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‎.github/workflows/miss_hit.yml‎ renamed to ‎.github/workflows/miss_hit_quality.yml‎

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name: miss_hit
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name: miss_hit_quality
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on:
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push:
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run: |
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python -m pip install --upgrade pip setuptools
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pip3 install -r requirements.txt
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- name: MISS_HIT Code style
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run: |
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mh_style --process-slx
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cd tests
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make data
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- name: MISS_HIT Metrics
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run: |

‎.github/workflows/miss_hit_style.yml‎

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name: miss_hit_style
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on:
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push:
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branches:
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- master
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pull_request:
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branches: '*'
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: true
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fetch-depth: 1
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- name: Set up Python 3.6
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uses: actions/setup-python@v2
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with:
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python-version: 3.6
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip setuptools
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pip3 install -r requirements.txt
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cd tests
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make data
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- name: MISS_HIT Code style
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run: |
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mh_style

‎.github/workflows/run_tests.yml‎

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name: tests and coverage
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# Uses the cron schedule for github actions
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#
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#
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# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
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#
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#
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# ┌───────────── minute (0 - 59)
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# │ ┌───────────── hour (0 - 23)
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# │ │ ┌───────────── day of the month (1 - 31)
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# │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
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# │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
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# │ │ │ │ │
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# │ │ │ │ │
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# │ │ │ │ │
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# │ │ │ │ │
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# * * * * *
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on:
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push:
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branches:
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- dev
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- '*'
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pull_request:
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branches: '*'
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schedule:
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sudo apt-get -y install octave liboctave-dev
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sudo apt-get -y install nodejs npm
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- name: Clone cpp_spm
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- name: Clone cpp_spm
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uses: actions/checkout@v2
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with:
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submodules: true
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git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
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make -C MOxUnit install
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git clone https://github.com/MOcov/MOcov.git --depth 1
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make -C MOcov install
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make -C MOcov install
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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: |
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git clone https://github.com/bids-standard/bids-matlab.git --depth 1
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- name: Update octave path
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octave $OCTFLAGS --eval "initCppRoi; savepath();"
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octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'bids-matlab')); savepath();"
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octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'bids-matlab')); savepath();"
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- name: Run tests
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octave $OCTFLAGS --eval "run_tests"
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cat test_report.log | grep 0
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bash <(curl -s https://codecov.io/bash)
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bash <(curl -s https://codecov.io/bash)

‎.gitignore‎

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demos/*/*.json
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demos/*/*/*.json
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demos/*/derivatives
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‎.pre-commit-config.yaml‎

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repos:
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- repo: local
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hooks:
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- id: mh_style
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name: mh_style
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entry: mh_style
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args: [--process-slx, --fix]
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files: ^(.*\.(m|slx))$
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language: python
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additional_dependencies: [miss_hit_core]
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- id: mh_metric
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name: mh_metric
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entry: mh_metric
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args: [--ci]
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files: ^(.*\.(m|slx))$
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language: python
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additional_dependencies: [miss_hit_core]
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- id: mh_lint
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name: mh_lint
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entry: mh_lint
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files: ^(.*\.(m|slx))$
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language: python
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additional_dependencies: [miss_hit]
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v2.0.0
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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

‎.readthedocs.yml‎

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python:
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version: 3.7
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install:
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- requirements: requirements.txt
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- requirements: requirements.txt

‎README.md‎

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- Can help generate ROI based on:
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- the SPM Anatomy toolbox (INSERT URL)
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- the SPM neuromorphometric atlas
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- neurosynth probabilty maps
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- the probabilistic maps of visual topography in human cortex:
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- https://scholar.princeton.edu/napl/resources
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- Yeo's 7 networks "atlas"
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- add REF and URL
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## Contributing
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## Contributors

