lib/bids-matlab && git checkout dev
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git clone https://github.com/bids-standard/bids-matlab.git --branch dev lib/bids-matlab
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lib/JSONio:
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git clone https://github.com/gllmflndn/JSONio.git --depth 1 lib/JSONio
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clean:
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clean: clean_doc clean_tests
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rm -rf lib/bids-matlab
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rm -rf lib/JSONio
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rm -rf version.txt
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clean_doc:
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cd docs && make clean
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clean_tests:
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rm -rf coverage_html
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rm -f coverage.xml
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rm -f *.log
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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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‎docs/Makefile‎

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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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clean:
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rm -rf build

‎docs/source/index.rst‎

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general_information
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function_details
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mapping

‎docs/source/mapping.md‎

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<!--
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THIS FILE IS AUTOMATICALLY GENERATED!
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DO NOT EDIT MANUALLY!
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-->
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# Mapping
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| input | output |
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| - | - |
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| m\*.\* | \*space-individual_desc-biascor_\*.\* |
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| c1\*.\* | \*space-individual_label-GM_probseg.\* |
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| c2\*.\* | \*space-individual_label-WM_probseg.\* |
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| c3\*.\* | \*space-individual_label-CSF_probseg.\* |
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| iy_\*.\* | \*from-IXI549Space_to-T1w_mode-image_xfm.\* |
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| y_\*.\* | \*from-T1w_to-IXI549Space_mode-image_xfm.\* |
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| segparam_\*.\* | \*segparam.\* |
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| a\*.\* | \*space-individual_desc-stc_\*.\* |
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| au\*.\* | \*space-individual_desc-stc_\*.\* |
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| unwarpparam_\*.\* | \*unwarpparam.\* |
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| u\*.\* | \*space-individual_desc-realignUnwarp_\*.\* |
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| ua\*.\* | \*space-individual_desc-realignUnwarp_\*.\* |
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| rp_\*.\* | \*motion.tsv |
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| rp_a\*.\* | \*motion.tsv |
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| rp_au\*.\* | \*motion.tsv |
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| wc1\*.\* | \*space-IXI549Space_label-GM_probseg.\* |
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| wc2\*.\* | \*space-IXI549Space_label-WM_probseg.\* |
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| wc3\*.\* | \*space-IXI549Space_label-CSF_probseg.\* |
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| s\*.\* | \*space-individual_desc-smth_\*.\* |
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| sua\*.\* | \*space-individual_desc-smth_\*.\* |
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| sau\*.\* | \*space-individual_desc-smth_\*.\* |
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| sra\*.\* | \*space-individual_desc-smth_\*.\* |
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| su\*.\* | \*space-individual_desc-smth_\*.\* |
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| sr\*.\* | \*space-individual_desc-smth_\*.\* |
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| sw\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| swua\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| swau\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| swra\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| swu\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| swr\*.\* | \*space-IXI549Space_desc-smth_\*.\* |
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| w\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| wm\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| wau\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| wua\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| wra\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| wu\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| wr\*.\* | \*space-IXI549Space_desc-preproc_\*.\* |
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| mean\*.\* | \*space-individual_desc-mean_\*.\* |
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| meanu\*.\* | \*space-individual_desc-mean_\*.\* |
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| meanua\*.\* | \*space-individual_desc-mean_\*.\* |
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| meanau\*.\* | \*space-individual_desc-mean_\*.\* |
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| wmeanu\*.\* | \*space-IXI549Space_desc-mean_\*.\* |
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| wmeanua\*.\* | \*space-IXI549Space_desc-mean_\*.\* |
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| wmeanau\*.\* | \*space-IXI549Space_desc-mean_\*.\* |

‎init_spm_2_bids.m‎

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end
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% TODO check if bids-matlab is there ?
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add_dependencies();
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disp('Correct matlab/octave verions and added to the path!');

‎miss_hit.cfg‎

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# metric for code quality
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metric "cnest": limit 5
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metric "file_length": limit 500
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metric "cyc": limit 13
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metric "parameters": limit 5
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metric "cyc": limit 16
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metric "parameters": limit 6

‎run_tests.m‎

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% (C) Copyright 2019 spm_2_bids developers
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folderToCover = fullfile(pwd, 'src');
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testFolder = fullfile(pwd, 'tests');
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thisDir = fullfile(fileparts(mfilename('fullpath')));
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if isdir(fullfile(thisDir, 'lib', 'bids-matlab'))
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addpath(fullfile(thisDir, 'lib', 'bids-matlab'));
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end
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folderToCover = fullfile(thisDir, 'src');
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testFolder = fullfile(thisDir, 'tests');
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success = moxunit_runtests(testFolder, ...
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'-verbose', '-recursive', '-with_coverage', ...

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