‎atlas/space-IXI549Space_desc-neuromorphometrics_dseg.csv‎

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label,ROI
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4,3rd Ventricle
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11,4th Ventricle
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23,Right Accumbens Area
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30,Left Accumbens Area
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31,Right Amygdala
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32,Left Amygdala
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35,Brain Stem
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36,Right Caudate
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37,Left Caudate
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38,Right Cerebellum Exterior
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39,Left Cerebellum Exterior
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40,Right Cerebellum White Matter
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41,Left Cerebellum White Matter
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44,Right Cerebral White Matter
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45,Left Cerebral White Matter
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46,CSF
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47,Right Hippocampus
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48,Left Hippocampus
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49,Right Inf Lat Vent
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50,Left Inf Lat Vent
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51,Right Lateral Ventricle
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52,Left Lateral Ventricle
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55,Right Pallidum
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56,Left Pallidum
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57,Right Putamen
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58,Left Putamen
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59,Right Thalamus Proper
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60,Left Thalamus Proper
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61,Right Ventral DC
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62,Left Ventral DC
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63,Right vessel
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64,Left vessel
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69,Optic Chiasm
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71,Cerebellar Vermal Lobules I-V
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72,Cerebellar Vermal Lobules VI-VII
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73,Cerebellar Vermal Lobules VIII-X
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75,Left Basal Forebrain
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76,Right Basal Forebrain
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100,Right ACgG anterior cingulate gyrus
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101,Left ACgG anterior cingulate gyrus
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102,Right AIns anterior insula
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103,Left AIns anterior insula
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104,Right AOrG anterior orbital gyrus
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105,Left AOrG anterior orbital gyrus
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106,Right AnG angular gyrus
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107,Left AnG angular gyrus
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108,Right Calc calcarine cortex
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109,Left Calc calcarine cortex
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112,Right CO central operculum
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113,Left CO central operculum
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114,Right Cun cuneus
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115,Left Cun cuneus
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116,Right Ent entorhinal area
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117,Left Ent entorhinal area
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118,Right FO frontal operculum
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119,Left FO frontal operculum
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120,Right FRP frontal pole
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121,Left FRP frontal pole
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122,Right FuG fusiform gyrus
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123,Left FuG fusiform gyrus
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124,Right GRe gyrus rectus
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125,Left GRe gyrus rectus
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128,Right IOG inferior occipital gyrus
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129,Left IOG inferior occipital gyrus
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132,Right ITG inferior temporal gyrus
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133,Left ITG inferior temporal gyrus
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134,Right LiG lingual gyrus
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135,Left LiG lingual gyrus
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136,Right LOrG lateral orbital gyrus
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137,Left LOrG lateral orbital gyrus
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138,Right MCgG middle cingulate gyrus
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139,Left MCgG middle cingulate gyrus
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140,Right MFC medial frontal cortex
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141,Left MFC medial frontal cortex
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142,Right MFG middle frontal gyrus
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143,Left MFG middle frontal gyrus
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144,Right MOG middle occipital gyrus
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145,Left MOG middle occipital gyrus
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146,Right MOrG medial orbital gyrus
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147,Left MOrG medial orbital gyrus
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148,Right MPoG postcentral gyrus medial segment
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149,Left MPoG postcentral gyrus medial segment
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150,Right MPrG precentral gyrus medial segment
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151,Left MPrG precentral gyrus medial segment
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152,Right MSFG superior frontal gyrus medial segment
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153,Left MSFG superior frontal gyrus medial segment
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154,Right MTG middle temporal gyrus
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155,Left MTG middle temporal gyrus
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156,Right OCP occipital pole
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157,Left OCP occipital pole
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160,Right OFuG occipital fusiform gyrus
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161,Left OFuG occipital fusiform gyrus
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162,Right OpIFG opercular part of the inferior frontal gyrus
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163,Left OpIFG opercular part of the inferior frontal gyrus
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164,Right OrIFG orbital part of the inferior frontal gyrus
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165,Left OrIFG orbital part of the inferior frontal gyrus
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166,Right PCgG posterior cingulate gyrus
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167,Left PCgG posterior cingulate gyrus
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168,Right PCu precuneus
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169,Left PCu precuneus
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170,Right PHG parahippocampal gyrus
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171,Left PHG parahippocampal gyrus
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172,Right PIns posterior insula
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173,Left PIns posterior insula
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174,Right PO parietal operculum
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175,Left PO parietal operculum
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176,Right PoG postcentral gyrus
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177,Left PoG postcentral gyrus
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178,Right POrG posterior orbital gyrus
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179,Left POrG posterior orbital gyrus
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180,Right PP planum polare
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181,Left PP planum polare
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182,Right PrG precentral gyrus
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183,Left PrG precentral gyrus
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184,Right PT planum temporale
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185,Left PT planum temporale
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186,Right SCA subcallosal area
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187,Left SCA subcallosal area
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190,Right SFG superior frontal gyrus
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191,Left SFG superior frontal gyrus
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192,Right SMC supplementary motor cortex
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193,Left SMC supplementary motor cortex
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194,Right SMG supramarginal gyrus
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195,Left SMG supramarginal gyrus
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196,Right SOG superior occipital gyrus
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197,Left SOG superior occipital gyrus
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198,Right SPL superior parietal lobule
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199,Left SPL superior parietal lobule
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200,Right STG superior temporal gyrus
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201,Left STG superior temporal gyrus
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202,Right TMP temporal pole
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203,Left TMP temporal pole
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204,Right TrIFG triangular part of the inferior frontal gyrus
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205,Left TrIFG triangular part of the inferior frontal gyrus
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206,Right TTG transverse temporal gyrus
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207,Left TTG transverse temporal gyrus

‎demos/atlas/create_roi_from_atlas.m‎

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spm_mkdir(opt.roi.dir);
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hemi = {'lh', 'rh'};
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hemi = {'L', 'H'};
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for iHemi = 1:numel(hemi)
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‎demos/roi/other_demo.m‎ renamed to ‎demos/roi/neurosynth_left_right_rois.m‎

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% (C) Copyright 2021 CPP ROI developers
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% small demo to show how to create and rename ROIs that come from neurosynth
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% and how to only keep the data from one hemisphere of an image.
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run ../../initCppRoi;
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gunzip(fullfile('inputs', '*.gz'));
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roiImage = thresholdToMask(zMap, 5);
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% keep only one hemisphere and appends a 'hs--[hemisphere label]'
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leftRoiImage = keepHemisphere(roiImage, 'lh');
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rightRoiImage = keepHemisphere(roiImage, 'rh');
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leftRoiImage = keepHemisphere(roiImage, 'L');
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rightRoiImage = keepHemisphere(roiImage, 'R');
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% change the label entity and remove the hs one
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leftRoiImage = renameFile(leftRoiImage, ...
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struct('entities', struct( ...
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'label', 'ns left motion', ...
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'hs', '')));
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'hemi', '')));
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rightRoiImage = renameFile(rightRoiImage, ...
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struct('entities', struct( ...
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'label', 'ns right motion', ...
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'hs', '')));
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'hemi', '')));

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